Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase

Jigar N Bandaria; Samrat Dutta; Michael W Nydegger; William Rock; Amnon Kohen; Christopher M Cheatum

doi:10.1073/pnas.0912190107

Back

Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase

Journal article

Open access

Peer reviewed

Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase

Jigar N Bandaria, Samrat Dutta, Michael W Nydegger, William Rock, Amnon Kohen and Christopher M Cheatum

Proceedings of the National Academy of Sciences - PNAS, Vol.107(42), pp.17974-17979

10/19/2010

DOI: 10.1073/pnas.0912190107

PMCID: PMC2964212

PMID: 20876138

Files and links (1)

url

https://doi.org/10.1073/pnas.0912190107View

Published (Version of record) Open Access

Abstract

The potential for femtosecond to picosecond time-scale motions to influence the rate of the intrinsic chemical step in enzyme-catalyzed reactions is a source of significant controversy. Among the central challenges in resolving this controversy is the difficulty of experimentally characterizing thermally activated motions at this time scale in functionally relevant enzyme complexes. We report a series of measurements to address this problem using two-dimensional infrared spectroscopy to characterize the time scales of active-site motions in complexes of formate dehydrogenase with the transition-state-analog inhibitor azide (N(3)(-)). We observe that the frequency-frequency time correlation functions (FFCF) for the ternary complexes with NAD(+) and NADH decay completely with slow time constants of 3.2 ps and 4.6 ps, respectively. This result suggests that in the vicinity of the transition state, the active-site enzyme structure samples a narrow and relatively rigid conformational distribution indicating that the transition-state structure is well organized for the reaction. In contrast, for the binary complex, we observe a significant static contribution to the FFCF similar to what is seen in other enzymes, indicating the presence of the slow motions that occur on time scales longer than our measurement window.

Catalytic Domain

Formate Dehydrogenases - chemistry

Formate Dehydrogenases - metabolism

Models, Molecular

NAD - metabolism

NADP - metabolism

Spectrophotometry, Infrared

Details

Title: Subtitle: Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase
Creators: Jigar N Bandaria - Department of Chemistry and Optical Science and Technology Center, University of Iowa, Iowa City, IA 52242, USA
Samrat Dutta
Michael W Nydegger
William Rock
Amnon Kohen
Christopher M Cheatum
Resource Type: Journal article
Publication Details: Proceedings of the National Academy of Sciences - PNAS, Vol.107(42), pp.17974-17979
DOI: 10.1073/pnas.0912190107
PMID: 20876138
PMCID: PMC2964212
NLM abbreviation: Proc Natl Acad Sci U S A
ISSN: 0027-8424
eISSN: 1091-6490
Publisher: National Academy of Sciences
Grant note: R01 GM65368 / NIGMS NIH HHS R01 GM065368 / NIGMS NIH HHS
Language: English
Date published: 10/19/2010
Academic Unit: Liberal Arts and Science Admin; Chemistry
Record Identifier: 9984216598602771

Metrics

21 Record Views

68 Times Cited - Web of Science