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Uversky VN. Marc H. V. van Regenmortel, a virtual friend and a real colleague. J Mol Recognit 2024; 37:e3079. [PMID: 38419129 DOI: 10.1002/jmr.3079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 03/02/2024]
Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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Zagrovic B, Adlhart M, Kapral TH. Coding From Binding? Molecular Interactions at the Heart of Translation. Annu Rev Biophys 2023; 52:69-89. [PMID: 36626765 DOI: 10.1146/annurev-biophys-090622-102329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The mechanism and the evolution of DNA replication and transcription, the key elements of the central dogma of biology, are fundamentally well explained by the physicochemical complementarity between strands of nucleic acids. However, the determinants that have shaped the third part of the dogma-the process of biological translation and the universal genetic code-remain unclear. We review and seek parallels between different proposals that view the evolution of translation through the prism of weak, noncovalent interactions between biological macromolecules. In particular, we focus on a recent proposal that there exists a hitherto unrecognized complementarity at the heart of biology, that between messenger RNA coding regions and the proteins that they encode, especially if the two are unstructured. Reflecting the idea that the genetic code evolved from intrinsic binding propensities between nucleotides and amino acids, this proposal promises to forge a link between the distant past and the present of biological systems.
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Affiliation(s)
- Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs & University of Vienna, Vienna, Austria;
| | - Marlene Adlhart
- Department of Structural and Computational Biology, Max Perutz Labs & University of Vienna, Vienna, Austria;
| | - Thomas H Kapral
- Department of Structural and Computational Biology, Max Perutz Labs & University of Vienna, Vienna, Austria;
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
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Biological soft matter: intrinsically disordered proteins in liquid-liquid phase separation and biomolecular condensates. Essays Biochem 2022; 66:831-847. [PMID: 36350034 DOI: 10.1042/ebc20220052] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/10/2022]
Abstract
The facts that many proteins with crucial biological functions do not have unique structures and that many biological processes are compartmentalized into the liquid-like biomolecular condensates, which are formed via liquid-liquid phase separation (LLPS) and are not surrounded by the membrane, are revolutionizing the modern biology. These phenomena are interlinked, as the presence of intrinsic disorder represents an important requirement for a protein to undergo LLPS that drives biogenesis of numerous membrane-less organelles (MLOs). Therefore, one can consider these phenomena as crucial constituents of a new IDP-LLPS-MLO field. Furthermore, intrinsically disordered proteins (IDPs), LLPS, and MLOs represent a clear link between molecular and cellular biology and soft matter and condensed soft matter physics. Both IDP and LLPS/MLO fields are undergoing explosive development and generate the ever-increasing mountain of crucial data. These new data provide answers to so many long-standing questions that it is difficult to imagine that in the very recent past, protein scientists and cellular biologists operated without taking these revolutionary concepts into account. The goal of this essay is not to deliver a comprehensive review of the IDP-LLPS-MLO field but to provide a brief and rather subjective outline of some of the recent developments in these exciting fields.
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Dayhoff GW, Uversky VN. Rapid prediction and analysis of protein intrinsic disorder. Protein Sci 2022; 31:e4496. [PMID: 36334049 PMCID: PMC9679974 DOI: 10.1002/pro.4496] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/07/2022]
Abstract
Protein intrinsic disorder is found in all kingdoms of life and is known to underpin numerous physiological and pathological processes. Computational methods play an important role in characterizing and identifying intrinsically disordered proteins and protein regions. Herein, we present a new high-efficiency web-based disorder predictor named Rapid Intrinsic Disorder Analysis Online (RIDAO) that is designed to facilitate the application of protein intrinsic disorder analysis in genome-scale structural bioinformatics and comparative genomics/proteomics. RIDAO integrates six established disorder predictors into a single, unified platform that reproduces the results of individual predictors with near-perfect fidelity. To demonstrate the potential applications, we construct a test set containing more than one million sequences from one hundred organisms comprising over 420 million residues. Using this test set, we compare the efficiency and accessibility (i.e., ease of use) of RIDAO to five well-known and popular disorder predictors, namely: AUCpreD, IUPred3, metapredict V2, flDPnn, and SPOT-Disorder2. We show that RIDAO yields per-residue predictions at a rate two to six orders of magnitude greater than the other predictors and completely processes the test set in under an hour. RIDAO can be accessed free of charge at https://ridao.app.
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Affiliation(s)
- Guy W. Dayhoff
- Department of ChemistryUniversity of South FloridaTampaFloridaUSA
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research InstituteUniversity of South FloridaTampaFloridaUSA
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Štambuk N, Konjevoda P, Pavan J. Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research. Int J Mol Sci 2021; 22:9106. [PMID: 34502016 PMCID: PMC8431130 DOI: 10.3390/ijms22179106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 01/01/2023] Open
Abstract
Antisense peptide technology (APT) is based on a useful heuristic algorithm for rational peptide design. It was deduced from empirical observations that peptides consisting of complementary (sense and antisense) amino acids interact with higher probability and affinity than the randomly selected ones. This phenomenon is closely related to the structure of the standard genetic code table, and at the same time, is unrelated to the direction of its codon sequence translation. The concept of complementary peptide interaction is discussed, and its possible applications to diagnostic tests and bioengineering research are summarized. Problems and difficulties that may arise using APT are discussed, and possible solutions are proposed. The methodology was tested on the example of SARS-CoV-2. It is shown that the CABS-dock server accurately predicts the binding of antisense peptides to the SARS-CoV-2 receptor binding domain without requiring predefinition of the binding site. It is concluded that the benefits of APT outweigh the costs of random peptide screening and could lead to considerable savings in time and resources, especially if combined with other computational and immunochemical methods.
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Affiliation(s)
- Nikola Štambuk
- Center for Nuclear Magnetic Resonance, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Paško Konjevoda
- Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Josip Pavan
- Department of Ophthalmology, University Hospital Dubrava, Avenija Gojka Šuška 6, HR-10000 Zagreb, Croatia
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Van Regenmortel MHV. Design in biology and rational design in vaccinology: A conceptual analysis. Methods 2021; 195:120-127. [PMID: 34352372 DOI: 10.1016/j.ymeth.2021.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/20/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022] Open
Abstract
This review discusses the philosophical foundations of what used to be called "the scientific method" and is nowadays often known as the scientific attitude. It used to be believed that scientific theories and methods aimed at the truth especially in the case of physics, chemistry and astronomy because these sciences were able to develop numerous scientific laws that made it possible to understand and predict many physical phenomena. The situation is different in the case of the biological sciences which deal with highly complex living organisms made up of huge numbers of constituents that undergo continuous dynamic processes; this leads to novel emergent properties in organisms that cannot be predicted because they are not present in the constituents before they have interacted with each other. This is one of the reasons why there are no universal scientific laws in biology. Furthermore, all scientific theories can only achieve a restricted level of predictive success because they remain valid only under the limited range of conditions that were used for establishing the theory' in the first place. Many theories that used to be accepted were subsequently shown to be false, demonstrating that scientific theories always remain tentative and can never be proven beyond and doubt. It is ironical that as scientists have finally accepted that approximate truths are perfectly adequate and that absolute truth is an illusion, a new irrational sociological phenomenon called Post-Truth conveyed by social media, the Internet and fake news has developed in the Western world that is convincing millions of people that truth simply does not exist. Misleading information is circulated with the intention to deceive and science denialism is promoted by denying the remarkable achievements of science and technology during the last centuries. Although the concept of intentional design is widely used to describe the methods that biologists use to make discoveries and inventions, it will be argued that the term is not appropriate for explaining the appearance of life on our planet nor for describing the scientific creativity of scientific investigators. The term rational for describing the development of new vaccines is also unjustified. Because the analysis of the COVID-19 pandemic requires contributions from biomedical and psycho-socioeconomic sciences, one scientific method alone would be insufficient for combatting the pandemic.
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Kutyshenko VP, Prokhorov DA, Mikoulinskaia GV, Molochkov NV, Yegorov AY, Paskevich SI, Uversky VN. Comparative analysis of the active sites of orthologous endolysins of the Escherichia lytic bacteriophages T5, RB43, and RB49. Int J Biol Macromol 2020; 166:1096-1105. [PMID: 33159938 DOI: 10.1016/j.ijbiomac.2020.10.264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/31/2020] [Indexed: 10/23/2022]
Abstract
The methods of solution NMR, circular dichroism (CD), and differential scanning calorimetry (DSC) were used to study two zinc-containing L-alanyl-D-glutamate peptidases - endolysins of the pseudo T-even myoviruses RB43 and RB49 (EndoRB43 and EndoRB49, respectively), which are orthologous to the EndoT5, which is a zinc-containing L-alanyl-D-glutamate peptidase of the T5 siphovirus. The spatial conservation of the Zn2+-binding sites for the enzymes EndoT5, EndoRB43, and EndoRB49 was established, and the key role of Zn2+ ions in the stabilization of the spatial structures of these three peptidases was confirmed. We are showing here that the binding of the Zn2+ ion in the active center of EndoRB49 peptidase causes conformational rearrangements similar to those observed in the EndoT5 peptidase upon binding of Zn2+ and Ca2+ ions and lead to the formation of a catalytically active form of the enzyme. Therefore, the binding of the Zn2+ ion to the active site of EndoRB49 peptidase is a necessary and sufficient condition for functioning of this protein.
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Affiliation(s)
- Victor P Kutyshenko
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
| | - Dmitry A Prokhorov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Galina V Mikoulinskaia
- Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Nikolai V Molochkov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Alexander Y Yegorov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Svetlana I Paskevich
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Vladimir N Uversky
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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