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Fragment molecular orbital study of the cAMP-dependent protein kinase catalyzed phosphoryl transfer: a comparison with the differential transition state stabilization method
KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.ORCID iD: 0000-0003-2673-075X
2016 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 22, 15153-15161 p.Article in journal (Refereed) Published
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Abstract [en]

The importance of key residues to the activity of the cAMP-dependent protein kinase catalyzed phosphoryl transfer and to the stabilization of the transition state of the reaction has been investigated by means of the fragment molecular orbital (FMO) method. To evaluate the accuracy of the method and its capability of fragmenting covalent bonds, we have compared stabilization energies due to the interactions between individual residues and the reaction center to results obtained with the differential transition state stabilization method (Szarek, et al., J. Phys. Chem. B, 2008, 112, 11819-11826) and observe, despite a size difference in the fragment describing the reaction center, near-quantitative agreement. We have also computed deletion energies to investigate the effect of virtual deletion of key residues on the activation energy. These results are consistent with the stabilization energies and yield additional information as they clearly capture the effect of secondary interactions, i. e. interactions in the second coordination layer of the reaction center. We find that using FMO to calculate deletion energies is a powerful and time efficient approach to analyze the importance of key residues to the activity of an enzyme catalyzed reaction.

Place, publisher, year, edition, pages
2016. Vol. 18, no 22, 15153-15161 p.
National Category
Physical Chemistry
Research subject
Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-189810DOI: 10.1039/c6cp02623kISI: 000378273500045PubMedID: 27197750Scopus ID: 2-s2.0-84973655854OAI: oai:DiVA.org:kth-189810DiVA: diva2:949459
Funder
Swedish Research Council
Note

QC 20160719

Available from: 2016-07-19 Created: 2016-07-15 Last updated: 2017-03-20Bibliographically approved

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