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The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Bioorganic Chemistry".

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 42941

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Dr. Marilisa Leone

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Institute of Biostructures and Bioimaging (IBB), National Research Council of Italy (CNR), Via Mezzocannone 16, 80134 Naples, Italy
Interests: structural biology; NMR; drug discovery; conformational analysis of proteins and peptides; protein–protein interactions (PPIs); design and evaluation of PPI inhibitors; structure-based drug design; molecular modeling; docking; cancer
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Dear Colleagues,

Proteins represent one of the most abundant classes of biological macromolecules and play crucial roles in a vast array of physiological and pathological processes. The knowledge of the 3D structure of a protein, as well as the possible conformational transitions occurring upon interaction with diverse ligands, are essential to fully comprehend its biological function.
A part for globular well folded proteins, over the past few years, intrinsically disordered proteins (IDPs) have been put in the spotlight. IDPs are usually aggregation-prone and may form toxic amyloid fibers and oligomers associated with several human pathologies. Structural characterizations of these aggregates along with the search for novel techniques to easily perform such investigations have recently been the subject of intensive studies. Interestingly, IDPs may as well undergo a disorder to order transition upon binding to their targets and produce specific outcomes in a cellular context.
Peptides are smaller in size than proteins but similarly represent key elements of cells. A few peptides are able to work as tumor markers and find applications in the diagnostic and therapeutic fields. Conformational analysis of bioactive peptides is important to design novel potential drugs acting as selective modulators of specific receptors or enzymes. Nevertheless, synthetic peptides reproducing different protein fragments have frequently been implemented as model systems in folding studies relying on structural investigations in water and/or other environments.
This Special Issue will be focused on the above described topics and looks for contributions (communications, full papers, and reviews) related to the latest trends in structural biology. In detail, the issue intends to collect original conformational studies on globular folded proteins, IDPs and bioactive peptides. Works conducted through multidisciplinary approaches—combining several experimental techniques (including but not limited to NMR, X-Ray crystallography, FT-IR, CD, fluorescence spectroscopy) along with computational molecular modeling methodologies—are highly welcome.

Dr. Marilisa Leone
Guest Editor

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Keywords

Protein (peptide) structure and dynamics
Intrinsically disordered proteins
Globular proteins
Protein (peptide)-protein (small molecule) interactions
Structure-based drug design
Multidisciplinary approaches
Structure-activity relationship
Conformational switch
Therapeutic targets

Published Papers (13 papers)

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Editorial

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5 pages, 178 KiB

Open AccessEditorial

Special Issue—The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder

by Marilisa Leone

Molecules 2021, 26(12), 3716; https://doi.org/10.3390/molecules26123716 - 18 Jun 2021

Cited by 1 | Viewed by 1255

Abstract

Among biological macromolecules, proteins hold prominent roles in a vast array of physiological and pathological processes [...] Full article

(This article belongs to the Special Issue The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder)

Research

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21 pages, 39201 KiB

Open AccessArticle

Structure of Nanobody Nb23

by Mathias Percipalle, Yamanappa Hunashal, Jan Steyaert, Federico Fogolari and Gennaro Esposito

Molecules 2021, 26(12), 3567; https://doi.org/10.3390/molecules26123567 - 11 Jun 2021

Cited by 6 | Viewed by 4489

Abstract

Background: Nanobodies, or VHHs, are derived from heavy chain-only antibodies (hcAbs) found in camelids. They overcome some of the inherent limitations of monoclonal antibodies (mAbs) and derivatives thereof, due to their smaller molecular size and higher stability, and thus present an alternative to mAbs for therapeutic use. Two nanobodies, Nb23 and Nb24, have been shown to similarly inhibit the self-aggregation of very amyloidogenic variants of β2-microglobulin. Here, the structure of Nb23 was modeled with the Chemical-Shift (CS)-Rosetta server using chemical shift assignments from nuclear magnetic resonance (NMR) spectroscopy experiments, and used as prior knowledge in PONDEROSA restrained modeling based on experimentally assessed internuclear distances. Further validation was comparatively obtained with the results of molecular dynamics trajectories calculated from the resulting best energy-minimized Nb23 conformers. Methods: 2D and 3D NMR spectroscopy experiments were carried out to determine the assignment of the backbone and side chain hydrogen, nitrogen and carbon resonances to extract chemical shifts and interproton separations for restrained modeling. Results: The solution structure of isolated Nb23 nanobody was determined. Conclusions: The structural analysis indicated that isolated Nb23 has a dynamic CDR3 loop distributed over different orientations with respect to Nb24, which could determine differences in target antigen affinity or complex lability. Full article

(This article belongs to the Special Issue The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder)

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11 pages, 1181 KiB

Open AccessArticle

Patterns in Protein Flexibility: A Comparison of NMR “Ensembles”, MD Trajectories, and Crystallographic B-Factors

by Christopher Reinknecht, Anthony Riga, Jasmin Rivera and David A. Snyder

Molecules 2021, 26(5), 1484; https://doi.org/10.3390/molecules26051484 - 9 Mar 2021

Cited by 5 | Viewed by 2844

Abstract

Proteins are molecular machines requiring flexibility to function. Crystallographic B-factors and Molecular Dynamics (MD) simulations both provide insights into protein flexibility on an atomic scale. Nuclear Magnetic Resonance (NMR) lacks a universally accepted analog of the B-factor. However, a lack of convergence in atomic coordinates in an NMR-based structure calculation also suggests atomic mobility. This paper describes a pattern in the coordinate uncertainties of backbone heavy atoms in NMR-derived structural “ensembles” first noted in the development of FindCore2 (previously called Expanded FindCore: DA Snyder, J Grullon, YJ Huang, R Tejero, GT Montelione, Proteins: Structure, Function, and Bioinformatics 82 (S2), 219–230) and demonstrates that this pattern exists in coordinate variances across MD trajectories but not in crystallographic B-factors. This either suggests that MD trajectories and NMR “ensembles” capture motional behavior of peptide bond units not captured by B-factors or indicates a deficiency common to force fields used in both NMR and MD calculations. Full article

(This article belongs to the Special Issue The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder)

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15 pages, 2563 KiB

Open AccessArticle

Swapping the Positions in a Cross-Strand Lateral Ion-Pairing Interaction between Ammonium- and Carboxylate-Containing Residues in a β-Hairpin

by Cheng-Hsin Huang, Tong Wai Wong, Chen-Hsu Yu, Jing-Yuan Chang, Shing-Jong Huang, Shou-Ling Huang and Richard P. Cheng

Molecules 2021, 26(5), 1346; https://doi.org/10.3390/molecules26051346 - 3 Mar 2021

Cited by 7 | Viewed by 1972

Abstract

Cross-strand lateral ion-pairing interactions are important for antiparallel β-sheet stability. Statistical studies suggested that swapping the position of cross-strand lateral residues should not significantly affect the interaction. Herein, we swapped the position of ammonium- and carboxylate-containing residues with different side-chain lengths in a cross-strand lateral ion-pairing interaction in a β-hairpin. The peptides were analyzed by 2D-NMR. The fraction folded population and folding free energy were derived from the chemical shift data. The ion-pairing interaction energy was derived using double mutant cycle analysis. The general trends for the fraction folded population and interaction energetics remained similar upon swapping the position of the interacting charged residues. The most stabilizing cross-strand interactions were between short residues, similar to the unswapped study. However, the fraction folded populations for most of the swapped peptides were higher compared to the corresponding unswapped peptides. Furthermore, subtle differences in the ion-pairing interaction energy upon swapping were observed, most likely due to the “unleveled” relative positioning of the interacting residues created by the inherent right-handed twist of the structure. These results should be useful for developing functional peptides that rely on lateral ion-pairing interactions across antiparallel β-strands. Full article

(This article belongs to the Special Issue The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder)

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16 pages, 4506 KiB

Open AccessArticle

Dynamic Preference for NADP/H Cofactor Binding/Release in E. coli YqhD Oxidoreductase

by Rajni Verma, Jonathan M. Ellis and Katie R. Mitchell-Koch

Molecules 2021, 26(2), 270; https://doi.org/10.3390/molecules26020270 - 7 Jan 2021

Cited by 4 | Viewed by 2361

Abstract

YqhD, an E. coli alcohol/aldehyde oxidoreductase, is an enzyme able to produce valuable bio-renewable fuels and fine chemicals from a broad range of starting materials. Herein, we report the first computational solution-phase structure-dynamics analysis of YqhD, shedding light on the effect of oxidized and reduced NADP/H cofactor binding on the conformational dynamics of the biocatalyst using molecular dynamics (MD) simulations. The cofactor oxidation states mainly influence the interdomain cleft region conformations of the YqhD monomers, involved in intricate cofactor binding and release. The ensemble of NADPH-bound monomers has a narrower average interdomain space resulting in more hydrogen bonds and rigid cofactor binding. NADP-bound YqhD fluctuates between open and closed conformations, while it was observed that NADPH-bound YqhD had slower opening/closing dynamics of the cofactor-binding cleft. In the light of enzyme kinetics and structural data, simulation findings have led us to postulate that the frequently sampled open conformation of the cofactor binding cleft with NADP leads to the more facile release of NADP while increased closed conformation sampling during NADPH binding enhances cofactor binding affinity and the aldehyde reductase activity of the enzyme. Full article

(This article belongs to the Special Issue The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder)

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20 pages, 27079 KiB

Open AccessArticle

Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

by Lijun Lang and Alberto Perez

Molecules 2021, 26(1), 198; https://doi.org/10.3390/molecules26010198 - 2 Jan 2021

Cited by 12 | Viewed by 2705

Abstract

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (

Δ G_{c o n f o r m a t i o n}

) and the interaction between interface residues (

Δ G_{i n t e r a c t i o n}

). Full article

(This article belongs to the Special Issue The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder)

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23 pages, 3951 KiB

Open AccessArticle

Possible Transmission Flow of SARS-CoV-2 Based on ACE2 Features

by Sk. Sarif Hassan, Shinjini Ghosh, Diksha Attrish, Pabitra Pal Choudhury, Alaa A. A. Aljabali, Bruce D. Uhal, Kenneth Lundstrom, Nima Rezaei, Vladimir N. Uversky, Murat Seyran, Damiano Pizzol, Parise Adadi, Antonio Soares, Tarek Mohamed Abd El-Aziz, Ramesh Kandimalla, Murtaza M. Tambuwala, Gajendra Kumar Azad, Samendra P. Sherchan, Wagner Baetas-da-Cruz, Kazuo Takayama, Ángel Serrano-Aroca, Gaurav Chauhan, Giorgio Palu and Adam M. Brufsky Show full author list Hide full author list

Molecules 2020, 25(24), 5906; https://doi.org/10.3390/molecules25245906 - 13 Dec 2020

Cited by 29 | Viewed by 4954

Abstract

Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that is engendering the severe coronavirus disease 2019 (COVID-19) pandemic. The spike (S) protein receptor-binding domain (RBD) of SARS-CoV-2 binds to the three sub-domains viz. amino acids (aa) 22–42, aa 79–84, and aa 330–393 of ACE2 on human cells to initiate entry. It was reported earlier that the receptor utilization capacity of ACE2 proteins from different species, such as cats, chimpanzees, dogs, and cattle, are different. A comprehensive analysis of ACE2 receptors of nineteen species was carried out in this study, and the findings propose a possible SARS-CoV-2 transmission flow across these nineteen species. Full article

(This article belongs to the Special Issue The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder)

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16 pages, 3650 KiB

Open AccessArticle

Mass Spectrometric Analysis of Antibody—Epitope Peptide Complex Dissociation: Theoretical Concept and Practical Procedure of Binding Strength Characterization

by Bright D. Danquah, Kwabena F. M. Opuni, Claudia Roewer, Cornelia Koy and Michael O. Glocker

Molecules 2020, 25(20), 4776; https://doi.org/10.3390/molecules25204776 - 17 Oct 2020

Cited by 10 | Viewed by 2598

Abstract

Electrospray mass spectrometry is applied to determine apparent binding energies and quasi equilibrium dissociation constants of immune complex dissociation reactions in the gas phase. Myoglobin, a natural protein-ligand complex, has been used to develop the procedure which starts from determining mean charge states [...] Read more.

K_{D m 0 g}^{#} =

3.60 × 10⁻¹² for the gas phase heme dissociation process was calculated from the mass spectrometry data and by subsequent extrapolation to room temperature to mimic collision conditions for neutral and resting myoglobin. Similarly, for RNAse S dissociation at room temperature a

K_{D m 0 g}^{#} =

4.03 × 10⁻¹² was determined. The protocol was tested with two immune complexes consisting of epitope peptides and monoclonal antibodies. For the epitope peptide dissociation reaction of the FLAG peptide from the antiFLAG antibody complex an apparent gas phase dissociation constant

K_{D m 0 g}^{#} =

4.04 × 10⁻¹² was calculated. Likewise, an apparent

K_{D m 0 g}^{#} =

4.58 × 10⁻¹² was calculated for the troponin I epitope peptide—antiTroponin I antibody immune complex dissociation. Electrospray mass spectrometry is a rapid method, which requires small sample amounts for either identification of protein-bound ligands or for determination of the apparent gas phase protein-ligand complex binding strengths. Full article

(This article belongs to the Special Issue The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder)

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Review

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22 pages, 4305 KiB

Open AccessReview

Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins

by Elisia A. Paiz, Karen A. Lewis and Steven T. Whitten

Molecules 2021, 26(3), 634; https://doi.org/10.3390/molecules26030634 - 26 Jan 2021

Cited by 1 | Viewed by 2382

Abstract

The α and polyproline II (PPII) basins are the two most populated regions of the Ramachandran map when constructed from the protein coil library, a widely used denatured state model built from the segments of irregular structure found in the Protein Data Bank. This indicates the α and PPII conformations are dominant components of the ensembles of denatured structures that exist in solution for biological proteins, an observation supported in part by structural studies of short, and thus unfolded, peptides. Although intrinsic conformational propensities have been determined experimentally for the common amino acids in short peptides, and estimated from surveys of the protein coil library, the ability of these intrinsic conformational propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs), an increasingly important class of proteins in cell function, has thus far proven elusive to establish. Recently, we demonstrated that the sequence dependence of the mean hydrodynamic size of IDPs in water and the impact of heat on the coil dimensions, provide access to both the sequence dependence and thermodynamic energies that are associated with biases for the α and PPII backbone conformations. Here, we compare results from peptide-based studies of intrinsic conformational propensities and surveys of the protein coil library to those of the sequence-based analysis of heat effects on IDP hydrodynamic size, showing that a common structural and thermodynamic description of the protein denatured state is obtained. Full article

(This article belongs to the Special Issue The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder)

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17 pages, 2268 KiB

Open AccessReview

Combining High-Pressure Perturbation with NMR Spectroscopy for a Structural and Dynamical Characterization of Protein Folding Pathways

by Cécile Dubois, Isaline Herrada, Philippe Barthe and Christian Roumestand

Molecules 2020, 25(23), 5551; https://doi.org/10.3390/molecules25235551 - 26 Nov 2020

Cited by 14 | Viewed by 3591

Abstract

High-hydrostatic pressure is an alternative perturbation method that can be used to destabilize globular proteins. Generally perfectly reversible, pressure exerts local effects on regions or domains of a protein containing internal voids, contrary to heat or chemical denaturant that destabilize protein structures uniformly. When combined with NMR spectroscopy, high pressure (HP) allows one to monitor at a residue-level resolution the structural transitions occurring upon unfolding and to determine the kinetic properties of the process. The use of HP-NMR has long been hampered by technical difficulties. Owing to the recent development of commercially available high-pressure sample cells, HP-NMR experiments can now be routinely performed. This review summarizes recent advances of HP-NMR techniques for the characterization at a quasi-atomic resolution of the protein folding energy landscape. Full article

(This article belongs to the Special Issue The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder)

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24 pages, 1855 KiB

Open AccessReview

Structure-Function Insights of Jaburetox and Soyuretox: Novel Intrinsically Disordered Polypeptides Derived from Plant Ureases

by Matheus V. Coste Grahl, Fernanda Cortez Lopes, Anne H. Souza Martinelli, Celia R. Carlini and Leonardo L. Fruttero

Molecules 2020, 25(22), 5338; https://doi.org/10.3390/molecules25225338 - 16 Nov 2020

Cited by 6 | Viewed by 3144

Abstract

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) do not have a stable 3D structure but still have important biological activities. Jaburetox is a recombinant peptide derived from the jack bean (Canavalia ensiformis) urease and presents entomotoxic and antimicrobial actions. The structure of Jaburetox was elucidated using nuclear magnetic resonance which reveals it is an IDP with small amounts of secondary structure. Different approaches have demonstrated that Jaburetox acquires certain folding upon interaction with lipid membranes, a characteristic commonly found in other IDPs and usually important for their biological functions. Soyuretox, a recombinant peptide derived from the soybean (Glycine max) ubiquitous urease and homologous to Jaburetox, was also characterized for its biological activities and structural properties. Soyuretox is also an IDP, presenting more secondary structure in comparison with Jaburetox and similar entomotoxic and fungitoxic effects. Moreover, Soyuretox was found to be nontoxic to zebra fish, while Jaburetox was innocuous to mice and rats. This profile of toxicity affecting detrimental species without damaging mammals or the environment qualified them to be used in biotechnological applications. Both peptides were employed to develop transgenic crops and these plants were active against insects and nematodes, unveiling their immense potentiality for field applications. Full article

(This article belongs to the Special Issue The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder)

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24 pages, 6447 KiB

Open AccessReview

ATP Analogues for Structural Investigations: Case Studies of a DnaB Helicase and an ABC Transporter

by Denis Lacabanne, Thomas Wiegand, Nino Wili, Maria I. Kozlova, Riccardo Cadalbert, Daniel Klose, Armen Y. Mulkidjanian, Beat H. Meier and Anja Böckmann

Molecules 2020, 25(22), 5268; https://doi.org/10.3390/molecules25225268 - 12 Nov 2020

Cited by 19 | Viewed by 5824

Abstract

Nucleoside triphosphates (NTPs) are used as chemical energy source in a variety of cell systems. Structural snapshots along the NTP hydrolysis reaction coordinate are typically obtained by adding stable, nonhydrolyzable adenosine triphosphate (ATP) -analogues to the proteins, with the goal to arrest a state that mimics as closely as possible a physiologically relevant state, e.g., the pre-hydrolytic, transition and post-hydrolytic states. We here present the lessons learned on two distinct ATPases on the best use and unexpected pitfalls observed for different analogues. The proteins investigated are the bacterial DnaB helicase from Helicobacter pylori and the multidrug ATP binding cassette (ABC) transporter BmrA from Bacillus subtilis, both belonging to the same division of P-loop fold NTPases. We review the magnetic-resonance strategies which can be of use to probe the binding of the ATP-mimics, and present carbon-13, phosphorus-31, and vanadium-51 solid-state nuclear magnetic resonance (NMR) spectra of the proteins or the bound molecules to unravel conformational and dynamic changes upon binding of the ATP-mimics. Electron paramagnetic resonance (EPR), and in particular W-band electron-electron double resonance (ELDOR)-detected NMR, is of complementary use to assess binding of vanadate. We discuss which analogues best mimic the different hydrolysis states for the DnaB helicase and the ABC transporter BmrA. These might be relevant also to structural and functional studies of other NTPases. Full article

(This article belongs to the Special Issue The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder)

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18 pages, 861 KiB

Open AccessReview

The TRIOBP Isoforms and Their Distinct Roles in Actin Stabilization, Deafness, Mental Illness, and Cancer

by Beti Zaharija, Bobana Samardžija and Nicholas J. Bradshaw

Molecules 2020, 25(21), 4967; https://doi.org/10.3390/molecules25214967 - 27 Oct 2020

Cited by 11 | Viewed by 3312

Abstract

The TRIOBP (TRIO and F-actin Binding Protein) gene encodes multiple proteins, which together play crucial roles in modulating the assembly of the actin cytoskeleton. Splicing of the TRIOBP gene is complex, with the two most studied TRIOBP protein isoforms sharing no overlapping amino acid sequence with each other. TRIOBP-1 (also known as TARA or TAP68) is a mainly structured protein that is ubiquitously expressed and binds to F-actin, preventing its depolymerization. It has been shown to be important for many processes including in the cell cycle, adhesion junctions, and neuronal differentiation. TRIOBP-1 has been implicated in schizophrenia through the formation of protein aggregates in the brain. In contrast, TRIOBP-4 is an entirely disordered protein with a highly specialized expression pattern. It is known to be crucial for the bundling of actin in the stereocilia of the inner ear, with mutations in it causing severe or profound hearing loss. Both of these isoforms are implicated in cancer. Additional longer isoforms of TRIOBP exist, which overlap with both TRIOBP-1 and 4. These appear to participate in the functions of both shorter isoforms, while also possessing unique functions in the inner ear. In this review, the structures and functions of all of these isoforms are discussed, with a view to understanding how they operate, both alone and in combination, to modulate actin and their consequences for human illness. Full article

(This article belongs to the Special Issue The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder)

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