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Biomolecules
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Molecular Phase Transitions in Physiology and Pathology: Freezing and Precipitation...
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Molecular Phase Transitions in Physiology and Pathology: Freezing and Precipitation in Biology

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biological Factors".

Deadline for manuscript submissions: closed (25 May 2022) | Viewed by 8049

Special Issue Editors

Prof. Dr. Alexei V. Finkelstein

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Guest Editor
Laboratory of Protein Physics, Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
Interests: protein physics; protein structure; protein folding; protein folding intermediates; protein design; phase transitions; phase transition kinetics; transition states; antifreeze proteins; amyloids; protein bioinformatics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Roman G. Efremov

E-Mail Website
Guest Editor
Biomolecular Systems Modeling Laboratory, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences, 117997 Moscow, Russia
Interests: biophysics; membranes; membrane proteins; NMR; molecular modeling; computer simulations

Special Issue Information

Dear Colleagues,

We are pleased to invite you to take part in this Special Issue of Biomolecules dedicated to the biological phenomena that are connected to phase transitions.

Phase transitions, such as the freezing of water upon lowering temperature, or precipitation upon increasing solute concentration, are familiar physical phenomena. Such collective processes are also of importance to living systems. Spontaneous intramolecular phase transitions define the folding of globular proteins and maybe chromatin too; intermolecular phase transitions are the behind-the-scenes players in protein aggregation, the formation of amyloid fibrils, liquid–liquid or liquid–gel phase transitions associated with the biogenesis of membranes, as well as in membraneless organelles in the cells, with the formation of atherosclerotic plaques, blood clots, etc. The new phases can be nucleated in bulk liquid and on various interfaces and “impurities”, etc.

This Special Issue aims to provide an overview and analysis of the as-yet still limited understanding of the phase behavior in and around biological objects.

In this Special Issue, original research articles and reviews are welcome. Research areas may include (but are not limited to) the phase transition phenomena connected to proteins, nucleic acids, membranes, and biological liquid–liquid and liquid–gel phase transitions.

We look forward to receiving your contributions.

Prof. Dr. Alexei V. Finkelstein
Prof. Dr. Roman Efremov
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. Biomolecules 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 2700 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

  • phase transitions
  • proteins
  • membranes
  • freezing
  • precipitation
  • liquid–liquid phase transition
  • liquid–gel phase transition

Published Papers (3 papers)

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Research

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13 pages, 2178 KiB  
Article
How Can Ice Emerge at 0 °C?
by Alexei V. Finkelstein, Sergiy O. Garbuzynskiy and Bogdan S. Melnik
Biomolecules 2022, 12(7), 981; https://doi.org/10.3390/biom12070981 - 13 Jul 2022
Cited by 4 | Viewed by 1482 | Correction
Abstract
The classical nucleation theory shows that bulk water freezing does not occur at temperatures above ≈ −30 °C, and that at higher temperatures ice nucleation requires the presence of some ice-binding surfaces. The temperature and rate of ice nucleation depend on the size [...] Read more.
The classical nucleation theory shows that bulk water freezing does not occur at temperatures above ≈ −30 °C, and that at higher temperatures ice nucleation requires the presence of some ice-binding surfaces. The temperature and rate of ice nucleation depend on the size and level of complementarity between the atomic structure of these surfaces and various H-bond-rich/depleted crystal planes. In our experiments, the ice nucleation temperature was within a range from −8 °C to −15 °C for buffer and water in plastic test tubes. Upon the addition of ice-initiating substances (i.e., conventional AgI or CuO investigated here), ice appeared in a range from −3 °C to −7 °C, and in the presence of the ice-nucleating bacterium Pseudomonas syringae from −1 °C to −2 °C. The addition of an antifreeze protein inhibited the action of the tested ice-initiating agents. Full article
(This article belongs to the Special Issue Molecular Phase Transitions in Physiology and Pathology: Freezing and Precipitation in Biology)
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19 pages, 5285 KiB  
Article
Differences in Medium-Induced Conformational Plasticity Presumably Underlie Different Cytotoxic Activity of Ricin and Viscumin
by Pavel Volynsky, Diana Maltseva, Valentin Tabakmakher, Eduard V. Bocharov, Maria Raygorodskaya, Galina Zakharova, Elena Britikova, Alexander Tonevitsky and Roman Efremov
Biomolecules 2022, 12(2), 295; https://doi.org/10.3390/biom12020295 - 11 Feb 2022
Cited by 1 | Viewed by 2118
Abstract
Structurally similar catalytic subunits A of ricin (RTA) and viscumin (MLA) exhibit cytotoxic activity through ribosome inactivation. Ricin is more cytotoxic than viscumin, although the molecular mechanisms behind this difference are still poorly understood. To shed more light on this problem, we used [...] Read more.
Structurally similar catalytic subunits A of ricin (RTA) and viscumin (MLA) exhibit cytotoxic activity through ribosome inactivation. Ricin is more cytotoxic than viscumin, although the molecular mechanisms behind this difference are still poorly understood. To shed more light on this problem, we used a combined biochemical/molecular modeling approach to assess possible relationships between the activity of toxins and their structural/dynamic properties. Based on bioassay measurements, it was suggested that the differences in activity are associated with the ability of RTA and MLA to undergo structural/hydrophobic rearrangements during trafficking through the endoplasmic reticulum (ER) membrane. Molecular dynamics simulations and surface hydrophobicity mapping of both proteins in different media showed that RTA rearranges its structure in a membrane-like environment much more efficiently than MLA. Their refolded states also drastically differ in terms of hydrophobic organization. We assume that the higher conformational plasticity of RTA is favorable for the ER-mediated translocation pathway, which leads to a higher rate of toxin penetration into the cytoplasm. Full article
(This article belongs to the Special Issue Molecular Phase Transitions in Physiology and Pathology: Freezing and Precipitation in Biology)
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Review

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23 pages, 1612 KiB  
Review
Getting Closer to Decrypting the Phase Transitions of Bacterial Biomolecules
by Katarzyna Sołtys, Aneta Tarczewska, Dominika Bystranowska and Nikola Sozańska
Biomolecules 2022, 12(7), 907; https://doi.org/10.3390/biom12070907 - 28 Jun 2022
Cited by 8 | Viewed by 3885
Abstract
Liquid–liquid phase separation (LLPS) of biomolecules has emerged as a new paradigm in cell biology, and the process is one proposed mechanism for the formation of membraneless organelles (MLOs). Bacterial cells have only recently drawn strong interest in terms of studies on both [...] Read more.
Liquid–liquid phase separation (LLPS) of biomolecules has emerged as a new paradigm in cell biology, and the process is one proposed mechanism for the formation of membraneless organelles (MLOs). Bacterial cells have only recently drawn strong interest in terms of studies on both liquid-to-liquid and liquid-to-solid phase transitions. It seems that these processes drive the formation of prokaryotic cellular condensates that resemble eukaryotic MLOs. In this review, we present an overview of the key microbial biomolecules that undergo LLPS, as well as the formation and organization of biomacromolecular condensates within the intracellular space. We also discuss the current challenges in investigating bacterial biomacromolecular condensates. Additionally, we highlight a summary of recent knowledge about the participation of bacterial biomolecules in a phase transition and provide some new in silico analyses that can be helpful for further investigations. Full article
(This article belongs to the Special Issue Molecular Phase Transitions in Physiology and Pathology: Freezing and Precipitation in Biology)
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