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Dynamic Connection ...
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Ojeda-May, PedroUmeå universitet,Kemiska institutionen,Högpresterande beräkningscentrum norr (HPC2N)
(author)
Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions
- Article/chapterEnglish2021
Publisher, publication year, extent ...
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2021-07-12
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American Chemical Society (ACS),2021
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printrdacarrier
Numbers
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LIBRIS-ID:oai:DiVA.org:umu-187197
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https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-187197URI
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https://doi.org/10.1021/acs.biochem.1c00221DOI
Supplementary language notes
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Language:English
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Summary in:English
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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Enzymes employ a wide range of protein motions to achieve efficient catalysis of chemical reactions. While the role of collective protein motions in substrate binding, product release, and regulation of enzymatic activity is generally understood, their roles in catalytic steps per se remain uncertain. Here, molecular dynamics simulations, enzyme kinetics, X-ray crystallography, and nuclear magnetic resonance spectroscopy are combined to elucidate the catalytic mechanism of adenylate kinase and to delineate the roles of catalytic residues in catalysis and the conformational change in the enzyme. This study reveals that the motions in the active site, which occur on a time scale of picoseconds to nanoseconds, link the catalytic reaction to the slow conformational dynamics of the enzyme by modulating the free energy landscapes of subdomain motions. In particular, substantial conformational rearrangement occurs in the active site following the catalytic reaction. This rearrangement not only affects the reaction barrier but also promotes a more open conformation of the enzyme after the reaction, which then results in an accelerated opening of the enzyme compared to that of the reactant state. The results illustrate a linkage between enzymatic catalysis and collective protein motions, whereby the disparate time scales between the two processes are bridged by a cascade of intermediate-scale motion of catalytic residues modulating the free energy landscapes of the catalytic and conformational change processes.
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Ul Mushtaq, AmeeqUmeå universitet,Kemiska institutionen(Swepub:umu)amul0005
(author)
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Rogne, PerUmeå universitet,Kemiska institutionen(Swepub:umu)pero0018
(author)
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Verma, ApoorvUmeå universitet,Kemiska institutionen(Swepub:umu)apve0002
(author)
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Ovchinnikov, Victor
(author)
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Grundström, ChristinUmeå universitet,Kemiska institutionen(Swepub:umu)chgr0001
(author)
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Dulko-Smith, Beata
(author)
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Sauer, Uwe H.Umeå universitet,Kemiska institutionen(Swepub:umu)uwsa0001
(author)
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Wolf-Watz, Magnus,1971-Umeå universitet,Kemiska institutionen(Swepub:umu)maswoz04
(author)
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Nam, Kwangho
(author)
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Umeå universitetKemiska institutionen
(creator_code:org_t)
Related titles
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In:Biochemistry: American Chemical Society (ACS)60:28, s. 2246-22580006-29601520-4995
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- By the author/editor
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Ojeda-May, Pedro
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Ul Mushtaq, Amee ...
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Rogne, Per
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Verma, Apoorv
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Ovchinnikov, Vic ...
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Grundström, Chri ...
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Dulko-Smith, Bea ...
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Sauer, Uwe H.
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Wolf-Watz, Magnu ...
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Nam, Kwangho
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Biochemistry and ...
- Articles in the publication
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Biochemistry
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Umeå University