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Advances in Protein Dynamics

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: 31 August 2024 | Viewed by 5663

Special Issue Editors


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Guest Editor
1. Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
2. Center of Excellence of the Hungarian Academy of Sciences, 1117 Budapest, Hungary
Interests: protein structures; protein dynamics; protein conformation; protein folding; protein bioinformatics; protein interactions; membrane proteins; protein stability; intrinsically disordered proteins; protein biophysics; protein binding; molecular biophysics; protein refolding; membrane transport proteins; computational structural biology; structural bioinformatics
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
Interests: protein bioinformatics; protein stability; intrinsically disordered proteins; protein structure; protein structure modeling; protein dynamics; molecular dynamics simulation; protein conformation; computational structural biology; structural bioinformatics; drug design; structure based drug design
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Proteins are essential building blocks of living organisms, and knowledge regarding their structure is crucial for understanding their function. In many cases, proteins have several relevant conformations, and a static structure cannot account for all their behavior. The number of known protein structures is growing rapidly, the number of deposited PDB structures has set a new record, and artificial intelligence has found its way into protein structure research in recent years. Disordered proteins and proteins participating in liquid–liquid phase separation showing dynamical behavior are also intensively researched. Understanding the structural dynamics of proteins can be challenging, but time-resolved experimental background and theoretical possibilities are also continuously developing. Computational power has significantly increased in the last decade and seems to be increasing further with orders of magnitude. As guest editors of the “Advances in Protein Dynamics” Special Issue of IJMS, we would like to invite you to contribute methodological or application papers related to protein dynamics.

Dr. Istvan Simon
Dr. Csaba Magyar
Guest Editors

Manuscript Submission Information

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Keywords

  • protein structure
  • protein structure modelling
  • protein structural dynamics
  • time-resolved methods
  • protein–protein interactions
  • structure-based drug design
  • structural background of protein function
  • structural background of protein stability
  • folded and disordered proteins

Published Papers (4 papers)

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Research

14 pages, 3946 KiB  
Article
Sequence Alignment-Based Prediction of Myosin 7A: Structural Implications and Protein Interactions
by Chan Jong Yu, Yoon Ho Park, Bumhan Ryu and Hyun Suk Jung
Int. J. Mol. Sci. 2024, 25(6), 3365; https://doi.org/10.3390/ijms25063365 - 16 Mar 2024
Viewed by 703
Abstract
Myosin, a superfamily of motor proteins, obtain the energy they require for movement from ATP hydrolysis to perform various functions by binding to actin filaments. Extensive studies have clarified the diverse functions performed by the different isoforms of myosin. However, the unavailability of [...] Read more.
Myosin, a superfamily of motor proteins, obtain the energy they require for movement from ATP hydrolysis to perform various functions by binding to actin filaments. Extensive studies have clarified the diverse functions performed by the different isoforms of myosin. However, the unavailability of resolved structures has made it difficult to understand the way in which their mechanochemical cycle and structural diversity give rise to distinct functional properties. With this study, we seek to further our understanding of the structural organization of the myosin 7A motor domain by modeling the tertiary structure of myosin 7A based on its primary sequence. Multiple sequence alignment and a comparison of the models of different myosin isoforms and myosin 7A not only enabled us to identify highly conserved nucleotide binding sites but also to predict actin binding sites. In addition, the actomyosin-7A complex was predicted from the protein–protein interaction model, from which the core interface sites of actin and the myosin 7A motor domain were defined. Finally, sequence alignment and the comparison of models were used to suggest the possibility of a pliant region existing between the converter domain and lever arm of myosin 7A. The results of this study provide insights into the structure of myosin 7A that could serve as a framework for higher resolution studies in future. Full article
(This article belongs to the Special Issue Advances in Protein Dynamics)
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15 pages, 3603 KiB  
Article
Insights into the Inhibitory Mechanisms of the Covalent Drugs for DNMT3A
by Wei Yang, Jingyuan Zhuang, Chen Li, Chen Bai and Guijuan Cheng
Int. J. Mol. Sci. 2023, 24(16), 12652; https://doi.org/10.3390/ijms241612652 - 10 Aug 2023
Viewed by 1277
Abstract
The perturbations of DNA methyltransferase 3 alpha (DNMT3A) may cause uncontrolled gene expression, resulting in cancers and tumors. The DNMT inhibitors Azacytidine (AZA) and Zebularine (ZEB) inhibit the DNMT family with no specificities, and consequently would bring side effects during the treatment. Therefore, [...] Read more.
The perturbations of DNA methyltransferase 3 alpha (DNMT3A) may cause uncontrolled gene expression, resulting in cancers and tumors. The DNMT inhibitors Azacytidine (AZA) and Zebularine (ZEB) inhibit the DNMT family with no specificities, and consequently would bring side effects during the treatment. Therefore, it is vital to understand the inhibitory mechanisms in DNMT3A to inform the new inhibitor design for DNMTs. Herein, we carried out molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) simulations to investigate the inhibitory mechanisms of the AZA and ZEB. The results were compared to the methyl transfer of cytosine. We showed how the AZA might stop the methyl transfer process, whereas the ZEB might be stuck in a methyl-transferred intermediate (IM3). The IM3 state then fails the elimination due to the unique protein dynamics that result in missing the catalytic water chain. Our results brought atomic-level insights into the mechanisms of the two drugs in DNMT3A, which could benefit the new generation of drug design for the DNMTs. Full article
(This article belongs to the Special Issue Advances in Protein Dynamics)
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8 pages, 653 KiB  
Article
Molecular Dynamics Simulation as a Tool to Identify Mutual Synergistic Folding Proteins
by Csaba Magyar, Bálint Zoltán Németh, Miklós Cserző and István Simon
Int. J. Mol. Sci. 2023, 24(2), 1790; https://doi.org/10.3390/ijms24021790 - 16 Jan 2023
Cited by 1 | Viewed by 1616
Abstract
Mutual synergistic folding (MSF) proteins belong to a recently emerged subclass of disordered proteins, which are disordered in their monomeric forms but become ordered in their oligomeric forms. They can be identified by experimental methods following their unfolding, which happens in a single-step [...] Read more.
Mutual synergistic folding (MSF) proteins belong to a recently emerged subclass of disordered proteins, which are disordered in their monomeric forms but become ordered in their oligomeric forms. They can be identified by experimental methods following their unfolding, which happens in a single-step cooperative process, without the presence of stable monomeric intermediates. Only a limited number of experimentally validated MSF proteins are accessible. The amino acid composition of MSF proteins shows high similarity to globular ordered proteins, rather than to disordered ones. However, they have some special structural features, which makes it possible to distinguish them from globular proteins. Even in the possession of their oligomeric three-dimensional structure, classification can only be performed based on unfolding experiments, which are frequently absent. In this work, we demonstrate a simple protocol using molecular dynamics simulations, which is able to indicate that a protein structure belongs to the MSF subclass. The presumption of the known atomic resolution quaternary structure is an obvious limitation of the method, and because of its high computational time requirements, it is not suitable for screening large databases; still, it is a valuable in silico tool for identification of MSF proteins. Full article
(This article belongs to the Special Issue Advances in Protein Dynamics)
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15 pages, 2399 KiB  
Article
Effects of Residual Composition and Distribution on the Structural Characteristics of the Protein
by Qiaoling Song, Zhenan Wu, Chenghao Jin, Zhichao Yu, Peng Xu and Zhouting Jiang
Int. J. Mol. Sci. 2022, 23(22), 14263; https://doi.org/10.3390/ijms232214263 - 17 Nov 2022
Cited by 1 | Viewed by 1099
Abstract
The effect of ratio and consecutive number of hydrophobic residues in the repeating unit of protein chains was investigated by MD simulation. The modified off-lattice HNP model was applied in this study. The protein chains constituted by different HNP ratios or different numbers [...] Read more.
The effect of ratio and consecutive number of hydrophobic residues in the repeating unit of protein chains was investigated by MD simulation. The modified off-lattice HNP model was applied in this study. The protein chains constituted by different HNP ratios or different numbers of consecutively hydrophobic residues with the same chain length were simulated under a broad temperature range. We concluded that the proteins with higher ratio or larger number of sequentially hydrophobic residues present more orientated and compact structure under a certain low temperature. It is attributed to the lower non-bonded potential energy between H-H residual pairs, especially more hydrophobic residues in a procession among the protein chain. Considering the microscopic structure of the protein, more residue contacts are achieved with the proteins with higher ratios and sequential H residues under the low temperature. Meanwhile, with the ratio and consecutive number of H residues increasing, the distribution of stem length showed a transition from exponential decline to unimodal and even multiple peaks, indicating the specific ordered structure formed. These results provide an insight into 3D structural properties of proteins from their residue sequences, which has a primary structure at molecular level and, ultimately, a practical possibility of applying in biotechnological applications. Full article
(This article belongs to the Special Issue Advances in Protein Dynamics)
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