Special Issue "Protein-Protein and Protein-Ligand Interaction"

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Proteins and Proteomics".

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 874

Special Issue Editor

Dr. Mateusz Banach
E-Mail Website1 Website2
Guest Editor
Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College, Medyczna 7, 30-688 Kraków, Poland
Interests: bioinformatics; computational geometry; computer science; data analysis; data visualization; hydrophobic core; optimization algorithms; protein folding; protein-protein interaction; python programming; web services and databases

Special Issue Information

Dear Colleagues,

The biological function of many proteins depends on the formation of a multimeric quaternary structure or the binding of smaller molecules, or both. Other partners include nucleic acids and nearby segments of the cell wall. In addition to kind and number of substrates and their spatial arrangement, protein complexes also have a temporal context: being permanent or transitory. Finally, some proteins act only as monomers, with or without ligand-related activity.

Algorithms, simulations, models, and databases provide an invaluable support for experimental methods, allowing cost-effective, reproducible, large-scale analysis and prediction. Thanks to computers it is possible to gauge whether two or more proteins may interact, or if an introduction of additional factors (a mutation in the sequence or the presence of another molecule) could promote or hinder the construction of such complexes. This situation can be observed from a broad perspective, which is the purpose of protein–protein interaction networks, but also very focused—down to the atomic level—when one tries to pinpoint residues engaged in contact. Possibilities regarding ligand binding are similar, ranging from the exploration of structural features (binding pockets) and the search for molecules that may fit them, to the construction of compound databases for drug candidate screening.

In this Special Issue we are looking forward to submissions in the form of original articles, reviews, and communications presenting recent results of not necessarily purely in silico research, but contributing to the expansion of scientific knowledge in the areas of protein–protein and protein–ligand interaction. 

Dr. Mateusz Banach
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. Life 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 1800 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

  • bioinformatics
  • computational biology
  • drug design
  • ligand binding
  • machine learning
  • molecular docking
  • molecular dynamics 
  • protein–protein interaction
  • proteomics
  • theoretical models

Published Papers (1 paper)

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Research

Article
Identifying the Hot Spot Residues of the SARS-CoV-2 Main Protease Using MM-PBSA and Multiple Force Fields
Life 2022, 12(1), 54; https://doi.org/10.3390/life12010054 - 31 Dec 2021
Cited by 1 | Viewed by 433
Abstract
In this study, we investigated the binding affinities between the main protease of SARS-CoV-2 virus (Mpro) and its various ligands to identify the hot spot residues of the protease. To benchmark the influence of various force fields on hot spot [...] Read more.
In this study, we investigated the binding affinities between the main protease of SARS-CoV-2 virus (Mpro) and its various ligands to identify the hot spot residues of the protease. To benchmark the influence of various force fields on hot spot residue identification and binding free energy calculation, we performed MD simulations followed by MM-PBSA analysis with three different force fields: CHARMM36, AMBER99SB, and GROMOS54a7. We performed MD simulations with 100 ns for 11 protein–ligand complexes. From the series of MD simulations and MM-PBSA calculations, it is identified that the MM-PBSA estimations using different force fields are weakly correlated to each other. From a comparison between the force fields, AMBER99SB and GROMOS54a7 results are fairly correlated while CHARMM36 results show weak or almost no correlations with the others. Our results suggest that MM-PBSA analysis results strongly depend on force fields and should be interpreted carefully. Additionally, we identified the hot spot residues of Mpro, which play critical roles in ligand binding through energy decomposition analysis. It is identified that the residues of the S4 subsite of the binding site, N142, M165, and R188, contribute strongly to ligand binding. In addition, the terminal residues, D295, R298, and Q299 are identified to have attractive interactions with ligands via electrostatic and solvation energy. We believe that our findings will help facilitate developing the novel inhibitors of SARS-CoV-2. Full article
(This article belongs to the Special Issue Protein-Protein and Protein-Ligand Interaction)
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