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Kargatov AM. A strained N-capping motif in α-helices of βαβ-units. J Struct Biol 2024; 216:108063. [PMID: 38246580 DOI: 10.1016/j.jsb.2024.108063] [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: 09/19/2023] [Revised: 12/29/2023] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
A novel helical N-capping motif has been considered. It occurs in the βα-arches of right-handed βαβ-units and contains an N-cap residue in a sterically strained conformation. Moreover, this amino acid position contains almost no glycines, that could relieve strain. It was shown that the N-cap adopts this conformation as a result of the unusual convergence between the second and third amino acid positions of the α-helix (counting from the N-cap) and the second position of the preceding β-strand. This is achieved by the presence of glycines in the specified positions (i.e. positions i - 2, i + 2 and i + 3, if N-cap is i). The N-cap conformation is stabilized by a hydrogen bond between the backbone amide group in the second position of the α-helix and the carbonyl group in the first position of the β-strand. The occurrence of similar N-capping motifs in different types of βαβ-units was compared and their structural differences caused by the influence of the environment were described. Study results may be useful for protein design and ab initio prediction of the 3D protein structure.
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Affiliation(s)
- Anton M Kargatov
- Instituteof Protein Research RAS, Institutskaya street, 4, Pushchino, Moscow region 142290, Russian Federation.
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2
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Li H, Sheng RC, Zhang CN, Wang LC, Li M, Wang YH, Qiao YH, Klosterman SJ, Chen JY, Kong ZQ, Subbarao KV, Chen FM, Zhang DD. Two zinc finger proteins, VdZFP1 and VdZFP2, interact with VdCmr1 to promote melanized microsclerotia development and stress tolerance in Verticillium dahliae. BMC Biol 2023; 21:237. [PMID: 37904147 PMCID: PMC10617112 DOI: 10.1186/s12915-023-01697-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/08/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND Melanin plays important roles in morphological development, survival, host-pathogen interactions and in the virulence of phytopathogenic fungi. In Verticillum dahliae, increases in melanin are recognized as markers of maturation of microsclerotia which ensures the long-term survival and stress tolerance, while decreases in melanin are correlated with increased hyphal growth in the host. The conserved upstream components of the VdCmr1-regulated pathway controlling melanin production in V. dahliae have been extensively identified, but the direct activators of this pathway are still unclear. RESULTS We identified two genes encoding conserved C2H2-type zinc finger proteins VdZFP1 and VdZFP2 adjacent to VdPKS9, a gene encoding a negative regulator of both melanin biosynthesis and microsclerotia formation in V. dahliae. Both VdZFP1 and VdZFP2 were induced during microsclerotia development and were involved in melanin deposition. Their localization changed from cytoplasmic to nuclear in response to osmotic pressure. VdZFP1 and VdZFP2 act as modulators of microsclerotia melanization in V. dahliae, as confirmed by melanin biosynthesis inhibition and supplementation with the melanin pathway intermediate scytalone in albino strains. The results indicate that VdZFP1 and VdZFP2 participate in melanin biosynthesis by positively regulating VdCmr1. Based on the results obtained with yeast one- and two-hybrid (Y1H and Y2H) and bimolecular fluorescence complementation (BiFC) systems, we determined the melanin biosynthesis relies on the direct interactions among VdZFP1, VdZFP2 and VdCmr1, and these interactions occur on the cell walls of microsclerotia. Additionally, VdZFP1 and/or VdZFP2 mutants displayed increased sensitivity to stress factors rather than alterations in pathogenicity, reflecting the importance of melanin in stress tolerance of V. dahliae. CONCLUSIONS Our results revealed that VdZFP1 and VdZFP2 positively regulate VdCmr1 to promote melanin deposition during microsclerotia development, providing novel insight into the regulation of melanin biosynthesis in V. dahliae.
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Affiliation(s)
- Huan Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ruo-Cheng Sheng
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Chen-Ning Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Li-Chao Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Min Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Ya-Hong Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Yu-Hang Qiao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Steven J Klosterman
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA, USA
| | - Jie-Yin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Zhi-Qiang Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, c/o United States Agricultural Research Station,, Salinas, CA, USA.
| | - Feng-Mao Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
| | - Dan-Dan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
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3
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3β-Corner Stability by Comparative Molecular Dynamics Simulations. Int J Mol Sci 2022; 23:ijms231911674. [PMID: 36232976 PMCID: PMC9570037 DOI: 10.3390/ijms231911674] [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: 08/25/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
This study explored the mechanisms by which the stability of super-secondary structures of the 3β-corner type autonomously outside the protein globule are maintained in an aqueous environment. A molecular dynamic (MD) study determined the behavioral diversity of a large set of non-homologous 3β-corner structures of various origins. We focused on geometric parameters such as change in gyration radius, solvent-accessible area, major conformer lifetime and torsion angles, and the number of hydrogen bonds. Ultimately, a set of 3β-corners from 330 structures was characterized by a root mean square deviation (RMSD) of less than 5 Å, a change in the gyration radius of no more than 5%, and the preservation of amino acid residues positioned within the allowed regions on the Ramachandran map. The studied structures retained their topologies throughout the MD experiments. Thus, the 3β-corner structure was found to be rather stable per se in a water environment, i.e., without the rest of a protein molecule, and can act as the nucleus or “ready-made” building block in protein folding. The 3β-corner can also be considered as an independent object for study in field of structural biology.
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4
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Chirgadze YN, Boshkova EA, Kargatov AM, Chirgadze NY. Functional identification of 'hypothetical protein' structures with unknown function. J Biomol Struct Dyn 2022:1-5. [PMID: 35694832 DOI: 10.1080/07391102.2022.2085806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Y N Chirgadze
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - E A Boshkova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - A M Kargatov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - N Y Chirgadze
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada.,X-CHIP Technologies Inc, Toronto, Ontario, Canada
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5
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Rudnev VR, Kulikova LI, Nikolsky KS, Malsagova KA, Kopylov AT, Kaysheva AL. Current Approaches in Supersecondary Structures Investigation. Int J Mol Sci 2021; 22:11879. [PMID: 34769310 PMCID: PMC8584461 DOI: 10.3390/ijms222111879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022] Open
Abstract
Proteins expressed during the cell cycle determine cell function, topology, and responses to environmental influences. The development and improvement of experimental methods in the field of structural biology provide valuable information about the structure and functions of individual proteins. This work is devoted to the study of supersecondary structures of proteins and determination of their structural motifs, description of experimental methods for their detection, databases, and repositories for storage, as well as methods of molecular dynamics research. The interest in the study of supersecondary structures in proteins is due to their autonomous stability outside the protein globule, which makes it possible to study folding processes, conformational changes in protein isoforms, and aberrant proteins with high productivity.
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Affiliation(s)
- Vladimir R. Rudnev
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (V.R.R.); (L.I.K.); (K.S.N.); (A.T.K.); (A.L.K.)
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Liudmila I. Kulikova
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (V.R.R.); (L.I.K.); (K.S.N.); (A.T.K.); (A.L.K.)
- 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
| | - Kirill S. Nikolsky
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (V.R.R.); (L.I.K.); (K.S.N.); (A.T.K.); (A.L.K.)
| | - Kristina A. Malsagova
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (V.R.R.); (L.I.K.); (K.S.N.); (A.T.K.); (A.L.K.)
| | - Arthur T. Kopylov
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (V.R.R.); (L.I.K.); (K.S.N.); (A.T.K.); (A.L.K.)
| | - Anna L. Kaysheva
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (V.R.R.); (L.I.K.); (K.S.N.); (A.T.K.); (A.L.K.)
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6
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Alvarez-Carreño C, Penev PI, Petrov AS, Williams LD. Fold Evolution before LUCA: Common Ancestry of SH3 Domains and OB Domains. Mol Biol Evol 2021; 38:5134-5143. [PMID: 34383917 PMCID: PMC8557408 DOI: 10.1093/molbev/msab240] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
SH3 and OB are the simplest, oldest, and most common protein domains within the translation system. SH3 and OB domains are β-barrels that are structurally similar but are topologically distinct. To transform an OB domain to a SH3 domain, β-strands must be permuted in a multistep and evolutionarily implausible mechanism. Here, we explored relationships between SH3 and OB domains of ribosomal proteins, initiation, and elongation factors using a combined sequence- and structure-based approach. We detect a common core of SH3 and OB domains, as a region of significant structure and sequence similarity. The common core contains four β-strands and a loop, but omits the fifth β-strand, which is variable and is absent from some OB and SH3 domain proteins. The structure of the common core immediately suggests a simple permutation mechanism for interconversion between SH3 and OB domains, which appear to share an ancestor. The OB domain was formed by duplication and adaptation of the SH3 domain core, or vice versa, in a simple and probable transformation. By employing the folding algorithm AlphaFold2, we demonstrated that an ancestral reconstruction of a permuted SH3 sequence folds into an OB structure, and an ancestral reconstruction of a permuted OB sequence folds into a SH3 structure. The tandem SH3 and OB domains in the universal ribosomal protein uL2 share a common ancestor, suggesting that the divergence of these two domains occurred before the last universal common ancestor.
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Affiliation(s)
- Claudia Alvarez-Carreño
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Petar I Penev
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anton S Petrov
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Loren Dean Williams
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
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7
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Konagurthu AS, Subramanian R, Allison L, Abramson D, Stuckey PJ, Garcia de la Banda M, Lesk AM. Universal Architectural Concepts Underlying Protein Folding Patterns. Front Mol Biosci 2021; 7:612920. [PMID: 33996891 PMCID: PMC8120156 DOI: 10.3389/fmolb.2020.612920] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022] Open
Abstract
What is the architectural “basis set” of the observed universe of protein structures? Using information-theoretic inference, we answer this question with a dictionary of 1,493 substructures—called concepts—typically at a subdomain level, based on an unbiased subset of known protein structures. Each concept represents a topologically conserved assembly of helices and strands that make contact. Any protein structure can be dissected into instances of concepts from this dictionary. We dissected the Protein Data Bank and completely inventoried all the concept instances. This yields many insights, including correlations between concepts and catalytic activities or binding sites, useful for rational drug design; local amino-acid sequence–structure correlations, useful for ab initio structure prediction methods; and information supporting the recognition and exploration of evolutionary relationships, useful for structural studies. An interactive site, Proçodic, at http://lcb.infotech.monash.edu.au/prosodic (click), provides access to and navigation of the entire dictionary of concepts and their usages, and all associated information. This report is part of a continuing programme with the goal of elucidating fundamental principles of protein architecture, in the spirit of the work of Cyrus Chothia.
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Affiliation(s)
- Arun S Konagurthu
- Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC, Australia
| | - Ramanan Subramanian
- Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC, Australia
| | - Lloyd Allison
- Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC, Australia
| | - David Abramson
- Research Computing Center, University of Queensland, Brisbane, QLD, Australia
| | - Peter J Stuckey
- Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC, Australia.,School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, Australia
| | - Maria Garcia de la Banda
- Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC, Australia
| | - Arthur M Lesk
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States.,MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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8
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Exploring Protein Fold Space. Biomolecules 2020; 10:biom10020193. [PMID: 32012781 PMCID: PMC7072414 DOI: 10.3390/biom10020193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 11/17/2022] Open
Abstract
The model of protein folding proposed by Ptitsyn and colleagues involves the accretion of secondary structures around a nucleus. As developed by Efimov, this model also provides a useful way to view the relationships among structures. Although somewhat eclipsed by later databases based on the pairwise comparison of structures, Efimov’s approach provides a guide for the more automatic comparison of proteins based on an encoding of their topology as a string. Being restricted to layers of secondary structures based on beta sheets, this too has limitations which are partly overcome by moving to a more generalised secondary structure lattice that can encompass both open and closed (barrel) sheets as well as helical packing of the type encoded by Murzin and Finkelstein on small polyhedra. Regular (crystalline) lattices, such as close-packed hexagonals, were found to be too limited so pseudo-latticses were investigated including those found in quasicrystals and the Bernal tetrahedron-based lattice that he used to represent liquid water. The Bernal lattice was considered best and used to generate model protein structures. These were much more numerous than those seen in Nature, posing the open question of why this might be.
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9
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Structural features of split and unsplit βαβ-units. J Struct Biol 2020; 209:107427. [PMID: 31756457 DOI: 10.1016/j.jsb.2019.107427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 11/06/2019] [Accepted: 11/16/2019] [Indexed: 11/21/2022]
Abstract
In this study, 1064 nonhomologous "unsplit", "one-strand split" and "two-strand split" right-handed βαβ-units having standard α-helices and loops up to seven residues in length have been analyzed. It was found that the α-helices in these kinds of βαβ-units have different distributions of the hydrophobic and hydrophilic amino acid residues along the chain. In the unsplit βαβ-units, most α-helices have hydrophobic residues in positions N4-N7-N8-N11 or N6-N7-N10, where N1 is the first N-terminal residue. In the one-strand split βαβ-units, most α-helices have hydrophobic residues in positions N4-N7-N8-N11 and those in two-strand split βαβ-units in positions N4-N5-N8-N12. On the other hand, in all kinds of βαβ-units, there are commonly occurring hydrophobic stripes of type C4-C7-C8 at the C-terminal parts of the α-helices. As a rule, the C- and N-terminal hydrophobic stripes overlap and the extent of their overlapping determine the length of α-helices.
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10
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Engineering protein assemblies with allosteric control via monomer fold-switching. Nat Commun 2019; 10:5703. [PMID: 31836707 PMCID: PMC6911049 DOI: 10.1038/s41467-019-13686-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 11/15/2019] [Indexed: 12/14/2022] Open
Abstract
The macromolecular machines of life use allosteric control to self-assemble, dissociate and change shape in response to signals. Despite enormous interest, the design of nanoscale allosteric assemblies has proven tremendously challenging. Here we present a proof of concept of allosteric assembly in which an engineered fold switch on the protein monomer triggers or blocks assembly. Our design is based on the hyper-stable, naturally monomeric protein CI2, a paradigm of simple two-state folding, and the toroidal arrangement with 6-fold symmetry that it only adopts in crystalline form. We engineer CI2 to enable a switch between the native and an alternate, latent fold that self-assembles onto hexagonal toroidal particles by exposing a favorable inter-monomer interface. The assembly is controlled on demand via the competing effects of temperature and a designed short peptide. These findings unveil a remarkable potential for structural metamorphosis in proteins and demonstrate key principles for engineering protein-based nanomachinery. The design of protein assemblies is a major thrust for biomolecular engineering and nanobiotechnology. Here the authors demonstrate a general mechanism for designing allosteric macromolecular assemblies and showcase a proof of concept for engineered allosteric protein assembly.
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11
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A global map of the protein shape universe. PLoS Comput Biol 2019; 15:e1006969. [PMID: 30978181 PMCID: PMC6481876 DOI: 10.1371/journal.pcbi.1006969] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/24/2019] [Accepted: 03/20/2019] [Indexed: 11/19/2022] Open
Abstract
Proteins are involved in almost all functions in a living cell, and functions of proteins are realized by their tertiary structures. Obtaining a global perspective of the variety and distribution of protein structures lays a foundation for our understanding of the building principle of protein structures. In light of the rapid accumulation of low-resolution structure data from electron tomography and cryo-electron microscopy, here we map and classify three-dimensional (3D) surface shapes of proteins into a similarity space. Surface shapes of proteins were represented with 3D Zernike descriptors, mathematical moment-based invariants, which have previously been demonstrated effective for biomolecular structure similarity search. In addition to single chains of proteins, we have also analyzed the shape space occupied by protein complexes. From the mapping, we have obtained various new insights into the relationship between shapes, main-chain folds, and complex formation. The unique view obtained from shape mapping opens up new ways to understand design principles, functions, and evolution of proteins. Proteins are the major molecules involved in almost all cellular processes. In this work, we present a novel mapping of protein shapes that represents the variety and the similarities of 3D shapes of proteins and their assemblies. This mapping provides various novel insights into protein shapes including determinant factors of protein 3D shapes, which enhance our understanding of the design principles of protein shapes. The mapping will also be a valuable resource for artificial protein design as well as references for classifying medium- to low-resolution protein structure images of determined by cryo-electron microscopy and tomography.
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12
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Kargatov AM, Efimov AV. Left-handed βαβ-units: frequency of occurrence and arrangement in protein structure. J Biomol Struct Dyn 2019; 38:1230-1233. [PMID: 30938660 DOI: 10.1080/07391102.2019.1591306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anton M Kargatov
- Institute of Protein Research, Russian Academy of Sciences, Moscow Region, Russian Federation
| | - Alexander V Efimov
- Institute of Protein Research, Russian Academy of Sciences, Moscow Region, Russian Federation
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13
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Efimov AV. Handedness of structural units depends on their mutual arrangement in protein structure. J Biomol Struct Dyn 2019; 38:604-608. [PMID: 30776980 DOI: 10.1080/07391102.2019.1580220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alexander V Efimov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
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14
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Kargatov AM, Brazhnikov EV, Efimov AV. Structure and Features of Amino Acid Sequences of L-Modules in SH3-Like Folds. Mol Biol 2018. [DOI: 10.1134/s0026893318060092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Chouhan BPS, Maimaiti S, Gade M, Laurino P. Rossmann-Fold Methyltransferases: Taking a "β-Turn" around Their Cofactor, S-Adenosylmethionine. Biochemistry 2018; 58:166-170. [PMID: 30406995 DOI: 10.1021/acs.biochem.8b00994] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Methyltransferases (MTases) are superfamilies of enzymes that catalyze the transfer of a methyl group from S-adenosylmethionine (SAM), a nucleoside-based cofactor, to a wide variety of substrates such as DNA, RNA, proteins, small molecules, and lipids. Depending upon their structural features, the MTases can be further classified into different classes; we consider exclusively the largest class of MTases, the Rossmann-fold MTases. It has been shown that the nucleoside cofactor-binding Rossmann enzymes, particularly the nicotinamide adenine dinucleotide (NAD)-, flavin adenine dinucleotide (FAD)-, and SAM-binding MTases enzymes, share common binding motifs that include a Gly-rich loop region that interacts with the cofactor and a highly conserved acidic residue (Asp/Glu) that interacts with the ribose moiety of the cofactor. Here, we observe that the Gly-rich loop region of the Rossmann MTases adapts a specific type II' β-turn in the proximity of the cofactor (<4 Å), and it appears to be a key feature of these superfamilies. Additionally, we demonstrate that the conservation of this β-turn could play a critical role in the enzyme-cofactor interaction, thereby shedding new light on the structural conformation of the Gly-rich loop region from Rossmann MTases.
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Affiliation(s)
- Bhanu Pratap Singh Chouhan
- Okinawa Institute of Science and Technology Graduate University , 1919-1 Tancha, Onna-son , Okinawa 904-0412 , Japan
| | - Shayida Maimaiti
- Okinawa Institute of Science and Technology Graduate University , 1919-1 Tancha, Onna-son , Okinawa 904-0412 , Japan
| | - Madhuri Gade
- Okinawa Institute of Science and Technology Graduate University , 1919-1 Tancha, Onna-son , Okinawa 904-0412 , Japan
| | - Paola Laurino
- Okinawa Institute of Science and Technology Graduate University , 1919-1 Tancha, Onna-son , Okinawa 904-0412 , Japan
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16
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Efimov AV. Chirality and Handedness of Protein Structures. BIOCHEMISTRY (MOSCOW) 2018; 83:S103-S110. [DOI: 10.1134/s0006297918140092] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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17
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Efimov AV. Structural motifs in which β-strands are clipped together with the П-like module. Proteins 2017; 85:1925-1930. [PMID: 28677205 DOI: 10.1002/prot.25346] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/20/2017] [Accepted: 07/02/2017] [Indexed: 11/08/2022]
Abstract
In this study, the structural motifs that can be represented as combinations of small motifs such as β-hairpins, S-, and Z-like β-sheets and βαβ-units, and the П-like module are described and analyzed. The П-module consists of connected elements of the β-strand-loop-β-strand type arranged in space so that its overall fold resembles a clip or the Greek letter П. In proteins, the П-module itself and the structural motifs containing it exhibit unique overall folds and have specific sequence patterns of the key hydrophobic, hydrophilic and glycine residues. All this together enables us to conclude that these structural motifs can fold independently of the remaining part of the molecule and can act as nuclei and/or "ready-made" building blocks in protein folding.
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Affiliation(s)
- Alexander V Efimov
- Institute of Protein Research, Russian Academy of Sciences, Moscow Region, Russian Federation
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18
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Caetano-Anollés D, Caetano-Anollés G. Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks. Life (Basel) 2016; 6:life6040043. [PMID: 27918435 PMCID: PMC5198078 DOI: 10.3390/life6040043] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 11/21/2016] [Accepted: 11/29/2016] [Indexed: 01/10/2023] Open
Abstract
The origin of biomolecular machinery likely centered around an ancient and central molecule capable of interacting with emergent macromolecular complexity. tRNA is the oldest and most central nucleic acid molecule of the cell. Its co-evolutionary interactions with aminoacyl-tRNA synthetase protein enzymes define the specificities of the genetic code and those with the ribosome their accurate biosynthetic interpretation. Phylogenetic approaches that focus on molecular structure allow reconstruction of evolutionary timelines that describe the history of RNA and protein structural domains. Here we review phylogenomic analyses that reconstruct the early history of the synthetase enzymes and the ribosome, their interactions with RNA, and the inception of amino acid charging and codon specificities in tRNA that are responsible for the genetic code. We also trace the age of domains and tRNA onto ancient tRNA homologies that were recently identified in rRNA. Our findings reveal a timeline of recruitment of tRNA building blocks for the formation of a functional ribosome, which holds both the biocatalytic functions of protein biosynthesis and the ability to store genetic memory in primordial RNA genomic templates.
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Affiliation(s)
- Derek Caetano-Anollés
- Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, 24306 Plön, Germany.
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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19
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Extension of the classical classification of β-turns. Sci Rep 2016; 6:33191. [PMID: 27627963 PMCID: PMC5024104 DOI: 10.1038/srep33191] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/22/2016] [Indexed: 11/29/2022] Open
Abstract
The functional properties of a protein primarily depend on its three-dimensional (3D) structure. These properties have classically been assigned, visualized and analysed on the basis of protein secondary structures. The β-turn is the third most important secondary structure after helices and β-strands. β-turns have been classified according to the values of the dihedral angles φ and ψ of the central residue. Conventionally, eight different types of β-turns have been defined, whereas those that cannot be defined are classified as type IV β-turns. This classification remains the most widely used. Nonetheless, the miscellaneous type IV β-turns represent 1/3rd of β-turn residues. An unsupervised specific clustering approach was designed to search for recurrent new turns in the type IV category. The classical rules of β-turn type assignment were central to the approach. The four most frequently occurring clusters defined the new β-turn types. Unexpectedly, these types, designated IV1, IV2, IV3 and IV4, represent half of the type IV β-turns and occur more frequently than many of the previously established types. These types show convincing particularities, in terms of both structures and sequences that allow for the classical β-turn classification to be extended for the first time in 25 years.
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20
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Abstract
Globular proteins typically fold into tightly packed arrays of regular secondary structures. We developed a model to approximate the compact parallel and antiparallel arrangement of α-helices and β-strands, enumerated all possible topologies formed by up to five secondary structural elements (SSEs), searched for their occurrence in spatial structures of proteins, and documented their frequencies of occurrence in the PDB. The enumeration model grows larger super-secondary structure patterns (SSPs) by combining pairs of smaller patterns, a process that approximates a potential path of protein fold evolution. The most prevalent SSPs are typically present in superfolds such as the Rossmann-like fold, the ferredoxin-like fold, and the Greek key motif, whereas the less frequent SSPs often possess uncommon structure features such as split β-sheets, left-handed connections, and crossing loops. This complete SSP enumeration model, for the first time, allows us to investigate which theoretically possible SSPs are not observed in available protein structures. All SSPs with up to four SSEs occurred in proteins. However, among the SSPs with five SSEs, approximately 20% (218) are absent from existing folds. Of these unobserved SSPs, 80% contain two or more uncommon structure features. To facilitate future efforts in protein structure classification, engineering, and design, we provide the resulting patterns and their frequency of occurrence in proteins at: http://prodata.swmed.edu/ssps/.
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21
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Laurino P, Tóth-Petróczy Á, Meana-Pañeda R, Lin W, Truhlar DG, Tawfik DS. An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors. PLoS Biol 2016; 14:e1002396. [PMID: 26938925 PMCID: PMC4777477 DOI: 10.1371/journal.pbio.1002396] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 01/29/2016] [Indexed: 01/30/2023] Open
Abstract
Nucleoside-based cofactors are presumed to have preceded proteins. The Rossmann fold is one of the most ancient and functionally diverse protein folds, and most Rossmann enzymes utilize nucleoside-based cofactors. We analyzed an omnipresent Rossmann ribose-binding interaction: a carboxylate side chain at the tip of the second β-strand (β2-Asp/Glu). We identified a canonical motif, defined by the β2-topology and unique geometry. The latter relates to the interaction being bidentate (both ribose hydroxyls interacting with the carboxylate oxygens), to the angle between the carboxylate and the ribose, and to the ribose's ring configuration. We found that this canonical motif exhibits hallmarks of divergence rather than convergence. It is uniquely found in Rossmann enzymes that use different cofactors, primarily SAM (S-adenosyl methionine), NAD (nicotinamide adenine dinucleotide), and FAD (flavin adenine dinucleotide). Ribose-carboxylate bidentate interactions in other folds are not only rare but also have a different topology and geometry. We further show that the canonical geometry is not dictated by a physical constraint--geometries found in noncanonical interactions have similar calculated bond energies. Overall, these data indicate the divergence of several major Rossmann-fold enzyme classes, with different cofactors and catalytic chemistries, from a common pre-LUCA (last universal common ancestor) ancestor that possessed the β2-Asp/Glu motif.
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Affiliation(s)
- Paola Laurino
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Ágnes Tóth-Petróczy
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Rubén Meana-Pañeda
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Wei Lin
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Dan S. Tawfik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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22
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Efimov AV, Boshkova EA. [Two mechanisms of protein folding: theoretical analysis]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2015; 40:665-72. [PMID: 25895362 DOI: 10.1134/s1068162014060077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the present study, two possible mechanisms of protein folding are analized. One of them is based on the hypothesis that at the first step of protein folding a nucleus is formed and then the remaining part of the molecule or domain is folded around it. For example, β-proteins containing 3β-corners can fold in this way. According to the other mechanism, the three-dimensional structure of proteins is formed as a result of interactions between "ready-made" building blocks. Analysis of structural features of the 3β-corners and features of their amino asid sequences enable us to conclude that the 3β-corner can fold into its unique structure per se and can act as a nucleus or "ready-made" building block in protein folding. The larger protein structures can be obtained by stepwise addition of β-strands to the 3β-corner in accordance with a restricted set of rules as shown in the corresponding structural tree, which is available at http://strees.protres.ru/. On the other hand, complementary interactions of the two 3β-corners can result in formation of the fold that is observed in the serine protease domain and similar proteins.
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23
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Lhota J, Hauptman R, Hart T, Ng C, Xie L. A new method to improve network topological similarity search: applied to fold recognition. Bioinformatics 2015; 31:2106-14. [PMID: 25717198 DOI: 10.1093/bioinformatics/btv125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/21/2015] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Similarity search is the foundation of bioinformatics. It plays a key role in establishing structural, functional and evolutionary relationships between biological sequences. Although the power of the similarity search has increased steadily in recent years, a high percentage of sequences remain uncharacterized in the protein universe. Thus, new similarity search strategies are needed to efficiently and reliably infer the structure and function of new sequences. The existing paradigm for studying protein sequence, structure, function and evolution has been established based on the assumption that the protein universe is discrete and hierarchical. Cumulative evidence suggests that the protein universe is continuous. As a result, conventional sequence homology search methods may be not able to detect novel structural, functional and evolutionary relationships between proteins from weak and noisy sequence signals. To overcome the limitations in existing similarity search methods, we propose a new algorithmic framework-Enrichment of Network Topological Similarity (ENTS)-to improve the performance of large scale similarity searches in bioinformatics. RESULTS We apply ENTS to a challenging unsolved problem: protein fold recognition. Our rigorous benchmark studies demonstrate that ENTS considerably outperforms state-of-the-art methods. As the concept of ENTS can be applied to any similarity metric, it may provide a general framework for similarity search on any set of biological entities, given their representation as a network. AVAILABILITY AND IMPLEMENTATION Source code freely available upon request CONTACT : lxie@iscb.org.
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Affiliation(s)
- John Lhota
- Hunter College High School, New York, NY 10128, U.S.A., Department of Computer Science, Hunter College, The City University of New York, New York, NY 10065, U.S.A., Department of Biological Sciences, Hunter College, The City University of New York New York, NY 10065, U.S.A. and The Graduate Center, The City University of New York, New York, NY 10016, U.S.A
| | - Ruth Hauptman
- Hunter College High School, New York, NY 10128, U.S.A., Department of Computer Science, Hunter College, The City University of New York, New York, NY 10065, U.S.A., Department of Biological Sciences, Hunter College, The City University of New York New York, NY 10065, U.S.A. and The Graduate Center, The City University of New York, New York, NY 10016, U.S.A
| | - Thomas Hart
- Hunter College High School, New York, NY 10128, U.S.A., Department of Computer Science, Hunter College, The City University of New York, New York, NY 10065, U.S.A., Department of Biological Sciences, Hunter College, The City University of New York New York, NY 10065, U.S.A. and The Graduate Center, The City University of New York, New York, NY 10016, U.S.A
| | - Clara Ng
- Hunter College High School, New York, NY 10128, U.S.A., Department of Computer Science, Hunter College, The City University of New York, New York, NY 10065, U.S.A., Department of Biological Sciences, Hunter College, The City University of New York New York, NY 10065, U.S.A. and The Graduate Center, The City University of New York, New York, NY 10016, U.S.A
| | - Lei Xie
- Hunter College High School, New York, NY 10128, U.S.A., Department of Computer Science, Hunter College, The City University of New York, New York, NY 10065, U.S.A., Department of Biological Sciences, Hunter College, The City University of New York New York, NY 10065, U.S.A. and The Graduate Center, The City University of New York, New York, NY 10016, U.S.A. Hunter College High School, New York, NY 10128, U.S.A., Department of Computer Science, Hunter College, The City University of New York, New York, NY 10065, U.S.A., Department of Biological Sciences, Hunter College, The City University of New York New York, NY 10065, U.S.A. and The Graduate Center, The City University of New York, New York, NY 10016, U.S.A
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24
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Minami S, Sawada K, Chikenji G. How a spatial arrangement of secondary structure elements is dispersed in the universe of protein folds. PLoS One 2014; 9:e107959. [PMID: 25243952 PMCID: PMC4171485 DOI: 10.1371/journal.pone.0107959] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 08/18/2014] [Indexed: 11/18/2022] Open
Abstract
It has been known that topologically different proteins of the same class sometimes share the same spatial arrangement of secondary structure elements (SSEs). However, the frequency by which topologically different structures share the same spatial arrangement of SSEs is unclear. It is important to estimate this frequency because it provides both a deeper understanding of the geometry of protein folds and a valuable suggestion for predicting protein structures with novel folds. Here we clarified the frequency with which protein folds share the same SSE packing arrangement with other folds, the types of spatial arrangement of SSEs that are frequently observed across different folds, and the diversity of protein folds that share the same spatial arrangement of SSEs with a given fold, using a protein structure alignment program MICAN, which we have been developing. By performing comprehensive structural comparison of SCOP fold representatives, we found that approximately 80% of protein folds share the same spatial arrangement of SSEs with other folds. We also observed that many protein pairs that share the same spatial arrangement of SSEs belong to the different classes, often with an opposing N- to C-terminal direction of the polypeptide chain. The most frequently observed spatial arrangement of SSEs was the 2-layer α/β packing arrangement and it was dispersed among as many as 27% of SCOP fold representatives. These results suggest that the same spatial arrangements of SSEs are adopted by a wide variety of different folds and that the spatial arrangement of SSEs is highly robust against the N- to C-terminal direction of the polypeptide chain.
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Affiliation(s)
- Shintaro Minami
- Department of Complex Systems Science, Nagoya University, Nagoya, Aichi, Japan
| | - Kengo Sawada
- Department of Applied Physics, Nagoya University, Nagoya, Aichi, Japan
| | - George Chikenji
- Department of Computational Science and Engineering, Nagoya University, Nagoya, Aichi, Japan
- * E-mail:
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25
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Boshkova EA, Gordeev AB, Efimov AV. A novel structural tree for wrap-proteins, a subclass of (α+β)-proteins. J Biomol Struct Dyn 2013; 32:222-5. [PMID: 23383708 DOI: 10.1080/07391102.2012.760107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this paper, a novel structural subclass of (α+β)-proteins is presented. A characteristic feature of these proteins and domains is that they consist of strongly twisted and coiled β-sheets wrapped around one or two α-helices, so they are referred to here as wrap-proteins. It is shown that overall folds of the wrap-proteins can be obtained by stepwise addition of α-helices and/or β-strands to the strongly twisted and coiled β-hairpin taken as the starting structure in modeling. As a result of modeling, a structural tree for the wrap-proteins was constructed that includes 201 folds of which 49 occur in known nonhomologous proteins.
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Affiliation(s)
- Eugenia A Boshkova
- a Institute of Protein Research, Russian Academy of Sciences , Pushchino , Moscow Region , 142290 , Russian Federation
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26
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Gordeev AB, Efimov AV. Modeling of folds and folding pathways for some protein families of (α + β)- and (α/β)-classes. J Biomol Struct Dyn 2013; 31:4-16. [PMID: 22800569 DOI: 10.1080/07391102.2012.691341] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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27
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Tang YH, Han SP, Kassahn KS, Skarshewski A, Rothnagel JA, Smith R. Complex evolutionary relationships among four classes of modular RNA-binding splicing regulators in eukaryotes: the hnRNP, SR, ELAV-like and CELF proteins. J Mol Evol 2012. [PMID: 23179353 DOI: 10.1007/s00239-012-9533-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Alternative RNA splicing in multicellular organisms is regulated by a large group of proteins of mainly unknown origin. To predict the functions of these proteins, classification of their domains at the sequence and structural level is necessary. We have focused on four groups of splicing regulators, the heterogeneous nuclear ribonucleoprotein (hnRNP), serine-arginine (SR), embryonic lethal, abnormal vision (ELAV)-like, and CUG-BP and ETR-like factor (CELF) proteins, that show increasing diversity among metazoa. Sequence and phylogenetic analyses were used to obtain a broader understanding of their evolutionary relationships. Surprisingly, when we characterised sequence similarities across full-length sequences and conserved domains of ten metazoan species, we found some hnRNPs were more closely related to SR, ELAV-like and CELF proteins than to other hnRNPs. Phylogenetic analyses and the distribution of the RRM domains suggest that these proteins diversified before the last common ancestor of the metazoans studied here through domain acquisition and duplication to create genes of mixed evolutionary origin. We propose that these proteins were derived independently rather than through the expansion of a single protein family. Our results highlight inconsistencies in the current classification system for these regulators, which does not adequately reflect their evolutionary relationships, and suggests that a domain-based classification scheme may have more utility.
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Affiliation(s)
- Yue Hang Tang
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia.
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28
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Abstract
A characteristic feature of the polypeptide chain is its ability to form a restricted set of commonly occurring folding units composed of two or more elements of secondary structure that are adjacent along the chain. Some of these super-secondary structures exhibit a unique handedness and a unique overall fold irrespective of whether they occur in homologous or nonhomologous proteins. Such super-secondary structures are of particular value since they can be used as starting structures in protein modeling. The larger protein folds can be obtained by stepwise addition of other secondary structural elements to the starting structures taking into account a set of simple rules inferred from known principles of protein structure.
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Affiliation(s)
- Alexander V Efimov
- Institute of Protein Research, Russian Academy of Sciences, Moscow Region, Russia.
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29
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Efimov AV. Structures closed into cycles in globular proteins. BIOCHEMISTRY. BIOKHIMIIA 2011; 76:1385-1390. [PMID: 22339594 DOI: 10.1134/s0006297911130025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Different types of structures closed into cycles are widespread at all the levels of structural organization of proteins. β-Hairpins, triple-stranded β-sheets, and βαβ-units represent simple structural motifs closed into cycles by systems of hydrogen bonds. Secondary closing of these simple motifs into larger cycles by means of different superhelices, split β-hairpins, or SS-bridges results in formation of complex structural motifs such as abcd-units, φ-motifs, five- and seven-segment α/β-motifs, etc. At the level of tertiary structure many proteins and domains fold into structures closed into cylinders. Apparently, closing the motifs and domains into cycles and cylinders results in formation of more cooperative and stable structures as compared with open ones, and this may be the reason for high frequencies of occurrence of the motifs in proteins.
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Affiliation(s)
- A V Efimov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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30
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COMIN MATTEO, GUERRA CONCETTINA, ZANOTTI GIUSEPPE. MINING OVERREPRESENTED 3D PATTERNS OF SECONDARY STRUCTURES IN PROTEINS. J Bioinform Comput Biol 2011; 6:1067-87. [DOI: 10.1142/s0219720008003849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 03/05/2008] [Accepted: 04/09/2008] [Indexed: 11/18/2022]
Abstract
We consider the problem of finding overrepresented arrangements of secondary structure elements (SSEs) in a given dataset of representative protein structures. While most papers in the literature study the distribution of geometrical properties, in particular angles and distances, between pairs of interacting SSEs, in this paper we focus on the distribution of angles of all quartets of SSEs and on the extraction of overrepresented angular patterns. We propose a variant of the Apriori method that obtains overrepresented arrangements of quartets of SSEs by combining arrangements of triplets of SSEs. This specific case will pose the basis for a natural extension of the problem to any given number of SSEs. We analyze the results of our method on a dataset of 300 nonredundant proteins. Supplementary material is available at .
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Affiliation(s)
- MATTEO COMIN
- Department of Information Engineering, University of Padova, 35131 Padova, Italy
| | - CONCETTINA GUERRA
- Department of Information Engineering, University of Padova, 35131 Padova, Italy
- College of Computing, Georgia Institute of Technology, Atlanta, GA 30332-0280, USA
| | - GIUSEPPE ZANOTTI
- Department of Chemistry and VIMM, University of Padova, Padova 35131, Italy
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31
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Reeder PJ, Huang YM, Dordick JS, Bystroff C. A rewired green fluorescent protein: folding and function in a nonsequential, noncircular GFP permutant. Biochemistry 2010; 49:10773-9. [PMID: 21090791 DOI: 10.1021/bi100975z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sequential order of secondary structural elements in proteins affects the folding and activity to an unknown extent. To test the dependence on sequential connectivity, we reconnected secondary structural elements by their solvent-exposed ends, permuting their sequential order, called "rewiring". This new protein design strategy changes the topology of the backbone without changing the core side chain packing arrangement. While circular and noncircular permutations have been observed in protein structures that are not related by sequence homology, to date no one has attempted to rationally design and construct a protein with a sequence that is noncircularly permuted while conserving three-dimensional structure. Herein, we show that green fluorescent protein can be rewired, still functionally fold, and exhibit wild-type fluorescence excitation and emission spectra.
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Affiliation(s)
- Philippa J Reeder
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
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32
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Boshkova EA, Efimov AV. Structures closed into cycles in proteins containing 3β-corners. BIOCHEMISTRY (MOSCOW) 2010; 75:1258-63. [DOI: 10.1134/s000629791010007x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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On the evolutionary origins of "Fold Space Continuity": a study of topological convergence and divergence in mixed alpha-beta domains. J Struct Biol 2010; 172:244-52. [PMID: 20691788 DOI: 10.1016/j.jsb.2010.07.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 06/25/2010] [Accepted: 07/31/2010] [Indexed: 11/21/2022]
Abstract
Existing protein structure classifications group proteins by overall structural similarity at the highest level and by evolutionary relationships at the lowest level, deriving higher-level groups by pairwise structure comparison. For this to be successful requires that large changes in structure are relatively rare in evolution and that proteins with no detectable evolutionary relationship do not converge on similar global chain conformations since this creates conflicts between structural and evolutionary consistency. Analysis of global structural changes using core topological descriptions for 4261 domains from classes C and D of the SCOP database and new measures of topological distance and consistency of classification showed that the topological consistency of SCOP folds is highly variable with some folds having no consistent description and significant overlaps between groups including some members of separate folds with identical topological descriptions. Topological clustering shows that including sufficient indels to allow family members to be joined would also require joining several distinct folds. We conclude that evolutionary changes in the global topology of protein domains are the root cause of many difficulties for present approaches to structure classification using pairwise comparison. As a resolution we propose that a purely structural classification should be created using an approach similar to that adopted by the Gene Ontology in which proteins are assigned labels describing structure.
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34
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Efimov AV. Structural motifs are closed into cycles in proteins. Biochem Biophys Res Commun 2010; 399:412-5. [DOI: 10.1016/j.bbrc.2010.07.089] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 07/25/2010] [Indexed: 11/25/2022]
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35
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Abstract
It is well known that the set of observed topological arrangements of secondary structures in globular proteins is highly limited. These limitations have been explained as the consequence of several rules of thumb including a strong preference for right-handed connections, against crossing loops and certain beta strand patterns. We present a critical evaluation of the power of these rules to distinguish known from possible topologies in a large set of two- and three-layer protein structures and determine that although these rules are still largely valid, an increasing number of exceptions can be found to many of them. The rules are then used to construct a generalised linear model for assessing the probability of occurrence of an arbitrary topology in the PDB. Application of the model to a large set of topologies generated during structure prediction showed that many had a similar probability of occurrence to known PDB folds.
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Affiliation(s)
- Ben Grainger
- Division of Mathematical Biology, National Institute for Medical Research, London, United Kingdom.
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36
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Gordeev AB, Kargatov AM, Efimov AV. PCBOST: Protein classification based on structural trees. Biochem Biophys Res Commun 2010; 397:470-1. [PMID: 20573601 DOI: 10.1016/j.bbrc.2010.05.136] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 05/27/2010] [Indexed: 11/17/2022]
Abstract
In this paper, we present the protein classification based on structural trees (PCBOST). This is a novel hierarchical classification of proteins that is primarily based on similarity of overall folds of proteins as well as on the modeled folding pathways of proteins. Amino acid sequences, functions of proteins and their evolutionary relationship are not taken into account in this classification. To date the database includes 3847 proteins and domains grouped into six categories having structural similarity and forming six structural trees (total 10,547 PDB-entries). The work on extension of the database and construction of novel structural trees is in progress. The service is free for all users and available at the URL <http://strees.protres.ru/>.
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Affiliation(s)
- Alexey B Gordeev
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation
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Kargatov AM, Efimov AV. A novel structural motif and structural trees for proteins containing it. BIOCHEMISTRY (MOSCOW) 2010; 75:249-56. [DOI: 10.1134/s0006297910020161] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ito JI, Sonobe Y, Ikeda K, Tomii K, Higo J. Universal partitioning of the hierarchical fold network of 50-residue segments in proteins. BMC STRUCTURAL BIOLOGY 2009; 9:34. [PMID: 19454039 PMCID: PMC2693521 DOI: 10.1186/1472-6807-9-34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Accepted: 05/20/2009] [Indexed: 11/23/2022]
Abstract
Background Several studies have demonstrated that protein fold space is structured hierarchically and that power-law statistics are satisfied in relation between the numbers of protein families and protein folds (or superfamilies). We examined the internal structure and statistics in the fold space of 50 amino-acid residue segments taken from various protein folds. We used inter-residue contact patterns to measure the tertiary structural similarity among segments. Using this similarity measure, the segments were classified into a number (Kc) of clusters. We examined various Kc values for the clustering. The special resolution to differentiate the segment tertiary structures increases with increasing Kc. Furthermore, we constructed networks by linking structurally similar clusters. Results The network was partitioned persistently into four regions for Kc ≥ 1000. This main partitioning is consistent with results of earlier studies, where similar partitioning was reported in classifying protein domain structures. Furthermore, the network was partitioned naturally into several dozens of sub-networks (i.e., communities). Therefore, intra-sub-network clusters were mutually connected with numerous links, although inter-sub-network ones were rarely done with few links. For Kc ≥ 1000, the major sub-networks were about 40; the contents of the major sub-networks were conserved. This sub-partitioning is a novel finding, suggesting that the network is structured hierarchically: Segments construct a cluster, clusters form a sub-network, and sub-networks constitute a region. Additionally, the network was characterized by non-power-law statistics, which is also a novel finding. Conclusion Main findings are: (1) The universe of 50 residue segments found here was characterized by non-power-law statistics. Therefore, the universe differs from those ever reported for the protein domains. (2) The 50-residue segments were partitioned persistently and universally into some dozens (ca. 40) of major sub-networks, irrespective of the number of clusters. (3) These major sub-networks encompassed 90% of all segments. Consequently, the protein tertiary structure is constructed using the dozens of elements (sub-networks).
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Relative stabilities of conserved and non-conserved structures in the OB-fold superfamily. Int J Mol Sci 2009; 10:2412-2430. [PMID: 19564956 PMCID: PMC2695284 DOI: 10.3390/ijms10052412] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 05/16/2009] [Accepted: 05/19/2009] [Indexed: 11/17/2022] Open
Abstract
The OB-fold is a diverse structure superfamily based on a beta-barrel motif that is often supplemented with additional non-conserved secondary structures. Previous deletion mutagenesis and NMR hydrogen exchange studies of three OB-fold proteins showed that the structural stabilities of sites within the conserved beta-barrels were larger than sites in non-conserved segments. In this work we examined a database of 80 representative domain structures currently classified as OB-folds, to establish the basis of this effect. Residue-specific values were obtained for the number of Calpha-Calpha distance contacts, sequence hydrophobicities, crystallographic B-factors, and theoretical B-factors calculated from a Gaussian Network Model. All four parameters point to a larger average flexibility for the non-conserved structures compared to the conserved beta-barrels. The theoretical B-factors and contact densities show the highest sensitivity. Our results suggest a model of protein structure evolution in which novel structural features develop at the periphery of conserved motifs. Core residues are more resistant to structural changes during evolution since their substitution would disrupt a larger number of interactions. Similar factors are likely to account for the differences in stability to unfolding between conserved and non-conserved structures.
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Pascual-García A, Abia D, Ortiz ÁR, Bastolla U. Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures. PLoS Comput Biol 2009; 5:e1000331. [PMID: 19325884 PMCID: PMC2654728 DOI: 10.1371/journal.pcbi.1000331] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Accepted: 02/11/2009] [Indexed: 11/19/2022] Open
Abstract
Structural classifications of proteins assume the existence of the fold, which is an intrinsic equivalence class of protein domains. Here, we test in which conditions such an equivalence class is compatible with objective similarity measures. We base our analysis on the transitive property of the equivalence relationship, requiring that similarity of A with B and B with C implies that A and C are also similar. Divergent gene evolution leads us to expect that the transitive property should approximately hold. However, if protein domains are a combination of recurrent short polypeptide fragments, as proposed by several authors, then similarity of partial fragments may violate the transitive property, favouring the continuous view of the protein structure space. We propose a measure to quantify the violations of the transitive property when a clustering algorithm joins elements into clusters, and we find out that such violations present a well defined and detectable cross-over point, from an approximately transitive regime at high structure similarity to a regime with large transitivity violations and large differences in length at low similarity. We argue that protein structure space is discrete and hierarchic classification is justified up to this cross-over point, whereas at lower similarities the structure space is continuous and it should be represented as a network. We have tested the qualitative behaviour of this measure, varying all the choices involved in the automatic classification procedure, i.e., domain decomposition, alignment algorithm, similarity score, and clustering algorithm, and we have found out that this behaviour is quite robust. The final classification depends on the chosen algorithms. We used the values of the clustering coefficient and the transitivity violations to select the optimal choices among those that we tested. Interestingly, this criterion also favours the agreement between automatic and expert classifications. As a domain set, we have selected a consensus set of 2,890 domains decomposed very similarly in SCOP and CATH. As an alignment algorithm, we used a global version of MAMMOTH developed in our group, which is both rapid and accurate. As a similarity measure, we used the size-normalized contact overlap, and as a clustering algorithm, we used average linkage. The resulting automatic classification at the cross-over point was more consistent than expert ones with respect to the structure similarity measure, with 86% of the clusters corresponding to subsets of either SCOP or CATH superfamilies and fewer than 5% containing domains in distinct folds according to both SCOP and CATH. Almost 15% of SCOP superfamilies and 10% of CATH superfamilies were split, consistent with the notion of fold change in protein evolution. These results were qualitatively robust for all choices that we tested, although we did not try to use alignment algorithms developed by other groups. Folds defined in SCOP and CATH would be completely joined in the regime of large transitivity violations where clustering is more arbitrary. Consistently, the agreement between SCOP and CATH at fold level was lower than their agreement with the automatic classification obtained using as a clustering algorithm, respectively, average linkage (for SCOP) or single linkage (for CATH). The networks representing significant evolutionary and structural relationships between clusters beyond the cross-over point may allow us to perform evolutionary, structural, or functional analyses beyond the limits of classification schemes. These networks and the underlying clusters are available at http://ub.cbm.uam.es/research/ProtNet.php Making order of the fast-growing information on proteins is essential for gaining evolutionary and functional knowledge. The most successful approaches to this task are based on classifications of protein structures, such as SCOP and CATH, which assume a discrete view of the protein structure space as a collection of separated equivalence classes (folds). However, several authors proposed that protein domains should be regarded as assemblies of polypeptide fragments, which implies that the protein–structure space is continuous. Here, we assess these views of domain space through the concept of transitivity; i.e., we test whether structure similarity of A with B and B with C implies that A and C are similar, as required for consistent classification. We find that the domain space is approximately transitive and discrete at high similarity and continuous at low similarity, where transitivity is severely violated. Comparing our classification at the cross-over similarity with CATH and SCOP, we find that they join proteins at low similarity where classification is inconsistent. Part of this discrepancy is due to structural divergence of homologous domains, which are forced to be in a single cluster in CATH and SCOP. Structural and evolutionary relationships between consistent clusters are represented as a network in our approach, going beyond current protein classification schemes. We conjecture that our results are related to a change of evolutionary regime, from uniparental divergent evolution for highly related domains to assembly of large fragments for which the classical tree representation is unsuitable.
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Affiliation(s)
| | - David Abia
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - Ángel R. Ortiz
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - Ugo Bastolla
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, Madrid, Spain
- * E-mail:
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Papatheodorou TS, Fokas AS. Systematic construction and prediction of the arrangement of the strands of sandwich proteins. J R Soc Interface 2009; 6:63-73. [PMID: 18586634 DOI: 10.1098/rsif.2008.0192] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The problem of predicting the three-dimensional structure of a protein starting from its amino acid sequence is regarded as one of the most important open problems in biology. Here, we solve aspects of this problem for the so-called sandwich proteins that constitute a large class of proteins consisting of only beta-strands arranged in two sheets. A breakthrough for this class of proteins was announced in Kister et al. (Kister et al. 2002 Proc. Natl Acad. Sci. USA 99, 14 137-14 141), in which it was shown that sandwich proteins contain a certain invariant substructure called interlock. It was later noted that approximately 90% of the observed sandwich proteins are canonical, namely they are generated by certain geometrical structures. Here, employing a topological investigation, we prove that interlocks and geometrical structures are the direct consequence of certain biologically motivated fundamental principles. Furthermore, we construct all possible canonical motifs involving 6-10 strands. This construction limits dramatically the number of possible motifs. For example, for sandwich proteins with nine strands, the a priori number of possible canonical motifs exceeds 360000, whereas our construction yields only 49 geometrical structures and 625 canonical motifs.
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Affiliation(s)
- T S Papatheodorou
- Department of Computer Engineering and Informatics, University of Patras, 265 04 Patras, Greece.
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Abstract
Contemporary protein architectures can be regarded as molecular fossils, historical imprints that mark important milestones in the history of life. Whereas sequences change at a considerable pace, higher-order structures are constrained by the energetic landscape of protein folding, the exploration of sequence and structure space, and complex interactions mediated by the proteostasis and proteolytic machineries of the cell. The survey of architectures in the living world that was fuelled by recent structural genomic initiatives has been summarized in protein classification schemes, and the overall structure of fold space explored with novel bioinformatic approaches. However, metrics of general structural comparison have not yet unified architectural complexity using the 'shared and derived' tenet of evolutionary analysis. In contrast, a shift of focus from molecules to proteomes and a census of protein structure in fully sequenced genomes were able to uncover global evolutionary patterns in the structure of proteins. Timelines of discovery of architectures and functions unfolded episodes of specialization, reductive evolutionary tendencies of architectural repertoires in proteomes and the rise of modularity in the protein world. They revealed a biologically complex ancestral proteome and the early origin of the archaeal lineage. Studies also identified an origin of the protein world in enzymes of nucleotide metabolism harbouring the P-loop-containing triphosphate hydrolase fold and the explosive discovery of metabolic functions that recapitulated well-defined prebiotic shells and involved the recruitment of structures and functions. These observations have important implications for origins of modern biochemistry and diversification of life.
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Keren I, Klipcan L, Bezawork-Geleta A, Kolton M, Shaya F, Ostersetzer-Biran O. Characterization of the molecular basis of group II intron RNA recognition by CRS1-CRM domains. J Biol Chem 2008; 283:23333-42. [PMID: 18559344 DOI: 10.1074/jbc.m710488200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CRM (chloroplast RNA splicing and ribosome maturation) is a recently recognized RNA-binding domain of ancient origin that has been retained in eukaryotic genomes only within the plant lineage. Whereas in bacteria CRM domains exist as single domain proteins involved in ribosome maturation, in plants they are found in a family of proteins that contain between one and four repeats. Several members of this family with multiple CRM domains have been shown to be required for the splicing of specific plastidic group II introns. Detailed biochemical analysis of one of these factors in maize, CRS1, demonstrated its high affinity and specific binding to the single group II intron whose splicing it facilitates, the plastid-encoded atpF intron RNA. Through its association with two intronic regions, CRS1 guides the folding of atpF intron RNA into its predicted "catalytically active" form. To understand how multiple CRM domains cooperate to achieve high affinity sequence-specific binding to RNA, we analyzed the RNA binding affinity and specificity associated with each individual CRM domain in CRS1; whereas CRM3 bound tightly to the RNA, CRM1 associated specifically with a unique region found within atpF intron domain I. CRM2, which demonstrated only low binding affinity, also seems to form specific interactions with regions localized to domains I, III, and IV. We further show that CRM domains share structural similarities and RNA binding characteristics with the well known RNA recognition motif domain.
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Affiliation(s)
- Ido Keren
- Institute of Plant Sciences, Agricultural Research Organization, Bet Dagan 50250, Israel
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Abstract
In the present study, a novel structural motif of proteins referred to as the phi-motif is considered, and two novel structural trees in which the phi-motif is taken as the root structure have been constructed. The simplest phi-motif is formed by three adjacent beta-strands connected by loops and packed in one beta-sheet so that its overall fold resembles the Greek letter phi. Construction of the structural trees and modeling of folding pathways have shown that all structures of the protein superfamilies can be obtained by stepwise addition of alpha-helices and/or beta-strands to the root phi-motif taking into account a restricted set of rules inferred from known principles of protein structure. The structural trees are a good tool for structure comparison, structural classification of proteins, as well as for searching for all possible protein folds and folding pathways.
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Affiliation(s)
- A V Efimov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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Gordeev AB, Kondratova MS, Efimov AV. Novel structural tree of β-proteins containing abcd units. Mol Biol 2008. [DOI: 10.1134/s0026893308020155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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47
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Garbuzynskiy S, Kondratova M. Structural features of protein folding nuclei. FEBS Lett 2008; 582:768-72. [DOI: 10.1016/j.febslet.2008.01.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Revised: 12/10/2007] [Accepted: 01/29/2008] [Indexed: 10/22/2022]
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De Brevern AG, Etchebest C, Benros C, Hazout S. "Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence. J Biosci 2007; 32:51-70. [PMID: 17426380 DOI: 10.1007/s12038-007-0006-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The description of protein 3D structures can be performed through a library of 3D fragments, named a structural alphabet. Our structural alphabet is composed of 16 small protein fragments of 5 C alpha in length, called protein blocks (PBs). It allows an efficient approximation of the 3D protein structures and a correct prediction of the local structure. The 72 most frequent series of 5 consecutive PBs, called structural words (SWs)are able to cover more than 90% of the 3D structures. PBs are highly conditioned by the presence of a limited number of transitions between them. In this study, we propose a new method called "pinning strategy" that used this specific feature to predict long protein fragments. Its goal is to define highly probable successions of PBs. It starts from the most probable SW and is then extended with overlapping SWs. Starting from an initial prediction rate of 34.4%, the use of the SWs instead of the PBs allows a gain of 4.5%. The pinning strategy simply applied to the SWs increases the prediction accuracy to 39.9%. In a second step, the sequence-structure relationship is optimized, the prediction accuracy reaches 43.6%.
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Affiliation(s)
- A G De Brevern
- 1 INSERM, U726, Equipe de Bioinformatique Genomique et Moleculaire (EBGM), Universite Paris 7,case 7113, 2, place Jussieu, 75251 Paris Cedex 05, France.
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Taylor WR. Evolutionary transitions in protein fold space. Curr Opin Struct Biol 2007; 17:354-61. [PMID: 17580115 DOI: 10.1016/j.sbi.2007.06.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Revised: 04/11/2007] [Accepted: 06/06/2007] [Indexed: 10/23/2022]
Abstract
With the number of known protein folds potentially approaching completion, the problems associated with their systematic classification are evaluated. It is argued that it will be difficult, if not impossible, to find a general metric based on pairwise comparison that will provide a satisfactory classification. It is suggested that some progress may be made through comparison against a library of idealised 'template' folds, but a proper solution can only be attained if this includes a model of the underlying evolutionary processes. These processes are considered with examples of some unexpected relationships among folds, including circular permutations. The problem is finally set in the wider context of the genetic environment, introducing complications relating to introns, gene fixation and population size.
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Affiliation(s)
- William R Taylor
- Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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Gelly JC, Etchebest C, Hazout S, de Brevern A. Protein Peeling 2: a web server to convert protein structures into series of protein units. Nucleic Acids Res 2006; 34:W75-8. [PMID: 16845113 PMCID: PMC1538916 DOI: 10.1093/nar/gkl292] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Protein Peeling 2 (PP2) is a web server for the automatic identification of protein units (PUs) given the 3D coordinates of a protein. PUs are an intermediate level of protein structure description between protein domains and secondary structures. It is a new tool to better understand and analyze the organization of protein structures. PP2 uses only the matrices of protein contact probabilities and cuts the protein structures optimally using Matthews' coefficient correlation. An index assesses the compactness quality of each PU. Results are given both textually and graphically using JMol and PyMol softwares. The server can be accessed from .
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Affiliation(s)
| | - C. Etchebest
- INSERM, U726, Equipe de Bioinformatique Génomique et Moléculaire (EBGM)Université Paris 7, case 7113, 2, place Jussieu, 75251 Paris Cedex 05, France
| | - S. Hazout
- INSERM, U726, Equipe de Bioinformatique Génomique et Moléculaire (EBGM)Université Paris 7, case 7113, 2, place Jussieu, 75251 Paris Cedex 05, France
| | - A.G. de Brevern
- INSERM, U726, Equipe de Bioinformatique Génomique et Moléculaire (EBGM)Université Paris 7, case 7113, 2, place Jussieu, 75251 Paris Cedex 05, France
- To whom correspondence should be addressed. Tel: +33 1 44 27 77 31; Fax: +33 1 43 26 38 30;
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