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Rostam N, Ghosh S, Chow CFW, Hadarovich A, Landerer C, Ghosh R, Moon H, Hersemann L, Mitrea DM, Klein IA, Hyman AA, Toth-Petroczy A. CD-CODE: crowdsourcing condensate database and encyclopedia. Nat Methods 2023; 20:673-676. [PMID: 37024650 PMCID: PMC10172118 DOI: 10.1038/s41592-023-01831-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 02/27/2023] [Indexed: 04/08/2023]
Abstract
The discovery of biomolecular condensates transformed our understanding of intracellular compartmentalization of molecules. To integrate interdisciplinary scientific knowledge about the function and composition of biomolecular condensates, we developed the crowdsourcing condensate database and encyclopedia ( cd-code.org ). CD-CODE is a community-editable platform, which includes a database of biomolecular condensates based on the literature, an encyclopedia of relevant scientific terms and a crowdsourcing web application. Our platform will accelerate the discovery and validation of biomolecular condensates, and facilitate efforts to understand their role in disease and as therapeutic targets.
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Affiliation(s)
- Nadia Rostam
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Soumyadeep Ghosh
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Chi Fung Willis Chow
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - Anna Hadarovich
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Cedric Landerer
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Rajat Ghosh
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - HongKee Moon
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Lena Hersemann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | | | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - Agnes Toth-Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology Dresden, Dresden, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
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Hadarovich A, Chakravarty D, Tuzikov AV, Ben-Tal N, Kundrotas PJ, Vakser IA. Structural motifs in protein cores and at protein-protein interfaces are different. Protein Sci 2020; 30:381-390. [PMID: 33166001 DOI: 10.1002/pro.3996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/30/2020] [Accepted: 10/31/2020] [Indexed: 11/10/2022]
Abstract
Structures of proteins and protein-protein complexes are determined by the same physical principles and thus share a number of similarities. At the same time, there could be differences because in order to function, proteins interact with other molecules, undergo conformations changes, and so forth, which might impose different restraints on the tertiary versus quaternary structures. This study focuses on structural properties of protein-protein interfaces in comparison with the protein core, based on the wealth of currently available structural data and new structure-based approaches. The results showed that physicochemical characteristics, such as amino acid composition, residue-residue contact preferences, and hydrophilicity/hydrophobicity distributions, are similar in protein core and protein-protein interfaces. On the other hand, characteristics that reflect the evolutionary pressure, such as structural composition and packing, are largely different. The results provide important insight into fundamental properties of protein structure and function. At the same time, the results contribute to better understanding of the ways to dock proteins. Recent progress in predicting structures of individual proteins follows the advancement of deep learning techniques and new approaches to residue coevolution data. Protein core could potentially provide large amounts of data for application of the deep learning to docking. However, our results showed that the core motifs are significantly different from those at protein-protein interfaces, and thus may not be directly useful for docking. At the same time, such difference may help to overcome a major obstacle in application of the coevolutionary data to docking-discrimination of the intramolecular information not directly relevant to docking.
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Affiliation(s)
- Anna Hadarovich
- Computational Biology Program, The University of Kansas, Lawrence, Kansas, USA.,United Institute of Informatics Problems, National Academy of Sciences, Minsk, Belarus
| | - Devlina Chakravarty
- Computational Biology Program, The University of Kansas, Lawrence, Kansas, USA.,Department of Chemistry, Rutgers University, Camden, New Jersey, USA
| | - Alexander V Tuzikov
- United Institute of Informatics Problems, National Academy of Sciences, Minsk, Belarus
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Petras J Kundrotas
- Computational Biology Program, The University of Kansas, Lawrence, Kansas, USA
| | - Ilya A Vakser
- Computational Biology Program, The University of Kansas, Lawrence, Kansas, USA.,Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, USA
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Hadarovich A, Anishchenko I, Tuzikov AV, Kundrotas PJ, Vakser IA. Gene ontology improves template selection in comparative protein docking. Proteins 2018; 87:245-253. [PMID: 30520123 DOI: 10.1002/prot.25645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 10/21/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023]
Abstract
Structural characterization of protein-protein interactions is essential for our ability to study life processes at the molecular level. Computational modeling of protein complexes (protein docking) is important as the source of their structure and as a way to understand the principles of protein interaction. Rapidly evolving comparative docking approaches utilize target/template similarity metrics, which are often based on the protein structure. Although the structural similarity, generally, yields good performance, other characteristics of the interacting proteins (eg, function, biological process, and localization) may improve the prediction quality, especially in the case of weak target/template structural similarity. For the ranking of a pool of models for each target, we tested scoring functions that quantify similarity of Gene Ontology (GO) terms assigned to target and template proteins in three ontology domains-biological process, molecular function, and cellular component (GO-score). The scoring functions were tested in docking of bound, unbound, and modeled proteins. The results indicate that the combined structural and GO-terms functions improve the scoring, especially in the twilight zone of structural similarity, typical for protein models of limited accuracy.
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Affiliation(s)
- Anna Hadarovich
- Computational Biology Program, The University of Kansas, Lawrence, Kansas.,United Institute of Informatics Problems, National Academy of Sciences, Minsk, Belarus
| | - Ivan Anishchenko
- Computational Biology Program, The University of Kansas, Lawrence, Kansas
| | - Alexander V Tuzikov
- United Institute of Informatics Problems, National Academy of Sciences, Minsk, Belarus
| | - Petras J Kundrotas
- Computational Biology Program, The University of Kansas, Lawrence, Kansas
| | - Ilya A Vakser
- Computational Biology Program, The University of Kansas, Lawrence, Kansas.,Department of Molecular Biosciences, The University of Kansas, Kansas, Lawrence
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