Promoting Vibrations and the Function of Enzymes. Emerging Theoretical and Experimental Convergence

Vern L. Schramm, Steven D. Schwartz

Research output: Contribution to journalReview article

7 Citations (Scopus)

Abstract

A complete understanding of enzyme catalysis requires knowledge of both transition state features and the detailed motions of atoms that cause reactant molecules to form and traverse the transition state. The seeming intractability of the problem arises from the femtosecond lifetime of chemical transition states, preventing most experimental access. Computational chemistry is admirably suited to short time scale analysis but can be misled by inappropriate starting points or by biased assumptions. Kinetic isotope effects provide an experimental approach to transition state structure and a method for obtaining transition state analogues but, alone, do not inform how that transition state is reached. Enzyme structures with transition state analogues provide computational starting points near the transition state geometry. These well-conditioned starting points, combined with the unbiased computational method of transition path sampling, provide realistic atomistic motions involved in transition state formation and passage. In many, but not all, enzymatic systems, femtosecond local protein motions near the catalytic site are linked to transition state formation. These motions are not inherently revealed by most approaches of transition state theory, because transition state theory replaces dynamics with the statistics of the transition state. Experimental and theoretical convergence of the link between local catalytic site vibrational modes and catalysis comes from heavy atom ("Born-Oppenheimer") enzymes. Fully labeled and catalytic site local heavy atom labels perturb the probability of finding enzymatic transition states in ways that can be analyzed and predicted by transition path sampling. Recent applications of these experimental and computational approaches reveal how subpicosecond local catalytic site protein modes play important roles in creating the transition state.

Original languageEnglish (US)
Pages (from-to)3299-3308
Number of pages10
JournalBiochemistry
Volume57
Issue number24
DOIs
StatePublished - Jun 19 2018

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Vibration
Catalytic Domain
Atoms
Catalysis
Enzymes
Computational chemistry
Sampling
Computational methods
Isotopes
Labels
Proteins
Statistics
Molecules
Kinetics
Geometry

ASJC Scopus subject areas

  • Biochemistry

Cite this

Promoting Vibrations and the Function of Enzymes. Emerging Theoretical and Experimental Convergence. / Schramm, Vern L.; Schwartz, Steven D.

In: Biochemistry, Vol. 57, No. 24, 19.06.2018, p. 3299-3308.

Research output: Contribution to journalReview article

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