Special Issue "Physics of Protein Folding, Misfolding, and Intrinsic Disorder: A Themed Issue in Honour of Professor Vladimir Uversky on the Occasion of His 60th Birthday"

A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: 15 September 2022 | Viewed by 2560

Special Issue Editors

Dr. Stefania Brocca
E-Mail Website
Guest Editor
Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
Interests: intrinsically disordered proteins; phase separations; charge-induced conformational transitions; structural and functional properties of hydrolytic enzymes
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Keith Dunker
E-Mail Website
Guest Editor
Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
Interests: intrinsically disordered proteins
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Professor Vladimir Uversky

The discovery of intrinsically disordered proteins (IDPs) has changed our perception of proteins as existing either in their native, folded and, hence, active state or as denatured, unfolded, and non-functional state. We now know that proteins may exist as dynamic conformational ensembles with little or no secondary and tertiary structure and yet be functional. Although apparently posing a challenge to Anfinsen’s postulate, IDPs in fact represent the limits of the structure–function paradigm.

IDPs also pose an additional challenge. Structural disorder is not easily tractable/detectable experimentally using techniques and approaches traditionally used by structuralists, and these techniques need to be enriched and complemented by those typically used by polymer physicists and chemists. Indeed, for the same reason, IDPs, which are prevalent in all three kingdoms of life and comprise almost half the human proteome, are often referred to as constituents of the ‘dark’ matter of biology. Over the past almost thirty years, studies on IDPs have fuelled crosstalk between biochemists, structuralists, and molecular biologists on one hand, and physicists and chemists on the other. These different communities have therefore faced the need to understand each other while speaking different languages.

Prof. Vladimir Uversky, one of the pioneers in the IDP field, realised the necessity of this dialogue and published an eloquent and thought-provoking paper, ‘Natively unfolded proteins: a point where biology waits for physics’ (Protein Sci. 2002). Today, twenty years later, to stimulate reflections on this issue and ponder the role of physical sciences in unravelling the structure–function paradigm, Biomolecules will be publishing this Special Issue on the occasion of Prof. Uversky’s 60th birthday celebrating his many contributions to the IDP field. This Special Issue aims to present the state of the art and invites contributions from those researchers who have known Prof. Vladimir Uversky personally.

Prof. Dr. Prakash Kulkarni
Dr. Stefania Brocca
Prof. Dr. Keith Dunker
Dr. Sonia Longhi
Guest Editors

Manuscript Submission Information

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Keywords

  • intrinsically disordered proteins (IDPs)
  • intrinsically disordered regions (IDRs)
  • intrinsic disorder prediction
  • intrinsic disorder characterization & methodological developments
  • molecular recognition & regulation mediated by structural disorder
  • conformational ensembles
  • energy landscape of IDPs
  • modeling of IDPs
  • conformational and binding properties of IDPs
  • folding upon binding
  • liquid-liquid phase separation
  • fibrillation
  • IDPs in nanotechnoogy and biotechnology
  • intrinsic disorder in disease and evolution

Published Papers (2 papers)

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Research

Article
Identification of Intrinsically Disordered Proteins and Regions in a Non-Model Insect Species Ostrinia nubilalis (Hbn.)
Biomolecules 2022, 12(4), 592; https://doi.org/10.3390/biom12040592 - 18 Apr 2022
Viewed by 583
Abstract
Research in previous decades has shown that intrinsically disordered proteins (IDPs) and regions in proteins (IDRs) are as ubiquitous as highly ordered proteins. Despite this, research on IDPs and IDRs still has many gaps left to fill. Here, we present an approach that [...] Read more.
Research in previous decades has shown that intrinsically disordered proteins (IDPs) and regions in proteins (IDRs) are as ubiquitous as highly ordered proteins. Despite this, research on IDPs and IDRs still has many gaps left to fill. Here, we present an approach that combines wet lab methods with bioinformatics tools to identify and analyze intrinsically disordered proteins in a non-model insect species that is cold-hardy. Due to their known resilience to the effects of extreme temperatures, these proteins likely play important roles in this insect’s adaptive mechanisms to sub-zero temperatures. The approach involves IDP enrichment by sample heating and double-digestion of proteins, followed by peptide and protein identification. Next, proteins are bioinformatically analyzed for disorder content, presence of long disordered regions, amino acid composition, and processes they are involved in. Finally, IDP detection is validated with an in-house 2D PAGE. In total, 608 unique proteins were identified, with 39 being mostly disordered, 100 partially disordered, 95 nearly ordered, and 374 ordered. One-third contain at least one long disordered segment. Functional information was available for only 90 proteins with intrinsic disorders out of 312 characterized proteins. Around half of the 90 proteins are cytoskeletal elements or involved in translational processes. Full article
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Article
Distribution of Charged Residues Affects the Average Size and Shape of Intrinsically Disordered Proteins
Biomolecules 2022, 12(4), 561; https://doi.org/10.3390/biom12040561 - 09 Apr 2022
Viewed by 854
Abstract
Intrinsically disordered proteins (IDPs) are ensembles of interconverting conformers whose conformational properties are governed by several physico-chemical factors, including their amino acid composition and the arrangement of oppositely charged residues within the primary structure. In this work, we investigate the effects of charge [...] Read more.
Intrinsically disordered proteins (IDPs) are ensembles of interconverting conformers whose conformational properties are governed by several physico-chemical factors, including their amino acid composition and the arrangement of oppositely charged residues within the primary structure. In this work, we investigate the effects of charge patterning on the average compactness and shape of three model IDPs with different proline content. We model IDP ensemble conformations as ellipsoids, whose size and shape are calculated by combining data from size-exclusion chromatography and native mass spectrometry. For each model IDP, we analyzed the wild-type protein and two synthetic variants with permuted positions of charged residues, where positive and negative amino acids are either evenly distributed or segregated. We found that charge clustering induces remodeling of the conformational ensemble, promoting compaction and/or increasing spherical shape. Our data illustrate that the average shape and volume of the ensembles depend on the charge distribution. The potential effect of other factors, such as chain length, number of proline residues, and secondary structure content, is also discussed. This methodological approach is a straightforward way to model IDP average conformation and decipher the salient sequence attributes influencing IDP structural properties. Full article
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: To be determined
Authors:
Keith Dunker; et al.
Affiliation:
Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA

Title: To be determined
Authors: Prakash Kulkarni; et al.
Affiliation: Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA 91010, USA

Title: To be determined
Authors: Benjamin Schuler; et al.
Affiliation: Department of Biochemistry and Department of Physics, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.

Title: To be determined
Authors: Jin Wang; et al.
Affiliation: Department of Chemistry and Physics, Stony Brook University, Stony Brook, NY 11794, USA

Title: To be determined
Authors: Bogdan Melnik; et al.
Affiliation: Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia

Title: To be determined
Authors: Remy Loris; et al.
Affiliation: Department of Biotechnology, Vrije Universiteit Brussel, B-1050 Brussel, Belgium

Title: The difference of structural state between canonical proteins and their isoforms established by proteome-wide bioinformatics analysis
Authors: Zarifa Osmanli 1,2, Theo Falgarone1, Turkan Samadova2, Jeremy Lecrecq1,  Ilham Shahmuradov2 and Andrey V Kajava1
Affiliation: 1 CRBM, Université de Montpellier, CNRS, Montpellier, France; 2 Institute of Biophysics, ANAS, Baku, Azerbaijan

Title: To be determined
Authors: Rita Grandori; et al.
Affiliation: Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy

Title: To be determined
Authors: Salvador Ventura; et al.
Affiliation: Institut de Biotecnologia i Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain

Title: To be determined
Authors: Stefano Gianni; et al.
Affiliation: Department of Biochemical Sciences “Rossi Fanelli”, Institute of Biology and Molecular Pathology of CNR, Sapienza University of Rome, 00185 Rome, Italy

Title: To be determined
Authors: David Eliezer; et al.
Affiliation: Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA.

Title: To be determined
Authors: Vincent J Hilser; et al.
Affiliation: Johns Hopkins University, USA

Title: To be determined
Authors: Elisar Barbar; et al.
Affiliation: Department of Biochemistry & Biophysics, College of Science, Corvallis, OR 97331, USA

Title: To be determined
Authors: Stefano Ciurli; Barbara Zambelli; et al.
Affiliation: Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy

Title: To be determined
Authors: Michele Vendruscolo; Johnny Habchi; et al.
Affiliation: University of Cambridge, Cambridge CB2 1EW, UK

Title: To be determined
Authors: Birthe Kragelund; Kresten Lindorff-Larsen; et al.
Affiliation: Københavns Universitet, Copenhagen, Denmark

Title: To be determined
Authors: Nathalie Sibille; et al.
Affiliation: Centre de Biochimie Structurale (CBS), CNRS, INSERM, University of Montpellier, Montpellier, France

Title: To be determined
Authors: Eugene A. Permyakov; et al.
Affiliation: Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Russia

Title: A trajectory of discovery: metabolic regulation by the conditionally disordered chloroplast protein, CP12
Authors: Cassy Gérard; Frédéric Carrière; Véronqiue Receveur-Bréchot; Hélène Launay*; Brigitte Gontero*
Affiliation: Aix Marseille Univ, CNRS, BIP, UMR 7281, 31 Chemin J. Aiguier, 13 402 Marseille Cedex 20, France

Title: To be determined
Authors: Isabelle Callebaut; et al.
Affiliation: Institut de Minéralogie de Physique des Matériaux et de Cosmochimie (IMPMC), Muséum National d’Histoire Naturelle, UMR CNRS 7590, Sorbonne Université, F-75005 Paris, France

Title: To be determined
Authors: Rohit V.Pappu; et al.
Affiliation: Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, MO 63130, USA

Title: To be determined
Authors: Gary W. Daughdrill; et al.
Affiliation: Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, USA

Title: A novel tandem-tag purification strategy for challenging disordered proteins
Authors: Peter Tompa; Attila Meszaros; et al.
Affiliation: Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium

Title: To be determined
Authors: Carine Van Heijenoort; et al.
Affiliation: ICSN-CNRS, Université Paris-Saclay, Gif-sur-Yvette, France

Title: To be determined
Authors: Thierry Michon; et al.
Affiliation: INRAE, Biologie du Fruit et Pathologie, University of Bordeaux, UMR 1332, F-33140 Villenave d'Ornon, France

Title: To be determined
Authors: Tanja Mittag; et al.
Affiliation: Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA

Title: To be determined
Authors: Martin Blackledge; et al.
Affiliation: Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France

Title: To be determined
Authors: Konstantin K. Turoverov; et al.
Affiliation: Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia

Title: To be determined
Authors: Andrzej Ożyhar; et al.
Affiliation: Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland

Title: To be determined
Authors: Garegin A Papoian; et al.
Affiliation: University of Maryland, College Park, MD 20742, USA

Title: To be determined
Authors: Christopher J. Oldfield; et al.
Affiliation: Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA

Title: To be determined
Authors: Ashok A Deniz; et al.
Affiliation: Department of Integrative and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA

Title: To be determined
Authors: Steven J Metallo; et al.
Affiliation: Department of Chemistry, Georgetown University, Washington, DC, USA

Title: To be determined
Authors: Jean Baum; et al.
Affiliation: Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA

Title: To be determined
Authors: Stephan M. Feller; et al.
Affiliation: Institute of Molecular Medicine, Tumor Biology, Martin-Luther-University of Halle-Wittenberg, Germany

Title: To be determined
Authors: Yaakov Levy; et al.
Affiliation: Department of Structural Biology, Weizmann Institute of Science, 76100, Rehovot, Israel

Title: To be determined
Authors: Mark E Bowen; et al.
Affiliation: Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA

Title: To be determined
Authors: Julie D. Forman-Kay; et al.
Affiliation: Molecular Medicine Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada

Title: To be determined
Authors: Zsuzsanna Dosztányi; et al.
Affiliation: Department of Biochemistry, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary

Title: To be determined
Authors: Galina A. Zhouravleva; et al.
Affiliation: St. Petersburg State University, 199034 St. Petersburg, Russia

Title: To be determined
Authors: Roberta Pierattelli; Isabella C. Felli; et al.
Affiliation: Department of Chemistry “Ugo Schiff” and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy

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