Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds
Vastly divergent sequences populate a majority of protein folds. In the quest to identify features that are conserved within protein domains belonging to the same fold, we set out to examine the entire protein universe on a fold-by-fold basis. We report that the atomic interaction network in the sol...
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| Other Authors: | |
| Format: | Article |
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Public Library of Science (PLoS)
2018
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| Online Access: | http://hdl.handle.net/1721.1/116196 https://orcid.org/0000-0002-2085-7840 |
| _version_ | 1826204752413720576 |
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| author | Soundararajan, Venkataramanan Raman, Rahul Raguram, S Sasisekharan, Viswanathan Sasisekharan, Ram |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Soundararajan, Venkataramanan Raman, Rahul Raguram, S Sasisekharan, Viswanathan Sasisekharan, Ram |
| author_sort | Soundararajan, Venkataramanan |
| collection | MIT |
| description | Vastly divergent sequences populate a majority of protein folds. In the quest to identify features that are conserved within protein domains belonging to the same fold, we set out to examine the entire protein universe on a fold-by-fold basis. We report that the atomic interaction network in the solvent-unexposed core of protein domains are fold-conserved, extraordinary sequence divergence notwithstanding. Further, we find that this feature, termed protein core atomic interaction network (or PCAIN) is significantly distinguishable across different folds, thus appearing to be "signature" of a domain's native fold. As part of this study, we computed the PCAINs for 8698 representative protein domains from families across the 1018 known protein folds to construct our seed database and an automated framework was developed for PCAIN-based characterization of the protein fold universe. A test set of randomly selected domains that are not in the seed database was classified with over 97% accuracy, independent of sequence divergence. As an application of this novel fold signature, a PCAIN-based scoring scheme was developed for comparative (homology-based) structure prediction, with 1-2 angstroms (mean 1.61A) Cα RMSD generally observed between computed structures and reference crystal structures. Our results are consistent across the full spectrum of test domains including those from recent CASP experiments and most notably in the 'twilight' and 'midnight' zones wherein < 30% and < 10% target-template sequence identity prevails (mean twilight RMSD of 1.69A). We further demonstrate the utility of the PCAIN protocol to derive biological insight into protein structure-function relationships, by modeling the structure of the YopM effector novel E3 ligase (NEL) domain from plaguecausative bacterium Yersinia Pestis and discussing its implications for host adaptive and innate immune modulation by the pathogen. Considering the several high-throughput, sequence-identity-independent applications demonstrated in this work, we suggest that the PCAIN is a fundamental fold feature that could be a valuable addition to the arsenal of protein modeling and analysis tools. |
| first_indexed | 2024-09-23T13:00:51Z |
| format | Article |
| id | mit-1721.1/116196 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T13:00:51Z |
| publishDate | 2018 |
| publisher | Public Library of Science (PLoS) |
| record_format | dspace |
| spelling | mit-1721.1/1161962022-09-28T11:28:32Z Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds Soundararajan, Venkataramanan Raman, Rahul Raguram, S Sasisekharan, Viswanathan Sasisekharan, Ram Massachusetts Institute of Technology. Department of Biology Koch Institute for Integrative Cancer Research at MIT Soundararajan, Venkataramanan Raman, Rahul Raguram, S Sasisekharan, Viswanathan Sasisekharan, Ram Vastly divergent sequences populate a majority of protein folds. In the quest to identify features that are conserved within protein domains belonging to the same fold, we set out to examine the entire protein universe on a fold-by-fold basis. We report that the atomic interaction network in the solvent-unexposed core of protein domains are fold-conserved, extraordinary sequence divergence notwithstanding. Further, we find that this feature, termed protein core atomic interaction network (or PCAIN) is significantly distinguishable across different folds, thus appearing to be "signature" of a domain's native fold. As part of this study, we computed the PCAINs for 8698 representative protein domains from families across the 1018 known protein folds to construct our seed database and an automated framework was developed for PCAIN-based characterization of the protein fold universe. A test set of randomly selected domains that are not in the seed database was classified with over 97% accuracy, independent of sequence divergence. As an application of this novel fold signature, a PCAIN-based scoring scheme was developed for comparative (homology-based) structure prediction, with 1-2 angstroms (mean 1.61A) Cα RMSD generally observed between computed structures and reference crystal structures. Our results are consistent across the full spectrum of test domains including those from recent CASP experiments and most notably in the 'twilight' and 'midnight' zones wherein < 30% and < 10% target-template sequence identity prevails (mean twilight RMSD of 1.69A). We further demonstrate the utility of the PCAIN protocol to derive biological insight into protein structure-function relationships, by modeling the structure of the YopM effector novel E3 ligase (NEL) domain from plaguecausative bacterium Yersinia Pestis and discussing its implications for host adaptive and innate immune modulation by the pathogen. Considering the several high-throughput, sequence-identity-independent applications demonstrated in this work, we suggest that the PCAIN is a fundamental fold feature that could be a valuable addition to the arsenal of protein modeling and analysis tools. 2018-06-11T14:40:57Z 2018-06-11T14:40:57Z 2010-02 2009-12 2018-06-08T17:45:49Z Article http://purl.org/eprint/type/JournalArticle 1932-6203 http://hdl.handle.net/1721.1/116196 Soundararajan, Venkataramanan et al. “Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds.” Edited by Neeraj Vij. PLoS ONE 5, 2 (February 2010): e9391 © 2010 Soundararajan et al https://orcid.org/0000-0002-2085-7840 http://dx.doi.org/10.1371/journal.pone.0009391 PLoS ONE Attribution 4.0 International (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/ application/pdf Public Library of Science (PLoS) PLoS |
| spellingShingle | Soundararajan, Venkataramanan Raman, Rahul Raguram, S Sasisekharan, Viswanathan Sasisekharan, Ram Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds |
| title | Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds |
| title_full | Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds |
| title_fullStr | Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds |
| title_full_unstemmed | Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds |
| title_short | Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds |
| title_sort | atomic interaction networks in the core of protein domains and their native folds |
| url | http://hdl.handle.net/1721.1/116196 https://orcid.org/0000-0002-2085-7840 |
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