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Molecular Insights into Macromolecules Structure, Function, and Regulation: 2nd Edition

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: 30 June 2024 | Viewed by 1229

Special Issue Editor

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our Special Issue titled “Molecular Insights into Macromolecules Structure, Function, and Regulation”.

Macromolecules are large molecules, with a diameter ranging from approximately 10 to 1000 nm. Proteins are common macromolecules in living organisms. Protein structures determine function, and the regulation of this structure often affects its function. In this Special Issue, we will focus on the structure, function and regulation of biomolecular proteins.

Nowadays, protein structure prediction/modeling has been routinely applied in drug discovery to increase its effectiveness. It provides essential contributions in successful predictions (e.g., antivirals for COVID-19), leading a battle against the pandemic and understanding the functional complexity of living systems. However, there are two main issues to be solved in order to implement reliable predictions: (i) accurate modeling of the protein structure and “binding pocket”; and (ii) correct incorporation of the intrinsically dynamic behavior of proteins. Moreover, protein structure and function can be altered by mutations, hence understanding the effects of mutations on protein structure and function is important for the prevention of related diseases and the development of therapeutic drugs. A variety of algorithms and strategies have been developed for the ever-improving estimation of structural modeling and drug discovery, accounting for conformational dynamics, including molecular simulation, deep learning, NMR, cryo-electron microscopy and single-molecule fluorescence techniques.

Accordingly, the aim of this Special Issue is to collect a series of state-of-the-art examples of the recent advances in this rapidly changing field, and uncover the ligand–protein/peptide–protein/protein–protein interaction modulations. Papers that explore all aspects are welcome, including current efforts in theoretical developments.

Dr. Zhiwei Yang
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

  • conformational dynamics
  • structural modeling
  • docking
  • molecular recognition
  • regulation mechanism
  • rational design
  • molecular dynamic simulation

Published Papers (1 paper)

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Research

13 pages, 6359 KiB  
Article
The Inhibition Effect of Epigallocatechin-3-Gallate on the Co-Aggregation of Amyloid-β and Human Islet Amyloid Polypeptide Revealed by Replica Exchange Molecular Dynamics Simulations
by Xuhua Li, Yu Zhang, Zhiwei Yang, Shengli Zhang and Lei Zhang
Int. J. Mol. Sci. 2024, 25(3), 1636; https://doi.org/10.3390/ijms25031636 - 29 Jan 2024
Viewed by 959
Abstract
Alzheimer’s disease and Type 2 diabetes are two epidemiologically linked diseases which are closely associated with the misfolding and aggregation of amyloid proteins amyloid-β (Aβ) and human islet amyloid polypeptide (hIAPP), respectively. The co-aggregation of the two amyloid proteins is regarded as the [...] Read more.
Alzheimer’s disease and Type 2 diabetes are two epidemiologically linked diseases which are closely associated with the misfolding and aggregation of amyloid proteins amyloid-β (Aβ) and human islet amyloid polypeptide (hIAPP), respectively. The co-aggregation of the two amyloid proteins is regarded as the fundamental molecular mechanism underlying their pathological association. The green tea extract epigallocatechin-3-gallate (EGCG) has been extensively demonstrated to inhibit the amyloid aggregation of Aβ and hIAPP proteins. However, its potential role in amyloid co-aggregation has not been thoroughly investigated. In this study, we employed the enhanced-sampling replica exchange molecular dynamics simulation (REMD) method to investigate the effect of EGCG on the co-aggregation of Aβ and hIAPP. We found that EGCG molecules substantially diminish the β-sheet structures within the amyloid core regions of Aβ and hIAPP in their co-aggregates. Through hydrogen-bond, π–π and cation–π interactions targeting polar and aromatic residues of Aβ and hIAPP, EGCG effectively attenuates both inter-chain and intra-chain interactions within the co-aggregates. All these findings indicated that EGCG can effectively inhibit the co-aggregation of Aβ and hIAPP. Our study expands the potential applications of EGCG as an anti-amyloidosis agent and provides therapeutic options for the pathological association of amyloid misfolding disorders. Full article
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