Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
4.7
2.7
Journals
Entropy
Special Issues
Molecular Dynamics Simulations of Biomolecules
entropy-logo
Submit to Entropy Review for Entropy Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Molecular Dynamics Simulations of Biomolecules

A special issue of Entropy (ISSN 1099-4300). This special issue belongs to the section "Statistical Physics".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 11696

Special Issue Editors

Dr. Donald J. Jacobs

E-Mail Website
Guest Editor
Department of Physics and Optical Science, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
Interests: statistical physics; biophysics; intelligent algorithms; adaptive control; inverse problems; optimization; simulation, computational modeling; multiscale modeling; data analytics; stochastic processes; extreme statistics; data reduction; machine learning
Special Issues, Collections and Topics in MDPI journals
Dr. Amar Singh

E-Mail Website
Guest Editor
Center for Computational Biology, The University of Kansas, Lawrence, KS 66047, USA
Interests: molecular dynamics; biophysics; computational biology; protein-protein interactions; nucleic acid structure & dynamics

Special Issue Information

Dear Colleagues,

Understanding the dynamics and interactions of biomolecules is fundamental in life sciences. Over the past 50 years, Molecular dynamics (MD) simulations have been elucidating these interactions and underling conformational transitions. Since that time, MD computational studies have played a critical role in both detailed atomic-scale and coarse-grained level information of a physical system. The MD simulation techniques have established their relevance in modern drug development processes, all-atom simulations of protein folding, protein–ligand docking, and mechanisms of large biomolecular networks. In life sciences, MD simulations are used to mimic the molecular motions and interactions of biological molecules over a given period of time, to gain insight into the behavior of an actual physical process, and to understand a wide range of chemical and biological functions. With remarkable advances in computing hardware and theoretical advancement, it is now possible to run longer MD simulations and thus a highly promising future of MD simulations.

Within the framework of the above overview, Entropy presents a Special Issue on “Molecular Dynamics Simulations of Biomolecules”. The aim of this Special Issue is to present recent applications of MD simulations in life sciences, especially in the context of interactions and free energy landscapes. This Special Issue is open to researchers working with MD simulations at any of these levels: a) thermodynamics, b) dynamics, and c) structural or conformational transitions. Original research papers and review articles that address the MD simulations of biomolecules are all welcome.

Dr. Donald Jacobs
Dr. Amar Singh
Guest Editors

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. Entropy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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 dynamics simulations
  • all-atom or coarse-grained simulations
  • force field development
  • free energy landscape
  • protein structure and dynamics
  • nucleic acid structure and dynamics
  • protein–ligand interaction
  • protein–protein interactions
  • lipid–drug interaction
  • statistical ensembles
  • thermodynamics of biomolecules
  • entropy and phase transitions
  • Monte Carlo simulations
  • enhanced sampling techniques

Published Papers (4 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

13 pages, 6152 KiB  
Article
Oleuropein as a Potent Compound against Neurological Complications Linked with COVID-19: A Computational Biology Approach
by Talib Hussain, Alaa Hamed Habib, Misbahuddin M. Rafeeq, Ahmed Alafnan, El-Sayed Khafagy, Danish Iqbal, Qazi Mohammad Sajid Jamal, Rahamat Unissa, Dinesh C. Sharma, Afrasim Moin and Syed Mohd Danish Rizvi
Entropy 2022, 24(7), 881; https://doi.org/10.3390/e24070881 - 26 Jun 2022
Cited by 4 | Viewed by 2846
Abstract
The association of COVID-19 with neurological complications is a well-known fact, and researchers are endeavoring to investigate the mechanistic perspectives behind it. SARS-CoV-2 can bind to Toll-like receptor 4 (TLR-4) that would eventually lead to α-synuclein aggregation in neurons and stimulation of neurodegeneration [...] Read more.
The association of COVID-19 with neurological complications is a well-known fact, and researchers are endeavoring to investigate the mechanistic perspectives behind it. SARS-CoV-2 can bind to Toll-like receptor 4 (TLR-4) that would eventually lead to α-synuclein aggregation in neurons and stimulation of neurodegeneration pathways. Olive leaves have been reported as a promising phytotherapy or co-therapy against COVID-19, and oleuropein is one of the major active components of olive leaves. In the current study, oleuropein was investigated against SARS-CoV-2 target (main protease 3CLpro), TLR-4 and Prolyl Oligopeptidases (POP), to explore oleuropein potency against the neurological complications associated with COVID-19. Docking experiments, docking validation, interaction analysis, and molecular dynamic simulation analysis were performed to provide insight into the binding pattern of oleuropein with the three target proteins. Interaction analysis revealed strong bonding between oleuropein and the active site amino acid residues of the target proteins. Results were further compared with positive control lopinavir (3CLpro), resatorvid (TLR-4), and berberine (POP). Moreover, molecular dynamic simulation was performed using YASARA structure tool, and AMBER14 force field was applied to examine an 100 ns trajectory run. For each target protein-oleuropein complex, RMSD, RoG, and total potential energy were estimated, and 400 snapshots were obtained after each 250 ps. Docking analyses showed binding energy as −7.8, −8.3, and −8.5 kcal/mol for oleuropein-3CLpro, oleuropein-TLR4, and oleuropein-POP interactions, respectively. Importantly, target protein-oleuropein complexes were stable during the 100 ns simulation run. However, an experimental in vitro study of the binding of oleuropein to the purified targets would be necessary to confirm the present study outcomes. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Biomolecules)
►▼ Show Figures

Figure 1

22 pages, 2767 KiB  
Article
Functional Dynamics of Substrate Recognition in TEM Beta-Lactamase
by Chris Avery, Lonnie Baker and Donald J. Jacobs
Entropy 2022, 24(5), 729; https://doi.org/10.3390/e24050729 - 20 May 2022
Cited by 3 | Viewed by 2151
Abstract
The beta-lactamase enzyme provides effective resistance to beta-lactam antibiotics due to substrate recognition controlled by point mutations. Recently, extended-spectrum and inhibitor-resistant mutants have become a global health problem. Here, the functional dynamics that control substrate recognition in TEM beta-lactamase are investigated using all-atom [...] Read more.
The beta-lactamase enzyme provides effective resistance to beta-lactam antibiotics due to substrate recognition controlled by point mutations. Recently, extended-spectrum and inhibitor-resistant mutants have become a global health problem. Here, the functional dynamics that control substrate recognition in TEM beta-lactamase are investigated using all-atom molecular dynamics simulations. Comparisons are made between wild-type TEM-1 and TEM-2 and the extended-spectrum mutants TEM-10 and TEM-52, both in apo form and in complex with four different antibiotics (ampicillin, amoxicillin, cefotaxime and ceftazidime). Dynamic allostery is predicted based on a quasi-harmonic normal mode analysis using a perturbation scan. An allosteric mechanism known to inhibit enzymatic function in TEM beta-lactamase is identified, along with other allosteric binding targets. Mechanisms for substrate recognition are elucidated using multivariate comparative analysis of molecular dynamics trajectories to identify changes in dynamics resulting from point mutations and ligand binding, and the conserved dynamics, which are functionally important, are extracted as well. The results suggest that the H10-H11 loop (residues 214-221) is a secondary anchor for larger extended spectrum ligands, while the H9-H10 loop (residues 194-202) is distal from the active site and stabilizes the protein against structural changes. These secondary non-catalytically-active loops offer attractive targets for novel noncompetitive inhibitors of TEM beta-lactamase. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Biomolecules)
►▼ Show Figures

Graphical abstract

19 pages, 9906 KiB  
Article
Soyasapogenol-B as a Potential Multitarget Therapeutic Agent for Neurodegenerative Disorders: Molecular Docking and Dynamics Study
by Danish Iqbal, Syed Mohd Danish Rizvi, Md Tabish Rehman, M. Salman Khan, Abdulaziz Bin Dukhyil, Mohamed F. AlAjmi, Bader Mohammed Alshehri, Saeed Banawas, Qamar Zia, Mohammed Alsaweed, Yahya Madkhali, Suliman A. Alsagaby and Wael Alturaiki
Entropy 2022, 24(5), 593; https://doi.org/10.3390/e24050593 - 23 Apr 2022
Cited by 10 | Viewed by 2793
Abstract
Neurodegenerative disorders involve various pathophysiological pathways, and finding a solution for these issues is still an uphill task for the scientific community. In the present study, a combination of molecular docking and dynamics approaches was applied to target different pathways leading to neurodegenerative [...] Read more.
Neurodegenerative disorders involve various pathophysiological pathways, and finding a solution for these issues is still an uphill task for the scientific community. In the present study, a combination of molecular docking and dynamics approaches was applied to target different pathways leading to neurodegenerative disorders such as Alzheimer’s disease. Initially, abrineurin natural inducers were screened using physicochemical properties and toxicity assessment. Out of five screened compounds, a pentacyclic triterpenoid, i.e., Soyasapogenol B appeared to be the most promising after molecular docking and simulation analysis. Soyasapogenol B showed low TPSA (60.69), high absorption (82.6%), no Lipinski rule violation, and no toxicity. Docking interaction analysis revealed that Soyasapogenol B bound effectively to all of the targeted proteins (AChE, BuChE MAO-A, MAO-B, GSK3β, and NMDA), in contrast to other screened abrineurin natural inducers and inhibitors. Importantly, Soyasapogenol B bound to active site residues of the targeted proteins in a similar pattern to the native ligand inhibitor. Further, 100 ns molecular dynamics simulations analysis showed that Soyasapogenol B formed stable complexes against all of the targeted proteins. RMSD analysis showed that the Soyasapogenol B–protein complex exhibited average RMSD values of 1.94 Å, 2.11 Å, 5.07 Å, 2.56 Å, 3.83 Å and 4.07 Å. Furthermore, the RMSF analysis and secondary structure analysis also indicated the stability of the Soyasapogenol B–protein complexes. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Biomolecules)
►▼ Show Figures

Figure 1

Review

Jump to: Research

24 pages, 1250 KiB  
Review
Structure and Dynamics of dsDNA in Cell-like Environments
by Amar Singh, Arghya Maity and Navin Singh
Entropy 2022, 24(11), 1587; https://doi.org/10.3390/e24111587 - 01 Nov 2022
Cited by 6 | Viewed by 2298
Abstract
Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA’s structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. [...] Read more.
Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA’s structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. Stability and structural dynamics of dsDNA play an important role in molecular biology. In vivo, DNA molecules are folded in a tightly confined space, such as a cell chamber or a channel, and are highly dense in solution; their conformational properties are restricted, which affects their thermodynamics and mechanical properties. There are also many technical medical purposes for which DNA is placed in a confined space, such as gene therapy, DNA encapsulation, DNA mapping, etc. Physiological conditions and the nature of confined spaces have a significant influence on the opening or denaturation of DNA base pairs. In this review, we summarize the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions. We include studies on various thermal and mechanical properties of dsDNA in ionic solutions, molecular crowded environments, and confined spaces. By providing a better understanding of melting and unzipping of dsDNA in different environments, this review provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA/RNA nanostructures. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Biomolecules)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-4
Back to TopTop