Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis

The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains un...

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Vydané v:	PLoS computational biology Ročník 15; číslo 2; s. e1006801
Hlavní autori:	Zhou, Hongyu, Dong, Zheng, Verkhivker, Gennady, Zoltowski, Brian D., Tao, Peng
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	United States Public Library of Science 01.02.2019 Public Library of Science (PLoS)
Predmet:	Algorithms Allosteric properties Allosteric proteins Artificial intelligence Biology and Life Sciences Chemical bonds Circadian rhythm Circadian rhythms Classification Computer and Information Sciences Computer applications Covalent bonds Gene expression Investigations Learning algorithms Light Linear algebra Machine learning Markov chains Mathematical models Neural networks Novels Observations Photosensitivity Physical Sciences Physiological aspects Protein binding Proteins Quantitative analysis Research and Analysis Methods United States > US Texas California
ISSN:	1553-7358, 1553-734X, 1553-7358
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Abstract	The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains unclear, which hinders the further development of VVD as an optogenetic tool. We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an atomistic allosteric mechanism leading to the discovery of the unexpected importance of A'α/Aβ and previously overlooked Eα/Fα loops in the conformational change. This approach could be applicable to other allosteric proteins in general to provide interpretable atomistic representations of their otherwise elusive allosteric mechanisms.
AbstractList	The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains unclear, which hinders the further development of VVD as an optogenetic tool. We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an atomistic allosteric mechanism leading to the discovery of the unexpected importance of A'[alpha]/A[beta] and previously overlooked E[alpha]/F[alpha] loops in the conformational change. This approach could be applicable to other allosteric proteins in general to provide interpretable atomistic representations of their otherwise elusive allosteric mechanisms. The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains unclear, which hinders the further development of VVD as an optogenetic tool. We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an atomistic allosteric mechanism leading to the discovery of the unexpected importance of A'α/Aβ and previously overlooked Eα/Fα loops in the conformational change. This approach could be applicable to other allosteric proteins in general to provide interpretable atomistic representations of their otherwise elusive allosteric mechanisms.The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains unclear, which hinders the further development of VVD as an optogenetic tool. We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an atomistic allosteric mechanism leading to the discovery of the unexpected importance of A'α/Aβ and previously overlooked Eα/Fα loops in the conformational change. This approach could be applicable to other allosteric proteins in general to provide interpretable atomistic representations of their otherwise elusive allosteric mechanisms. The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains unclear, which hinders the further development of VVD as an optogenetic tool. We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an atomistic allosteric mechanism leading to the discovery of the unexpected importance of A'α/Aβ and previously overlooked Eα/Fα loops in the conformational change. This approach could be applicable to other allosteric proteins in general to provide interpretable atomistic representations of their otherwise elusive allosteric mechanisms. The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains unclear, which hinders the further development of VVD as an optogenetic tool. We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an atomistic allosteric mechanism leading to the discovery of the unexpected importance of A’α/Aβ and previously overlooked Eα/Fα loops in the conformational change. This approach could be applicable to other allosteric proteins in general to provide interpretable atomistic representations of their otherwise elusive allosteric mechanisms. Allostery is an important but elusive property that governs critical functionality of many proteins. Quantitative analysis is needed to provide significant insight into protein allostery and lead to better prediction power of this ubiquitous phenomenon. We developed machine learning methods based on robust Markov state model to delineate allosteric mechanism of Vivid as an allosteric protein in the filamentous fungus Neurospora crassa, regulating circadian rhythm of this organism. We accurately reconstructed the equilibrium distributions for two allosteric configurations of Vivid, and determined structural differences among these states. Intriguingly, the novel community analysis derived from machine learning methods reveals the importance of two loop regions for Vivid allostery through quantitative evaluations with statistical significance.
Audience	Academic
Author	Dong, Zheng Zoltowski, Brian D. Tao, Peng Verkhivker, Gennady Zhou, Hongyu
AuthorAffiliation	2 Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America University of Maryland School of Pharmacy, UNITED STATES 3 Chapman University School of Pharmacy, Irvine, California, United States of America 1 Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States of America
AuthorAffiliation_xml	– name: 3 Chapman University School of Pharmacy, Irvine, California, United States of America – name: 1 Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States of America – name: 2 Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America – name: University of Maryland School of Pharmacy, UNITED STATES
Author_xml	– sequence: 1 givenname: Hongyu surname: Zhou fullname: Zhou, Hongyu – sequence: 2 givenname: Zheng surname: Dong fullname: Dong, Zheng – sequence: 3 givenname: Gennady orcidid: 0000-0002-4507-4471 surname: Verkhivker fullname: Verkhivker, Gennady – sequence: 4 givenname: Brian D. orcidid: 0000-0001-6749-0743 surname: Zoltowski fullname: Zoltowski, Brian D. – sequence: 5 givenname: Peng orcidid: 0000-0002-2488-0239 surname: Tao fullname: Tao, Peng
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/30779735$$D View this record in MEDLINE/PubMed
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Snippet	The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal...
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SubjectTerms	Algorithms Allosteric properties Allosteric proteins Artificial intelligence Biology and Life Sciences Chemical bonds Circadian rhythm Circadian rhythms Classification Computer and Information Sciences Computer applications Covalent bonds Gene expression Investigations Learning algorithms Light Linear algebra Machine learning Markov chains Mathematical models Neural networks Novels Observations Photosensitivity Physical Sciences Physiological aspects Protein binding Proteins Quantitative analysis Research and Analysis Methods
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Title	Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis
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