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Advances in Biomolecular Simulation
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Advances in Biomolecular Simulation

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry, Theoretical and Computational Chemistry".

Deadline for manuscript submissions: closed (30 April 2012) | Viewed by 70624

Special Issue Editor

Dr. Sang Kyu Kwak

E-Mail Website
Guest Editor
School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea
Interests: molecular modeling and simulation methods; multidimensional carbon materials; CO2 capture; catalysis

Special Issue Information

Dear Colleagues,

Molecular modeling and simulation studies have been adopted in the fields of biochemistry, molecular biology, and biophysics since its first successful application into the protein simulation. Its well-descriptive ability on atomistic details is the key nature of the welcome acceptance in such scientifically driven fields. Certainly this trend has been significantly increased with the inextricable help of the advance of computer technology and the development of various simulation methodologies. Towards great discoveries of biological systems and phenomena using the biomolecular simulation approaches, we invite scientific research papers and reviews, which particularly concentrate on two main themes. The first theme is about theoretical analysis and determination of protein structures (i.e. primary to quaternary), properties (i.e. physical, chemical, electrical), complexes (i.e. macromolecules with nucleic acids), interactions (i.e. solvent effects, agglomeration, crystallization, folding/unfolding), and functionalities (i.e. roles in cells or through cell membranes, possible mutation). The second theme is about development and application of biomolecular simulation methods, which include sampling, force-field, multiscale approach (i.e. ab-intio, atomistic, coarse-grained) including parallel programming. Addition to indicated themes, it is highly recommended in this special issue if new advanced simulation techniques are introduced, new biological phenomena are found, and entire cell is simulated at atomistic level.

Dr. Sang Kyu Kwak
Guest Editor

Keywords

  • protein structures, properties, complexes, and functionalities
  • protein-cell interaction
  • protein aggregation and crystallization
  • molecular dynamics simulation
  • Monte Carlo simulation
  • multiscale and parallel approach for biological macromolecules

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Published Papers (9 papers)

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Research

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1437 KiB  
Article
Homology Modeling and Analysis of Structure Predictions of the Bovine Rhinitis B Virus RNA Dependent RNA Polymerase (RdRp)
by Devendra K. Rai and Elizabeth Rieder
Int. J. Mol. Sci. 2012, 13(7), 8998-9013; https://doi.org/10.3390/ijms13078998 - 19 Jul 2012
Cited by 19 | Viewed by 8851
Abstract
Bovine Rhinitis B Virus (BRBV) is a picornavirus responsible for mild respiratory infection of cattle. It is probably the least characterized among the aphthoviruses. BRBV is the closest relative known to Foot and Mouth Disease virus (FMDV) with a ~43% identical polyprotein sequence [...] Read more.
Bovine Rhinitis B Virus (BRBV) is a picornavirus responsible for mild respiratory infection of cattle. It is probably the least characterized among the aphthoviruses. BRBV is the closest relative known to Foot and Mouth Disease virus (FMDV) with a ~43% identical polyprotein sequence and as much as 67% identical sequence for the RNA dependent RNA polymerase (RdRp), which is also known as 3D polymerase (3Dpol). In the present study we carried out phylogenetic analysis, structure based sequence alignment and prediction of three-dimensional structure of BRBV 3Dpol using a combination of different computational tools. Model structures of BRBV 3Dpol were verified for their stereochemical quality and accuracy. The BRBV 3Dpol structure predicted by SWISS-MODEL exhibited highest scores in terms of stereochemical quality and accuracy, which were in the range of 2Å resolution crystal structures. The active site, nucleic acid binding site and overall structure were observed to be in agreement with the crystal structure of unliganded as well as template/primer (T/P), nucleotide tri-phosphate (NTP) and pyrophosphate (PPi) bound FMDV 3Dpol (PDB, 1U09 and 2E9Z). The closest proximity of BRBV and FMDV 3Dpol as compared to human rhinovirus type 16 (HRV-16) and rabbit hemorrhagic disease virus (RHDV) 3Dpols is also substantiated by phylogeny analysis and root-mean square deviation (RMSD) between C-α traces of the polymerase structures. The absence of positively charged α-helix at C terminal, significant differences in non-covalent interactions especially salt bridges and CH-pi interactions around T/P channel of BRBV 3Dpol compared to FMDV 3Dpol, indicate that despite a very high homology to FMDV 3Dpol, BRBV 3Dpol may adopt a different mechanism for handling its substrates and adapting to physiological requirements. Our findings will be valuable in the design of structure-function interventions and identification of molecular targets for drug design applicable to Aphthovirus RdRps. Full article
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
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1081 KiB  
Communication
Target Molecular Simulations of RecA Family Protein Filaments
by Zhi-Yuan Su, Wen-Jay Lee, Wan-Sheng Su and Yeng-Tseng Wang
Int. J. Mol. Sci. 2012, 13(6), 7138-7148; https://doi.org/10.3390/ijms13067138 - 11 Jun 2012
Cited by 3 | Viewed by 6376
Abstract
Modeling of the RadA family mechanism is crucial to understanding the DNA SOS repair process. In a 2007 report, the archaeal RadA proteins function as rotary motors (linker region: I71-K88) such as shown in Figure 1. Molecular simulations approaches help to shed further [...] Read more.
Modeling of the RadA family mechanism is crucial to understanding the DNA SOS repair process. In a 2007 report, the archaeal RadA proteins function as rotary motors (linker region: I71-K88) such as shown in Figure 1. Molecular simulations approaches help to shed further light onto this phenomenon. We find 11 rotary residues (R72, T75-K81, M84, V86 and K87) and five zero rotary residues (I71, K74, E82, R83 and K88) in the simulations. Inclusion of our simulations may help to understand the RadA family mechanism. Full article
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
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198 KiB  
Article
Pharmacological Classification and Activity Evaluation of Furan and Thiophene Amide Derivatives Applying Semi-Empirical ab initio Molecular Modeling Methods
by Leszek Bober, Piotr Kawczak and Tomasz Baczek
Int. J. Mol. Sci. 2012, 13(6), 6665-6678; https://doi.org/10.3390/ijms13066665 - 30 May 2012
Cited by 15 | Viewed by 6618
Abstract
Pharmacological and physicochemical classification of the furan and thiophene amide derivatives by multiple regression analysis and partial least square (PLS) based on semi-empirical ab initio molecular modeling studies and high-performance liquid chromatography (HPLC) retention data is proposed. Structural parameters obtained from the PCM [...] Read more.
Pharmacological and physicochemical classification of the furan and thiophene amide derivatives by multiple regression analysis and partial least square (PLS) based on semi-empirical ab initio molecular modeling studies and high-performance liquid chromatography (HPLC) retention data is proposed. Structural parameters obtained from the PCM (Polarizable Continuum Model) method and the literature values of biological activity (antiproliferative for the A431 cells) expressed as LD50 of the examined furan and thiophene derivatives was used to search for relationships. It was tested how variable molecular modeling conditions considered together, with or without HPLC retention data, allow evaluation of the structural recognition of furan and thiophene derivatives with respect to their pharmacological properties. Full article
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
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519 KiB  
Article
Poisson Parameters of Antimicrobial Activity: A Quantitative Structure-Activity Approach
by Radu E. Sestraş, Lorentz Jäntschi and Sorana D. Bolboacă
Int. J. Mol. Sci. 2012, 13(4), 5207-5229; https://doi.org/10.3390/ijms13045207 - 24 Apr 2012
Cited by 7 | Viewed by 7869
Abstract
A contingency of observed antimicrobial activities measured for several compounds vs. a series of bacteria was analyzed. A factor analysis revealed the existence of a certain probability distribution function of the antimicrobial activity. A quantitative structure-activity relationship analysis for the overall antimicrobial [...] Read more.
A contingency of observed antimicrobial activities measured for several compounds vs. a series of bacteria was analyzed. A factor analysis revealed the existence of a certain probability distribution function of the antimicrobial activity. A quantitative structure-activity relationship analysis for the overall antimicrobial ability was conducted using the population statistics associated with identified probability distribution function. The antimicrobial activity proved to follow the Poisson distribution if just one factor varies (such as chemical compound or bacteria). The Poisson parameter estimating antimicrobial effect, giving both mean and variance of the antimicrobial activity, was used to develop structure-activity models describing the effect of compounds on bacteria and fungi species. Two approaches were employed to obtain the models, and for every approach, a model was selected, further investigated and found to be statistically significant. The best predictive model for antimicrobial effect on bacteria and fungi species was identified using graphical representation of observed vs. calculated values as well as several predictive power parameters. Full article
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
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Graphical abstract

745 KiB  
Article
The Effect of C-Terminal Helix on the Stability of FF Domain Studied by Molecular Dynamics Simulation
by Liling Zhao, Zanxia Cao and Jihua Wang
Int. J. Mol. Sci. 2012, 13(2), 1720-1732; https://doi.org/10.3390/ijms13021720 - 7 Feb 2012
Cited by 1 | Viewed by 6302
Abstract
To investigate the effect of C-terminal helix on the stability of the FF domain, we studied the native domain FF3-71 from human HYPA/FBP11 and the truncated version FF3-60 with C-terminal helix being deleted by molecular dynamics simulations with GROMACS package and [...] Read more.
To investigate the effect of C-terminal helix on the stability of the FF domain, we studied the native domain FF3-71 from human HYPA/FBP11 and the truncated version FF3-60 with C-terminal helix being deleted by molecular dynamics simulations with GROMACS package and GROMOS 43A1 force field. The results indicated that the structures of truncated version FF3-60 were evident different from those of native partner FF3-71. Compared with FF3-71, the FF3-60 lost some native contacts and exhibited some similar structural characters to those of intermediate state. The C-terminal helix played a major role in stabilizing the FF3-71 domain. To a certain degree, the FF domain had a tendency to form an intermediate state without the C-terminal helix. In our knowledge, this was the first study to examine the role of C-terminal helix of FF domain in detail by molecular dynamics simulations, which was useful to understand the three-state folding mechanism of the small FF domain. Full article
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
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Graphical abstract

717 KiB  
Article
Effects of Different Force Fields and Temperatures on the Structural Character of Abeta (12–28) Peptide in Aqueous Solution
by Zanxia Cao, Lei Liu, Liling Zhao and Jihua Wang
Int. J. Mol. Sci. 2011, 12(11), 8259-8274; https://doi.org/10.3390/ijms12118259 - 21 Nov 2011
Cited by 20 | Viewed by 6601
Abstract
The aim of this work is to investigate the effects of different force fields and temperatures on the structural character of Aβ (12–28) peptide in aqueous solution. Moreover, the structural character of Aβ (12–28) peptide is compared with other amyloid peptides (such as [...] Read more.
The aim of this work is to investigate the effects of different force fields and temperatures on the structural character of Aβ (12–28) peptide in aqueous solution. Moreover, the structural character of Aβ (12–28) peptide is compared with other amyloid peptides (such as H1 and α-syn12 peptide). The two independent temperature replica exchange molecular dynamics (T-REMD) simulations were completed by using two different models (OPLS-AA/TIP4P and GROMOS 43A1/SPC). We compared the models by analyzing the distributions of backbone dihedral angles, the secondary structure propensity, the free energy surface and the formation of β-hairpin. The results show that the mostly populated conformation state is random coil for both models. The population of β-hairpin is below 8 percent for both models. However, the peptide modeled by GROMOS 43A1 form β-hairpin with turn located at residues F19-E22, while the peptide modeled by OPLS-AA form β-hairpin with turn located at residues L17-F20. Full article
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
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Review

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628 KiB  
Review
Multiscale Models of the Antimicrobial Peptide Protegrin-1 on Gram-Negative Bacteria Membranes
by Dan S. Bolintineanu, Victor Vivcharuk and Yiannis N. Kaznessis
Int. J. Mol. Sci. 2012, 13(9), 11000-11011; https://doi.org/10.3390/ijms130911000 - 5 Sep 2012
Cited by 15 | Viewed by 7047
Abstract
Antimicrobial peptides (AMPs) are naturally-occurring molecules that exhibit strong antibiotic properties against numerous infectious bacterial strains. Because of their unique mechanism of action, they have been touted as a potential source for novel antibiotic drugs. We present a summary of computational investigations in [...] Read more.
Antimicrobial peptides (AMPs) are naturally-occurring molecules that exhibit strong antibiotic properties against numerous infectious bacterial strains. Because of their unique mechanism of action, they have been touted as a potential source for novel antibiotic drugs. We present a summary of computational investigations in our lab aimed at understanding this unique mechanism of action, in particular the development of models that provide a quantitative connection between molecular-level biophysical phenomena and relevant biological effects. Our work is focused on protegrins, a potent class of AMPs that attack bacteria by associating with the bacterial membrane and forming transmembrane pores that facilitate the unrestricted transport of ions. Using fully atomistic molecular dynamics simulations, we have computed the thermodynamics of peptide-membrane association and insertion, as well as peptide aggregation. We also present a multi-scale analysis of the ion transport properties of protegrin pores, ranging from atomistic molecular dynamics simulations to mesoscale continuum models of single-pore electrodiffusion to models of transient ion transport from bacterial cells. Overall, this work provides a quantitative mechanistic description of the mechanism of action of protegrin antimicrobial peptides across multiple length and time scales. Full article
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
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625 KiB  
Review
Molecular Dynamic Simulation Insights into the Normal State and Restoration of p53 Function
by Ting Fu, Hanyi Min, Yong Xu, Jianzhong Chen and Guohui Li
Int. J. Mol. Sci. 2012, 13(8), 9709-9740; https://doi.org/10.3390/ijms13089709 - 3 Aug 2012
Cited by 27 | Viewed by 10347
Abstract
As a tumor suppressor protein, p53 plays a crucial role in the cell cycle and in cancer prevention. Almost 50 percent of all human malignant tumors are closely related to a deletion or mutation in p53. The activity of p53 is inhibited by [...] Read more.
As a tumor suppressor protein, p53 plays a crucial role in the cell cycle and in cancer prevention. Almost 50 percent of all human malignant tumors are closely related to a deletion or mutation in p53. The activity of p53 is inhibited by over-active celluar antagonists, especially by the over-expression of the negative regulators MDM2 and MDMX. Protein-protein interactions, or post-translational modifications of the C-terminal negative regulatory domain of p53, also regulate its tumor suppressor activity. Restoration of p53 function through peptide and small molecular inhibitors has become a promising strategy for novel anti-cancer drug design and development. Molecular dynamics simulations have been extensively applied to investigate the conformation changes of p53 induced by protein-protein interactions and protein-ligand interactions, including peptide and small molecular inhibitors. This review focuses on the latest MD simulation research, to provide an overview of the current understanding of interactions between p53 and its partners at an atomic level. Full article
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
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6798 KiB  
Review
Spatial Simulations in Systems Biology: From Molecules to Cells
by Michael Klann and Heinz Koeppl
Int. J. Mol. Sci. 2012, 13(6), 7798-7827; https://doi.org/10.3390/ijms13067798 - 21 Jun 2012
Cited by 46 | Viewed by 9900
Abstract
Cells are highly organized objects containing millions of molecules. Each biomolecule has a specific shape in order to interact with others in the complex machinery. Spatial dynamics emerge in this system on length and time scales which can not yet be modeled with [...] Read more.
Cells are highly organized objects containing millions of molecules. Each biomolecule has a specific shape in order to interact with others in the complex machinery. Spatial dynamics emerge in this system on length and time scales which can not yet be modeled with full atomic detail. This review gives an overview of methods which can be used to simulate the complete cell at least with molecular detail, especially Brownian dynamics simulations. Such simulations require correct implementation of the diffusion-controlled reaction scheme occurring on this level. Implementations and applications of spatial simulations are presented, and finally it is discussed how the atomic level can be included for instance in multi-scale simulation methods. Full article
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
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