@inbook{e54a2945ec214f07baac8e20225f514c,
title = "Atomistic description of the relationship between protein dynamics and catalysis with transition path sampling",
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.",
keywords = "Catalysis, Enzyme dynamics, Protein design, Transition path sampling",
author = "Dimitri Antoniou and Ioanna Zoi and Schwartz, {Steven D.}",
note = "Funding Information: All computer simulations were performed at the University of Arizona High Performance Computing Center, on a Penguin Altus XE2242 supercomputer. This research was supported through the NIH grants R01GM127594 and R35GM145213. Publisher Copyright: {\textcopyright} 2023 Elsevier Inc.",
year = "2023",
month = jan,
doi = "10.1016/bs.mie.2023.03.005",
language = "English (US)",
isbn = "9780443152764",
series = "Methods in Enzymology",
publisher = "Academic Press Inc.",
pages = "319--340",
editor = "Richard, {John P.} and Moran, {Graham R.}",
booktitle = "New Experimental Probes for Enzyme Specificity and Mechanism",
}