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Molecular Simulation of Protein Structure and Interactions
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Molecular Simulation of Protein Structure and Interactions

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

Deadline for manuscript submissions: closed (31 December 2024) | Viewed by 1859

Special Issue Editors

Prof. Dr. Ricardo L. Mancera

E-Mail Website
Guest Editor
Curtin Medical School, Curtin University, Perth, WA 6845, Australia
Interests: molecular dynamics simulation; biological membranes; protein structure and dynamics; protein-protein and protein-ligand interactions; structure-based drug design
Special Issues, Collections and Topics in MDPI journals
Dr. Nevena Todorova

E-Mail Website
Guest Editor
School of Engineering, RMIT University, GPO Box 2476, Melbourne, VIC 3001, Australia
Interests: protein and nanomaterial interactions; protein structure and function; molecular dynamics simulations; enhanced sampling techniques

Special Issue Information

Dear Colleagues,

Molecular simulation methods allow the study of biomolecules in exquisite atomistic detail, enabling the characterisation of molecular mechanisms and their associated thermodynamics and kinetics properties. Developments in force fields and enhanced sampling methods, alongside the wider availability of exascale computing resources, are facilitating the investigation of much more complex systems at substantially larger time and length scales. The interface of biology and materials in molecular sciences are also being increasingly characterised by various molecular simulation and artificial intelligence approaches.

This special issue is aimed at recent research using molecular simulation approaches to study complex biomolecular systems such as intrinsically disordered proteins, protein aggregation, liquid-liquid phase separation, membrane receptor activation, peptide- and protein-membrane interactions, macrobiomolecular complex formation and interactions, protein-surface interactions, and proteins in biomaterials. New methods and force fields developed for these systems, including the use of artificial intelligence, are also of particular interest.

Prof. Dr. Ricardo L. Mancera
Dr. Nevena Todorova
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. 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

  • conformation and interactions of intrinsically disordered proteins
  • protein aggregation in disease
  • activation of membrane receptors
  • interactions of peptides and proteins with model cell membranes
  • formation, stability and interactions of biomacromolecular complexes
  • proteins in biomaterials
  • enhanced sampling methods
  • protein force fields

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Published Papers (1 paper)

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Research

21 pages, 4112 KiB  
Article
Computational Study of Molecular Mechanism for the Involvement of Human Serum Albumin in the Renin–Angiotensin–Aldosterone System
by Daria A. Belinskaia, Natalia N. Shestakova, Kamila V. Samodurova and Nikolay V. Goncharov
Int. J. Mol. Sci. 2024, 25(19), 10260; https://doi.org/10.3390/ijms251910260 - 24 Sep 2024
Cited by 3 | Viewed by 1184
Abstract
Human serum albumin (HSA) is an endogenous inhibitor of angiotensin I-converting enzyme (ACE) and, thus, plays a key role in the renin–angiotensin–aldosterone system (RAAS). However, little is known about the mechanism of interaction between these proteins, and the structure of the HSA–ACE complex [...] Read more.
Human serum albumin (HSA) is an endogenous inhibitor of angiotensin I-converting enzyme (ACE) and, thus, plays a key role in the renin–angiotensin–aldosterone system (RAAS). However, little is known about the mechanism of interaction between these proteins, and the structure of the HSA–ACE complex has not yet been obtained experimentally. The purpose of the presented work is to apply computer modeling methods to study the interaction of HSA with ACE in order to obtain preliminary details about the mechanism of their interaction. Ten possible HSA–ACE complexes were obtained by the procedure of macromolecular docking. Based on the number of steric and polar contacts between the proteins, three leading complexes were selected, the stabilities of which were then tested by molecular dynamics (MD) simulation. Based on the results of MD simulation, the two most probable conformations of the HSA–ACE complex were selected. The analysis of these conformations revealed that the processes of oxidation of the thiol group of Cys34 of HSA and the binding of albumin to ACE can reciprocally affect each other. Known point mutations in the albumin molecules Glu82Lys, Arg114Gly, Glu505Lys, Glu565Lys and Lys573Glu can also affect the interaction with ACE. According to the result of MD simulation, the known ACE mutations, albeit associated with various diseases, do not affect the HSA–ACE interaction. A comparative analysis was performed of the resulting HSA–ACE complexes with those obtained by AlphaFold 3 as well as with the crystal structure of the HSA and the neonatal Fc receptor (FcRn) complex. It was found that domains DI and DIII of albumin are involved in binding both ACE and FcRn. The obtained results of molecular modeling outline the direction for further study of the mechanisms of HSA–ACE interaction in vitro. Information about these mechanisms will help in the design and improvement of pharmacotherapy aimed at modulation of the physiological activity of ACE. Full article
(This article belongs to the Special Issue Molecular Simulation of Protein Structure and Interactions)
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