Publications by authors named "Dimitri Antoniou"

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The Shaping of Enzymatic Free Energy Barriers through the Creation of Rate-Promoting Vibrations via Inter-Residue Cross-Talk on Multiple Time Scales.
Rakesh K Roy, Dimitri Antoniou, Steven D Schwartz

J Phys Chem B· October 2025

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Transition Path Sampling Based Free Energy Calculations of Evolution's Effect on Rates in β-Lactamase: The Contributions of Rapid Protein Dynamics to Rate.
Clara F Frost, Dimitri Antoniou, Steven D Schwartz

J Phys Chem B· November 2024

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The Evolution of the Acylation Mechanism in -Lactamase and Rapid Protein Dynamics.
Clara F Frost, Dimitri Antoniou, Steven D Schwartz

ACS Catal· September 2024

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Atomistic description of the relationship between protein dynamics and catalysis with transition path sampling.
Dimitri Antoniou, Ioanna Zoi, Steven D Schwartz

Methods Enzymol· May 2023

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Connecting Conformational Motions to Rapid Dynamics in Human Purine Nucleoside Phosphorylase.
Clara F Frost, Sree Ganesh Balasubramani, Dimitri Antoniou, Steven D Schwartz

J Phys Chem B· January 2023

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Method for Identifying Common Features in Reactive Trajectories of a Transition Path Sampling Ensemble.
Dimitri Antoniou, Steven D Schwartz

J Chem Theory Comput· June 2022

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Inverse heavy enzyme isotope effects in methylthioadenosine nucleosidases.
Morais Brown, Ioanna Zoi, Dimitri Antoniou, Hilda A Namanja-Magliano, Steven D Schwartz

Proc Natl Acad Sci U S A· October 2021

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Role of Protein Motions in Catalysis by Formate Dehydrogenase.
Dimitri Antoniou, Steven D Schwartz

J Phys Chem B· October 2020

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Optimization of the Turnover in Artificial Enzymes via Directed Evolution Results in the Coupling of Protein Dynamics to Chemistry.
Joseph W Schafer, Ioanna Zoi, Dimitri Antoniou, Steven D Schwartz

J Am Chem Soc· July 2019

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Inverse enzyme isotope effects in human purine nucleoside phosphorylase with heavy asparagine labels.
Rajesh K Harijan, Ioanna Zoi, Dimitri Antoniou, Steven D Schwartz, Vern L Schramm

Proc Natl Acad Sci U S A· July 2018

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Electric Fields and Fast Protein Dynamics in Enzymes.
Ioanna Zoi, Dimitri Antoniou, Steven D Schwartz

J Phys Chem Lett· December 2017

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Incorporating Fast Protein Dynamics into Enzyme Design: A Proposed Mutant Aromatic Amine Dehydrogenase.
Ioanna Zoi, Dimitri Antoniou, Steven D Schwartz

J Phys Chem B· August 2017

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Catalytic-site design for inverse heavy-enzyme isotope effects in human purine nucleoside phosphorylase.
Rajesh K Harijan, Ioanna Zoi, Dimitri Antoniou, Steven D Schwartz, Vern L Schramm

Proc Natl Acad Sci U S A· June 2017

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Modulating Enzyme Catalysis through Mutations Designed to Alter Rapid Protein Dynamics.
Ioanna Zoi, Javier Suarez, Dimitri Antoniou, Scott A Cameron, Vern L Schramm

J Am Chem Soc· March 2016

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Hydride Transfer in DHFR by Transition Path Sampling, Kinetic Isotope Effects, and Heavy Enzyme Studies.
Zhen Wang, Dimitri Antoniou, Steven D Schwartz, Vern L Schramm

Biochemistry· January 2016

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Phase Space Bottlenecks in Enzymatic Reactions.
Dimitri Antoniou, Steven D Schwartz

J Phys Chem B· January 2016

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Another Look at the Mechanisms of Hydride Transfer Enzymes with Quantum and Classical Transition Path Sampling.
Michael W Dzierlenga, Dimitri Antoniou, Steven D Schwartz

J Phys Chem Lett· April 2015

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Enzyme homologues have distinct reaction paths through their transition states.
Ioanna Zoi, Matthew W Motley, Dimitri Antoniou, Vern L Schramm, Steven D Schwartz

J Phys Chem B· March 2015

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Mass Modulation of Protein Dynamics Associated with Barrier Crossing in Purine Nucleoside Phosphorylase.
Dimitri Antoniou, Xiaoxia Ge, Vern L Schramm, Steven D Schwartz

J Phys Chem Lett· December 2012

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Barrier Crossing in Dihydrofolate Reductasedoes not involve a rate-promoting vibration.
Mariangela Dametto, Dimitri Antoniou, Steven D Schwartz

Mol Phys· May 2012

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Protein dynamics and enzymatic chemical barrier passage.
Dimitri Antoniou, Steven D Schwartz

J Phys Chem B· December 2011

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The promoting vibration in human heart lactate dehydrogenase is a preferred vibrational channel.
Ardy Davarifar, Dimitri Antoniou, Steven D Schwartz

J Phys Chem B· December 2011

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Response to Comment on "Towards identification of the reaction coordinate directly from the transition state ensemble using the kernel PCA method" by D. Antoniou and S. Schwartz, J. Phys. Chem. B. 115, 2465-2469 (2011).
Dimitri Antoniou, Steven D Schwartz

J Phys Chem B· November 2011

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Toward Identification of the reaction coordinate directly from the transition state ensemble using the kernel PCA method.
Dimitri Antoniou, Steven D Schwartz

J Phys Chem B· March 2011

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Slow conformational motions that favor sub-picosecond motions important for catalysis.
J R Exequiel T Pineda, Dimitri Antoniou, Steven D Schwartz

J Phys Chem B· December 2010

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