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Molecular Dynamics Simulations of Biomacromolecules

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

Deadline for manuscript submissions: 30 June 2024 | Viewed by 3521

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Dr. Song Wang

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Guest Editor

Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
Interests: molecular dynamics simulation; computational biology; theoretical chemistry; calculational chemistry; biomacromolecule

Dr. Hao Zhang

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Guest Editor

Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
Interests: molecular dynamics simulation; computational biology; theoretical chemistry; calculational chemistry; biomacromolecule

Special Issue Information

Dear Colleagues,

Molecular dynamics simulation is an important method used to study the structure and properties of molecular systems, and it has been widely used in chemistry, biomedicine, materials science and engineering, physics and other disciplines. This Special Issue focuses on various aspects of the molecular dynamics simulation of biological macromolecules, including, but not limited to, biology, medicine, food, materials, environment, etc. Research methods include, but are not limited to, three-dimensional protein model construction, structural biology research, molecular docking, dynamic result analysis, etc., aiming to understand the internal mechanism of biological macromolecules. Papers focusing on innovative approaches to molecular dynamics are also welcome. We hope that this Special Issue will stimulate the interest of authors and readers and make an important contribution to the field of computational biology.

Dr. Song Wang
Dr. Hao Zhang
Guest Editors

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Keywords

molecular dynamics simulation
computational biology
theoretical chemistry
calculational chemistry
biomacromolecule

Published Papers (5 papers)

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Research

24 pages, 2446 KiB

Open AccessArticle

Molecular Dynamics Simulation of Kir6.2 Variants Reveals Potential Association with Diabetes Mellitus

by Mohamed E. Elangeeb, Imadeldin Elfaki, Ali M. S. Eleragi, Elsadig Mohamed Ahmed, Rashid Mir, Salem M. Alzahrani, Ruqaiah I. Bedaiwi, Zeyad M. Alharbi, Mohammad Muzaffar Mir, Mohammad Rehan Ajmal, Faris Jamal Tayeb and Jameel Barnawi

Molecules 2024, 29(8), 1904; https://doi.org/10.3390/molecules29081904 - 22 Apr 2024

Viewed by 339

Abstract

Diabetes mellitus (DM) represents a problem for the healthcare system worldwide. DM has very serious complications such as blindness, kidney failure, and cardiovascular disease. In addition to the very bad socioeconomic impacts, it influences patients and their families and communities. The global costs of DM and its complications are huge and expected to rise by the year 2030. DM is caused by genetic and environmental risk factors. Genetic testing will aid in early diagnosis and identification of susceptible individuals or populations using ATP-sensitive potassium (K_ATP) channels present in different tissues such as the pancreas, myocardium, myocytes, and nervous tissues. The channels respond to different concentrations of blood sugar, stimulation by hormones, or ischemic conditions. In pancreatic cells, they regulate the secretion of insulin and glucagon. Mutations in the KCNJ11 gene that encodes the Kir6.2 protein (a major constituent of K_ATP channels) were reported to be associated with Type 2 DM, neonatal diabetes mellitus (NDM), and maturity-onset diabetes of the young (MODY). Kir6.2 harbors binding sites for ATP and phosphatidylinositol 4,5-diphosphate (PIP2). The ATP inhibits the K_ATP channel, while the (PIP2) activates it. A Kir6.2 mutation at tyrosine330 (Y330) was demonstrated to reduce ATP inhibition and predisposes to NDM. In this study, we examined the effect of mutations on the Kir6.2 structure using bioinformatics tools and molecular dynamic simulations (SIFT, PolyPhen, SNAP2, PANTHER, PhD&SNP, SNP&Go, I-Mutant, MuPro, MutPred, ConSurf, HOPE, and GROMACS). Our results indicated that M199R, R201H, R206H, and Y330H mutations influence Kir6.2 structure and function and therefore may cause DM. We conclude that MD simulations are useful techniques to predict the effects of mutations on protein structure. In addition, the M199R, R201H, R206H, and Y330H variant in the Kir6.2 protein may be associated with DM. These results require further verification in protein–protein interactions, Kir6.2 function, and case-control studies. Full article

(This article belongs to the Special Issue Molecular Dynamics Simulations of Biomacromolecules)

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13 pages, 2922 KiB

Open AccessArticle

The Recognition Pathway of the SARS-CoV-2 Spike Receptor-Binding Domain to Human Angiotensin-Converting Enzyme 2

by Can Peng, Xinyue Lv, Zhiqiang Zhang, Jianping Lin and Dongmei Li

Molecules 2024, 29(8), 1875; https://doi.org/10.3390/molecules29081875 - 19 Apr 2024

Viewed by 228

Abstract

COVID-19 caused by SARS-CoV-2 has spread around the world. The receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 is a critical component that directly interacts with host ACE2. Here, we simulate the ACE2 recognition processes of RBD of the WT, Delta, and OmicronBA.2 variants using our recently developed supervised Gaussian accelerated molecular dynamics (Su-GaMD) approach. We show that RBD recognizes ACE2 through three contact regions (regions I, II, and III), which aligns well with the anchor–locker mechanism. The higher binding free energy in State d of the RBD_OmicronBA.₂-ACE2 system correlates well with the increased infectivity of OmicronBA.2 in comparison with other variants. For RBD_Delta, the T478K mutation affects the first step of recognition, while the L452R mutation, through its nearby Y449, affects the RBD_Delta-ACE2 binding in the last step of recognition. For RBD_OmicronBA.₂, the E484A mutation affects the first step of recognition, the Q493R, N501Y, and Y505H mutations affect the binding free energy in the last step of recognition, mutations in the contact regions affect the recognition directly, and other mutations indirectly affect recognition through dynamic correlations with the contact regions. These results provide theoretical insights for RBD-ACE2 recognition and may facilitate drug design against SARS-CoV-2. Full article

(This article belongs to the Special Issue Molecular Dynamics Simulations of Biomacromolecules)

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14 pages, 7979 KiB

Open AccessArticle

Mechanism of Mutation-Induced Effects on the Catalytic Function of TEV Protease: A Molecular Dynamics Study

by Jingyao Wang, Yicong Xu, Xujian Wang, Jiahuang Li and Zichun Hua

Molecules 2024, 29(5), 1071; https://doi.org/10.3390/molecules29051071 - 29 Feb 2024

Viewed by 637

Abstract

Tobacco etch virus protease (TEVp) is wildly exploited for various biotechnological applications. These applications take advantage of TEVp’s ability to cleave specific substrate sequences to study protein function and interactions. A major limitation of this enzyme is its relatively slow catalytic rate. In this study, MD simulations were conducted on TEV enzymes and known highly active mutants (eTEV and uTEV3) to explore the relationship between mutation, conformation, and catalytic function. The results suggest that mutations distant from the active site can influence the substrate-binding pocket through interaction networks. MD analysis of eTEV demonstrates that, by stabilizing the orientation of the substrate at the catalytic site, mutations that appropriately enlarge the substrate-binding pocket will be beneficial for Kcat, enhancing the catalytic efficiency of the enzyme. On the contrary, mutations in uTEV3 reduced the flexibility of the active pocket and increased the hydrogen bonding between the substrate and enzyme, resulting in higher affinity. At the same time, the MD simulation demonstrates that mutations outside of the active site residues could affect the dynamic movement of the binding pocket by altering residue networks and communication pathways, thereby having a profound impact on reactivity. These findings not only provide a molecular mechanistic explanation for the excellent mutants, but also serve as a guiding framework for rational computational design. Full article

(This article belongs to the Special Issue Molecular Dynamics Simulations of Biomacromolecules)

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21 pages, 12912 KiB

Open AccessArticle

Insight into the Inhibitory Mechanism of Embryonic Ectoderm Development Subunit by Triazolopyrimidine Derivatives as Inhibitors through Molecular Dynamics Simulation

by Jianan Ju, Hao Zhang, Shanshan Guan, Chang Liu, Juan Du, Xiaoli Shen and Song Wang

Molecules 2023, 28(24), 7997; https://doi.org/10.3390/molecules28247997 - 07 Dec 2023

Viewed by 700

Abstract

Inhibition of the Embryonic Ectoderm Development (EED) subunit in Polycomb Repressive Complex 2 (PRC2) can inhibit tumor growth. In this paper, we selected six experimentally designed EED competitive Inhibitors of the triazolopyrimidine derivatives class. We investigated the difference in the binding mode of the natural substrate to the Inhibitors and the effects of differences in the parent nuclei, heads, and tails of the Inhibitors on the inhibitory capacity. The results showed that the binding free energy of this class of Inhibitors was close to or lower compared to the natural substrate, providing an energetic basis for competitive inhibition. For the Inhibitors, the presence of a strong negatively charged group at the 6-position of the parent nucleus or the 8′-position of the head would make the hydrogen atom on the head imino group prone to flip, resulting in the vertical movement of the parent nucleus, which significantly decreased the inhibitory ability. When the 6-position of the parent nucleus was a nonpolar group, the parent nucleus would move horizontally, slightly decreasing the inhibitory ability. When the 8′-position of the head was methylene, it formed an intramolecular hydrophobic interaction with the benzene ring on the tail, resulting in a significant increase in inhibition ability. Full article

(This article belongs to the Special Issue Molecular Dynamics Simulations of Biomacromolecules)

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21 pages, 4192 KiB

Open AccessArticle

Exploring the Potential of Plant Bioactive Compounds against Male Infertility: An In Silico and In Vivo Study

by Muhammad Jahangeer, Ghulam Mustafa, Naveed Munir, Sibtain Ahmed and Khalid Mashai Al-Anazi

Molecules 2023, 28(23), 7693; https://doi.org/10.3390/molecules28237693 - 21 Nov 2023

Viewed by 1067

Abstract

Infertility is a well-recognized multifactorial problem affecting the majority of people who struggle with infertility issues. In recent times, among infertility cases, the male factor has acquired importance, and now it contributes to approximately half of the infertility cases because of different abnormalities. In the current study, we used natural phytochemicals as potential drug-lead compounds to target different receptor proteins that are involved in the onset of male infertility. A set of 210 plant phytochemicals were docked counter to active site residues of sex hormone-binding globulin, a disintegrin and metalloproteinase 17, and DNase I as receptor proteins. On the basis of binding scores and molecular dynamics simulation, the phytochemicals tricin, quercetin, malvidin, rhamnetin, isorhamnetin, gallic acid, kaempferol, esculin, robinetin, and okanin were found to be the potential drug candidates to treat male infertility. Molecular dynamics simulation showed tricin as a strong inhibitor of all selected receptor proteins because the ligand–protein complexes remained stabilized during the entire simulation time of 100 ns. Further, an in vivo study was designed to evaluate the effect of tricin in male rats with nicotine-induced infertility. It was explored that a high dose of tricin significantly reduced the levels of alanine transaminase, aspartate transaminase, urea, creatinine, cholesterol, triglyceride, and low-density lipoprotein and raised the level of high-density lipoprotein in intoxicated male rats. A high dose of tricin also increased the reproductive hormones (i.e., testosterone, luteinizing hormone, follicle-stimulating hormone, and prolactin) and reduced the level of DHEA-SO4. The phytochemical (tricin, 10 mg/kg body weight) also showed significant improvement in the histo-architecture after nicotine intoxication in rats. From the current study, it is concluded that the phytochemical tricin could serve as a potential drug candidate to cure male infertility. Full article

(This article belongs to the Special Issue Molecular Dynamics Simulations of Biomacromolecules)

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