Atomistic description of the relationship between protein dynamics and catalysis with transition path sampling.

Dimitri Antoniou, Ioanna Zoi, Steven D Schwartz

Abstract readReview

In one paragraph

Review in Methods in enzymology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Dimitri AntoniouDepartment of Biochemistry, University of Arizona, Tucson, AZ, United States.

Ioanna ZoiDepartment of Biochemistry, University of Arizona, Tucson, AZ, United States.

Steven D SchwartzDepartment of Biochemistry, University of Arizona, Tucson, AZ, United States. Electronic address: sschwartz@email.arizona.edu.

Funding

Protein dynamics from femtoseconds to milliseconds as crafted by natural and laboratory evolution: towards enzyme designR35GM145213 · NIGMS · UNIVERSITY OF ARIZONA · PI STEVEN D SCHWARTZ · 2022 to 2026

$2.1M

Rapid protein dynamics and catalysis: modulation by laboratory evolution, designed mutation, and protein control of electric field environmentR01GM127594 · NIGMS · UNIVERSITY OF ARIZONA · PI SCHWARTZ, STEVEN D · 2019 to 2022

$1.4M

NIGMS NIH HHS R01 GM127594NIGMS NIH HHS R35 GM145213

6 · The paper itself

Abstract

Despite initial resistance, it has been increasingly accepted that protein dynamics plays a role in enzymatic catalysis. There have been two lines of research. Some works study slow conformational motions that are not coupled to the reaction coordinate, but guide the system towards catalytically competent conformations. Understanding at the atomistic level how this is accomplished has remained elusive except for a few systems. In this review we focus on fast sub-picosecond motions that are coupled to the reaction coordinate. The use of Transition Path Sampling has allowed us an atomistic description of how these rate-promoting vibrational motions are incorporated in the reaction mechanism. We will also show how we used insights from rate-promoting motions in protein design.

Indexed as

ProteinsVibrationCatalysisMolecular ConformationMotionProtein ConformationProteinsCatalysisEnzyme dynamicsProtein designTransition path sampling

Identifiers

PMID37245906

DOI10.1016/bs.mie.2023.03.005

PMCPMC10228753

What OpenQuestion holds

Textmetadata

LicenceTDM

Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.