1
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Pietrangeli P, Marcocci L, Pennacchietti V, Diop A, Di Felice M, Pagano L, Malagrinò F, Toto A, Brunori M, Gianni S. The Mechanism of Folding of Human Frataxin in Comparison to the Yeast Homologue - Broad Energy Barriers and the General Properties of the Transition State. J Mol Biol 2024; 436:168555. [PMID: 38552947 DOI: 10.1016/j.jmb.2024.168555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024]
Abstract
The funneled energy landscape theory suggests that the folding pathway of homologous proteins should converge at the late stages of folding. In this respect, proteins displaying a broad energy landscape for folding are particularly instructive, allowing inferring both the early, intermediate and late stages of folding. In this paper we explore the folding mechanisms of human frataxin, an essential mitochondrial protein linked to the neurodegenerative disorder Friedreich's ataxia. Building upon previous studies on the yeast homologue, the folding pathway of human frataxin is thoroughly examined, revealing a mechanism implying the presence of a broad energy barrier, reminiscent of the yeast counterpart. Through an extensive site-directed mutagenesis, we employed a Φ -value analysis to map native-like contacts in the folding transition state. The presence of a broad energy barrier facilitated the exploration of such contacts in both early and late folding events. We compared results from yeast and human frataxin providing insights into the impact of native topology on the folding mechanism and elucidating the properties of the underlying free energy landscape. The findings are discussed in the context of the funneled energy landscape theory of protein folding.
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Affiliation(s)
- Paola Pietrangeli
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185 Rome, Italy
| | - Lucia Marcocci
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185 Rome, Italy
| | - Valeria Pennacchietti
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185 Rome, Italy
| | - Awa Diop
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185 Rome, Italy
| | - Mariana Di Felice
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185 Rome, Italy
| | - Livia Pagano
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185 Rome, Italy
| | - Francesca Malagrinò
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze Della Vita e Dell'ambiente, Università dell'Aquila, Piazzale Salvatore Tommasi 1, 67010 L'Aquila - Coppito, Italy
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185 Rome, Italy
| | - Maurizio Brunori
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185 Rome, Italy
| | - Stefano Gianni
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185 Rome, Italy.
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2
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Bychkova VE, Dolgikh DA, Balobanov VA. Function of the Conserved Non-Functional Residues in Apomyoglobin - to Determine and to Preserve Correct Topology of the Protein. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1905-1909. [PMID: 38105207 DOI: 10.1134/s0006297923110184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 07/18/2023] [Accepted: 08/31/2023] [Indexed: 12/19/2023]
Abstract
In this paper the answer to O. B. Ptitsyn's question "What is the role of conserved non-functional residues in apomyoglobin" is presented, which is based on the research results of three laboratories. The role of conserved non-functional apomyoglobin residues in formation of native topology in the molten globule state of this protein is revealed. This fact allows suggesting that the conserved non-functional residues in this protein are indispensable for fixation and maintaining main elements of the correct topology of its secondary structure in the intermediate state. The correct topology is a native element in the intermediate state of the protein.
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Affiliation(s)
- Valentina E Bychkova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Dmitry A Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117871, Russia
| | - Vitalii A Balobanov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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3
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Wijker S, Palmans ARA. Protein-Inspired Control over Synthetic Polymer Folding for Structured Functional Nanoparticles in Water. Chempluschem 2023; 88:e202300260. [PMID: 37417828 DOI: 10.1002/cplu.202300260] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/06/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023]
Abstract
The folding of proteins into functional nanoparticles with defined 3D structures has inspired chemists to create simple synthetic systems mimicking protein properties. The folding of polymers into nanoparticles in water proceeds via different strategies, resulting in the global compaction of the polymer chain. Herein, we review the different methods available to control the conformation of synthetic polymers and collapse/fold them into structured, functional nanoparticles, such as hydrophobic collapse, supramolecular self-assembly, and covalent cross-linking. A comparison is made between the design principles of protein folding to synthetic polymer folding and the formation of structured nanocompartments in water, highlighting similarities and differences in design and function. We also focus on the importance of structure for functional stability and diverse applications in complex media and cellular environments.
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Affiliation(s)
- Stefan Wijker
- Institute for Complex Molecular Systems, Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Anja R A Palmans
- Institute for Complex Molecular Systems, Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
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4
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Santorelli D, Marcocci L, Pennacchietti V, Nardella C, Diop A, Pietrangeli P, Pagano L, Toto A, Malagrinò F, Gianni S. Understanding the molecular basis of folding cooperativity through a comparative analysis of a multidomain protein and its isolated domains. J Biol Chem 2023; 299:102983. [PMID: 36739950 PMCID: PMC10017356 DOI: 10.1016/j.jbc.2023.102983] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/05/2023] Open
Abstract
Although cooperativity is a well-established and general property of folding, our current understanding of this feature in multidomain folding is still relatively limited. In fact, there are contrasting results indicating that the constituent domains of a multidomain protein may either fold independently on each other or exhibit interdependent supradomain phenomena. To address this issue, here we present the comparative analysis of the folding of a tandem repeat protein, comprising two contiguous PDZ domains, in comparison to that of its isolated constituent domains. By analyzing in detail the equilibrium and kinetics of folding at different experimental conditions, we demonstrate that despite each of the PDZ domains in isolation being capable of independent folding, at variance with previously characterized PDZ tandem repeats, the full-length construct folds and unfolds as a single cooperative unit. By exploiting quantitatively, the comparison of the folding of the tandem repeat to those observed for its constituent domains, as well as by characterizing a truncated variant lacking a short autoinhibitory segment, we successfully rationalize the molecular basis of the observed cooperativity and attempt to infer some general conclusions for multidomain systems.
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Affiliation(s)
- Daniele Santorelli
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Lucia Marcocci
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Valeria Pennacchietti
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Caterina Nardella
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Awa Diop
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Paola Pietrangeli
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Livia Pagano
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Francesca Malagrinò
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Naples, Italy.
| | - Stefano Gianni
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy.
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5
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Ginell GM, Holehouse AS. An Introduction to the Stickers-and-Spacers Framework as Applied to Biomolecular Condensates. Methods Mol Biol 2023; 2563:95-116. [PMID: 36227469 DOI: 10.1007/978-1-0716-2663-4_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Cellular organization is determined by a combination of membrane-bound and membrane-less biomolecular assemblies that range from clusters of tens of molecules to micrometer-sized cellular bodies. Over the last decade, membrane-less assemblies have come to be referred to as biomolecular condensates, reflecting their ability to condense specific molecules with respect to the remainder of the cell. In many cases, the physics of phase transitions provides a conceptual framework and a mathematical toolkit to describe the assembly, maintenance, and dissolution of biomolecular condensates. Among the various quantitative and qualitative models applied to understand intracellular phase transitions, the stickers-and-spacers framework offers an intuitive yet rigorous means to map biomolecular sequences and structure to the driving forces needed for higher-order assembly. This chapter introduces the fundamental concepts behind the stickers-and-spacers model, considers its application to different biological systems, and discusses limitations and misconceptions around the model.
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Affiliation(s)
- Garrett M Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA.
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6
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Finkelstein AV, Bogatyreva NS, Ivankov DN, Garbuzynskiy SO. Protein folding problem: enigma, paradox, solution. Biophys Rev 2022; 14:1255-1272. [PMID: 36659994 PMCID: PMC9842845 DOI: 10.1007/s12551-022-01000-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/19/2022] [Indexed: 01/22/2023] Open
Abstract
The ability of protein chains to spontaneously form their three-dimensional structures is a long-standing mystery in molecular biology. The most conceptual aspect of this mystery is how the protein chain can find its native, "working" spatial structure (which, for not too big protein chains, corresponds to the global free energy minimum) in a biologically reasonable time, without exhaustive enumeration of all possible conformations, which would take billions of years. This is the so-called "Levinthal's paradox." In this review, we discuss the key ideas and discoveries leading to the current understanding of protein folding kinetics, including folding landscapes and funnels, free energy barriers at the folding/unfolding pathways, and the solution of Levinthal's paradox. A special role here is played by the "all-or-none" phase transition occurring at protein folding and unfolding and by the point of thermodynamic (and kinetic) equilibrium between the "native" and the "unfolded" phases of the protein chain (where the theory obtains the simplest form). The modern theory provides an understanding of key features of protein folding and, in good agreement with experiments, it (i) outlines the chain length-dependent range of protein folding times, (ii) predicts the observed maximal size of "foldable" proteins and domains. Besides, it predicts the maximal size of proteins and domains that fold under solely thermodynamic (rather than kinetic) control. Complementarily, a theoretical analysis of the number of possible protein folding patterns, performed at the level of formation and assembly of secondary structures, correctly outlines the upper limit of protein folding times.
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Affiliation(s)
- Alexei V. Finkelstein
- Institute of Protein Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Biotechnology Department of the Lomonosov Moscow State University, 4 Institutskaya Str, 142290 Pushchino, Moscow Region, Russia
- Biology Department of the Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia
| | - Natalya S. Bogatyreva
- Institute of Protein Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Dmitry N. Ivankov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Sergiy O. Garbuzynskiy
- Institute of Protein Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
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7
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Tajana M, Trovato A, Tiana G. Key interaction patterns in proteins revealed by cluster expansion of the partition function. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2022; 45:95. [PMID: 36447074 DOI: 10.1140/epje/s10189-022-00250-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/19/2022] [Indexed: 06/16/2023]
Abstract
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence design. To achieve this goal, we employed a cluster expansion of the partition function in the space of sequences and evaluated numerically the statistical importance of each cluster. An important feature of this procedure is that it is applied to a dense finite system. We found that patterns that contribute most to the partition function are cycles with even numbers of nodes, while cliques are typically detrimental. Each cluster also gives a contribute to the sequence entropy, which is a measure of the evolutionary designability of a fold. We compared the entropies associated with different interaction patterns to their abundances in the native structures of real proteins.
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Affiliation(s)
- Matteo Tajana
- Department of Physics, Università degli Studi di Milano, Via Celoria 16, 20133, Milan, Italy
| | - Antonio Trovato
- Department of Physics and Astronomy "G. Galilei", Università degli Studi di Padova and INFN, Via Marzolo 8, 35121, Padova, Italy
| | - Guido Tiana
- Department of Physics and Center for Complexity and Biosystems, Università degli Studi di Milano and INFN, Via Celoria 16, 20133, Milan, Italy.
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8
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Petrovsky DV, Rudnev VR, Nikolsky KS, Kulikova LI, Malsagova KM, Kopylov AT, Kaysheva AL. PSSNet-An Accurate Super-Secondary Structure for Protein Segmentation. Int J Mol Sci 2022; 23:ijms232314813. [PMID: 36499138 PMCID: PMC9740782 DOI: 10.3390/ijms232314813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
A super-secondary structure (SSS) is a spatially unique ensemble of secondary structural elements that determine the three-dimensional shape of a protein and its function, rendering SSSs attractive as folding cores. Understanding known types of SSSs is important for developing a deeper understanding of the mechanisms of protein folding. Here, we propose a universal PSSNet machine-learning method for SSS recognition and segmentation. For various types of SSS segmentation, this method uses key characteristics of SSS geometry, including the lengths of secondary structural elements and the distances between them, torsion angles, spatial positions of Cα atoms, and primary sequences. Using four types of SSSs (βαβ-unit, α-hairpin, β-hairpin, αα-corner), we showed that extensive SSS sets could be reliably selected from the Protein Data Bank and AlphaFold 2.0 database of protein structures.
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9
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Kondratyev M, Rudnev VR, Nikolsky KS, Stepanov AA, Petrovsky DV, Kulikova LI, Kopylov AT, Malsagova KA, Kaysheva AL. Atomic Simulation of the Binding of JAK1 and JAK2 with the Selective Inhibitor Ruxolitinib. Int J Mol Sci 2022; 23:ijms231810466. [PMID: 36142375 PMCID: PMC9504736 DOI: 10.3390/ijms231810466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/23/2022] Open
Abstract
Rheumatoid arthritis belongs to the group of chronic systemic autoimmune diseases characterized by the development of destructive synovitis and extra-articular manifestations. Cytokines regulate a wide range of inflammatory processes involved in the pathogenesis of rheumatoid arthritis and contribute to the induction of autoimmunity and chronic inflammation. Janus-associated kinase (JAK) and signal transducer and activator of transcription (STAT) proteins mediate cell signaling from cytokine receptors, and are involved in the pathogenesis of autoimmune and inflammatory diseases. Targeted small-molecule drugs that inhibit the functional activity of JAK proteins are used in clinical practice for the treatment of rheumatoid arthritis. In our study, we modeled the interactions of the small-molecule drug ruxolitinib with JAK1 and JAK2 isoforms and determined the binding selectivity using molecular docking. Molecular modeling data show that ruxolitinib selectively binds the JAK1 and JAK2 isoforms with a binding affinity of −8.3 and −8.0 kcal/mol, respectively. The stabilization of ligands in the cavity of kinases occurs primarily through hydrophobic interactions. The amino acid residues of the protein globules of kinases that are responsible for the correct positioning of the drug ruxolitinib and its retention have been determined.
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Affiliation(s)
- Maxim Kondratyev
- Institute of Cell Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Vladimir R. Rudnev
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Kirill S. Nikolsky
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia
| | - Alexander A. Stepanov
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia
| | - Denis V. Petrovsky
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia
| | - Liudmila I. Kulikova
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Mathematical Problems of Biology RAS—The Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Arthur T. Kopylov
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia
| | - Kristina A. Malsagova
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia
- Correspondence: ; Tel.: +7-(499)-764-98-78
| | - Anna L. Kaysheva
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia
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10
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Blaber M. Variable and Conserved Regions of Secondary Structure in the β-Trefoil Fold: Structure Versus Function. Front Mol Biosci 2022; 9:889943. [PMID: 35517858 PMCID: PMC9062101 DOI: 10.3389/fmolb.2022.889943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
β-trefoil proteins exhibit an approximate C3 rotational symmetry. An analysis of the secondary structure for members of this diverse superfamily of proteins indicates that it is comprised of remarkably conserved β-strands and highly-divergent turn regions. A fundamental “minimal” architecture can be identified that is devoid of heterogenous and extended turn regions, and is conserved among all family members. Conversely, the different functional families of β-trefoils can potentially be identified by their unique turn patterns (or turn “signature”). Such analyses provide clues as to the evolution of the β-trefoil family, suggesting a folding/stability role for the β-strands and a functional role for turn regions. This viewpoint can also guide de novo protein design of β-trefoil proteins having novel functionality.
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Affiliation(s)
- Michael Blaber
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, United States
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11
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Robson B. De novo protein folding on computers. Benefits and challenges. Comput Biol Med 2022; 143:105292. [PMID: 35158120 DOI: 10.1016/j.compbiomed.2022.105292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/05/2023]
Abstract
There has been recent success in prediction of the three-dimensional folded native structures of proteins, most famously by the AlphaFold Algorithm running on Google's/Alphabet's DeepMind computer. However, this largely involves machine learning of protein structures and is not a de novo protein structure prediction method for predicting three-dimensional structures from amino acid residue sequences. A de novo approach would be based almost entirely on general principles of energy and entropy that govern protein folding energetics, and importantly do so without the use of the amino acid sequences and structural features of other proteins. Most consider that problem as still unsolved even though it has occupied leading scientists for decades. Many consider that it remains one of the major outstanding issues in modern science. There is crucial continuing help from experimental findings on protein unfolding and refolding in the laboratory, but only to a limited extent because many researchers consider that the speed by which real proteins folds themselves, often from milliseconds to minutes, is itself still not fully understood. This is unfortunate, because a practical solution to the problem would probably have a major effect on personalized medicine, the pharmaceutical industry, biotechnology, and nanotechnology, including for example "smaller" tasks such as better modeling of flexible "unfolded" regions of the SARS-COV-2 spike glycoprotein when interacting with its cell receptor, antibodies, and therapeutic agents. Some important ideas from earlier studies are given before moving on to lessons from periodic and aperiodic crystals, and a possible role for quantum phenomena. The conclusion is that better computation of entropy should be the priority, though that is presented guardedly.
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Affiliation(s)
- Barry Robson
- Ingine Inc.Cleveland Ohio and The Dirac Foundation, Oxfordshire, UK.
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12
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Dahanayake R, Dormidontova EE. Hydrogen Bonding Sequence Directed Coil-Globule Transition in Water Soluble Thermoresponsive Polymers. PHYSICAL REVIEW LETTERS 2021; 127:167801. [PMID: 34723603 DOI: 10.1103/physrevlett.127.167801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
The origin of the coil-globule transition for water-soluble thermoresponsive polymers frequently used in nanomaterials remains elusive. Using polypropylene oxide as an example we demonstrate by means of atomistic molecular dynamics simulations that temperature-induced increase in the sequence length of monomers that are not hydrogen bonded to water drives the coil-globule transition. Longer chains statistically exhibit longer sequences which serve as nucleation sites for hydrophobic cluster formation, facilitating chain collapse at lower temperature in agreement with experimental data.
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Affiliation(s)
- Rasika Dahanayake
- Polymer Program, Institute of Materials Science and Physics Department, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Elena E Dormidontova
- Polymer Program, Institute of Materials Science and Physics Department, University of Connecticut, Storrs, Connecticut 06269, USA
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13
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Rose GD. Protein folding - seeing is deceiving. Protein Sci 2021; 30:1606-1616. [PMID: 33938055 PMCID: PMC8284583 DOI: 10.1002/pro.4096] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/24/2021] [Accepted: 04/30/2021] [Indexed: 11/13/2022]
Abstract
This Perspective is intended to raise questions about the conventional interpretation of protein folding. According to the conventional interpretation, developed over many decades, a protein population can visit a vast number of conformations under unfolding conditions, but a single dominant native population emerges under folding conditions. Accordingly, folding comes with a substantial loss of conformational entropy. How is this price paid? The conventional answer is that favorable interactions between and among the side chains can compensate for entropy loss, and moreover, these interactions are responsible for the structural particulars of the native conformation. Challenging this interpretation, the Perspective introduces a proposal that high energy (i.e., unfavorable) excluding interactions winnow the accessible population substantially under physical-chemical conditions that favor folding. Both steric clash and unsatisfied hydrogen bond donors and acceptors are classified as excluding interactions, so called because conformers with such disfavored interactions will be largely excluded from the thermodynamic population. Both excluding interactions and solvent factors that induce compactness are somewhat nonspecific, yet together they promote substantial chain organization. Moreover, proteins are built on a backbone scaffold consisting of α-helices and strands of β-sheet, where the number of hydrogen bond donors and acceptors is exactly balanced. These repetitive secondary structural elements are the only two conformers that can be both completely hydrogen-bond satisfied and extended indefinitely without encountering a steric clash. Consequently, the number of fundamental folds is limited to no more than ~10,000 for a protein domain. Once excluding interactions are taken into account, the issue of "frustration" is largely eliminated and the Levinthal paradox is resolved. Putting the "bottom line" at the top: it is likely that hydrogen-bond satisfaction represents a largely under-appreciated parameter in protein folding models.
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Affiliation(s)
- George D. Rose
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
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14
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Especial JNC, Faísca PFN. A Specific Set of Heterogeneous Native Interactions Yields Efficient Knotting in Protein Folding. J Phys Chem B 2021; 125:7359-7367. [PMID: 34197706 DOI: 10.1021/acs.jpcb.1c03127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Native interactions are crucial for folding, and non-native interactions appear to be critical for efficiently knotting proteins. Therefore, it is important to understand both their roles in the folding of knotted proteins. It has been proposed that non-native interactions drive the correct order of contact formation, which is essential to avoid backtracking and efficiently self-tie. In this study, we ask if non-native interactions are strictly necessary to tangle a protein or if the correct order of contact formation can be assured by a specific set of native, but otherwise heterogeneous (i.e., having distinct energies), interactions. In order to address this problem, we conducted extensive Monte Carlo simulations of lattice models of protein-like sequences designed to fold into a preselected knotted conformation embedding a trefoil knot. We were able to identify a specific set of heterogeneous native interactions that drives efficient knotting and is able to fold the protein when combined with the remaining native interactions modeled as homogeneous. This specific set of heterogeneous native interactions is strictly enough to efficiently self-tie. A distinctive feature of these native interactions is that they do not backtrack because their energies ensure the correct order of contact formation. Furthermore, they stabilize a knotted intermediate state, which is en route to the native structure. Our results thus show that-at least in the context of the adopted model-non-native interactions are not necessary to knot a protein. However, when they are taken into account in protein energetics, it is possible to find specific, nonlocal non-native interactions that operate as a scaffold that assists the knotting step.
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Affiliation(s)
- João N C Especial
- Departamento de Física, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal.,BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal
| | - Patrícia F N Faísca
- Departamento de Física, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal.,BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal
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15
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Gianni S, Freiberger MI, Jemth P, Ferreiro DU, Wolynes PG, Fuxreiter M. Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly. Acc Chem Res 2021; 54:1251-1259. [PMID: 33550810 PMCID: PMC8023570 DOI: 10.1021/acs.accounts.0c00813] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Indexed: 12/20/2022]
Abstract
Are all protein interactions fully optimized? Do suboptimal interactions compromise specificity? What is the functional impact of frustration? Why does evolution not optimize some contacts? Proteins and their complexes are best described as ensembles of states populating an energy landscape. These ensembles vary in breadth from narrow ensembles clustered around a single average X-ray structure to broader ensembles encompassing a few different functional "taxonomic" states on to near continua of rapidly interconverting conformations, which are called "fuzzy" or even "intrinsically disordered". Here we aim to provide a comprehensive framework for confronting the structural and dynamical continuum of protein assemblies by combining the concepts of energetic frustration and interaction fuzziness. The diversity of the protein structural ensemble arises from the frustrated conflicts between the interactions that create the energy landscape. When frustration is minimal after folding, it results in a narrow ensemble, but residual frustrated interactions result in fuzzy ensembles, and this fuzziness allows a versatile repertoire of biological interactions. Here we discuss how fuzziness and frustration play off each other as proteins fold and assemble, viewing their significance from energetic, functional, and evolutionary perspectives.We demonstrate, in particular, that the common physical origin of both concepts is related to the ruggedness of the energy landscapes, intramolecular in the case of frustration and intermolecular in the case of fuzziness. Within this framework, we show that alternative sets of suboptimal contacts may encode specificity without achieving a single structural optimum. Thus, we demonstrate that structured complexes may not be optimized, and energetic frustration is realized via different sets of contacts leading to multiplicity of specific complexes. Furthermore, we propose that these suboptimal, frustrated, or fuzzy interactions are under evolutionary selection and expand the biological repertoire by providing a multiplicity of biological activities. In accord, we show that non-native interactions in folding or interaction landscapes can cooperate to generate diverse functional states, which are essential to facilitate adaptation to different cellular conditions. Thus, we propose that not fully optimized structures may actually be beneficial for biological activities of proteins via an alternative set of suboptimal interactions. The importance of such variability has not been recognized across different areas of biology.This account provides a modern view on folding, function, and assembly across the protein universe. The physical framework presented here is applicable to the structure and dynamics continuum of proteins and opens up new perspectives for drug design involving not fully structured, highly dynamic protein assemblies.
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Affiliation(s)
- Stefano Gianni
- Istituto
Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli” and Istituto di Biologia e Patologia
Molecolari del CNR, Sapienza Università
di Roma, 00185 Rome, Italy
| | - María Inés Freiberger
- Protein
Physiology Lab, Departamento de Química Biológica, Facultad
de Ciencias Exactas y Naturales, Universidad
de Buenos Aires-CONICET-IQUIBICEN, 1428 Buenos Aires, Argentina
| | - Per Jemth
- Department
of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, SE-75123 Uppsala, Sweden
| | - Diego U. Ferreiro
- Protein
Physiology Lab, Departamento de Química Biológica, Facultad
de Ciencias Exactas y Naturales, Universidad
de Buenos Aires-CONICET-IQUIBICEN, 1428 Buenos Aires, Argentina
| | - Peter G. Wolynes
- Center
for Theoretical Biological Physics, Rice
University, 6500 Main Street, Houston, Texas 77251-1892, United States
| | - Monika Fuxreiter
- MTA-DE
Laboratory of Protein Dynamics, Department of Biochemistry and Molecular
Biology, University of Debrecen, Nagyerdei krt 98, H-4032 Debrecen, Hungary
- Department
of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
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16
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Crippa M, Andreghetti D, Capelli R, Tiana G. Evolution of frustrated and stabilising contacts in reconstructed ancient proteins. EUROPEAN BIOPHYSICS JOURNAL 2021; 50:699-712. [PMID: 33569610 PMCID: PMC8260555 DOI: 10.1007/s00249-021-01500-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/14/2020] [Accepted: 01/13/2021] [Indexed: 11/30/2022]
Abstract
Energetic properties of a protein are a major determinant of its evolutionary fitness. Using a reconstruction algorithm, dating the reconstructed proteins and calculating the interaction network between their amino acids through a coevolutionary approach, we studied how the interactions that stabilise 890 proteins, belonging to five families, evolved for billions of years. In particular, we focused our attention on the network of most strongly attractive contacts and on that of poorly optimised, frustrated contacts. Our results support the idea that the cluster of most attractive interactions extends its size along evolutionary time, but from the data, we cannot conclude that protein stability or that the degree of frustration tends always to decrease.
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Affiliation(s)
- Martina Crippa
- Department of Physics and Center for Complexity and Biosystems, Università degli Studi di Milano and INFN, via Celoria 16, 20133, Milan, Italy
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Turin, Italy
| | - Damiano Andreghetti
- Department of Physics and Center for Complexity and Biosystems, Università degli Studi di Milano and INFN, via Celoria 16, 20133, Milan, Italy
| | - Riccardo Capelli
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Turin, Italy
| | - Guido Tiana
- Department of Physics and Center for Complexity and Biosystems, Università degli Studi di Milano and INFN, via Celoria 16, 20133, Milan, Italy.
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17
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Tenorio CA, Parker JB, Blaber M. Oligomerization of a symmetric β-trefoil protein in response to folding nucleus perturbation. Protein Sci 2020; 29:1629-1640. [PMID: 32362013 DOI: 10.1002/pro.3877] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 11/06/2022]
Abstract
Gene duplication and fusion events in protein evolution are postulated to be responsible for the common protein folds exhibiting internal rotational symmetry. Such evolutionary processes can also potentially yield regions of repetitive primary structure. Repetitive primary structure offers the potential for alternative definitions of critical regions, such as the folding nucleus (FN). In principle, more than one instance of the FN potentially enables an alternative folding pathway in the face of a subsequent deleterious mutation. We describe the targeted mutation of the carboxyl-terminal region of the (internally located) FN of the de novo designed purely-symmetric β-trefoil protein Symfoil-4P. This mutation involves wholesale replacement of a repeating trefoil-fold motif with a "blade" motif from a β-propeller protein, and postulated to trap that region of the Symfoil-4P FN in a nonproductive folding intermediate. The resulting protein (termed "Bladefoil") is shown to be cooperatively folding, but as a trimeric oligomer. The results illustrate how symmetric protein architectures have potentially diverse folding alternatives available to them, including oligomerization, when preferred pathways are perturbed.
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Affiliation(s)
- Connie A Tenorio
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, USA
| | - Joseph B Parker
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, USA
| | - Michael Blaber
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, USA
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18
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Toto A, Malagrinò F, Visconti L, Troilo F, Pagano L, Brunori M, Jemth P, Gianni S. Templated folding of intrinsically disordered proteins. J Biol Chem 2020; 295:6586-6593. [PMID: 32253236 DOI: 10.1074/jbc.rev120.012413] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Much of our current knowledge of biological chemistry is founded in the structure-function relationship, whereby sequence determines structure that determines function. Thus, the discovery that a large fraction of the proteome is intrinsically disordered, while being functional, has revolutionized our understanding of proteins and raised new and interesting questions. Many intrinsically disordered proteins (IDPs) have been determined to undergo a disorder-to-order transition when recognizing their physiological partners, suggesting that their mechanisms of folding are intrinsically different from those observed in globular proteins. However, IDPs also follow some of the classic paradigms established for globular proteins, pointing to important similarities in their behavior. In this review, we compare and contrast the folding mechanisms of globular proteins with the emerging features of binding-induced folding of intrinsically disordered proteins. Specifically, whereas disorder-to-order transitions of intrinsically disordered proteins appear to follow rules of globular protein folding, such as the cooperative nature of the reaction, their folding pathways are remarkably more malleable, due to the heterogeneous nature of their folding nuclei, as probed by analysis of linear free-energy relationship plots. These insights have led to a new model for the disorder-to-order transition in IDPs termed "templated folding," whereby the binding partner dictates distinct structural transitions en route to product, while ensuring a cooperative folding.
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Affiliation(s)
- Angelo Toto
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Francesca Malagrinò
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Lorenzo Visconti
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Francesca Troilo
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Livia Pagano
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Maurizio Brunori
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
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19
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Ivankov DN, Finkelstein AV. Solution of Levinthal's Paradox and a Physical Theory of Protein Folding Times. Biomolecules 2020; 10:biom10020250. [PMID: 32041303 PMCID: PMC7072185 DOI: 10.3390/biom10020250] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 12/19/2022] Open
Abstract
“How do proteins fold?” Researchers have been studying different aspects of this question for more than 50 years. The most conceptual aspect of the problem is how protein can find the global free energy minimum in a biologically reasonable time, without exhaustive enumeration of all possible conformations, the so-called “Levinthal’s paradox.” Less conceptual but still critical are aspects about factors defining folding times of particular proteins and about perspectives of machine learning for their prediction. We will discuss in this review the key ideas and discoveries leading to the current understanding of folding kinetics, including the solution of Levinthal’s paradox, as well as the current state of the art in the prediction of protein folding times.
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Affiliation(s)
- Dmitry N. Ivankov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Correspondence: or (D.N.I.); (A.V.F.); Tel.: +7-495-280-1481 (ext. 3320) (D.N.I.); +7-496-731-8412 (A.V.F.)
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Biology Department, Lomonosov Moscow State University, 119192 Moscow, Russia
- Biotechnology Department, Lomonosov Moscow State University, 142290 Pushchino, Moscow Region, Russia
- Correspondence: or (D.N.I.); (A.V.F.); Tel.: +7-495-280-1481 (ext. 3320) (D.N.I.); +7-496-731-8412 (A.V.F.)
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20
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Trotter D, Wallin S. Effects of Topology and Sequence in Protein Folding Linked via Conformational Fluctuations. Biophys J 2020; 118:1370-1380. [PMID: 32061276 DOI: 10.1016/j.bpj.2020.01.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/17/2019] [Accepted: 01/13/2020] [Indexed: 01/18/2023] Open
Abstract
Experiments have compared the folding of proteins with different amino acid sequences but the same basic structure, or fold. Results indicate that folding is robust to sequence variations for proteins with some nonlocal folds, such as all-β, whereas the folding of more local, all-α proteins typically exhibits a stronger sequence dependence. Here, we use a coarse-grained model to systematically study how variations in sequence perturb the folding energy landscapes of three model sequences with 3α, 4β + α, and β-barrel folds, respectively. These three proteins exhibit folding features in line with experiments, including expected rank order in the cooperativity of the folding transition and stability-dependent shifts in the location of the free-energy barrier to folding. Using a generalized-ensemble simulation approach, we determine the thermodynamics of around 2000 sequence variants representing all possible hydrophobic or polar single- and double-point mutations. From an analysis of the subset of stability-neutral mutations, we find that folding is perturbed in a topology-dependent manner, with the β-barrel protein being the most robust. Our analysis shows, in particular, that the magnitude of mutational perturbations of the transition state is controlled in part by the size or "width" of the underlying conformational ensemble. This result suggests that the mutational robustness of the folding of the β-barrel protein is underpinned by its conformationally restricted transition state ensemble, revealing a link between sequence and topological effects in protein folding.
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Affiliation(s)
- Daniel Trotter
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Stefan Wallin
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.
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21
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Troilo F, Malagrinò F, Visconti L, Toto A, Gianni S. The Effect of Proline cis- trans Isomerization on the Folding of the C-Terminal SH2 Domain from p85. Int J Mol Sci 2019; 21:E125. [PMID: 31878075 PMCID: PMC6982175 DOI: 10.3390/ijms21010125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 11/17/2022] Open
Abstract
SH2 domains are protein domains that modulate protein-protein interactions through a specific interaction with sequences containing phosphorylated tyrosines. In this work, we analyze the folding pathway of the C-terminal SH2 domain of the p85 regulatory subunit of the protein PI3K, which presents a proline residue in a cis configuration in the loop between the βE and βF strands. By employing single and double jump folding and unfolding experiments, we demonstrate the presence of an on-pathway intermediate that transiently accumulates during (un)folding. By comparing the kinetics of folding of the wild-type protein to that of a site-directed variant of C-SH2 in which the proline was replaced with an alanine, we demonstrate that this intermediate is dictated by the peptidyl prolyl cis-trans isomerization. The results are discussed in the light of previous work on the effect of peptidyl prolyl cis-trans isomerization on folding events.
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Affiliation(s)
- Francesca Troilo
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, 00161 Roma, Italy; (F.T.); (F.M.); (L.V.); (A.T.)
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Francesca Malagrinò
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, 00161 Roma, Italy; (F.T.); (F.M.); (L.V.); (A.T.)
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Lorenzo Visconti
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, 00161 Roma, Italy; (F.T.); (F.M.); (L.V.); (A.T.)
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Angelo Toto
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, 00161 Roma, Italy; (F.T.); (F.M.); (L.V.); (A.T.)
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Stefano Gianni
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, 00161 Roma, Italy; (F.T.); (F.M.); (L.V.); (A.T.)
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
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22
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Uversky VN, Finkelstein AV. Life in Phases: Intra- and Inter- Molecular Phase Transitions in Protein Solutions. Biomolecules 2019; 9:E842. [PMID: 31817975 PMCID: PMC6995567 DOI: 10.3390/biom9120842] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Proteins, these evolutionarily-edited biological polymers, are able to undergo intramolecular and intermolecular phase transitions. Spontaneous intramolecular phase transitions define the folding of globular proteins, whereas binding-induced, intra- and inter- molecular phase transitions play a crucial role in the functionality of many intrinsically-disordered proteins. On the other hand, intermolecular phase transitions are the behind-the-scenes players in a diverse set of macrosystemic phenomena taking place in protein solutions, such as new phase nucleation in bulk, on the interface, and on the impurities, protein crystallization, protein aggregation, the formation of amyloid fibrils, and intermolecular liquid-liquid or liquid-gel phase transitions associated with the biogenesis of membraneless organelles in the cells. This review is dedicated to the systematic analysis of the phase behavior of protein molecules and their ensembles, and provides a description of the major physical principles governing intramolecular and intermolecular phase transitions in protein solutions.
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Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Moscow, Russia
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow, Russia
- Biology Department, Lomonosov Moscow State University, 119192 Moscow, Russia
- Bioltechnogy Department, Lomonosov Moscow State University, 142290 Pushchino, Moscow, Russia
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23
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Tan Q, Duan M, Li M, Han L, Huo S. Approximating dynamic proximity with a hybrid geometry energy-based kernel for diffusion maps. J Chem Phys 2019; 151:105101. [PMID: 31521094 DOI: 10.1063/1.5100968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The diffusion map is a dimensionality reduction method. The reduction coordinates are associated with the leading eigenfunctions of the backward Fokker-Planck operator, providing a dynamic meaning for these coordinates. One of the key factors that affect the accuracy of diffusion map embedding is the dynamic measure implemented in the Gaussian kernel. A common practice in diffusion map study of molecular systems is to approximate dynamic proximity with RMSD (root-mean-square deviation). In this paper, we present a hybrid geometry-energy based kernel. Since high energy-barriers may exist between geometrically similar conformations, taking both RMSD and energy difference into account in the kernel can better describe conformational transitions between neighboring conformations and lead to accurate embedding. We applied our diffusion map method to the β-hairpin of the B1 domain of streptococcal protein G and to Trp-cage. Our results in β-hairpin show that the diffusion map embedding achieves better results with the hybrid kernel than that with the RMSD-based kernel in terms of free energy landscape characterization and a new correlation measure between the cluster center Euclidean distances in the reduced-dimension space and the reciprocals of the total net flow between these clusters. In addition, our diffusion map analysis of the ultralong molecular dynamics trajectory of Trp-cage has provided a unified view of its folding mechanism. These promising results demonstrate the effectiveness of our diffusion map approach in the analysis of the dynamics and thermodynamics of molecular systems. The hybrid geometry-energy criterion could be also useful as a general dynamic measure for other purposes.
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Affiliation(s)
- Qingzhe Tan
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, USA
| | - Mojie Duan
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, USA
| | - Minghai Li
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, USA
| | - Li Han
- Department of Math and Computer Science, Clark University, Worcester, Massachusetts 01610, USA
| | - Shuanghong Huo
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, USA
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24
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Sidky H, Chen W, Ferguson AL. High-Resolution Markov State Models for the Dynamics of Trp-Cage Miniprotein Constructed Over Slow Folding Modes Identified by State-Free Reversible VAMPnets. J Phys Chem B 2019; 123:7999-8009. [DOI: 10.1021/acs.jpcb.9b05578] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Hythem Sidky
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Wei Chen
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Andrew L. Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
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25
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Toto A, Troilo F, Visconti L, Malagrinò F, Bignon C, Longhi S, Gianni S. Binding induced folding: Lessons from the kinetics of interaction between N TAIL and XD. Arch Biochem Biophys 2019; 671:255-261. [PMID: 31326517 DOI: 10.1016/j.abb.2019.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/28/2019] [Accepted: 07/14/2019] [Indexed: 10/26/2022]
Abstract
Intrinsically Disordered Proteins (IDPs) are a class of protein that exert their function despite lacking a well-defined three-dimensional structure, which is sometimes achieved only upon binding to their natural ligands. This feature implies the folding of IDPs to be generally coupled with a binding event, representing an interesting challenge for kinetic studies. In this review, we recapitulate some of the most important findings of IDPs binding-induced folding mechanisms obtained by analyzing their binding kinetics. Furthermore, by focusing on the interaction between the Measles virus NTAIL protein, a prototypical IDP, and its physiological partner, the X domain, we recapitulate the major theoretical and experimental approaches that were used to describe binding induced folding.
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Affiliation(s)
- Angelo Toto
- Istituto Pasteur, Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Francesca Troilo
- Istituto Pasteur, Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Lorenzo Visconti
- Istituto Pasteur, Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Francesca Malagrinò
- Istituto Pasteur, Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Christophe Bignon
- Aix-Marseille University, CNRS, Architecture et Fonction des Macromolećules Biologiques (AFMB), UMR7257, Marseille, France
| | - Sonia Longhi
- Aix-Marseille University, CNRS, Architecture et Fonction des Macromolećules Biologiques (AFMB), UMR7257, Marseille, France.
| | - Stefano Gianni
- Istituto Pasteur, Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy.
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Visconti L, Malagrinò F, Gianni S, Toto A. Structural characterization of an on-pathway intermediate and transition state in the folding of the N-terminal SH2 domain from SHP2. FEBS J 2019; 286:4769-4777. [PMID: 31287606 DOI: 10.1111/febs.14990] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/29/2019] [Accepted: 07/06/2019] [Indexed: 12/23/2022]
Abstract
Src Homology 2 (SH2) domains are a class of protein domains that present a conserved three-dimensional structure and possess a crucial role in mediating protein-protein interactions. Despite their importance and abundance in the proteome, knowledge about the folding properties of SH2 domain is limited. Here we present an extensive mutational analysis (Φ value analysis) of the folding pathway of the N-SH2 domain of the Src homology region 2 domain-containing phosphatase-2 (SHP2) protein, a 104 residues domain that presents the classical SH2 domain fold (two α-helices flanking a central β-sheet composed of 3-5 antiparallel β-strands), with a fundamental role in mediating the interaction of SHP2 with its substrates and triggering key metabolic pathways in the cell. By analysing folding kinetic data we demonstrated that the folding pathway of N-SH2 presents an obligatory on-pathway intermediate that accumulates during the folding reaction. The production of 24 conservative site-directed variants allowed us to perform a Φ value analysis, by which we could fully characterize the intermediate and the transition state native-like interactions, providing a detailed quantitative analysis of the folding pathway of N-SH2. Results highlight the presence of a hydrophobic nucleus that stabilizes the intermediate, leading to a higher degree of native-like interactions in the transition state. Data are discussed and compared with previous works on SH2 domains.
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Affiliation(s)
- Lorenzo Visconti
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Italy
| | - Francesca Malagrinò
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Italy
| | - Stefano Gianni
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Italy
| | - Angelo Toto
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Italy
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Karlsson E, Andersson E, Dogan J, Gianni S, Jemth P, Camilloni C. A structurally heterogeneous transition state underlies coupled binding and folding of disordered proteins. J Biol Chem 2018; 294:1230-1239. [PMID: 30514761 PMCID: PMC6349112 DOI: 10.1074/jbc.ra118.005854] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/30/2018] [Indexed: 11/12/2022] Open
Abstract
Many intrinsically disordered proteins (IDPs) attain a well-defined structure in a coupled folding and binding reaction with another protein. Such reactions may involve early to late formation of different native structural regions along the reaction pathway. To obtain insights into the transition state for a coupled binding and folding reaction, we performed restrained molecular dynamics simulations using previously determined experimental binding Φb values of the interaction between two IDP domains: the activation domain from the p160 transcriptional co-activator for thyroid hormone and retinoid receptors (ACTR) and the nuclear co-activator binding domain (NCBD) of CREB-binding protein, each forming three well-defined α-helices upon binding. These simulations revealed that both proteins are largely disordered in the transition state for complex formation, except for two helices, one from each domain, that display a native-like structure. The overall transition state structure was extended and largely dynamic with many weakly populated contacts. To test the transition state model, we combined site-directed mutagenesis with kinetic experiments, yielding results consistent with overall diffuse interactions and formation of native intramolecular interactions in the third NCBD helix during the binding reaction. Our findings support the view that the transition state and, by inference, any encounter complex in coupled binding and folding reactions are structurally heterogeneous and largely independent of specific interactions. Furthermore, experimental Φb values and Brønsted plots suggested that the transition state is globally robust with respect to most mutations but can display more native-like features for some highly destabilizing mutations, possibly because of Hammond behavior or ground-state effects.
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Affiliation(s)
- Elin Karlsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jakob Dogan
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, 00185 Rome, Italy
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden.
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy.
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Rodriguez PM, Stratmann D, Duprat E, Papandreou N, Acuna R, Lacroix Z, Chomilier J. Correlating topology and thermodynamics to predict protein structure sensitivity to point mutations. BIO-ALGORITHMS AND MED-SYSTEMS 2018. [DOI: 10.1515/bams-2018-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe relation between distribution of hydrophobic amino acids along with protein chains and their structure is far from being completely understood. No reliable method allowsab initioprediction of the folded structure from this distribution of physicochemical properties, even when they are highly degenerated by considering only two classes: hydrophobic and polar. Establishment of long-range hydrophobic three dimension (3D) contacts is essential for the formation of the nucleus, a key process in the early steps of protein folding. Thus, a large number of 3D simulation studies were developed to challenge this issue. They are nowadays evaluated in a specific chapter of the molecular modeling competition, Critical Assessment of Protein Structure Prediction. We present here a simulation of the early steps of the folding process for 850 proteins, performed in a discrete 3D space, which results in peaks in the predicted distribution of intra-chain noncovalent contacts. The residues located at these peak positions tend to be buried in the core of the protein and are expected to correspond to critical positions in the sequence, important both for folding and structural (or similarly, energetic in the thermodynamic hypothesis) stability. The degree of stabilization or destabilization due to a point mutation at the critical positions involved in numerous contacts is estimated from the calculated folding free energy difference between mutated and native structures. The results show that these critical positions are not tolerant towards mutation. This simulation of the noncovalent contacts only needs a sequence as input, and this paper proposes a validation of the method by comparison with the prediction of stability by well-established programs.
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Krishnamoorthy G. Intramolecular Distance Distribution Reveals Mechanisms in Protein Folding and Dynamics. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES INDIA SECTION A-PHYSICAL SCIENCES 2018. [DOI: 10.1007/s40010-018-0525-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Jacobs WM, Shakhnovich EI. Accurate Protein-Folding Transition-Path Statistics from a Simple Free-Energy Landscape. J Phys Chem B 2018; 122:11126-11136. [PMID: 30091592 DOI: 10.1021/acs.jpcb.8b05842] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths-the rare trajectories that transit between the folded and unfolded ensembles-using only thermodynamic information, such as a low-dimensional equilibrium free-energy landscape. However, commonly used one-dimensional landscapes typically fall short of this aim, because an empirical coordinate-dependent diffusion coefficient has to be fit to transition-path trajectory data in order to reproduce the transition-path dynamics. We show that an alternative, first-principles free-energy landscape predicts transition-path statistics that agree well with simulations and single-molecule experiments without requiring dynamical data as an input. This "topological configuration" model assumes that distinct, native-like substructures assemble on a time scale that is slower than native-contact formation but faster than the folding of the entire protein. Using only equilibrium simulation data to determine the free energies of these coarse-grained intermediate states, we predict a broad distribution of transition-path transit times that agrees well with the transition-path durations observed in simulations. We further show that both the distribution of finite-time displacements on a one-dimensional order parameter and the ensemble of transition-path trajectories generated by the model are consistent with the simulated transition paths. These results indicate that a landscape based on transient folding intermediates, which are often hidden by one-dimensional projections, can form the basis of a predictive model of protein-folding transition-path dynamics.
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Affiliation(s)
- William M Jacobs
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
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Troilo F, Bonetti D, Camilloni C, Toto A, Longhi S, Brunori M, Gianni S. Folding Mechanism of the SH3 Domain from Grb2. J Phys Chem B 2018; 122:11166-11173. [DOI: 10.1021/acs.jpcb.8b06320] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Francesca Troilo
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Daniela Bonetti
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli studi di Milano, 20133 Milan, Italy
| | - Angelo Toto
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Sonia Longhi
- Aix-Marseille Univ, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR, 7257 Marseille, France
| | - Maurizio Brunori
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Stefano Gianni
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
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Possenti A, Vendruscolo M, Camilloni C, Tiana G. A method for partitioning the information contained in a protein sequence between its structure and function. Proteins 2018; 86:956-964. [PMID: 29790601 DOI: 10.1002/prot.25527] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/27/2018] [Accepted: 05/14/2018] [Indexed: 11/11/2022]
Abstract
Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance between the amount of information supplied by the sequence and that left after that the protein has folded into its structure. We study the amount of information necessary to specify the protein structure, providing an estimate that keeps into account the thermodynamic properties of protein folding. We thus show that the information remaining in the protein sequence after encoding for its structure (the 'information gap') is very close to what needed to encode for its function and interactions. Then, by predicting the information gap directly from the protein sequence, we show that it may be possible to use these insights from information theory to discriminate between ordered and disordered proteins, to identify unknown functions, and to optimize artificially-designed protein sequences.
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Affiliation(s)
- Andrea Possenti
- Center for Complexity and Biosystems and Department of Physics, Università degli Studi di Milano and INFN, via Celoria 16, 20133, Milan, Italy.,Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133, Milan, Italy
| | - Guido Tiana
- Center for Complexity and Biosystems and Department of Physics, Università degli Studi di Milano and INFN, via Celoria 16, 20133, Milan, Italy
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35
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36
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Fluorescence Lifetime Distribution Brings Out Mechanisms Involving Biomolecules While Quantifying Population Heterogeneity. REVIEWS IN FLUORESCENCE 2017 2018. [DOI: 10.1007/978-3-030-01569-5_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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37
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Kukic P, Pustovalova Y, Camilloni C, Gianni S, Korzhnev DM, Vendruscolo M. Structural Characterization of the Early Events in the Nucleation–Condensation Mechanism in a Protein Folding Process. J Am Chem Soc 2017; 139:6899-6910. [DOI: 10.1021/jacs.7b01540] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Predrag Kukic
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Yulia Pustovalova
- Department
of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Carlo Camilloni
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
- Technische Universität Mun̈chen Institute for Advanced Study & Department of Chemistry, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Stefano Gianni
- Istituto
Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia
Molecolari del CNR, Dipartimento di Scienze Biochimiche “A.
Rossi Fanelli”, Sapienza Università di Roma, Rome 00185, Italy
| | - Dmitry M. Korzhnev
- Department
of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
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The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution. Biophys J 2017; 112:1350-1365. [PMID: 28402878 DOI: 10.1016/j.bpj.2017.02.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/16/2017] [Accepted: 02/22/2017] [Indexed: 02/05/2023] Open
Abstract
Homology modeling is a powerful tool for predicting a protein's structure. This approach is successful because proteins whose sequences are only 30% identical still adopt the same structure, while structure similarity rapidly deteriorates beyond the 30% threshold. By studying the divergence of protein structure as sequence evolves in real proteins and in evolutionary simulations, we show that this nonlinear sequence-structure relationship emerges as a result of selection for protein folding stability in divergent evolution. Fitness constraints prevent the emergence of unstable protein evolutionary intermediates, thereby enforcing evolutionary paths that preserve protein structure despite broad sequence divergence. However, on longer timescales, evolution is punctuated by rare events where the fitness barriers obstructing structure evolution are overcome and discovery of new structures occurs. We outline biophysical and evolutionary rationale for broad variation in protein family sizes, prevalence of compact structures among ancient proteins, and more rapid structure evolution of proteins with lower packing density.
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Finkelstein AV, Badretdin AJ, Galzitskaya OV, Ivankov DN, Bogatyreva NS, Garbuzynskiy SO. There and back again: Two views on the protein folding puzzle. Phys Life Rev 2017; 21:56-71. [PMID: 28190683 DOI: 10.1016/j.plrev.2017.01.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/05/2017] [Accepted: 01/19/2017] [Indexed: 02/08/2023]
Abstract
The ability of protein chains to spontaneously form their spatial structures is a long-standing puzzle in molecular biology. Experimentally measured folding times of single-domain globular proteins range from microseconds to hours: the difference (10-11 orders of magnitude) is the same as that between the life span of a mosquito and the age of the universe. This review describes physical theories of rates of overcoming the free-energy barrier separating the natively folded (N) and unfolded (U) states of protein chains in both directions: "U-to-N" and "N-to-U". In the theory of protein folding rates a special role is played by the point of thermodynamic (and kinetic) equilibrium between the native and unfolded state of the chain; here, the theory obtains the simplest form. Paradoxically, a theoretical estimate of the folding time is easier to get from consideration of protein unfolding (the "N-to-U" transition) rather than folding, because it is easier to outline a good unfolding pathway of any structure than a good folding pathway that leads to the stable fold, which is yet unknown to the folding protein chain. And since the rates of direct and reverse reactions are equal at the equilibrium point (as follows from the physical "detailed balance" principle), the estimated folding time can be derived from the estimated unfolding time. Theoretical analysis of the "N-to-U" transition outlines the range of protein folding rates in a good agreement with experiment. Theoretical analysis of folding (the "U-to-N" transition), performed at the level of formation and assembly of protein secondary structures, outlines the upper limit of protein folding times (i.e., of the time of search for the most stable fold). Both theories come to essentially the same results; this is not a surprise, because they describe overcoming one and the same free-energy barrier, although the way to the top of this barrier from the side of the unfolded state is very different from the way from the side of the native state; and both theories agree with experiment. In addition, they predict the maximal size of protein domains that fold under solely thermodynamic (rather than kinetic) control and explain the observed maximal size of the "foldable" protein domains.
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Affiliation(s)
- Alexei V Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation.
| | - Azat J Badretdin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation
| | - Dmitry N Ivankov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation; Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Natalya S Bogatyreva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation; Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Sergiy O Garbuzynskiy
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation
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40
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Structural and thermodynamic characterisation of L94F mutant of horse cytochrome c. Int J Biol Macromol 2016; 92:202-212. [DOI: 10.1016/j.ijbiomac.2016.06.096] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/24/2016] [Accepted: 06/30/2016] [Indexed: 12/11/2022]
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41
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Sacquin-Mora S. Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus? J R Soc Interface 2016; 12:rsif.2015.0876. [PMID: 26577596 DOI: 10.1098/rsif.2015.0876] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The determination of a protein's folding nucleus, i.e. a set of native contacts playing an important role during its folding process, remains an elusive yet essential problem in biochemistry. In this work, we investigate the mechanical properties of 70 protein structures belonging to 14 protein families presenting various folds using coarse-grain Brownian dynamics simulations. The resulting rigidity profiles combined with multiple sequence alignments show that a limited set of rigid residues, which we call the consensus nucleus, occupy conserved positions along the protein sequence. These residues' side chains form a tight interaction network within the protein's core, thus making our consensus nuclei potential folding nuclei. A review of experimental and theoretical literature shows that most (above 80%) of these residues were indeed identified as folding nucleus member in earlier studies.
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Affiliation(s)
- Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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42
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Gianni S, Jemth P. Protein folding: Vexing debates on a fundamental problem. Biophys Chem 2016; 212:17-21. [DOI: 10.1016/j.bpc.2016.03.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 02/25/2016] [Accepted: 03/07/2016] [Indexed: 11/24/2022]
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Abstract
Allosteric transition, defined as conformational changes induced by ligand binding, is one of the fundamental properties of proteins. Allostery has been observed and characterized in many proteins, and has been recently utilized to control protein function via regulation of protein activity. Here, we review the physical and evolutionary origin of protein allostery, as well as its importance to protein regulation, drug discovery, and biological processes in living systems. We describe recently developed approaches to identify allosteric pathways, connected sets of pairwise interactions that are responsible for propagation of conformational change from the ligand-binding site to a distal functional site. We then present experimental and computational protein engineering approaches for control of protein function by modulation of allosteric sites. As an example of application of these approaches, we describe a synergistic computational and experimental approach to rescue the cystic-fibrosis-associated protein cystic fibrosis transmembrane conductance regulator, which upon deletion of a single residue misfolds and causes disease. This example demonstrates the power of allosteric manipulation in proteins to both elucidate mechanisms of molecular function and to develop therapeutic strategies that rescue those functions. Allosteric control of proteins provides a tool to shine a light on the complex cascades of cellular processes and facilitate unprecedented interrogation of biological systems.
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Affiliation(s)
- Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States
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44
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He E, Ren W, Wang J, Li W, Wang W. Effects of heme binding on myoglobin folding: Coarse grained molecular simulations. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633615500595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Many proteins contain cofactors, such as heme, ATP and metal ions. Binding of cofactors is not only essential for their biological functions, but also can reshape the intrinsic energy landscape of protein molecules and modulate the folding and stability. However, the molecular mechanism of cofactor coupled protein folding is not well understood. In this work, we study the cofactor coupled folding of myoglobin, which is a typical cofactor (heme) containing protein, by performing molecular dynamics simulations with a structure-based protein model developed based on the energy landscape theory. We showed that the heme binding increases the stability of the myoglobin. More importantly, the heme binding tends to increase the protein folding cooperativity, and switch the folding process from a “three-state” mechanism to a “two-state” mechanism. We also showed that the folding pathways of the myoglobin can be modulated by the heme binding. By performing comparative simulations, we revealed that the above effects of heme binding are resulted from the heme induced folding of F-helix, which is otherwise unstructured at apo state, and the heme mediated contacting interactions around the heme binding site. The simulation results are consistent with available experimental data, and provide insights into the molecular mechanism of the effects of cofactor binding on the protein folding and stability.
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Affiliation(s)
- Erbin He
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
| | - Weitong Ren
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
| | - Jun Wang
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
| | - Wenfei Li
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
| | - Wei Wang
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
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Xia X, Longo LM, Sutherland MA, Blaber M. Evolution of a protein folding nucleus. Protein Sci 2015; 25:1227-40. [PMID: 26610273 DOI: 10.1002/pro.2848] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/10/2015] [Indexed: 12/22/2022]
Abstract
The folding nucleus (FN) is a cryptic element within protein primary structure that enables an efficient folding pathway and is the postulated heritable element in the evolution of protein architecture; however, almost nothing is known regarding how the FN structurally changes as complex protein architecture evolves from simpler peptide motifs. We report characterization of the FN of a designed purely symmetric β-trefoil protein by ϕ-value analysis. We compare the structure and folding properties of key foldable intermediates along the evolutionary trajectory of the β-trefoil. The results show structural acquisition of the FN during gene fusion events, incorporating novel turn structure created by gene fusion. Furthermore, the FN is adjusted by circular permutation in response to destabilizing functional mutation. FN plasticity by way of circular permutation is made possible by the intrinsic C3 cyclic symmetry of the β-trefoil architecture, identifying a possible selective advantage that helps explain the prevalence of cyclic structural symmetry in the proteome.
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Affiliation(s)
- Xue Xia
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, 32306-4300
| | - Liam M Longo
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, 32306-4300.,Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Mason A Sutherland
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, 32306-4300
| | - Michael Blaber
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, 32306-4300
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Isaac AE, Sinha S. Analysis of core-periphery organization in protein contact networks reveals groups of structurally and functionally critical residues. J Biosci 2015; 40:683-99. [PMID: 26564971 DOI: 10.1007/s12038-015-9554-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The representation of proteins as networks of interacting amino acids, referred to as protein contact networks (PCN), and their subsequent analyses using graph theoretic tools, can provide novel insights into the key functional roles of specific groups of residues. We have characterized the networks corresponding to the native states of 66 proteins (belonging to different families) in terms of their core-periphery organization. The resulting hierarchical classification of the amino acid constituents of a protein arranges the residues into successive layers - having higher core order - with increasing connection density, ranging from a sparsely linked periphery to a densely intra-connected core (distinct from the earlier concept of protein core defined in terms of the three-dimensional geometry of the native state, which has least solvent accessibility). Our results show that residues in the inner cores are more conserved than those at the periphery. Underlining the functional importance of the network core, we see that the receptor sites for known ligand molecules of most proteins occur in the innermost core. Furthermore, the association of residues with structural pockets and cavities in binding or active sites increases with the core order. From mutation sensitivity analysis, we show that the probability of deleterious or intolerant mutations also increases with the core order. We also show that stabilization centre residues are in the innermost cores, suggesting that the network core is critically important in maintaining the structural stability of the protein. A publicly available Web resource for performing core-periphery analysis of any protein whose native state is known has been made available by us at http://www.imsc.res.in/ ~sitabhra/proteinKcore/index.html.
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Affiliation(s)
- Arnold Emerson Isaac
- Bioinformatics Division, School of Bio Sciences and Technology, VIT University, Vellore, India
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Layers: A molecular surface peeling algorithm and its applications to analyze protein structures. Sci Rep 2015; 5:16141. [PMID: 26553411 PMCID: PMC4639851 DOI: 10.1038/srep16141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 10/01/2015] [Indexed: 11/08/2022] Open
Abstract
We present an algorithm 'Layers' to peel the atoms of proteins as layers. Using Layers we show an efficient way to transform protein structures into 2D pattern, named residue transition pattern (RTP), which is independent of molecular orientations. RTP explains the folding patterns of proteins and hence identification of similarity between proteins is simple and reliable using RTP than with the standard sequence or structure based methods. Moreover, Layers generates a fine-tunable coarse model for the molecular surface by using non-random sampling. The coarse model can be used for shape comparison, protein recognition and ligand design. Additionally, Layers can be used to develop biased initial configuration of molecules for protein folding simulations. We have developed a random forest classifier to predict the RTP of a given polypeptide sequence. Layers is a standalone application; however, it can be merged with other applications to reduce the computational load when working with large datasets of protein structures. Layers is available freely at http://www.csb.iitkgp.ernet.in/applications/mol_layers/main.
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48
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Finkelstein AV, Garbuzynskiy SO. Reduction of the Search Space for the Folding of Proteins at the Level of Formation and Assembly of Secondary Structures: A New View on the Solution of Levinthal's Paradox. Chemphyschem 2015; 16:3375-8. [PMID: 26332344 DOI: 10.1002/cphc.201500700] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Indexed: 12/13/2022]
Abstract
The complete volume of the protein conformation space is, by many orders of magnitude, smaller at the level of secondary structure elements than that at the level of amino acid residues; the latter, according to Levinthal's estimate, scales approximately as 10(2 L), with L being the number of residues in the chain, whereas the former, as demonstrated in this paper, scales no faster than ∼L(N), with N being the number of the secondary structure elements, which is approximately equal to L/15. This drastic decrease in the exponent (L/15 instead of 2 L) explains why sampling of the conformation space does not contradict the ability of the protein chain to find its most stable fold.
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Affiliation(s)
- Alexei V Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya street 4, Pushchino, Russia.
| | - Sergiy O Garbuzynskiy
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya street 4, Pushchino, Russia
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Faísca PF. Knotted proteins: A tangled tale of Structural Biology. Comput Struct Biotechnol J 2015; 13:459-68. [PMID: 26380658 PMCID: PMC4556803 DOI: 10.1016/j.csbj.2015.08.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/31/2015] [Accepted: 08/07/2015] [Indexed: 01/19/2023] Open
Abstract
Knotted proteins have their native structures arranged in the form of an open knot. In the last ten years researchers have been making significant efforts to reveal their folding mechanism and understand which functional advantage(s) knots convey to their carriers. Molecular simulations have been playing a fundamental role in this endeavor, and early computational predictions about the knotting mechanism have just been confirmed in wet lab experiments. Here we review a collection of simulation results that allow outlining the current status of the field of knotted proteins, and discuss directions for future research.
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50
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Sikosek T, Chan HS. Biophysics of protein evolution and evolutionary protein biophysics. J R Soc Interface 2015; 11:20140419. [PMID: 25165599 DOI: 10.1098/rsif.2014.0419] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence-structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by 'hidden' conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution.
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Affiliation(s)
- Tobias Sikosek
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Physics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Physics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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