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Searching protein space for ancient sub-domain segments. Curr Opin Struct Biol 2021; 68:105-112. [PMID: 33476896 DOI: 10.1016/j.sbi.2020.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 11/29/2020] [Indexed: 01/08/2023]
Abstract
Evolutionary processes that formed the current protein universe left their traces, among them homologous segments that recur, or are 'reused,' in multiple proteins. These reused segments, called 'themes,' can be found at various scales, the best known of which is the domain. Yet, recent studies have begun to focus on the evolutionary insights that can be derived from sub-domain-scale themes, which are candidates for traces of more ancient events. Characterizing these may provide clues to the emergence of domains. Particularly interesting are themes that are reused across dissimilar contexts, that is, where the rest of the protein domain differs. We survey computational studies identifying reused themes within different contexts at the sub-domain level.
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Ferruz N, Lobos F, Lemm D, Toledo-Patino S, Farías-Rico JA, Schmidt S, Höcker B. Identification and Analysis of Natural Building Blocks for Evolution-Guided Fragment-Based Protein Design. J Mol Biol 2020; 432:3898-3914. [PMID: 32330481 PMCID: PMC7322520 DOI: 10.1016/j.jmb.2020.04.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 12/15/2022]
Abstract
Natural evolution has generated an impressively diverse protein universe via duplication and recombination from a set of protein fragments that served as building blocks. The application of these concepts to the design of new proteins using subdomain-sized fragments from different folds has proven to be experimentally successful. To better understand how evolution has shaped our protein universe, we performed an all-against-all comparison of protein domains representing all naturally existing folds and identified conserved homologous protein fragments. Overall, we found more than 1000 protein fragments of various lengths among different folds through similarity network analysis. These fragments are present in very different protein environments and represent versatile building blocks for protein design. These data are available in our web server called F(old P)uzzle (fuzzle.uni-bayreuth.de), which allows to individually filter the dataset and create customized networks for folds of interest. We believe that our results serve as an invaluable resource for structural and evolutionary biologists and as raw material for the design of custom-made proteins.
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Affiliation(s)
- Noelia Ferruz
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Francisco Lobos
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany; Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dominik Lemm
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Saacnicteh Toledo-Patino
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany; Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Steffen Schmidt
- Max Planck Institute for Developmental Biology, Tübingen, Germany; Computational Biochemistry, University of Bayreuth, Bayreuth, Germany.
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany; Max Planck Institute for Developmental Biology, Tübingen, Germany.
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3
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Navigating Among Known Structures in Protein Space. Methods Mol Biol 2018. [PMID: 30298400 DOI: 10.1007/978-1-4939-8736-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Present-day protein space is the result of 3.7 billion years of evolution, constrained by the underlying physicochemical qualities of the proteins. It is difficult to differentiate between evolutionary traces and effects of physicochemical constraints. Nonetheless, as a rule of thumb, instances of structural reuse, or focusing on structural similarity, are likely attributable to physicochemical constraints, whereas sequence reuse, or focusing on sequence similarity, may be more indicative of evolutionary relationships. Both types of relationships have been studied and can provide meaningful insights to protein biophysics and evolution, which in turn can lead to better algorithms for protein search, annotation, and maybe even design.In broad strokes, studies of protein space vary in the entities they represent, the similarity measure comparing these entities, and the representation used. The entities can be, for example, protein chains, domains, supra-domains, or smaller protein sub-parts denoted themes. The measures of similarity between the entities can be based on sequence, structure, function, or any combination of these. The representation can be global, encompassing the whole space, or local, focusing on a particular region surrounding protein(s) of interest. Global representations include lists of grouped proteins, protein networks, and maps. Networks are the abstraction that is derived most directly from the similarity data: each node is the protein entity (e.g., a domain), and edges connect similar domains. Selecting the entities, the similarity measure, and the abstraction are three intertwined decisions: the similarity measures allow us to identify the entities, and the selection of entities influences what is a meaningful similarity measure. Similarly, we seek entities that are related to each other in a way, for which a simple representation describes their relationships succinctly and accurately. This chapter will cover studies that rely on different entities, similarity measures, and a range of representations to better understand protein structure space. Scholars may use publicly available navigators offering a global representation, and in particular the hierarchical classifications SCOP, CATH, and ECOD, or a local representation, which encompass structural alignment algorithms. Alternatively, scholars can configure their own navigator using existing tools. To demonstrate this DIY (do it yourself) approach for navigating in protein space, we investigate substrate-binding proteins. By presenting sequence similarities among this large and diverse protein family as a network, we can infer that one member (pdb ID 4ntl; of yet unknown function) may bind methionine and suggest a putative binding mechanism.
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Budowski-Tal I, Kolodny R, Mandel-Gutfreund Y. A Novel Geometry-Based Approach to Infer Protein Interface Similarity. Sci Rep 2018; 8:8192. [PMID: 29844500 PMCID: PMC5974305 DOI: 10.1038/s41598-018-26497-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 05/10/2018] [Indexed: 11/21/2022] Open
Abstract
The protein interface is key to understand protein function, providing a vital insight on how proteins interact with each other and with other molecules. Over the years, many computational methods to compare protein structures were developed, yet evaluating interface similarity remains a very difficult task. Here, we present PatchBag – a geometry based method for efficient comparison of protein surfaces and interfaces. PatchBag is a Bag-Of-Words approach, which represents complex objects as vectors, enabling to search interface similarity in a highly efficient manner. Using a novel framework for evaluating interface similarity, we show that PatchBag performance is comparable to state-of-the-art alignment-based structural comparison methods. The great advantage of PatchBag is that it does not rely on sequence or fold information, thus enabling to detect similarities between interfaces in unrelated proteins. We propose that PatchBag can contribute to reveal novel evolutionary and functional relationships between protein interfaces.
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Affiliation(s)
- Inbal Budowski-Tal
- Faculty of Biology, Technion, Israel Institute of Technology, Haifa, 3200003, Israel.,Department of Computer Science, University of Haifa, Mount Carmel, Haifa, 3498838, Israel
| | - Rachel Kolodny
- Department of Computer Science, University of Haifa, Mount Carmel, Haifa, 3498838, Israel.
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion, Israel Institute of Technology, Haifa, 3200003, Israel.
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King IC, Gleixner J, Doyle L, Kuzin A, Hunt JF, Xiao R, Montelione GT, Stoddard BL, DiMaio F, Baker D. Precise assembly of complex beta sheet topologies from de novo designed building blocks. eLife 2015; 4. [PMID: 26650357 PMCID: PMC4737653 DOI: 10.7554/elife.11012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/08/2015] [Indexed: 01/22/2023] Open
Abstract
Design of complex alpha-beta protein topologies poses a challenge because of the large number of alternative packing arrangements. A similar challenge presumably limited the emergence of large and complex protein topologies in evolution. Here, we demonstrate that protein topologies with six and seven-stranded beta sheets can be designed by insertion of one de novo designed beta sheet containing protein into another such that the two beta sheets are merged to form a single extended sheet, followed by amino acid sequence optimization at the newly formed strand-strand, strand-helix, and helix-helix interfaces. Crystal structures of two such designs closely match the computational design models. Searches for similar structures in the SCOP protein domain database yield only weak matches with different beta sheet connectivities. A similar beta sheet fusion mechanism may have contributed to the emergence of complex beta sheets during natural protein evolution. DOI:http://dx.doi.org/10.7554/eLife.11012.001 A protein is made up of a sequence of amino acids and must fold into a specific three-dimensional structure if it is to work correctly. The structure is formed by segments of the protein adopting specific shapes, the two most common shapes being alpha helices and beta strands. Beta strands commonly interact with each other to form regions called beta sheets. Researchers trying to design proteins with new abilities have managed to create proteins that contain up to five beta strands and four alpha helices. Larger and more complex proteins are more challenging to make because there are many different ways that a protein can fold. It is also difficult to understand how complex structures such as large beta sheets emerged naturally, over the course of evolution. King et al. have now used computer modeling to explore how a large, complex beta sheet might form. In the model, one small, newly designed protein was inserted into another so that their beta sheets merged to form a single extended sheet. The model then stabilized this structure by changing the amino acids found at the points where the two proteins met. King et al. were then able to synthesize these new proteins in bacteria and use a technique called X-ray crystallography to determine the structure of two of them. The structures closely matched the computer models; one protein contained a six-stranded beta sheet, and the other had a seven-stranded beta sheet. The folds of the two designed proteins were then compared with those found in a database that classifies proteins on the basis of their structure. The beta sheets in the designed proteins did not match the protein structures in the database, which suggests that the designed proteins contained new types of folds. In the future, the technique used by King et al. could be used to design other large and complex beta sheet structures. Furthermore, the results suggest that such large structures could have evolved naturally through the combination of smaller, less complex proteins. DOI:http://dx.doi.org/10.7554/eLife.11012.002
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Affiliation(s)
- Indigo Chris King
- Institute for Protein Design, University of Washington, Seattle, United States
| | - James Gleixner
- Institute for Protein Design, University of Washington, Seattle, United States
| | - Lindsey Doyle
- Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Alexandre Kuzin
- Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, United States
| | - John F Hunt
- Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, United States
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, United States
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, United States
| | - Barry L Stoddard
- Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Frank DiMaio
- Institute for Protein Design, University of Washington, Seattle, United States
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, United States
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Scaiewicz A, Levitt M. The language of the protein universe. Curr Opin Genet Dev 2015; 35:50-6. [PMID: 26451980 DOI: 10.1016/j.gde.2015.08.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/20/2015] [Accepted: 08/25/2015] [Indexed: 11/17/2022]
Abstract
Proteins, the main cell machinery which play a major role in nearly every cellular process, have always been a central focus in biology. We live in the post-genomic era, and inferring information from massive data sets is a steadily growing universal challenge. The increasing availability of fully sequenced genomes can be regarded as the 'Rosetta Stone' of the protein universe, allowing the understanding of genomes and their evolution, just as the original Rosetta Stone allowed Champollion to decipher the ancient Egyptian hieroglyphics. In this review, we consider aspects of the protein domain architectures repertoire that are closely related to those of human languages and aim to provide some insights about the language of proteins.
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Affiliation(s)
- Andrea Scaiewicz
- Department of Structural Biology, Stanford University, Stanford, CA 94305-5126, United States
| | - Michael Levitt
- Department of Structural Biology, Stanford University, Stanford, CA 94305-5126, United States.
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Edwards H, Deane CM. Structural Bridges through Fold Space. PLoS Comput Biol 2015; 11:e1004466. [PMID: 26372166 PMCID: PMC4570669 DOI: 10.1371/journal.pcbi.1004466] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 07/12/2015] [Indexed: 12/05/2022] Open
Abstract
Several protein structure classification schemes exist that partition the protein universe into structural units called folds. Yet these schemes do not discuss how these units sit relative to each other in a global structure space. In this paper we construct networks that describe such global relationships between folds in the form of structural bridges. We generate these networks using four different structural alignment methods across multiple score thresholds. The networks constructed using the different methods remain a similar distance apart regardless of the probability threshold defining a structural bridge. This suggests that at least some structural bridges are method specific and that any attempt to build a picture of structural space should not be reliant on a single structural superposition method. Despite these differences all representations agree on an organisation of fold space into five principal community structures: all-α, all-β sandwiches, all-β barrels, α/β and α + β. We project estimated fold ages onto the networks and find that not only are the pairings of unconnected folds associated with higher age differences than bridged folds, but this difference increases with the number of networks displaying an edge. We also examine different centrality measures for folds within the networks and how these relate to fold age. While these measures interpret the central core of fold space in varied ways they all identify the disposition of ancestral folds to fall within this core and that of the more recently evolved structures to provide the peripheral landscape. These findings suggest that evolutionary information is encoded along these structural bridges. Finally, we identify four highly central pivotal folds representing dominant topological features which act as key attractors within our landscapes. Folds are considered to be the structural units which make up the protein universe. Structural classification schemes focus on the assignment and organisation of protein domains into folds. However, they do not suggest how different folds might relate to one another in a global way. We introduce the concept of bridges through fold space: significant similarities between these units. We consider four alignment methods and a dynamic approach to placing these bridges. A greater consensus between these methods cannot be achieved by simply increasing the stringency with which edges are assigned. Instead, we emphasise the importance of considering consensus maps and only report results where there is agreement across all networks. It is possible that a study of the bridges may reveal evolutionary relationships. Based on a phylogenetic analysis of structures, we find that bridges consistently fall between folds which evolved at similar times. Moreover, the landscapes all consist of a core of older folds, with younger structures more often seen at the periphery. Finally we identify four pivotal folds in the landscapes. They contain topological motifs which unite disparate regions of fold space.
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Affiliation(s)
- Hannah Edwards
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Charlotte M. Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Nepomnyachiy S, Ben-Tal N, Kolodny R. CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers. Structure 2015; 23:941-948. [PMID: 25865247 DOI: 10.1016/j.str.2015.02.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/20/2015] [Accepted: 02/24/2015] [Indexed: 12/18/2022]
Abstract
It can be informative to view biological data, e.g., protein-protein interactions within a large complex, in a network representation coupled with three-dimensional structural visualizations of individual molecular entities. CyToStruct, introduced here, provides a transparent interface between the Cytoscape platform for network analysis and molecular viewers, including PyMOL, UCSF Chimera, VMD, and Jmol. CyToStruct launches and passes scripts to molecular viewers from the network's edges and nodes. We provide demonstrations to analyze interactions among subunits in large protein/RNA/DNA complexes, and similarities among proteins. CyToStruct enriches the network tools of Cytoscape by adding a layer of structural analysis, offering all capabilities implemented in molecular viewers. CyToStruct is available at https://bitbucket.org/sergeyn/cytostruct/wiki/Home and in the Cytoscape App Store. Given the coordinates of a molecular complex, our web server (http://trachel-srv.cs.haifa.ac.il/rachel/ppi/) automatically generates all files needed to visualize the complex as a Cytoscape network with CyToStruct bridging to PyMOL, UCSF Chimera, VMD, and Jmol.
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Affiliation(s)
- Sergey Nepomnyachiy
- Department of Computer Science & Engineering, Polytechnic Institute of NYU, Brooklyn, NY 11201, USA
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.
| | - Rachel Kolodny
- Department of Computer Science, University of Haifa, Mount Carmel 31905, Israel.
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9
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Abstract
To explore protein space from a global perspective, we consider 9,710 SCOP (Structural Classification of Proteins) domains with up to 70% sequence identity and present all similarities among them as networks: In the "domain network," nodes represent domains, and edges connect domains that share "motifs," i.e., significantly sized segments of similar sequence and structure. We explore the dependence of the network on the thresholds that define the evolutionary relatedness of the domains. At excessively strict thresholds the network falls apart completely; for very lax thresholds, there are network paths between virtually all domains. Interestingly, at intermediate thresholds the network constitutes two regions that can be described as "continuous" versus "discrete." The continuous region comprises a large connected component, dominated by domains with alternating alpha and beta elements, and the discrete region includes the rest of the domains in isolated islands, each generally corresponding to a fold. We also construct the "motif network," in which nodes represent recurring motifs, and edges connect motifs that appear in the same domain. This network also features a large and highly connected component of motifs that originate from domains with alternating alpha/beta elements (and some all-alpha domains), and smaller isolated islands. Indeed, the motif network suggests that nature reuses such motifs extensively. The networks suggest evolutionary paths between domains and give hints about protein evolution and the underlying biophysics. They provide natural means of organizing protein space, and could be useful for the development of strategies for protein search and design.
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