Structure, Dynamics and Energetics of Biomolecular Processes: Forces Driving Macromolecular Association, Folding, and Recognition

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Biochemistry, Biophysics and Computational Biology".

Deadline for manuscript submissions: 29 November 2024 | Viewed by 1452

Special Issue Editors


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Guest Editor
Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, NJ 08854, USA
Interests: protein-ligand interactions; thermodynamic driving forces; drug discovery and optimization

E-Mail Website
Guest Editor
Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, NJ 08854, USA
Interests: macromolecular association and folding; ligand-receptor binding energetics; drug-DNA interactions

Special Issue Information

Dear Colleagues,

Living cells encompass an exceptionally complex and intricate network of macromolecular interactions that mediate an array of biochemical processes orchestrated within the cellular machinery. These interactions are governed by molecular, dynamic, and energetic forces that collectively operate with unprecedented precision to control and regulate cellular functions. A myriad of nucleic acids, proteins, and biologically active compounds participate in ligand–target interactions that are exquisitely modulated by the surrounding solvent environment within the cellular milieu. Apart from the well-established role of macromolecular association and folding on functional activity, a substantial body of evidence has recently challenged the classical structure–function paradigm whereby a more dynamic and flexible ensemble of conformational states are integral participants in the cellular recognition and assembly process. These findings underscore the relevance of intrinsically disordered proteins and/or regions in mediating liquid–liquid phase separation. While essential for spatial–temporal organization of intracellular space, the aberrant formation of biomolecular condensates may harbor clues to elucidate the origins of specific pathogenic conditions, such as neurodegeneration and tumorigenesis. Understanding dysregulation related to protein misfolding and disease is an area of paramount importance for the design, development, and optimization of effective therapeutic agents. Such discoveries have accelerated as a consequence of significant advances in biophysical, molecular biology, and structural approaches. This Special Issue welcomes the contribution of original articles and reviews that focus on the structure, dynamics, and energetics of biological processes with particular emphasis on macromolecular association, folding, and recognition. Our objective is to compile a comprehensive overview of experimental and theoretical techniques that are aimed at facilitating advancements in this fundamental area of research. These studies invoke a multidisciplinary array of biophysical, computational, and structural approaches including analytical ultracentrifugation, differential scanning and isothermal titration calorimetry, surface plasmon resonance, molecular docking and modeling, nuclear magnetic resonance spectroscopy, atomic force microscopy, X-ray crystallography, and related methodologies at the interface of core technologies.

Prof. Dr. Conceição A. Minetti
Prof. Dr. David P. Remeta
Guest Editors

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Keywords

  • molecular recognition and solvation
  • biomolecular structure and dynamics
  • ligand–receptor binding energetics
  • thermodynamic driving forces
  • macromolecular folding and stability
  • protein–nucleic acid interactions
  • intrinsically disordered proteins
  • liquid–liquid phase separation
  • protein aggregation and disease
  • drug discovery and optimization

Published Papers (1 paper)

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Research

14 pages, 5540 KiB  
Article
Modeling the Effect on a Novel Fungal Peptaibol Placed in an All-Atom Bacterial Membrane Mimicking System via Accelerated Molecular Dynamics Simulations
by Chetna Tyagi, Tamás Marik, András Szekeres, Csaba Vágvölgyi, László Kredics and Ferenc Ötvös
Life 2023, 13(12), 2288; https://doi.org/10.3390/life13122288 - 30 Nov 2023
Viewed by 939
Abstract
We previously reported on a novel peptaibol, named Tripleurin XIIc (TPN), an 18-residue long sequence produced by the fungus Trichoderma pleuroti. We elucidated its 3D structure via classical and accelerated molecular dynamics simulation (aMD) methods and reported the folding dynamics of TPN [...] Read more.
We previously reported on a novel peptaibol, named Tripleurin XIIc (TPN), an 18-residue long sequence produced by the fungus Trichoderma pleuroti. We elucidated its 3D structure via classical and accelerated molecular dynamics simulation (aMD) methods and reported the folding dynamics of TPN in water and chloroform solvents. Peptaibols, in general, are insoluble in water, as they are amphipathic and may prefer hydrophobic environments like transmembrane regions. In this study, we attempted to use aMD simulations to model an all-atom bacterial membrane system while placing a TPN molecule in its vicinity. The results highlighted that TPN was able to introduce some disorder into the membrane and caused lipid clustering. It could also enter the transmembrane region from the water-bilayer interface. The structural dynamics of TPN in the transmembrane region revealed a single energetically stable conformation similar to the one obtained from water and chloroform solvent simulations reported by us previously. However, this linear structure was found to be at the local energy minimum (stable) in water but at a metastable intermediate state (higher energy) in chloroform. Therefore, it could be said that the water solvent can be successfully used for folding simulations of peptaibols. Full article
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