Protein Biophysics

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Biophysics: Structure, Dynamics, and Function".

Deadline for manuscript submissions: 31 May 2026 | Viewed by 733

Special Issue Editors


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Guest Editor
Department of Molecular Medicine and USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
Interests: protein structure; protein folding; protein misfolding; intrinsically disordered proteins; conformational disease; partially folded protein; folding intermediate; protein aggregation
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Guest Editor
Molecular Biotehnology, Turkish-German University, Beykoz, Turkey
Interests: intrinsically disordered proteins and bio-inspired polymers
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Proteins are complex and versatile biological macromolecules with a myriad of structures and countless functions. Order and disorder are intricately intertwined in proteins, with many proteins being known to fold into unique structures in order to gain important functions, and with functions of many other proteins being dependent on the absence of unique structure and related ability to undergo disorder-to-order or order-to-disorder functional transitions. Being interaction specialists, proteins can act alone or require various partners for their functionality. They can assemble into highly specific proteinacous machines with sophisticated geometry or form liquid-like droplets. They can control and regulate countless biological processes, and, in turn, are tightly controlled and regulated themselves by a broad variety of cellular mechanisms. All this highlights the close link between protein science and different fields of molecular biophysics. This Special Issue entitled “Protein Biophysics” aims to collect high-quality research articles, short communications, and review articles in all fields of protein biophysics. We encourage scholars in related fields to contribute papers reflecting the latest progress in their research fields.

Topics of this Special Issue include, but are not limited to, the following:

  • Protein biophysics;
  • Protein engineering;
  • Protein folding;
  • Protein function;
  • Protein misfolding;
  • Protein stability;
  • Protein structure and prediction;
  • Protein structural and conformational dynamics;
  • Posttranslational modifications;
  • Peptide and protein aggregation;
  • Pathogenesis of proteinopathies;
  • Intrinsically disordered proteins;
  • Protein–ligand interactions;
  • Protein–protein interactions;
  • Protein–nucleic acid interactions;
  • Membrane proteins;
  • Liquid–liquid phase separation;
  • Biosensing, spectroscopy, and microfluidics;
  • Kinetics and thermodynamics;
  • Applications in biotechnology and bioengineering.

Prof. Dr. Vladimir N. Uversky
Dr. Orkid Coskuner-Weber
Guest Editors

Manuscript Submission Information

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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. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

  • protein function
  • protein folding
  • protein misfolding
  • protein structure
  • protein dynamics
  • protein stability
  • protein and peptide aggregation
  • posttranslational modifications
  • intrinsically disordered proteins
  • protein–ligand interactions
  • protein–protein interactions
  • protein–nucleic acid interactions
  • membrane proteins
  • liquid–liquid phase separation

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Published Papers (1 paper)

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Review

37 pages, 603 KB  
Review
Implicit Solvent Models and Their Applications in Biophysics
by Yusuf Bugra Severoglu, Betul Yuksel, Cagatay Sucu, Nese Aral, Vladimir N. Uversky and Orkid Coskuner-Weber
Biomolecules 2025, 15(9), 1218; https://doi.org/10.3390/biom15091218 - 23 Aug 2025
Viewed by 496
Abstract
Solvents represent the quiet majority in biomolecular systems, yet modeling their influence with both speed and ri:gor remains a central challenge. This study maps the state of the art in implicit solvent theory and practice, spanning classical continuum electrostatics (PB/GB; DelPhi, APBS), modern [...] Read more.
Solvents represent the quiet majority in biomolecular systems, yet modeling their influence with both speed and ri:gor remains a central challenge. This study maps the state of the art in implicit solvent theory and practice, spanning classical continuum electrostatics (PB/GB; DelPhi, APBS), modern nonpolar and cavity/dispersion treatments, and quantum–continuum models (PCM, COSMO/COSMO-RS, SMx/SMD). We highlight where these methods excel and where they falter, namely, around ion specificity, heterogeneous interfaces, entropic effects, and parameter sensitivity. We then spotlight two fast-moving frontiers that raise both accuracy and throughput: machine learning-augmented approaches that serve as PB-accurate surrogates, learn solvent-averaged potentials for MD, or supply residual corrections to GB/PB baselines, and quantum-centric workflows that couple continuum solvation methods, such as IEF-PCM, to sampling on real quantum hardware, pointing toward realistic solution-phase electronic structures at emerging scales. Applications across protein–ligand binding, nucleic acids, and intrinsically disordered proteins illustrate how implicit models enable rapid hypothesis testing, large design sweeps, and long-time sampling. Our perspective argues for hybridization as a best practice, meaning continuum cores refined by improved physics, such as multipolar water, ML correctors with uncertainty quantification and active learning, and quantum–continuum modules for chemically demanding steps. Full article
(This article belongs to the Special Issue Protein Biophysics)
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