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Liquid–Liquid Phase Transition and Self-Assembly of Biomacromolecules

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Macromolecules".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 6493

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Special Issue Editors

Dr. Pier Luigi San Biagio

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Guest Editor

Institute of Biophysics (IBF) of the National Research Council (CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy
Interests: biopolymer interaction and gelation; protein aggregation; liquid-liquid phase transition; static and dynamic light scattering; neurodegenerative diseases

Dr. Donatella Bulone

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Guest Editor

Institute of Biophysics (IBF) of the National Research Council (CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy
Interests: sol-gel transition; biomolecular self-assembly; dynamic properties and structural arrest of biomolecules in solution; protein folding and chaperon activity; liquid-liquid phase transition; gel matrices for drug delivery

Special Issue Information

Dear Colleagues,

Recently, it has been proposed that a liquid–liquid phase transition is responsible for the formation of membraneless organelles such as nucleoli, stress granules, and Cajal bodies. They form spontaneously in response to a variety of cellular signals, behave as liquid droplets, and allow the localization of specific biological functions. Many membraneless organelles contain proteins belonging to the class of intrinsically disordered proteins (IDP). These proteins have a low degree of structural order, which grants them the capacity of acting as a hub in the complex network of protein–protein interactions. It has been reported that IDP are directly involved either in the functional self-assembly of membraneless organelles or in the formation of insoluble pathological aggregates associated with various diseases. We invite interested colleagues to contribute to this Special Issue with original research articles and topical reviews with the aim of providing a compendium of the state of the art and encouraging further exploration of this fascinating theme.

Dr. Pier Luigi San Biagio
Dr. Donatella Bulone
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

intrinsically disordered proteins
self-assembly
protein–protein interactions
liquid–liquid phase transition
sol–gel transition
chaperon activity
protein-aggregation-related diseases

Published Papers (3 papers)

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Research

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21 pages, 3799 KiB

Open AccessArticle

Thermostable Proteins from HaCaT Keratinocytes Identify a Wide Breadth of Intrinsically Disordered Proteins and Candidates for Liquid–Liquid Phase Separation

by Michael L. Samulevich, Rambon Shamilov and Brian J. Aneskievich

Int. J. Mol. Sci. 2022, 23(22), 14323; https://doi.org/10.3390/ijms232214323 - 18 Nov 2022

Cited by 2 | Viewed by 2180

Abstract

Intrinsically disordered proteins (IDPs) move through an ensemble of conformations which allows multitudinous roles within a cell. Keratinocytes, the predominant cell type in mammalian epidermis, have had only a few individual proteins assessed for intrinsic disorder and its possible contribution to liquid–liquid phase separation (LLPS), especially in regard to what functions or structures these proteins provide. We took a holistic approach to keratinocyte IDPs starting with enrichment via the isolation of thermostable proteins. The keratinocyte protein involucrin, known for its resistance to heat denaturation, served as a marker. It and other thermostable proteins were identified by liquid chromatography tandem mass spectrometry and subjected to extensive bioinformatic analysis covering gene ontology, intrinsic disorder, and potential for LLPS. Numerous proteins unique to keratinocytes and other proteins with shared expression in multiple cell types were identified to have IDP traits (e.g., compositional bias, nucleic acid binding, and repeat motifs). Among keratinocyte-specific proteins, many that co-assemble with involucrin into the cell-specific structure known as the cornified envelope scored highly for intrinsic disorder and potential for LLPS. This suggests intrinsic disorder and LLPS are previously unrecognized traits for assembly of the cornified envelope, echoing the contribution of intrinsic disorder and LLPS to more widely encountered features such as stress granules and PML bodies. Full article

(This article belongs to the Special Issue Liquid–Liquid Phase Transition and Self-Assembly of Biomacromolecules)

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20 pages, 3313 KiB

Open AccessArticle

FUS Microphase Separation: Regulation by Nucleic Acid Polymers and DNA Repair Proteins

by Maria V. Sukhanova, Rashid O. Anarbaev, Ekaterina A. Maltseva, David Pastré and Olga I. Lavrik

Int. J. Mol. Sci. 2022, 23(21), 13200; https://doi.org/10.3390/ijms232113200 - 30 Oct 2022

Cited by 1 | Viewed by 1821

Abstract

Fused in sarcoma (FUS) is involved in the regulation of RNA and DNA metabolism. FUS participates in the formation of biomolecular condensates driven by phase transition. FUS is prone to self-aggregation and tends to undergo phase transition both with or without nucleic acid polymers. Using dynamic light scattering and fluorescence microscopy, we examined the formation of FUS high-order structures or FUS-rich microphases induced by the presence of RNA, poly(ADP-ribose), ssDNA, or dsDNA and evaluated effects of some nucleic-acid-binding proteins on the phase behavior of FUS–nucleic acid systems. Formation and stability of FUS-rich microphases only partially correlated with FUS’s affinity for a nucleic acid polymer. Some proteins—which directly interact with PAR, RNA, ssDNA, and dsDNA and are possible components of FUS-enriched cellular condensates—disrupted the nucleic-acid-induced assembly of FUS-rich microphases. We found that XRCC1, a DNA repair factor, underwent a microphase separation and formed own microdroplets and coassemblies with FUS in the presence of poly(ADP-ribose). These results probably indicated an important role of nucleic-acid-binding proteins in the regulation of FUS-dependent formation of condensates and imply the possibility of the formation of XRCC1-dependent phase-separated condensates in the cell. Full article

(This article belongs to the Special Issue Liquid–Liquid Phase Transition and Self-Assembly of Biomacromolecules)

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Review

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19 pages, 7293 KiB

Open AccessReview

Poly(ADP-ribose) in Condensates: The PARtnership of Phase Separation and Site-Specific Interactions

by Elizaveta E. Alemasova and Olga I. Lavrik

Int. J. Mol. Sci. 2022, 23(22), 14075; https://doi.org/10.3390/ijms232214075 - 15 Nov 2022

Cited by 2 | Viewed by 2112

Abstract

Biomolecular condensates are nonmembrane cellular compartments whose formation in many cases involves phase separation (PS). Despite much research interest in this mechanism of macromolecular self-organization, the concept of PS as applied to a live cell faces certain challenges. In this review, we discuss a basic model of PS and the role of site-specific interactions and percolation in cellular PS-related events. Using a multivalent poly(ADP-ribose) molecule as an example, which has high PS-driving potential due to its structural features, we consider how site-specific interactions and network formation are involved in the formation of phase-separated cellular condensates. Full article

(This article belongs to the Special Issue Liquid–Liquid Phase Transition and Self-Assembly of Biomacromolecules)

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