Special Issue "Protein Folding and Misfolding"

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A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (27 December 2013)

Special Issue Editor

Guest Editor
Prof. Dr. Alexeii Finkelstein

Laboratory of Protein Physics, Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
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Interests: protein physics; theoretical investigations of protein folding; molecular physics; molecular biology; biochemistry; biocomputing; protein engineering introduction

Special Issue Information

Dear Colleagues,

The ability of protein chains to spontaneously form their spatial structures was a long-standing puzzle in molecular biology, especially because the measured rates of spontaneous folding range from microseconds to hours: the difference (at least 11 orders of magnitude) is akin to the difference between the life span of a mosquito and the age of the universe. Now, when this puzzle is solved in its basics, the main interest has been shifted (1) to the "natively disordered" proteins, which usually obtain their definite structure only when interact with target molecules, and (2) to the ability of many protein chains to form not only the "native" (properly working) 3D structures, but also the other ("misfolded") structures, which is also often connected with interaction of these chains with the other molecules.

These reconstructions of protein structures sometimes cause deadly diseases, and therefore the problem of protein folding and misfolding attains a great medical interest. Many new challenges are waiting in the field.

To illustrate for the readers of “Biomolecules” the importance of the protein folding and misfolding problem as a multidisciplinary field of research, this special issue is intended to show the various aspects of protein folding, misfolding and unfolding.

We look forward to reading your contributions,

Prof. Dr. Alexei Finkelsteint
Guest Editor

Submission

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Keywords

  • protein folding
  • protein misfolding
  • protein unfolding
  • protein structure
  • natively disordered proteins
  • protein structure reconstruction
  • protein physics
  • protein engineering

Published Papers (22 papers)

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Research

Jump to: Review

Open AccessArticle Amino Acid Distribution Rules Predict Protein Fold: Protein Grammar for Beta-Strand Sandwich-Like Structures
Biomolecules 2015, 5(1), 41-59; doi:10.3390/biom5010041
Received: 13 October 2014 / Accepted: 31 December 2014 / Published: 23 January 2015
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Abstract
We present an alternative approach to protein 3D folding prediction based on determination of rules that specify distribution of “favorable” residues, that are mainly responsible for a given fold formation, and “unfavorable” residues, that are incompatible with that fold, in polypeptide sequences. The
[...] Read more.
We present an alternative approach to protein 3D folding prediction based on determination of rules that specify distribution of “favorable” residues, that are mainly responsible for a given fold formation, and “unfavorable” residues, that are incompatible with that fold, in polypeptide sequences. The process of determining favorable and unfavorable residues is iterative. The starting assumptions are based on the general principles of protein structure formation as well as structural features peculiar to a protein fold under investigation. The initial assumptions are tested one-by-one for a set of all known proteins with a given structure. The assumption is accepted as a “rule of amino acid distribution” for the protein fold if it holds true for all, or near all, structures. If the assumption is not accepted as a rule, it can be modified to better fit the data and then tested again in the next step of the iterative search algorithm, or rejected. We determined the set of amino acid distribution rules for a large group of beta sandwich-like proteins characterized by a specific arrangement of strands in two beta sheets. It was shown that this set of rules is highly sensitive (~90%) and very specific (~99%) for identifying sequences of proteins with specified beta sandwich fold structure. The advantage of the proposed approach is that it does not require that query proteins have a high degree of homology to proteins with known structure. So long as the query protein satisfies residue distribution rules, it can be confidently assigned to its respective protein fold. Another advantage of our approach is that it allows for a better understanding of which residues play an essential role in protein fold formation. It may, therefore, facilitate rational protein engineering design. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
Open AccessArticle Probing the Kinetic Stabilities of Friedreich’s Ataxia Clinical Variants Using a Solid Phase GroEL Chaperonin Capture Platform
Biomolecules 2014, 4(4), 956-979; doi:10.3390/biom4040956
Received: 5 February 2014 / Revised: 29 August 2014 / Accepted: 19 September 2014 / Published: 20 October 2014
Cited by 2 | PDF Full-text (67855 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Numerous human diseases are caused by protein folding defects where the protein may become more susceptible to degradation or aggregation. Aberrant protein folding can affect the kinetic stability of the proteins even if these proteins appear to be soluble in vivo. Experimental
[...] Read more.
Numerous human diseases are caused by protein folding defects where the protein may become more susceptible to degradation or aggregation. Aberrant protein folding can affect the kinetic stability of the proteins even if these proteins appear to be soluble in vivo. Experimental discrimination between functional properly folded and misfolded nonfunctional conformers is not always straightforward at near physiological conditions. The differences in the kinetic behavior of two initially folded frataxin clinical variants were examined using a high affinity chaperonin kinetic trap approach at 25 °C. The kinetically stable wild type frataxin (FXN) shows no visible partitioning onto the chaperonin. In contrast, the clinical variants FXN-p.Asp122Tyr and FXN-p.Ile154Phe kinetically populate partial folded forms that tightly bind the GroEL chaperonin platform. The initially soluble FXN-p.Ile154Phe variant partitions onto GroEL more rapidly and is more kinetically liable. These differences in kinetic stability were confirmed using differential scanning fluorimetry. The kinetic and aggregation stability differences of these variants may lead to the distinct functional impairments described in Friedreich’s ataxia, the neurodegenerative disease associated to frataxin functional deficiency. This chaperonin platform approach may be useful for identifying small molecule stabilizers since stabilizing ligands to frataxin variants should lead to a concomitant decrease in chaperonin binding. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
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Open AccessArticle Chaperonin GroEL Reassembly: An Effect of Protein Ligands and Solvent Composition
Biomolecules 2014, 4(2), 458-473; doi:10.3390/biom4020458
Received: 10 September 2013 / Revised: 28 March 2014 / Accepted: 2 April 2014 / Published: 22 April 2014
Cited by 2 | PDF Full-text (2071 KB) | HTML Full-text | XML Full-text
Abstract
Chaperonin GroEL is a complex oligomeric heat shock protein (Hsp60) assisting the correct folding and assembly of other proteins in the cell. An intriguing question is how GroEL folds itself. According to the literature, GroEL reassembly is dependent on chaperonin ligands and solvent
[...] Read more.
Chaperonin GroEL is a complex oligomeric heat shock protein (Hsp60) assisting the correct folding and assembly of other proteins in the cell. An intriguing question is how GroEL folds itself. According to the literature, GroEL reassembly is dependent on chaperonin ligands and solvent composition. Here we demonstrate dependence of GroEL reassembly efficiency on concentrations of the essential factors (Mg2+, ADP, ATP, GroES, ammonium sulfate, NaCl and glycerol). Besides, kinetics of GroEL oligomerization in various conditions was monitored by the light scattering technique and proved to be two-exponential, which suggested accumulation of a certain oligomeric intermediate. This intermediate was resolved as a heptamer by nondenaturing blue electrophoresis of GroEL monomers during their assembly in the presence of both Mg-ATP and co-chaperonin GroES. Presumably, this intermediate heptamer plays a key role in formation of the GroEL tetradecameric particle. The role of co-chaperonin GroES (Hsp10) in GroEL assembly is also discussed. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
Open AccessArticle Similar Structures to the E-to-H Helix Unit in the Globin-Like Fold are Found in Other Helical Folds
Biomolecules 2014, 4(1), 268-288; doi:10.3390/biom4010268
Received: 6 December 2013 / Revised: 11 February 2014 / Accepted: 13 February 2014 / Published: 27 February 2014
PDF Full-text (1628 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A protein in the globin-like fold contains six alpha-helices, A, B, E, F, G and H. Among them, the E-to-H helix unit (E, F, G and H helices) forms a compact structure. In this study, we searched similar structures to the E-to-H helix
[...] Read more.
A protein in the globin-like fold contains six alpha-helices, A, B, E, F, G and H. Among them, the E-to-H helix unit (E, F, G and H helices) forms a compact structure. In this study, we searched similar structures to the E-to-H helix of leghomoglobin in the whole protein structure space using the Dali program. Several similar structures were found in other helical folds, such as KaiA/RbsU domain and Type III secretion system domain. These observations suggest that the E-to-H helix unit may be a common subunit in the whole protein 3D structure space. In addition, the common conserved hydrophobic residues were found among the similar structures to the E-to-H helix unit. Hydrophobic interactions between the conserved residues may stabilize the 3D structures of the unit. We also predicted the possible compact regions of the units using the average distance method. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
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Open AccessArticle Reconstructing Protein Structures by Neural Network Pairwise Interaction Fields and Iterative Decoy Set Construction
Biomolecules 2014, 4(1), 160-180; doi:10.3390/biom4010160
Received: 24 December 2013 / Revised: 22 January 2014 / Accepted: 30 January 2014 / Published: 10 February 2014
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Abstract
Predicting the fold of a protein from its amino acid sequence is one of the grand problems in computational biology. While there has been progress towards a solution, especially when a protein can be modelled based on one or more known structures (templates),
[...] Read more.
Predicting the fold of a protein from its amino acid sequence is one of the grand problems in computational biology. While there has been progress towards a solution, especially when a protein can be modelled based on one or more known structures (templates), in the absence of templates, even the best predictions are generally much less reliable. In this paper, we present an approach for predicting the three-dimensional structure of a protein from the sequence alone, when templates of known structure are not available. This approach relies on a simple reconstruction procedure guided by a novel knowledge-based evaluation function implemented as a class of artificial neural networks that we have designed: Neural Network Pairwise Interaction Fields (NNPIF). This evaluation function takes into account the contextual information for each residue and is trained to identify native-like conformations from non-native-like ones by using large sets of decoys as a training set. The training set is generated and then iteratively expanded during successive folding simulations. As NNPIF are fast at evaluating conformations, thousands of models can be processed in a short amount of time, and clustering techniques can be adopted for model selection. Although the results we present here are very preliminary, we consider them to be promising, with predictions being generated at state-of-the-art levels in some of the cases. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
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Open AccessArticle Molecular Dynamics Simulations Capture the Misfolding of the Bovine Prion Protein at Acidic pH
Biomolecules 2014, 4(1), 181-201; doi:10.3390/biom4010181
Received: 9 January 2014 / Revised: 7 February 2014 / Accepted: 9 February 2014 / Published: 10 February 2014
Cited by 6 | PDF Full-text (1373 KB) | HTML Full-text | XML Full-text
Abstract
Bovine spongiform encephalopathy (BSE), or mad cow disease, is a fatal neurodegenerative disease that is transmissible to humans and that is currently incurable. BSE is caused by the prion protein (PrP), which adopts two conformers; PrPC is the native innocuous form, which
[...] Read more.
Bovine spongiform encephalopathy (BSE), or mad cow disease, is a fatal neurodegenerative disease that is transmissible to humans and that is currently incurable. BSE is caused by the prion protein (PrP), which adopts two conformers; PrPC is the native innocuous form, which is α-helix rich; and PrPSc is the β-sheet rich misfolded form, which is infectious and forms neurotoxic species. Acidic pH induces the conversion of PrPC to PrPSc. We have performed molecular dynamics simulations of bovine PrP at various pH regimes. An acidic pH environment induced conformational changes that were not observed in neutral pH simulations. Putative misfolded structures, with nonnative β-strands formed in the flexible N-terminal domain, were found in acidic pH simulations. Two distinct pathways were observed for the formation of nonnative β-strands: at low pH, hydrophobic contacts with M129 nucleated the nonnative β-strand; at mid-pH, polar contacts involving Q168 and D178 facilitated the formation of a hairpin at the flexible N-terminus. These mid- and low pH simulations capture the process of nonnative β-strand formation, thereby improving our understanding of how PrPC misfolds into the β-sheet rich PrPSc and how pH factors into the process. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
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Open AccessArticle A Firefly-Inspired Method for Protein Structure Prediction in Lattice Models
Biomolecules 2014, 4(1), 56-75; doi:10.3390/biom4010056
Received: 1 December 2013 / Revised: 17 December 2013 / Accepted: 27 December 2013 / Published: 7 January 2014
Cited by 7 | PDF Full-text (328 KB) | HTML Full-text | XML Full-text
Abstract
We introduce a Firefly-inspired algorithmic approach for protein structure prediction over two different lattice models in three-dimensional space. In particular, we consider three-dimensional cubic and three-dimensional face-centred-cubic (FCC) lattices. The underlying energy models are the Hydrophobic-Polar (H-P) model, the Miyazawa–Jernigan (M-J) model and
[...] Read more.
We introduce a Firefly-inspired algorithmic approach for protein structure prediction over two different lattice models in three-dimensional space. In particular, we consider three-dimensional cubic and three-dimensional face-centred-cubic (FCC) lattices. The underlying energy models are the Hydrophobic-Polar (H-P) model, the Miyazawa–Jernigan (M-J) model and a related matrix model. The implementation of our approach is tested on ten H-P benchmark problems of a length of 48 and ten M-J benchmark problems of a length ranging from 48 until 61. The key complexity parameter we investigate is the total number of objective function evaluations required to achieve the optimum energy values for the H-P model or competitive results in comparison to published values for the M-J model. For H-P instances and cubic lattices, where data for comparison are available, we obtain an average speed-up over eight instances of 2.1, leaving out two extreme values (otherwise, 8.8). For six M-J instances, data for comparison are available for cubic lattices and runs with a population size of 100, where, a priori, the minimum free energy is a termination criterion. The average speed-up over four instances is 1.2 (leaving out two extreme values, otherwise 1.1), which is achieved for a population size of only eight instances. The present study is a test case with initial results for ad hoc parameter settings, with the aim of justifying future research on larger instances within lattice model settings, eventually leading to the ultimate goal of implementations for off-lattice models. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
Open AccessArticle The Role of Non-Native Interactions in the Folding of Knotted Proteins: Insights from Molecular Dynamics Simulations
Biomolecules 2014, 4(1), 1-19; doi:10.3390/biom4010001
Received: 6 November 2013 / Revised: 10 December 2013 / Accepted: 20 December 2013 / Published: 24 December 2013
Cited by 6 | PDF Full-text (7311 KB) | HTML Full-text | XML Full-text
Abstract
For several decades, the presence of knots in naturally-occurring proteins was largely ruled out a priori for its supposed incompatibility with the efficiency and robustness of folding processes. For this very same reason, the later discovery of several unrelated families of knotted proteins
[...] Read more.
For several decades, the presence of knots in naturally-occurring proteins was largely ruled out a priori for its supposed incompatibility with the efficiency and robustness of folding processes. For this very same reason, the later discovery of several unrelated families of knotted proteins motivated researchers to look into the physico-chemical mechanisms governing the concerted sequence of folding steps leading to the consistent formation of the same knot type in the same protein location. Besides experiments, computational studies are providing considerable insight into these mechanisms. Here, we revisit a number of such recent investigations within a common conceptual and methodological framework. By considering studies employing protein models with different structural resolution (coarse-grained or atomistic) and various force fields (from pure native-centric to realistic atomistic ones), we focus on the role of native and non-native interactions. For various unrelated instances of knotted proteins, non-native interactions are shown to be very important for favoring the emergence of conformations primed for successful self-knotting events. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
Open AccessArticle Control of Collagen Stability and Heterotrimer Specificity through Repulsive Electrostatic Interactions
Biomolecules 2013, 3(4), 986-996; doi:10.3390/biom3040986
Received: 29 October 2013 / Revised: 27 November 2013 / Accepted: 28 November 2013 / Published: 6 December 2013
Cited by 4 | PDF Full-text (1336 KB) | HTML Full-text | XML Full-text
Abstract
Charge-pair interactions between acidic and basic residues on the surface of collagen can promote stability as well as control specificity of molecular recognition. Heterotrimeric collagen peptides have been engineered de novo using either rational or computational methods, which in both cases optimize networks
[...] Read more.
Charge-pair interactions between acidic and basic residues on the surface of collagen can promote stability as well as control specificity of molecular recognition. Heterotrimeric collagen peptides have been engineered de novo using either rational or computational methods, which in both cases optimize networks of favorable charge-pair interactions in the target structure. Less understood is the role of electrostatic repulsion between groups of like charge in destabilizing structure or directing molecular recognition. To study this, we apply a “charge crowding” approach, where repulsive interactions between multiple aspartate side chains are found to destabilize the homotrimer states in triple helical peptide system and can be utilized to promote the formation of heterotrimers. Neutralizing surface charge by increasing salt concentration or decreasing pH can enhance homotrimer stability, confirming the role of charge crowding on the destabilization of homotrimers via electrostatic repulsion. Charge crowding may be used in conjunction with other approaches to create specific collagen heterotrimers. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
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Open AccessArticle Unfolding Thermodynamics of Cysteine-Rich Proteins and Molecular Thermal-Adaptation of Marine Ciliates
Biomolecules 2013, 3(4), 967-985; doi:10.3390/biom3040967
Received: 9 September 2013 / Revised: 28 October 2013 / Accepted: 29 October 2013 / Published: 18 November 2013
Cited by 4 | PDF Full-text (961 KB) | HTML Full-text | XML Full-text
Abstract
Euplotes nobilii and Euplotes raikovi are phylogenetically closely allied species of marine ciliates, living in polar and temperate waters, respectively. Their evolutional relation and the sharply different temperatures of their natural environments make them ideal organisms to investigate thermal-adaptation. We perform a comparative
[...] Read more.
Euplotes nobilii and Euplotes raikovi are phylogenetically closely allied species of marine ciliates, living in polar and temperate waters, respectively. Their evolutional relation and the sharply different temperatures of their natural environments make them ideal organisms to investigate thermal-adaptation. We perform a comparative study of the thermal unfolding of disulfide-rich protein pheromones produced by these ciliates. Recent circular dichroism (CD) measurements have shown that the two psychrophilic (E. nobilii) and mesophilic (E. raikovi) protein families are characterized by very different melting temperatures, despite their close structural homology. The enhanced thermal stability of the E. raikovi pheromones is realized notwithstanding the fact that these proteins form, as a rule, a smaller number of disulfide bonds. We perform Monte Carlo (MC) simulations in a structure-based coarse-grained (CG) model to show that the higher stability of the E. raikovi pheromones is due to the lower locality of the disulfide bonds, which yields a lower entropy increase in the unfolding process. Our study suggests that the higher stability of the mesophilic E. raikovi phermones is not mainly due to the presence of a strongly hydrophobic core, as it was proposed in the literature. In addition, we argue that the molecular adaptation of these ciliates may have occurred from cold to warm, and not from warm to cold. To provide a testable prediction, we identify a point-mutation of an E. nobilii pheromone that should lead to an unfolding temperature typical of that of E. raikovi pheromones. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
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Open AccessArticle Variation in the Subcellular Localization and Protein Folding Activity among Arabidopsis thaliana Homologs of Protein Disulfide Isomerase
Biomolecules 2013, 3(4), 848-869; doi:10.3390/biom3040848
Received: 7 August 2013 / Revised: 27 September 2013 / Accepted: 12 October 2013 / Published: 21 October 2013
Cited by 2 | PDF Full-text (949 KB) | HTML Full-text | XML Full-text
Abstract
Protein disulfide isomerases (PDIs) catalyze the formation, breakage, and rearrangement of disulfide bonds to properly fold nascent polypeptides within the endoplasmic reticulum (ER). Classical animal and yeast PDIs possess two catalytic thioredoxin-like domains (a, a′) and two non-catalytic domains (
[...] Read more.
Protein disulfide isomerases (PDIs) catalyze the formation, breakage, and rearrangement of disulfide bonds to properly fold nascent polypeptides within the endoplasmic reticulum (ER). Classical animal and yeast PDIs possess two catalytic thioredoxin-like domains (a, a′) and two non-catalytic domains (b, b′), in the order a-b-b′-a′. The model plant, Arabidopsis thaliana, encodes 12 PDI-like proteins, six of which possess the classical PDI domain arrangement (AtPDI1 through AtPDI6). Three additional AtPDIs (AtPDI9, AtPDI10, AtPDI11) possess two thioredoxin domains, but without intervening b-b′ domains. C-terminal green fluorescent protein (GFP) fusions to each of the nine dual-thioredoxin PDI homologs localized predominantly to the ER lumen when transiently expressed in protoplasts. Additionally, expression of AtPDI9:GFP-KDEL and AtPDI10: GFP-KDDL was associated with the formation of ER bodies. AtPDI9, AtPDI10, and AtPDI11 mediated the oxidative folding of alkaline phosphatase when heterologously expressed in the Escherichia coli protein folding mutant, dsbA. However, only three classical AtPDIs (AtPDI2, AtPDI5, AtPDI6) functionally complemented dsbA. Interestingly, chemical inducers of the ER unfolded protein response were previously shown to upregulate most of the AtPDIs that complemented dsbA. The results indicate that Arabidopsis PDIs differ in their localization and protein folding activities to fulfill distinct molecular functions in the ER. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
Open AccessArticle Biophysical Characterization of α-Synuclein and Rotenone Interaction
Biomolecules 2013, 3(3), 703-732; doi:10.3390/biom3030703
Received: 13 September 2013 / Revised: 21 September 2013 / Accepted: 23 September 2013 / Published: 24 September 2013
Cited by 6 | PDF Full-text (1349 KB) | HTML Full-text | XML Full-text
Abstract
Previous studies revealed that pesticides interact with α-synuclein and accelerate the rate of fibrillation. These results are consistent with the prevailing hypothesis that the direct interaction of α-synuclein with pesticides is one of many suspected factors leading to α-synuclein fibrillation and ultimately to
[...] Read more.
Previous studies revealed that pesticides interact with α-synuclein and accelerate the rate of fibrillation. These results are consistent with the prevailing hypothesis that the direct interaction of α-synuclein with pesticides is one of many suspected factors leading to α-synuclein fibrillation and ultimately to Parkinson’s disease. In this study, the biophysical properties and fibrillation kinetics of α-synuclein in the presence of rotenone were investigated and, more specifically, the effects of rotenone on the early-stage misfolded forms of α-synuclein were considered. The thioflavine T (ThT) fluorescence assay studies provide evidence that early-phase misfolded α-synuclein forms are affected by rotenone and that the fibrillation process is accelerated. Further characterization by attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) shows that rotenone increases the amount of ordered secondary structure in this intrinsically disordered protein. Morphological characterization by transmission electron microscopy (TEM) and atomic force microscopy (AFM) provide visualization of the differences in the aggregated α-synuclein species developing during the early kinetics of the fibrillation process in the absence and presence of rotenone. We believe that these data provide useful information for a better understanding of the molecular basis of rotenone-induced misfolding and aggregation of α-synuclein. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)

Review

Jump to: Research

Open AccessReview Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor Interactions
Biomolecules 2014, 4(3), 725-773; doi:10.3390/biom4030725
Received: 4 February 2014 / Revised: 17 June 2014 / Accepted: 20 June 2014 / Published: 24 July 2014
Cited by 13 | PDF Full-text (5389 KB) | HTML Full-text | XML Full-text
Abstract
The discovery of Intrinsically Disordered Proteins, which contain significant levels of disorder yet perform complex biologically functions, as well as unwanted aggregation, has motivated numerous experimental and theoretical studies aimed at describing residue-level conformational ensembles. Multiple lines of evidence gathered over the last
[...] Read more.
The discovery of Intrinsically Disordered Proteins, which contain significant levels of disorder yet perform complex biologically functions, as well as unwanted aggregation, has motivated numerous experimental and theoretical studies aimed at describing residue-level conformational ensembles. Multiple lines of evidence gathered over the last 15 years strongly suggest that amino acids residues display unique and restricted conformational preferences in the unfolded state of peptides and proteins, contrary to one of the basic assumptions of the canonical random coil model. To fully understand residue level order/disorder, however, one has to gain a quantitative, experimentally based picture of conformational distributions and to determine the physical basis underlying residue-level conformational biases. Here, we review the experimental, computational and bioinformatic evidence for conformational preferences of amino acid residues in (mostly short) peptides that can be utilized as suitable model systems for unfolded states of peptides and proteins. In this context particular attention is paid to the alleged high polyproline II preference of alanine. We discuss how these conformational propensities may be modulated by peptide solvent interactions and so called nearest-neighbor interactions. The relevance of conformational propensities for the protein folding problem and the understanding of IDPs is briefly discussed. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
Open AccessReview Decoding F508del Misfolding in Cystic Fibrosis
Biomolecules 2014, 4(2), 498-509; doi:10.3390/biom4020498
Received: 28 February 2014 / Revised: 11 April 2014 / Accepted: 25 April 2014 / Published: 6 May 2014
Cited by 2 | PDF Full-text (675 KB) | HTML Full-text | XML Full-text
Abstract
The functional deficiency of the cystic fibrosis transmembrane conductance regulator (CFTR), a plasma membrane chloride channel, leads to the development of cystic fibrosis. The deletion of a phenylalanine at residue 508 (F508del) is the most common cause of CFTR misfolding leading to the
[...] Read more.
The functional deficiency of the cystic fibrosis transmembrane conductance regulator (CFTR), a plasma membrane chloride channel, leads to the development of cystic fibrosis. The deletion of a phenylalanine at residue 508 (F508del) is the most common cause of CFTR misfolding leading to the disease. The F508del misfolding originates in the first nucleotide-binding domain (NBD1), which induces a global conformational change in CFTR through NBD1’s interactions with other domains. Such global misfolding produces a mutant chloride channel that is impaired in exocytic trafficking, peripheral stability, and channel gating. The nature and atomic details of F508del misfolding have been subject to extensive research during the past decade. Current data support a central role for NBD1 in F508del misfolding and rescue. Many cis-acting NBD1 second-site mutations rescue F508del misfolding in the context of full-length CFTR. While some of these mutations appear to specifically counteract the F508del-induced misfolding, others release certain inherent conformational constraints of the human wild-type CFTR. Several small-molecule correctors were recently found to act on key interdomain interfaces of F508del CFTR. Potential rational approaches have been proposed in an attempt to develop highly effective small molecule modulators that improve the cell surface functional expression of F508del CFTR. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
Open AccessReview Kinetics and Thermodynamics of Membrane Protein Folding
Biomolecules 2014, 4(1), 354-373; doi:10.3390/biom4010354
Received: 31 December 2013 / Revised: 19 February 2014 / Accepted: 23 February 2014 / Published: 18 March 2014
Cited by 2 | PDF Full-text (554 KB) | HTML Full-text | XML Full-text
Abstract
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins. In comparison, advances in the membrane protein folding field
[...] Read more.
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins. In comparison, advances in the membrane protein folding field lag far behind. Although membrane proteins constitute about a third of the proteins encoded in known genomes, stability studies on membrane proteins have been impaired due to experimental limitations. Furthermore, no systematic experimental strategies are available for folding these biomolecules in vitro. Common denaturing agents such as chaotropes usually do not work on helical membrane proteins, and ionic detergents have been successful denaturants only in few cases. Refolding a membrane protein seems to be a craftsman work, which is relatively straightforward for transmembrane β-barrel proteins but challenging for α-helical membrane proteins. Additional complexities emerge in multidomain membrane proteins, data interpretation being one of the most critical. In this review, we will describe some recent efforts in understanding the folding mechanism of membrane proteins that have been reversibly refolded allowing both thermodynamic and kinetic analysis. This information will be discussed in the context of current paradigms in the protein folding field. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
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Open AccessReview Detecting Selection on Protein Stability through Statistical Mechanical Models of Folding and Evolution
Biomolecules 2014, 4(1), 291-314; doi:10.3390/biom4010291
Received: 25 December 2013 / Revised: 13 February 2014 / Accepted: 14 February 2014 / Published: 7 March 2014
Cited by 2 | PDF Full-text (241 KB) | HTML Full-text | XML Full-text
Abstract
The properties of biomolecules depend both on physics and on the evolutionary process that formed them. These two points of view produce a powerful synergism. Physics sets the stage and the constraints that molecular evolution has to obey, and evolutionary theory helps in
[...] Read more.
The properties of biomolecules depend both on physics and on the evolutionary process that formed them. These two points of view produce a powerful synergism. Physics sets the stage and the constraints that molecular evolution has to obey, and evolutionary theory helps in rationalizing the physical properties of biomolecules, including protein folding thermodynamics. To complete the parallelism, protein thermodynamics is founded on the statistical mechanics in the space of protein structures, and molecular evolution can be viewed as statistical mechanics in the space of protein sequences. In this review, we will integrate both points of view, applying them to detecting selection on the stability of the folded state of proteins. We will start discussing positive design, which strengthens the stability of the folded against the unfolded state of proteins. Positive design justifies why statistical potentials for protein folding can be obtained from the frequencies of structural motifs. Stability against unfolding is easier to achieve for longer proteins. On the contrary, negative design, which consists in destabilizing frequently formed misfolded conformations, is more difficult to achieve for longer proteins. The folding rate can be enhanced by strengthening short-range native interactions, but this requirement contrasts with negative design, and evolution has to trade-off between them. Finally, selection can accelerate functional movements by favoring low frequency normal modes of the dynamics of the native state that strongly correlate with the functional conformation change. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
Open AccessReview Heavy Metals and Metalloids As a Cause for Protein Misfolding and Aggregation
Biomolecules 2014, 4(1), 252-267; doi:10.3390/biom4010252
Received: 17 January 2014 / Revised: 14 February 2014 / Accepted: 19 February 2014 / Published: 25 February 2014
Cited by 21 | PDF Full-text (452 KB) | HTML Full-text | XML Full-text
Abstract
While the toxicity of metals and metalloids, like arsenic, cadmium, mercury, lead and chromium, is undisputed, the underlying molecular mechanisms are not entirely clear. General consensus holds that proteins are the prime targets; heavy metals interfere with the physiological activity of specific, particularly
[...] Read more.
While the toxicity of metals and metalloids, like arsenic, cadmium, mercury, lead and chromium, is undisputed, the underlying molecular mechanisms are not entirely clear. General consensus holds that proteins are the prime targets; heavy metals interfere with the physiological activity of specific, particularly susceptible proteins, either by forming a complex with functional side chain groups or by displacing essential metal ions in metalloproteins. Recent studies have revealed an additional mode of metal action targeted at proteins in a non-native state; certain heavy metals and metalloids have been found to inhibit the in vitro refolding of chemically denatured proteins, to interfere with protein folding in vivo and to cause aggregation of nascent proteins in living cells. Apparently, unfolded proteins with motile backbone and side chains are considerably more prone to engage in stable, pluridentate metal complexes than native proteins with their well-defined 3D structure. By interfering with the folding process, heavy metal ions and metalloids profoundly affect protein homeostasis and cell viability. This review describes how heavy metals impede protein folding and promote protein aggregation, how cells regulate quality control systems to protect themselves from metal toxicity and how metals might contribute to protein misfolding disorders. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
Open AccessReview Refolding Techniques for Recovering Biologically Active Recombinant Proteins from Inclusion Bodies
Biomolecules 2014, 4(1), 235-251; doi:10.3390/biom4010235
Received: 12 December 2013 / Revised: 23 January 2014 / Accepted: 10 February 2014 / Published: 20 February 2014
Cited by 16 | PDF Full-text (1232 KB) | HTML Full-text | XML Full-text
Abstract
Biologically active proteins are useful for studying the biological functions of genes and for the development of therapeutic drugs and biomaterials in a biotechnology industry. Overexpression of recombinant proteins in bacteria, such as Escherichia coli, often results in the formation of inclusion
[...] Read more.
Biologically active proteins are useful for studying the biological functions of genes and for the development of therapeutic drugs and biomaterials in a biotechnology industry. Overexpression of recombinant proteins in bacteria, such as Escherichia coli, often results in the formation of inclusion bodies, which are protein aggregates with non-native conformations. As inclusion bodies contain relatively pure and intact proteins, protein refolding is an important process to obtain active recombinant proteins from inclusion bodies. However, conventional refolding methods, such as dialysis and dilution, are time consuming and, often, recovered yields of active proteins are low, and a trial-and-error process is required to achieve success. Recently, several approaches have been reported to refold these aggregated proteins into an active form. The strategies largely aim at reducing protein aggregation during the refolding procedure. This review focuses on protein refolding techniques using chemical additives and laminar flow in microfluidic chips for the efficient recovery of active proteins from inclusion bodies. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
Figures

Open AccessReview Transient Non-Native Helix Formation during the Folding of β-Lactoglobulin
Biomolecules 2014, 4(1), 202-216; doi:10.3390/biom4010202
Received: 6 January 2014 / Revised: 5 February 2014 / Accepted: 10 February 2014 / Published: 13 February 2014
Cited by 2 | PDF Full-text (654 KB) | HTML Full-text | XML Full-text
Abstract
In ideal proteins, only native interactions are stabilized step-by-step in a smooth funnel-like energy landscape. In real proteins, however, the transient formation of non-native structures is frequently observed. In this review, the transient formation of non-native structures is described using the non-native helix
[...] Read more.
In ideal proteins, only native interactions are stabilized step-by-step in a smooth funnel-like energy landscape. In real proteins, however, the transient formation of non-native structures is frequently observed. In this review, the transient formation of non-native structures is described using the non-native helix formation during the folding of β-lactoglobulin as a prominent example. Although β-lactoglobulin is a predominantly β-sheet protein, it has been shown to form non-native helices during the early stage of folding. The location of non-native helices, their stabilization mechanism, and their role in the folding reaction are discussed. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
Figures

Open AccessReview Misfolding of Amyloidogenic Proteins and Their Interactions with Membranes
Biomolecules 2014, 4(1), 20-55; doi:10.3390/biom4010020
Received: 4 November 2013 / Revised: 13 December 2013 / Accepted: 17 December 2013 / Published: 27 December 2013
Cited by 4 | PDF Full-text (873 KB) | HTML Full-text | XML Full-text
Abstract
In this paper, we discuss amyloidogenic proteins, their misfolding, resulting structures, and interactions with membranes, which lead to membrane damage and subsequent cell death. Many of these proteins are implicated in serious illnesses such as Alzheimer’s disease and Parkinson’s disease. Misfolding of amyloidogenic
[...] Read more.
In this paper, we discuss amyloidogenic proteins, their misfolding, resulting structures, and interactions with membranes, which lead to membrane damage and subsequent cell death. Many of these proteins are implicated in serious illnesses such as Alzheimer’s disease and Parkinson’s disease. Misfolding of amyloidogenic proteins leads to the formation of polymorphic oligomers and fibrils. Oligomeric aggregates are widely thought to be the toxic species, however, fibrils also play a role in membrane damage. We focus on the structure of these aggregates and their interactions with model membranes. Study of interactions of amlyoidogenic proteins with model and natural membranes has shown the importance of the lipid bilayer in protein misfolding and aggregation and has led to the development of several models for membrane permeabilization by the resulting amyloid aggregates. We discuss several of these models: formation of structured pores by misfolded amyloidogenic proteins, extraction of lipids, interactions with receptors in biological membranes, and membrane destabilization by amyloid aggregates perhaps analogous to that caused by antimicrobial peptides. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
Figures

Open AccessReview Protein Stability, Folding and Misfolding in Human PGK1 Deficiency
Biomolecules 2013, 3(4), 1030-1052; doi:10.3390/biom3041030
Received: 21 October 2013 / Revised: 6 December 2013 / Accepted: 13 December 2013 / Published: 18 December 2013
Cited by 4 | PDF Full-text (873 KB) | HTML Full-text | XML Full-text
Abstract
Conformational diseases are often caused by mutations, altering protein folding and stability in vivo. We review here our recent work on the effects of mutations on the human phosphoglycerate kinase 1 (hPGK1), with a particular focus on thermodynamics and kinetics of protein
[...] Read more.
Conformational diseases are often caused by mutations, altering protein folding and stability in vivo. We review here our recent work on the effects of mutations on the human phosphoglycerate kinase 1 (hPGK1), with a particular focus on thermodynamics and kinetics of protein folding and misfolding. Expression analyses and in vitro biophysical studies indicate that disease-causing mutations enhance protein aggregation propensity. We found a strong correlation among protein aggregation propensity, thermodynamic stability, cooperativity and dynamics. Comparison of folding and unfolding properties with previous reports in PGKs from other species suggests that hPGK1 is very sensitive to mutations leading to enhance protein aggregation through changes in protein folding cooperativity and the structure of the relevant denaturation transition state for aggregation. Overall, we provide a mechanistic framework for protein misfolding of hPGK1, which is insightful to develop new therapeutic strategies aimed to target native state stability and foldability in hPGK1 deficient patients. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
Figures

Open AccessReview Toxin Instability and Its Role in Toxin Translocation from the Endoplasmic Reticulum to the Cytosol
Biomolecules 2013, 3(4), 997-1029; doi:10.3390/biom3040997
Received: 4 November 2013 / Revised: 26 November 2013 / Accepted: 27 November 2013 / Published: 10 December 2013
Cited by 4 | PDF Full-text (501 KB) | HTML Full-text | XML Full-text
Abstract
AB toxins enter a host cell by receptor-mediated endocytosis. The catalytic A chain then crosses the endosome or endoplasmic reticulum (ER) membrane to reach its cytosolic target. Dissociation of the A chain from the cell-binding B chain occurs before or during translocation to
[...] Read more.
AB toxins enter a host cell by receptor-mediated endocytosis. The catalytic A chain then crosses the endosome or endoplasmic reticulum (ER) membrane to reach its cytosolic target. Dissociation of the A chain from the cell-binding B chain occurs before or during translocation to the cytosol, and only the A chain enters the cytosol. In some cases, AB subunit dissociation is facilitated by the unique physiology and function of the ER. The A chains of these ER-translocating toxins are stable within the architecture of the AB holotoxin, but toxin disassembly results in spontaneous or assisted unfolding of the isolated A chain. This unfolding event places the A chain in a translocation-competent conformation that promotes its export to the cytosol through the quality control mechanism of ER-associated degradation. A lack of lysine residues for ubiquitin conjugation protects the exported A chain from degradation by the ubiquitin-proteasome system, and an interaction with host factors allows the cytosolic toxin to regain a folded, active state. The intrinsic instability of the toxin A chain thus influences multiple steps of the intoxication process. This review will focus on the host–toxin interactions involved with A chain unfolding in the ER and A chain refolding in the cytosol. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Type of Paper: Review
Title:
Protein Stability, Folding and Misfolding in Human PGK1 Deficiency
Authors:
Giovanna Valentini, Maristella Maggi and Angel L. Pey *
Affiliation: Department of Physical Chemistry, Faculty of Sciences, University of Granada, Granada 18071, Spain; * E-Mail: angelpey@ugr.es
Abstract:
Conformational diseases are often caused by mutations altering protein folding and stability in vivo. We review here our recent works on the effects of mutations on the thermodynamics and kinetics of folding and misfolding in the human phosphoglycerate kinase 1 (hPGK1). Expression analyses and in vitro biophysical studies indicate that disease causing mutations enhance protein aggregation propensity. We found a strong correlation between protein aggregation propensity, thermodynamic stability, cooperativity and dynamics. Comparison of folding and unfolding properties with previous reports in PGKs from other species suggests that hPGK1 is very sensitive to mutations leading to enhance protein aggregation through changes in protein folding cooperativity and the structure of the relevant denaturation transition state. Overall, we provide a mechanistic framework of protein misfolding of hPGK1 which is insightful to develop new therapeutic strategies aimed to target native state stability and foldability in hPGK1 deficient patients.

Type of Paper: Article
Title:
Variations in the Structure and Protein Folding Activity of Nine Endoplasmic Reticulum-Localized Protein Disulfide Isomerases in Arabidopsis
Authors:
Christen Y.L. Yuen, Kristie O. Matusumoto and David A. Christopher
Affiliation: Molecular Biosciences & Bioengineering, University of Hawaii, 1955 East-West Rd. AGsciences 218, Honolulu, HI 96822, USA; * E-Mail: dchr@hawaii.edu
Abstract:
Protein disulfide isomerases (PDIs) catalyze the formation, breakage, and rearrangement of disulfide bonds to properly fold nascent polypeptides within the endoplasmic reticulum (ER). Classical animal and yeast PDIs possess two catalytic thioredoxin-like domains (a, a’) and two non-catalytic domains (b, b’), in the order a-b-b’-a’. The model plant, Arabidopsis thaliana, encodes 12 PDI-like proteins, six of which possess the classical PDI domain arrangement (AtPDI1 through AtPDI6). Three additional AtPDIs (AtPDI9, AtPDI10, AtPDI11) possess two thioredoxin domains, but without intervening b-b’ domains. C-terminal green fluorescent protein (GFP) fusions to each of the nine dual-thioredoxin PDI homologs localized predominantly to the ER lumen when transiently expressed in protoplasts. Additionally, expression of AtPDI9:GFP-KDEL or AtPDI10:GFP-KDDL induced the formation of ER bodies. AtPDI9, AtPDI10, and AtPDI11 mediated the oxidative folding of alkaline phosphatase when heterologously expressed in the Escherichia coli protein folding mutant, dsbA. However, only three classical AtPDIs (AtPDI2, AtPDI5, AtPDI6) functionally complemented dsbA-. Interestingly, chemical inducers of the ER unfolded protein response were previously shown to upregulate most of AtPDIs that complemented dsbA-. The results indicate that Arabidopsis PDIs differ in their localization and protein folding activities to fulfill distinct molecular functions in the ER.

Type of Paper: Review
Title:
Refolding Techniques of Active Recombinant Proteins from Inclusion Bodies
Authors:
Hiroshi Yamaguchi and Masaya Miyazaki *
Affiliations
: Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1, Kasuga-Kouen, Kasuga, Japan; * E-Mail: m.miyazaki@aist.go.jp
Abstract:
Biologically active recombinant proteins are useful for studies of biological functions of genes and for the development of therapeutic drugs and biomaterials in the industries. Protein refolding is an important process to obtain active recombinant proteins from inclusion bodies that contain relatively pure and intact recombinant proteins. However, the conventional refolding method of dialysis or dilution is a time consuming procedure and often, recovering yields of active proteins are low. Recently, several approaches have been reported to refold these aggregated proteins into a biologically active form. In this review, we will focus on a protein refolding methods using chemical additives, solid phase-based techniques and laminar flow in microfluidic chips for efficient recovery of active proteins from inclusion bodies. Each technique (method) will be introduced by its principle, application, strong and weak points.

Type of Paper: Article
Title:
Two Peaks of Heat Capacity in a Short Peptide Chignolin Solution Related to Phase Transitions by an Enhanced Conformational Sampling Simulation
Author
s: Koji Umezawa 1,*, Mitsunori Takano, 1 and Junichi Higo 2
Affiliations
:
1
Graduate school of advanced science and engineering, Waseda University, Okubo 3-4-1, Shinjuku-Ku, Tokyo 169-8555, Japan;
2 Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan; * E-Mails: k.umezawa@aoni.waseda.jp (K.U.); mtkn@waseda.jp (M.T.); higo@protein.osaka-u.ac.jp (J.H.)
Abstract:
Phase-transition-like conformational change of a protein is a major topic in protein folding study. It has been reported experimentally that a 10-residue -hairpin peptide, chignolin, exhibits a transition at room temperature (312 K). We have performed a multicanonical molecular dynamics (McMD) simulation, one of enhanced conformational sampling methods, where the peptide was expressed by an all-atom model and surrounded by an explicit solvent. The McMD simulation has provided temperature dependence of thermodynamic quantities in a wide temperature range [140-700 K]. Interestingly, the heat capacity has exhibited two peaks at 310 K and 180 K. The 310-K peak was related to the folding-unfolding transition, below which chignolin adopted native-like structures. Thus, this transition likely corresponds to the experimentally observed one. The 180-K transition, which is incapable of being detected by an experiment, corresponded to an ordering-disordering transition of the solution structure surrounding chignolin. Free-energy landscapes of the system, derived from the McMD trajectory data, have characterized the phase transitions. In general, to reproduce a phase transition of a biological system by simulation is a difficult task even for a small peptide when it is represented by all-atom model immersed in an explicit solvent. The current study has shown that McMD can reproduce not only native-like structure but also its free-energy landscapes.

Type of Paper: Article
Title: Conformational Biases and Local Order in the Unfolded State: Mediation by Solvent and Nearest Neighbor Interactions
Authors: Siobhan Toal * and Reinhard Schweitzer-Stenner
Affiliation: Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA; E-Mails: siobhan.toal@gmail.com (S.T.); RSchweitzer-Stenner@drexel.edu (R.S.S.)
Abstract: The discovery of Intrinsically Disordered Proteins, which contain significant levels of disorder yet undergo complex biologically functions, as well as unwanted aggregation, has motivated numerous experimental and theoretical studies aimed at describing residue level conformational ensembles. It is now well established that amino acids residues display unique conformational preferences in the unfolded state. To fully understand residue level order/disorder, however, one has to address the physical basis underlying residue-level conformational bias. Here, we review the experimental and theoretical evidence for unique conformational propensities in the unfolded state as well as how these are modulated by peptide solvent interactions, co-solvation, and so called nearest neighbor interactions. We show that the thermodynamics governing the free energy landscape of intrinsic propensities displays enthalpy-entropy entropy compensation when solvated by water and that local order in the form of stable turns can be achieved in aqueous solution. We discuss the implications for local order/disorder in the unfolded state as well as for protein folding.

Type of Paper: Article
Title:
GroEL Chaperonin Reassembly: the Effect of the Protein Ligands and Solvent Composition
Author
: Gennady V. Semisotnov
Affiliation:
Institute of Protein Research, Russian Academy of Sciences, 142290, Russian Federation, Pushchino, Moscow Region, Institutskaya street, 4, Russia; E-Mail: siobhan nina@vega.protres.ru (G.V.S.)
Abstract:
GroEL chaperonin is complex oligomeric heat shock protein (Hsp60) assisting the correct folding and assembly of other proteins in the cell. One from intriguing questions is how GroEL folds itself. According to literary data GroEL reassembly is dependent on chaperonin’ ligands and solvent composition. Here we demonstrate the dependence of GroEL reassembly efficiency on concentration of the essential factors (Mg2+ ions, ADP, ATP, GroES, ammonium sulfate, NaCl and glycerol). Besides, GroEL oligomerization kinetics at various conditions were registrated by light scattering technique. These kinetics are two-exponential hinting on the accumulation of some oligomeric intermediate. This intermediate is resolved by nondenaturing electrophoresis of GroEL monomers in the presence of Mg-ATP and, probably, play a key role in the formation of GroEL tetradecameric particle. The role of co-chaperonin GroES in GroEL assembly is also discussed.

Type of Paper: Review
Title: Misfolding of Amyloidogenic Proteins and Their Interactions with Membranes
Authors: Annalisa Relini 1, Nadia Marano 1,2 and Alessandra Gliozzi 1
Affiliations:
1
Department of Physics, University of Genoa, Genoa, Italy
2 Department of Chemistry, Saint Lawrence University, Canton, NY, USA; E-Mail: gliozzi@fisica.unige.it (A.G.)
Abstract: We discuss amyloidogenic proteins, their misfolding, resulting structures, and interactions with membranes, which lead to membrane damage and subsequent cell death. Many of these proteins are implicated in serious illnesses such as Alzheimer’s disease and Parkinson’s disease. Because oligomeric aggregates are widely thought to be the toxic species, we focus on the structure of these aggregates and their interactions with model membranes. Study of interactions of amlyoidogenic proteins with model and natural membranes has led to a realization of the role of the lipid bilayer in protein misfolding and aggregation, and to the development of several models for membrane permeabilization by the resulting amyloid aggregates. We discuss several of these models: formation of structured pores by misfolded amyloidogenic proteins, extraction of lipids by these proteins, interactions of these proteins with receptors in biological membranes, and membrane destabilization perhaps analogous to that caused by antimicrobial peptides.

Type of Paper: Review
Title: Toxin Instability and Its Role in Toxin Translocation from the Endoplasmic Reticulum to the Cytosol
Author: Ken Teter
Affiliation: Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL  32826, USA; E-Mail: kteter@mail.ucf.edu
Abstract: AB toxins enter a host cell by receptor-mediated endocytosis.  The catalytic A chain then crosses the endosome or endoplasmic reticulum (ER) membrane to reach its cytosolic target.  Dissociation of the A chain from the cell-binding B chain occurs before or during translocation to the cytosol, and only the A chain enters the cytosol.  In some cases, AB subunit dissociation is facilitated by the unique physiology and function of the ER. The A chains of these ER-translocating toxins are stable within the architecture of the AB holotoxin, but toxin disassembly results in spontaneous or assisted unfolding of the isolated A chain.  This unfolding event places the A chain in a translocation-competent conformation that promotes its ER-to-cytosol export through the quality control mechanism of ER-associated degradation.  A lack of lysine residues for ubiquitin conjugation protects the exported A chain from degradation by the ubiquitin-proteasome system, and an interaction with host factors allows the cytosolic toxin to regain a folded, active state.  The intrinsic instability of the toxin A chain thus influences multiple steps of the intoxication process.  This review will focus on the host-toxin interactions involved with A chain unfolding in the ER and A chain refolding in the cytosol.

Type of Paper: Article
Title:
Folding Proteins by Neural Network Pairwise Interaction Fields and Iterative Decoy Set Construction
Author:
Gianluca Pollastri
Affiliation: Complex and Adaptive Systems Lab, School of Computer Science and Informatics, UCD Dublin, Belfield, Dublin 4, Ireland; E-Mail: gianluca.pollastri@ucd.ie
Abstract:
Predicting the fold of a protein from its amino acid sequence is one of the grand problems in computational biology. While there has been progress towards a solution, especially when a protein can be modelled based on one or more known structures (templates), in the absence of templates even the best predictions are generally much less reliable. In this paper we present a new approach to protein folding in the absence of templates. This approach relies on a reconstruction procedure guided by a potential function implemented as a class of Artificial Neural Networks we have designed: Neural Network Pairwise Interaction Fields (NNPIF). This potential function takes into account contextual information for each residue, and is trained to identify native-like conformations from non native-like ones by using large sets of decoys as a training set. The training set is iteratively expanded during successive folding simulations. As NNPIF are fast, thousands of models can be evaluated in a short amount of time and clustering techniques can be adopted for model selection. Although the results we present here are preliminary, we consider them to be promising, with predictions being generated at state of the art levels in some of the cases.

Type of Paper: Article
Title:
Kinetics and Thermodynamics of Membrane Protein Folding
Authors:
Ernesto A. Roman and F. Luis González Flecha
Affiliation:
Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Universidad de Buenos Aires-CONICET, Argentina; E-Mail: lgf@qb.ffyb.uba.ar (L.G.F.)
Abstract:
After Anfinsen work demonstrated that protein folding could be efficiently performed in vitro, characterization of protein unfolding and refolding has been extensively attempted. Over the past 40 years a lot of thermodynamic and kinetic studies have been performed addressing the stability of globular proteins. In comparison, advances in the membrane protein folding field has been slower. Although membrane proteins constitute about a third of the proteins encoded in known genomes, obtaining essential data on membrane protein stability has been impaired due to experimental limitations. Despite possible, folding membrane proteins in vitro hitherto lack of systematic experimental strategies. Common denaturing agents such as chaotropes usually do not work on membrane proteins, and ionic detergents have been successful only in few cases. Refolding a membrane protein seems to be a craftsman job; while transmembrane β-barrel proteins easily refold, folding α-helical membrane proteins is challenging. In multidomain membrane proteins additional complexities emerge, being data interpretation one of the most critical. In this review, we focus on membrane proteins that have been reversibly refolded allowing both thermodynamic and kinetic analysis. We will describe some of the better studied systems and discuss the obtained information, comparing it with current understanding of globular protein folding.

Type of Paper: Article
Title:
A Novel Branch-and-Bound Algorithm for the Protein Folding Problem in the 3D-HP Model
Author:
Hsin-Hung Chou 1,*, Chao-Wen Huang 2, Yueh-Chen Lin 2 and Sun-Yuan Hsieh 2
Affiliations:
1 Department of Information Management, Chang Jung Christian University, No.1, Changda Road, Gueiren District, Tainan City 71101, Taiwan; E-Mail: chouhh@mail.cjcu.edu.tw (H.-H. C.); 2 Department of Computer Science and Information Engineering, Institute of Medical Informatics, Institute of Manufacturing Information and Systems, National Cheng Kung University, No. 1, University Road, Tainan City 701, Taiwan; E-Mails: huang_c_w@hotmail.com (C.-W. H.); hsiehsy@mail.ncku.edu.tw (S.-Y. H.); hyde@iis.sinica.edu.tw (Y.-C. Lin.)
Abstract:
The protein folding problem is a fundamental issue in bioinformatics and biochemical physics. The object of the problem is to make a structure prediction of a protein from its amino acid sequence. The problem is a well-known NP-hard problem even under the simplified lattice model. Therefore, the existing algorithms for solving the problem can only predict a near-optimal structure from the benchmark sequences. In this paper, we propose a novel algorithm based on the branch-and-bound strategy to solve the protein folding problem in the 3D HP model. The experiment shows that our algorithm outperforms the other existing approaches.
Keywords:
Bioinformatics; Branch-and-bound algorithm; Computational biology; HP model; Protein folding problem

Type of Paper: Review
Title: Structure and Function of the LmbE-like Superfamily
Author: Marcy Hernick
Affiliation: Department of Pharmaceutical Sciences, Appalachian College of Pharmacy, Oakwood, VA 24631, USA; E-Mail: MHernick@acp.edu (M.H.)
Abstract: The LmbE-like superfamily is comprised of a series of enzymes that use a single catalytic metal ion to catalyze the hydrolysis various substrates. These substrates are often key metabolites for eukaryotes and prokaryotes, which makes the LmbE-like enzymes important targets for drug development. Herein we review the structure and function of the LmbE-like proteins identified to date. While this is the newest superfamily of metallohydrolases, a growing number of functionally interesting proteins from this superfamily have been characterized. Available crystal structures of LmbE-like proteins reveal a Rossman fold similar to lactate dehydrogenase, which represented a novel fold for (zinc) metallohydrolases at the time the initial structure was solved. There is remarkable structural diversity amongst the substrates for the LmbE-like enzymes that translates into functional diversity for this enzyme superfamily. The majority of enzymes identified to date are metal-dependent deacetylases that catalyze the hydrolysis of a N-acetylglucosamine moiety on substrate using a combination of amino acid side chains and a single bound metal ion, most commonly zinc or iron. Additionally, studies indicate that protein dynamics play important roles in regulating access to the active site and facilitating catalysis for at least two members of this protein superfamily.

Type of Paper: Review
Title:
Transient non-native helix formation during folding of b-lactoglobulin
Author:
Masamichi Ikeguchi
Affiliation:
Department of Bioinformatics, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan; E-Mail: ikeguchi@soka.ac.jp (M.I.)
Abstract:
For ideal proteins, only native interactions are stabilized step-by-step in a smooth funnel-like energy landscape. For real proteins, however, transient formation of non-native structures are frequently observed. In this review, transient formation of non-native structure, especially as a prominent example, the non-native helix formation during the folding of b-lactoglobulin is described. Although b-lactoglobulin is a predominantly b-sheet protein, it has been shown to form non-native helices during an early stage of folding. The location of non-native helices, their stabilization mechanism, and their role in the folding reaction will be discussed.

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