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Cited by 198Protein Structure and DynamicsElectron Spin Resonance StudiesEnzyme Structure and Function

Conformation of T4 Lysozyme in Solution. Hinge-Bending Motion and the Substrate-Induced Conformational Transition Studied by Site-Directed Spin Labeling

Mchaourab, Hassane S., Oh, Kyoung Joon, Fang, Celia J., Hubbell, Wayne L.·1997·Biochemistry
DOI 10.1021/bi962114m
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Abstract

T4 lysozyme and mutants thereof crystallize in different conformations that are related to each other by a bend about a hinge in the molecule. This observation suggests that the wild type protein may undergo a hinge-bending motion in solution to allow substrate access to an otherwise closed active site cleft [Faber, H.R., & Matthews, B.W. (1990) Nature 348, 263-266]. To test this hypothesis, either single or pairs of nitroxide side chains were introduced into the protein to monitor tertiary contact interactions and inter-residue distances, respectively, in solution. A set of constraints for these structural parameters was derived from a reference state, a covalent enzyme-substrate adduct where the enzyme is locked in the closed state. In the absence of substrate, differences in both inter-residue distances and tertiary contact interactions relative to this reference state are consistent with a hinge-bending motion that opens the active site cleft. Quantitative analysis of spin-spin interactions between nitroxide pairs reveals an 8 A relative domain movement upon substrate binding. In addition, it is demonstrated that the I3P mutation, which produces a large hinge-bending angle in the crystal, has no effect on the solution conformation. Thus, the hinge motion is not the result of the mutation but is an integral part of T4 lysozyme catalysis in solution, as suggested recently [Zhang, X.J., Wozniak, J.A., & Matthews, B.W. (1995) J. Mol. Biol. 250, 527-552]. The strategy employed here, based on site-directed spin labeling, should be generally applicable to the study of protein conformation and conformational changes in solution.

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  • The model learned evolutionary conservation patterns without being trained on explicit alignment information.

    “This indicates that the model has captured evolutionary conservation patterns without training on explicit alignment information such as with Potts models51, as implemented in direct coupling analysis7,52–55.”

    From Large language models generate functional protein sequences across diverse families (2023) · cites this paper as [51]

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Authors
Mchaourab, H. S., Oh, K. J., Fang, C. J., & Hubbell, W. L.
Affiliations
University of California, Los Angeles (US)
ORCID
Venue
Biochemistry
Publisher
American Chemical Society (ACS)
Published
1997-01-01
Volume
36
Issue
2
Pages
307-316
ISSN
  • 0006-2960 (ISSN-L)
  • 1520-4995
DOI
10.1021/bi962114m
OpenAlex
W2008954354
Cited by
198
References
11
Citations by year
2025: 3 · 2024: 1 · 2023: 9 · 2022: 8 · 2021: 4 · 2020: 5 · 2019: 5 · 2018: 1 · 2017: 6 · 2016: 3 · 2015: 12 · 2014: 11 · 2013: 9 · 2012: 11
FWCI
3.67
Type
journal article
Language
en
Open access
closed
Locations
  • Biochemistry (publishedVersion)
  • PubMed (publishedVersion)
Funders
National Eye Institute (EY 05216)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Electron Spin Resonance Studies
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords
T4 lysozyme, hinge-bending motion, site-directed spin labeling, protein conformation in solution, domain motion
MeSH terms
Electron Spin Resonance Spectroscopy, Models, Structural, Muramidase, Protein Conformation, Recombinant Proteins, Solutions, Spin Labels, Mutagenesis, Site-Directed, Bacteriophage T4, Point Mutation, Protein Structure, Secondary, Crystallography, X-Ray

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