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Biophysica
Special Issues
Role of Water in Biological Systems
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Role of Water in Biological Systems

A special issue of Biophysica (ISSN 2673-4125).

Deadline for manuscript submissions: closed (31 May 2021) | Viewed by 12072

Special Issue Editors

Dr. Boris Zaslavsky

E-Mail Website
Guest Editor
Cleveland Diagnostics, Cleveland, OH 44114, USA
Interests: water in biology; aqueous two-phase systems; early cancer detection; membrane-less organelles
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Vladimir N. Uversky

grade E-Mail Website
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 physics; protein folding; protein misfolding; intrinsically disordered proteins; protein function; protein interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Being the only natural liquid that exists on the surface of our planet in enormous quantities, water is the basis of life on Earth. In fact, water was the unique environment in which life originated. The processes that take place in the cells of all the organisms take place in an aqueous environment. Water is an active component of various biological processes ranging from enzymatic catalysis to protein folding, to the assembly of biological complexes, and to liquid–liquid phase transitions serving as a foundation of the biogenesis of various membrane-less organelles. To stress the inseparable link of biological processes with water, we have decided to launch a Special Issue titled “Role of Water in Biological Systems”.

In this Special Issue, we welcome the submission of papers focusing on both experimental and computational approaches to underscore the unique position of water in a variety of biological systems. Fields of interest include but are not limited to the roles of water in protein folding, enzymatic catalysis, the assembly and functionality of biological complexes, liquid–liquid phase transitions in aqueous media, the partition of various solutes in formed phases, the biogenesis of membrane-less organelles, as well as the structure of bulk water, the structure of hydration shell water, and the solvent properties of water.

Dr. Boris Y. Zaslavsky
Dr. Vladimir N. Uversky
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. Biophysica is an international peer-reviewed open access quarterly 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 1000 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

  • Water structure
  • Solvent properties of water
  • membrane-less organelles
  • liquid–liquid phase transition
  • phase separation
  • aqueous two-phase systems

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Published Papers (3 papers)

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Research

18 pages, 2655 KiB  
Article
Autologous Gradient Formation under Differential Interstitial Fluid Flow Environments
by Caleb A. Stine and Jennifer M. Munson
Biophysica 2022, 2(1), 16-33; https://doi.org/10.3390/biophysica2010003 - 4 Jan 2022
Cited by 4 | Viewed by 3263
Abstract
Fluid flow and chemokine gradients play a large part in not only regulating homeostatic processes in the brain, but also in pathologic conditions by directing cell migration. Tumor cells in particular are superior at invading into the brain resulting in tumor recurrence. One [...] Read more.
Fluid flow and chemokine gradients play a large part in not only regulating homeostatic processes in the brain, but also in pathologic conditions by directing cell migration. Tumor cells in particular are superior at invading into the brain resulting in tumor recurrence. One mechanism that governs cellular invasion is autologous chemotaxis, whereby pericellular chemokine gradients form due to interstitial fluid flow (IFF) leading cells to migrate up the gradient. Glioma cells have been shown to specifically use CXCL12 to increase their invasion under heightened interstitial flow. Computational modeling of this gradient offers better insight into the extent of its development around single cells, yet very few conditions have been modelled. In this paper, a computational model is developed to investigate how a CXCL12 gradient may form around a tumor cell and what conditions are necessary to affect its formation. Through finite element analysis using COMSOL and coupled convection-diffusion/mass transport equations, we show that velocity (IFF magnitude) has the largest parametric effect on gradient formation, multidirectional fluid flow causes gradient formation in the direction of the resultant which is governed by IFF magnitude, common treatments and flow patterns have a spatiotemporal effect on pericellular gradients, exogenous background concentrations can abrogate the autologous effect depending on how close the cell is to the source, that there is a minimum distance away from the tumor border required for a single cell to establish an autologous gradient, and finally that the development of a gradient formation is highly dependent on specific cell morphology. Full article
(This article belongs to the Special Issue Role of Water in Biological Systems)
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16 pages, 793 KiB  
Article
Water Thermodynamics and Its Effects on the Protein Stability and Activity
by Francesco Mallamace, Domenico Mallamace, Sow-Hsin Chen, Paola Lanzafame and Georgia Papanikolaou
Biophysica 2021, 1(4), 413-428; https://doi.org/10.3390/biophysica1040030 - 14 Oct 2021
Cited by 1 | Viewed by 3598
Abstract
We discuss a phenomenon regarding water that was until recently a subject of scientific interest: i.e., the dynamical crossover, from the fragile to strong glass forming material, for both bulk and protein hydration water. Such crossover is characterized by a temperature TL [...] Read more.
We discuss a phenomenon regarding water that was until recently a subject of scientific interest: i.e., the dynamical crossover, from the fragile to strong glass forming material, for both bulk and protein hydration water. Such crossover is characterized by a temperature TL in which significant dynamical changes like the decoupling (or the violation of the Stokes-Einstein relation) of homologous transport parameters, e.g., the density relaxation time τ and the viscosity η, occur in the system. On this respect we considered the dynamic properties of water-protein systems. More precisely, we focused our study on proteins and their hydration water, as far as bulk and confined water. In order to clarify the effects of the water dynamical crossover on the protein properties we considered and discussed in a comparative way previous and new experimental data, obtained from different techniques and molecular dynamic simulation (MD). We pointed out the reasons for different dynamical findings from the use of different experimental techniques. Full article
(This article belongs to the Special Issue Role of Water in Biological Systems)
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18 pages, 2805 KiB  
Article
Optimal Relabeling of Water Molecules and Single-Molecule Entropy Estimation
by Federico Fogolari and Gennaro Esposito
Biophysica 2021, 1(3), 279-296; https://doi.org/10.3390/biophysica1030021 - 30 Jun 2021
Cited by 2 | Viewed by 3289
Abstract
Estimation of solvent entropy from equilibrium molecular dynamics simulations is a long-standing problem in statistical mechanics. In recent years, methods that estimate entropy using k-th nearest neighbours (kNN) have been applied to internal degrees of freedom in biomolecular simulations, and for the [...] Read more.
Estimation of solvent entropy from equilibrium molecular dynamics simulations is a long-standing problem in statistical mechanics. In recent years, methods that estimate entropy using k-th nearest neighbours (kNN) have been applied to internal degrees of freedom in biomolecular simulations, and for the rigorous computation of positional-orientational entropy of one and two molecules. The mutual information expansion (MIE) and the maximum information spanning tree (MIST) methods were proposed and used to deal with a large number of non-independent degrees of freedom, providing estimates or bounds on the global entropy, thus complementing the kNN method. The application of the combination of such methods to solvent molecules appears problematic because of the indistinguishability of molecules and of their symmetric parts. All indistiguishable molecules span the same global conformational volume, making application of MIE and MIST methods difficult. Here, we address the problem of indistinguishability by relabeling water molecules in such a way that each water molecule spans only a local region throughout the simulation. Then, we work out approximations and show how to compute the single-molecule entropy for the system of relabeled molecules. The results suggest that relabeling water molecules is promising for computation of solvation entropy. Full article
(This article belongs to the Special Issue Role of Water in Biological Systems)
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