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Biological Liquid-Liquid Phase Separation, Biomolecular Condensates, and Membraneless Organelles (2nd Edition)

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: 20 December 2024 | Viewed by 3366

Special Issue Editor

Prof. Dr. Vladimir N. Uversky

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Guest Editor
Department of Molecular Medicine, USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd, MDC07, Tampa, FL 33612, USA
Interests: intrinsically disordered proteins; protein folding; protein misfolding; partially folded proteins; protein aggregation; protein structure; protein function; protein stability; protein biophysics; protein bioinformatics; conformational diseases; protein–ligand interactions; protein–protein interactions; liquid-liquid phase transitions
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Special Issue Information

Dear Colleagues,

Currently, there is immense interest among the scientific community in intracellular liquid–liquid phase separation (LLPS) and resulting biomolecular condensates (BMCs) and membrane-less organelles (MLOs). Obviously, such BMCs and MLOs, which do not have enclosing membranes, are mysterious subjects, whose components can directly contact, and exchange with, the exterior environment and whose biogenesis and structural integrity rely exclusively on protein–protein and/or protein–nucleic acid interactions. BMCs/MLOs, are large, highly dynamic, macromolecular ensembles visible under the light microscope as spherical micron-sized droplets. They demonstrate liquid-like behavior, being able to drip, formation of spherical structures upon fusion, and wetting. Therefore, MLOs are condensed liquid droplets formed as a result of reversible and highly controlled LLPS. MLOs are different in size, shape, and composition, and have important and diverse biological functions. Typically, MLOs are formed in response to specific cellular activities or stress. Alterations of their biogenesis might have pathological consequences, and many MLOs are associated with the pathogenesis of various diseases. Leading by Prof. Dr. Vladimir N. Uversky and assisting by our Topical Advisory Panel Member Dr. Zoltan Villanyi (University of Szeged), this Special Issue includes research papers and reviews dedicated to the different aspects of LLPS, BMCs, and MLOs.

Prof. Dr. Vladimir N. Uversky
Guest Editor

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Published Papers (2 papers)

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Research

18 pages, 13890 KiB  
Article
DNA Repair Protein XRCC1 Stimulates Activity of DNA Polymerase λ under Conditions of Microphase Separation
by Natalia A. Lebedeva, Rashid O. Anarbaev, Ekaterina A. Maltseva, Maria V. Sukhanova, Nadejda I. Rechkunova and Olga I. Lavrik
Int. J. Mol. Sci. 2024, 25(13), 6927; https://doi.org/10.3390/ijms25136927 - 25 Jun 2024
Viewed by 723
Abstract
Non-membrane compartments or biomolecular condensates play an important role in the regulation of cellular processes including DNA repair. Here, an ability of XRCC1, a scaffold protein involved in DNA base excision repair (BER) and single-strand break repair, to form protein-rich microphases in the [...] Read more.
Non-membrane compartments or biomolecular condensates play an important role in the regulation of cellular processes including DNA repair. Here, an ability of XRCC1, a scaffold protein involved in DNA base excision repair (BER) and single-strand break repair, to form protein-rich microphases in the presence of DNA duplexes was discovered. We also showed that the gap-filling activity of BER-related DNA polymerase λ (Pol λ) is significantly increased by the presence of XRCC1. The stimulation of the Pol λ activity was observed only at micromolar XRCC1 concentrations, which were well above the nanomolar dissociation constant determined for the XRCC1–Pol λ complex and pointed to the presence of an auxiliary stimulatory factor in addition to protein–protein interactions. Indeed, according to dynamic light scattering measurements, the stimulation of the Pol λ activity by XRCC1 was coupled with microphase separation in a protein–DNA mixture. Fluorescence microscopy revealed colocalization of Pol λ, XRCC1, and gapped DNA within the microphases. Thus, stimulation of Pol λ activity is caused both by its interaction with XRCC1 and by specific conditions of microphase separation; this phenomenon is shown for the first time. Full article
(This article belongs to the Special Issue Biological Liquid-Liquid Phase Separation, Biomolecular Condensates, and Membraneless Organelles (2nd Edition))
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28 pages, 11034 KiB  
Article
Nucleolar- and Nuclear-Stress-Induced Membrane-Less Organelles: A Proteome Analysis through the Prism of Liquid–Liquid Phase Separation
by Yakov I. Mokin, Anastasia A. Gavrilova, Anna S. Fefilova, Irina M. Kuznetsova, Konstantin K. Turoverov, Vladimir N. Uversky and Alexander V. Fonin
Int. J. Mol. Sci. 2023, 24(13), 11007; https://doi.org/10.3390/ijms241311007 - 2 Jul 2023
Cited by 5 | Viewed by 1808
Abstract
Radical changes in the idea of the organization of intracellular space that occurred in the early 2010s made it possible to consider the formation and functioning of so-called membrane-less organelles (MLOs) based on a single physical principle: the liquid–liquid phase separation (LLPS) of [...] Read more.
Radical changes in the idea of the organization of intracellular space that occurred in the early 2010s made it possible to consider the formation and functioning of so-called membrane-less organelles (MLOs) based on a single physical principle: the liquid–liquid phase separation (LLPS) of biopolymers. Weak non-specific inter- and intramolecular interactions of disordered polymers, primarily intrinsically disordered proteins, and RNA, play a central role in the initiation and regulation of these processes. On the other hand, in some cases, the “maturation” of MLOs can be accompanied by a “liquid–gel” phase transition, where other types of interactions can play a significant role in the reorganization of their structure. In this work, we conducted a bioinformatics analysis of the propensity of the proteomes of two membrane-less organelles, formed in response to stress in the same compartment, for spontaneous phase separation and examined their intrinsic disorder predispositions. These MLOs, amyloid bodies (A-bodies) formed in the response to acidosis and heat shock and nuclear stress bodies (nSBs), are characterized by a partially overlapping composition, but show different functional activities and morphologies. We show that the proteomes of these biocondensates are differently enriched in proteins, and many have high potential for spontaneous LLPS that correlates with the different morphology and function of these organelles. The results of these analyses allowed us to evaluate the role of weak interactions in the formation and functioning of these important organelles. Full article
(This article belongs to the Special Issue Biological Liquid-Liquid Phase Separation, Biomolecular Condensates, and Membraneless Organelles (2nd Edition))
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