CHARMM at 45: Enhancements in accessibility, functionality, and speed
Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …
computational biochemistry and biophysics. Commensurate with the developments in …
Engineered control of enzyme structural dynamics and function
Enzymes undergo a range of internal motions from local, active site fluctuations to large‐
scale, global conformational changes. These motions are often important for enzyme …
scale, global conformational changes. These motions are often important for enzyme …
The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release
Dihydrofolate reductase (DHFR) catalyzes the stereospecific reduction of 7, 8-dihydrofolate
(FH2) to (6s)-5, 6, 7, 8-tetrahydrofolate (FH4) via hydride transfer from NADPH. The …
(FH2) to (6s)-5, 6, 7, 8-tetrahydrofolate (FH4) via hydride transfer from NADPH. The …
Reaction coordinates and transition states in enzymatic catalysis
K Zinovjev, I Tuñón - Wiley Interdisciplinary Reviews …, 2018 - Wiley Online Library
Enzymatic reactions are complex chemical processes taking place in complex dynamic
environments. Theoretical characterization of these reactions requires the determination of …
environments. Theoretical characterization of these reactions requires the determination of …
Substrate and transition state binding in alkaline phosphatase analyzed by computation of oxygen isotope effects
Enzymes are powerful catalysts, and a thorough understanding of the sources of their
catalytic power will facilitate many medical and industrial applications. Here we have studied …
catalytic power will facilitate many medical and industrial applications. Here we have studied …
Machine Learning Quantum Mechanical/Molecular Mechanical Potentials: Evaluating Transferability in Dihydrofolate Reductase-Catalyzed Reactions
Integrating machine learning potentials (MLPs) with quantum mechanical/molecular
mechanical (QM/MM) free energy simulations has emerged as a powerful approach for …
mechanical (QM/MM) free energy simulations has emerged as a powerful approach for …
Covalent Adduct Formation as a Strategy for Efficient CO2 Fixation in Crotonyl-CoA Carboxylases/Reductases
Increasing levels of CO2 in the atmosphere have led to a growing interest into the various
ways nature transforms this greenhouse gas into valuable organic compounds. Crotonyl …
ways nature transforms this greenhouse gas into valuable organic compounds. Crotonyl …
Hydride transfer in DHFR by transition path sampling, kinetic isotope effects, and heavy enzyme studies
Escherichia coli dihydrofolate reductase (ecDHFR) is used to study fundamental principles
of enzyme catalysis. It remains controversial whether fast protein motions are coupled to the …
of enzyme catalysis. It remains controversial whether fast protein motions are coupled to the …
The role of the Met20 loop in the hydride transfer in Escherichia coli dihydrofolate reductase
AR Mhashal, A Vardi-Kilshtain, A Kohen… - Journal of Biological …, 2017 - ASBMB
A key question concerning the catalytic cycle of Escherichia coli dihydrofolate reductase
(ecDHFR) is whether the Met 20 loop is dynamically coupled to the chemical step during …
(ecDHFR) is whether the Met 20 loop is dynamically coupled to the chemical step during …
Evolutionary Effects on Bound Substrate pKa in Dihydrofolate Reductase
AR Mhashal, Y Pshetitsky, CM Cheatum… - Journal of the …, 2018 - ACS Publications
In the present study, we address the effect of active site structure and dynamics of different
dihydrofolate reductase (DHFR) isoforms on the p K a of the bound substrate 7, 8 …
dihydrofolate reductase (DHFR) isoforms on the p K a of the bound substrate 7, 8 …