Perspective: Path Sampling Methods Applied to Enzymatic Catalysis

SD Schwartz - Journal of chemical theory and computation, 2022 - ACS Publications
This Perspective reviews the use of Transition Path Sampling methods to study
enzymatically catalyzed chemical reactions. First applied by our group to an enzymatic …

Substrate Turnover Dynamics Guide Ketol-Acid Reductoisomerase Redesign for Increased Specific Activity

E Karvelis, C Swanson, B Tidor - ACS catalysis, 2024 - ACS Publications
The task of adapting enzymes for specific applications is often hampered by our incomplete
ability to tune and tailor catalytic functions, particularly when seeking increased activity …

Connecting conformational motions to rapid dynamics in human purine nucleoside phosphorylase

CF Frost, SG Balasubramani, D Antoniou… - The Journal of …, 2022 - ACS Publications
The influence of protein motions on enzyme catalysis remains a topic of active discussion.
Protein motions occur across a variety of time scales, from vibrational fluctuations in …

The Evolution of the Acylation Mechanism in β-Lactamase and Rapid Protein Dynamics

CF Frost, D Antoniou, SD Schwartz - ACS catalysis, 2024 - ACS Publications
β-Lactamases are a class of well-studied enzymes that are known to have existed since
billions of years ago, starting as a defense mechanism to stave off competitors and are now …

Myosin-Catalyzed ATP Hydrolysis in the Presence of Disease-Causing Mutations: Mavacamten as a Way to Repair Mechanism

A Chakraborti, JC Tardiff… - The Journal of Physical …, 2024 - ACS Publications
Hypertrophic cardiomyopathy is one of the most common forms of genetic cardiomyopathy.
Mavacamten is a first-in-class myosin modulator that was identified via activity screening on …

Transition Path Sampling Study of Engineered Enzymes That Catalyze the Morita–Baylis–Hillman Reaction: Why Is Enzyme Design so Difficult?

SG Balasubramani, K Korchagina… - Journal of Chemical …, 2024 - ACS Publications
It is hoped that artificial enzymes designed in laboratories can be efficient alternatives to
chemical catalysts that have been used to synthesize organic molecules. However, the …

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

D Antoniou, I Zoi, SD Schwartz - Methods in enzymology, 2023 - Elsevier
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 …

A Tale of Two Myofilaments: Molecular Insights into Cardiac Muscle Function in Health and Disease

A Chakraborti - 2024 - repository.arizona.edu
Cardiac muscle function is critical for the heart to function properly but the complex
mechanism behind it is still not well understood, especially at the molecular level …