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Advances in Molecular Biophysics of Protein-Protein Interactions
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Advances in Molecular Biophysics of Protein-Protein Interactions

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: closed (31 January 2024) | Viewed by 4711

Special Issue Editors

Dr. Hao-Bo Guo

E-Mail Website
Guest Editor
Air Force Research Laboratory (AFRL), 5135 Pearson Road, Building 10, WPAFB, Dayton, OH 45433, USA
Interests: biophysics; bioinformation; biochemistry; molecular biology; structural biology; network biology
Prof. Dr. Rajiv J. Berry

E-Mail Website
Guest Editor
Air Force Research Laboratory (AFRL), 5135 Pearson Road, Building 10, WPAFB, Dayton, OH 45433, USA
Interests: chemical physics; biological physics; biopolymers; molecular mechanics; quantum mechanics; molecular dynamics; free-energy simulations

Special Issue Information

Dear Colleagues,

Protein–protein interactions (PPIs) play a critical role in biological processes and can be mapped experimentally (e.g., yeast two-hybrid) or theoretically (e.g., protein–protein docking). Curated binary PPI networks (PINs), such as the BioGRID and STRING databases, often contain thousands or even millions of PPIs within a proteome or a set of proteins. Recent developments in molecular biophysics have enabled spatial and temporal PPI detection in cells. With the release of AlphaFold2 (AF2), the AF2 database (AFDB), and other tools (e.g., RoseTTAFold), accurate structure models of proteins and protein complexes have also become available.

This Special Issue focuses on recent advances in molecular biophysics regarding protein–protein interactions. Possible topics include, but are not limited to: single-molecular PPI detection, single-cell PPI mapping, the protein interaction network, the protein complex, protein aggregation, protein–protein docking, protein–protein binding affinity, and the evolution of PPIs. We welcome experimental and theoretical contributions reports, reviews, and perspectives.

Dr. Hao-Bo Guo
Prof. Dr. Rajiv J. Berry
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

  • protein–protein interaction
  • protein interaction network
  • protein complex
  • single-cell
  • single-molecular
  • binding affinity
  • binding pocket
  • protein domain
  • protein aggregation
  • protein multimerization
  • physical interaction
  • genetic interaction

Published Papers (3 papers)

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24 pages, 10156 KiB  
Article
Computational Prediction of the Interaction of Ivermectin with Fibrinogen
by Paola Vottero, Scott Tavernini, Alessandro D. Santin, David E. Scheim, Jack A. Tuszynski and Maral Aminpour
Int. J. Mol. Sci. 2023, 24(14), 11449; https://doi.org/10.3390/ijms241411449 - 14 Jul 2023
Viewed by 2390
Abstract
Hypercoagulability and formation of extensive and difficult-to-lyse microclots are a hallmark of both acute COVID-19 and long COVID. Fibrinogen, when converted to fibrin, is responsible for clot formation, but abnormal structural and mechanical clot properties can lead to pathologic thrombosis. Recent experimental evidence [...] Read more.
Hypercoagulability and formation of extensive and difficult-to-lyse microclots are a hallmark of both acute COVID-19 and long COVID. Fibrinogen, when converted to fibrin, is responsible for clot formation, but abnormal structural and mechanical clot properties can lead to pathologic thrombosis. Recent experimental evidence suggests that the spike protein (SP) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may directly bind to the blood coagulation factor fibrinogen and induce structurally abnormal blood clots with heightened proinflammatory activity. Accordingly, in this study, we used molecular docking and molecular dynamics simulations to explore the potential activity of the antiparasitic drug ivermectin (IVM) to prevent the binding of the SARS-CoV-2 SP to fibrinogen and reduce the occurrence of microclots. Our computational results indicate that IVM may bind with high affinity to multiple sites on the fibrinogen peptide, with binding more likely in the central, E region, and in the coiled-coil region, as opposed to the globular D region. Taken together, our in silico results suggest that IVM may interfere with SP–fibrinogen binding and, potentially, decrease the formation of fibrin clots resistant to degradation. Additional in vitro studies are warranted to validate whether IVM binding to fibrinogen is sufficiently stable to prevent interaction with the SP, and potentially reduce its thrombo-inflammatory effect in vivo. Full article
(This article belongs to the Special Issue Advances in Molecular Biophysics of Protein-Protein Interactions)
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16 pages, 1998 KiB  
Article
The Thermodynamic Fingerprints of Ultra-Tight Nanobody–Antigen Binding Probed via Two-Color Single-Molecule Coincidence Detection
by Benno Schedler, Olessya Yukhnovets, Lennart Lindner, Alida Meyer and Jörg Fitter
Int. J. Mol. Sci. 2023, 24(22), 16379; https://doi.org/10.3390/ijms242216379 - 15 Nov 2023
Viewed by 723
Abstract
Life on the molecular scale is based on a versatile interplay of biomolecules, a feature that is relevant for the formation of macromolecular complexes. Fluorescence-based two-color coincidence detection is widely used to characterize molecular binding and was recently improved by a brightness-gated version [...] Read more.
Life on the molecular scale is based on a versatile interplay of biomolecules, a feature that is relevant for the formation of macromolecular complexes. Fluorescence-based two-color coincidence detection is widely used to characterize molecular binding and was recently improved by a brightness-gated version which gives more accurate results. We developed and established protocols which make use of coincidence detection to quantify binding fractions between interaction partners labeled with fluorescence dyes of different colors. Since the applied technique is intrinsically related to single-molecule detection, the concentration of diffusing molecules for confocal detection is typically in the low picomolar regime. This makes the approach a powerful tool for determining bi-molecular binding affinities, in terms of KD values, in this regime. We demonstrated the reliability of our approach by analyzing very strong nanobody-EGFP binding. By measuring the affinity at different temperatures, we were able to determine the thermodynamic parameters of the binding interaction. The results show that the ultra-tight binding is dominated by entropic contributions. Full article
(This article belongs to the Special Issue Advances in Molecular Biophysics of Protein-Protein Interactions)
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14 pages, 3237 KiB  
Article
Conformation-Specific Association of Prion Protein Amyloid Aggregates with Tau Protein Monomers
by Mantas Ziaunys, Kamile Mikalauskaite, Lukas Krasauskas and Vytautas Smirnovas
Int. J. Mol. Sci. 2023, 24(11), 9277; https://doi.org/10.3390/ijms24119277 - 25 May 2023
Cited by 1 | Viewed by 1124
Abstract
Protein aggregation into amyloid fibrils is associated with several amyloidoses, including neurodegenerative Alzheimer’s and Parkinson’s diseases. Despite years of research and numerous studies, the process is still not fully understood, which significantly impedes the search for cures of amyloid-related disorders. Recently, there has [...] Read more.
Protein aggregation into amyloid fibrils is associated with several amyloidoses, including neurodegenerative Alzheimer’s and Parkinson’s diseases. Despite years of research and numerous studies, the process is still not fully understood, which significantly impedes the search for cures of amyloid-related disorders. Recently, there has been an increase in reports of amyloidogenic protein cross-interactions during the fibril formation process, which further complicates the already intricate process of amyloid aggregation. One of these reports displayed an interaction involving Tau and prion proteins, which prompted a need for further investigation into the matter. In this work, we generated five populations of conformationally distinct prion protein amyloid fibrils and examined their interaction with Tau proteins. We observed that there was a conformation-specific association between Tau monomers and prion protein fibrils, which increased the aggregate self-association and amyloidophilic dye binding capacity. We also determined that the interaction did not induce the formation of Tau protein amyloid aggregates, but rather caused their electrostatic adsorption to the prion protein fibril surface. Full article
(This article belongs to the Special Issue Advances in Molecular Biophysics of Protein-Protein Interactions)
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