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Atomistic and Coarse-Grained Simulations in Biological Systems

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (24 June 2019) | Viewed by 10280

Special Issue Editor


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Guest Editor
Institut de Physique de Rennes, Univ Rennes, F-35000 Rennes, France Rennes CEDEX 05, France
Interests: molecular simulation; confinement effects; water and ions transport; interfacial properties; hydration; hydrogen bonds

Special Issue Information

Dear colleagues, 

Classical molecular dynamics (MD) simulation of proteins has emerged as a complementary tool to experiments. Its appeal to fully describe biomolecular structures and dynamics at an atomistic level, combined with advancements in computer hardware and algorithms, have led to an ever-growing interest in simulations of increasing size and length.

These last two decades, molecular simulation has emerged as a very powerful method and complementary tool to experiments to investigate matter at the nanoscale and has greatly benefited the understanding of microscopic mechanisms ruling the biomolecular processes, such as folding protein, hydration biomolecules, supramolecular assemblies, etc. To correctly investigate them at the molecular level and to capture their structural, dynamical and thermodynamical properties, many computational efforts have been devoted to developing atomistic and mesoscopic models and methodologies to sample large time and spatial scales. The growing developments in these fields have motivated us to launch this Special Issue on "Atomistic and Coarse-grained Simulations in Biological Systems" in the International Journal of Molecular Sciences. We expect that it will offer the computational community an opportunity to expose and review the latest and most significant achievements in these domains.

As an expert in this field, we are very pleased to invite you to submit original papers, communications, and reviews for this Special Issue of IJMS, an MDPI open-access journal (IF 3.687). We have fixed a deadline for June 2019.

Thank you for your time and consideration, we look forward to hearing from you and receiving your contribution to this Special Issue.

Prof. Aziz Ghoufi
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular simulations
  • coarse graining
  • protein
  • hydration
  • biomolecules
  • folding
  • assemblies

Published Papers (2 papers)

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Research

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13 pages, 2195 KiB  
Article
The Observation of Ligand-Binding-Relevant Open States of Fatty Acid Binding Protein by Molecular Dynamics Simulations and a Markov State Model
by Yue Guo, Mojie Duan and Minghui Yang
Int. J. Mol. Sci. 2019, 20(14), 3476; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20143476 - 15 Jul 2019
Cited by 13 | Viewed by 3297
Abstract
As a member of the fatty acids transporter family, the heart fatty acid binding proteins (HFABPs) are responsible for many important biological activities. The binding mechanism of fatty acid with FABP is critical to the understanding of FABP functions. The uncovering of binding-relevant [...] Read more.
As a member of the fatty acids transporter family, the heart fatty acid binding proteins (HFABPs) are responsible for many important biological activities. The binding mechanism of fatty acid with FABP is critical to the understanding of FABP functions. The uncovering of binding-relevant intermediate states and interactions would greatly increase our knowledge of the binding process. In this work, all-atom molecular dynamics (MD) simulations were performed to characterize the structural properties of nativelike intermediate states. Based on multiple 6 μs MD simulations and Markov state model (MSM) analysis, several “open” intermediate states were observed. The transition rates between these states and the native closed state are in good agreement with the experimental measurements, which indicates that these intermediate states are binding relevant. As a common property in the open states, the partially unfolded α2 helix generates a larger portal and provides the driving force to facilitate ligand binding. On the other side, there are two kinds of open states for the ligand-binding HFABP: one has the partially unfolded α2 helix, and the other has the looser β-barrel with disjointing βD-βE strands. Our results provide atomic-level descriptions of the binding-relevant intermediate states and could improve our understanding of the binding mechanism. Full article
(This article belongs to the Special Issue Atomistic and Coarse-Grained Simulations in Biological Systems)
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Review

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21 pages, 788 KiB  
Review
Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications
by Nidhi Singh and Wenjin Li
Int. J. Mol. Sci. 2019, 20(15), 3774; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20153774 - 01 Aug 2019
Cited by 71 | Viewed by 6590
Abstract
Molecular dynamics simulations have emerged as a powerful tool to study biological systems at varied length and timescales. The conventional all-atom molecular dynamics simulations are being used by the wider scientific community in routine to capture the conformational dynamics and local motions. In [...] Read more.
Molecular dynamics simulations have emerged as a powerful tool to study biological systems at varied length and timescales. The conventional all-atom molecular dynamics simulations are being used by the wider scientific community in routine to capture the conformational dynamics and local motions. In addition, recent developments in coarse-grained models have opened the way to study the macromolecular complexes for time scales up to milliseconds. In this review, we have discussed the principle, applicability and recent development in coarse-grained models for biological systems. The potential of coarse-grained simulation has been reviewed through state-of-the-art examples of protein folding and structure prediction, self-assembly of complexes, membrane systems and carbohydrates fiber models. The multiscale simulation approaches have also been discussed in the context of their emerging role in unravelling hierarchical level information of biosystems. We conclude this review with the future scope of coarse-grained simulations as a constantly evolving tool to capture the dynamics of biosystems. Full article
(This article belongs to the Special Issue Atomistic and Coarse-Grained Simulations in Biological Systems)
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