@article{ajmera2025metalloenzyme,title={Designing an Artificial Metalloenzyme for Re(I)-Catalyzed CO2 Photoreduction},author={Ajmera, Pujan and Farley, Liam and Minnetian, Natalie and King, Ryan and Jayasekara, Hiran and Chaturvedi, Shobhit S. and Yang, Jenny and Alexandrova, Anastassia N. and Rovis, Tomislav},journal={ChemRxiv (Preprint)},year={2025},doi={10.26434/chemrxiv-2025-mhw1f/v2},}
Distinct Electric Fields Enable Common Catalytic Function in Structurally Diverse Enzymes
Shobhit S. Chaturvedi, Anubhav Goswami, Jiayi Qian, and 3 more authors
@article{chaturvedi2025distinct,title={Distinct Electric Fields Enable Common Catalytic Function in Structurally Diverse Enzymes},author={Chaturvedi, Shobhit S. and Goswami, Anubhav and Qian, Jiayi and Petersen, Ashley and Ajmera, Pujan and Alexandrova, Anastassia N.},journal={Journal of the American Chemical Society},volume={147},number={35},pages={32225--32237},year={2025},doi={10.1021/jacs.5c11931},}
PyCPET – Computing Heterogeneous 3D Protein Electric Fields and Their Dynamics
Pujan Ajmera, Santiago Vargas, Shobhit S. Chaturvedi, and 2 more authors
@article{ajmera2025pycpet,title={PyCPET -- Computing Heterogeneous 3D Protein Electric Fields and Their Dynamics},author={Ajmera, Pujan and Vargas, Santiago and Chaturvedi, Shobhit S. and Hennefarth, Matthew and Alexandrova, Anastassia N.},journal={Journal of Chemical Theory and Computation},volume={21},number={8},pages={4299--4308},year={2025},doi={10.1021/acs.jctc.5c00138},}
Methods for Theoretical Treatment of Local Fields in Proteins and Enzymes
@article{eberhart2025chemrev,title={Methods for Theoretical Treatment of Local Fields in Proteins and Enzymes},author={Eberhart, Mark E. and Alexandrova, Anastassia N. and Ajmera, Pujan and B{\'\i}m, Daniel and Chaturvedi, Shobhit S. and Vargas, Santiago and Wilson, Timothy R.},journal={Chemical Reviews},volume={125},number={7},pages={3772--3813},year={2025},doi={10.1021/acs.chemrev.4c00471},}
2024
Machine-Learning Prediction of Protein Function from the Portrait of Its Intramolecular Electric Field
@article{vargas2024ml,title={Machine-Learning Prediction of Protein Function from the Portrait of Its Intramolecular Electric Field},author={Vargas, Santiago and Chaturvedi, Shobhit S. and Alexandrova, Anastassia N.},journal={Journal of the American Chemical Society},volume={146},number={41},pages={28375--28383},year={2024},doi={10.1021/jacs.4c09549},}
Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field
Shobhit S. Chaturvedi, Santiago Vargas, Pujan Ajmera, and 1 more author
@article{chaturvedi2024protoglobin,title={Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field},author={Chaturvedi, Shobhit S. and Vargas, Santiago and Ajmera, Pujan and Alexandrova, Anastassia N.},journal={Journal of the American Chemical Society},volume={146},number={24},pages={16670--16680},year={2024},doi={10.1021/jacs.4c03914},}
The Unique Role of the Second Coordination Sphere to Unlock and Control Catalysis in Nonheme Fe(II)/2-Oxoglutarate Histone Demethylase KDM2A
Midhun George Thomas, Simahudeen Bathir Jaber Sathik Rifayee, Shobhit S. Chaturvedi, and 5 more authors
@article{thomas2024kdm2a,title={The Unique Role of the Second Coordination Sphere to Unlock and Control Catalysis in Nonheme Fe(II)/2-Oxoglutarate Histone Demethylase KDM2A},author={Thomas, Midhun George and Jaber Sathik Rifayee, Simahudeen Bathir and Chaturvedi, Shobhit S. and Gorantla, Koteswara Rao and White, Walter and Wildey, Jon and Schofield, Christopher J. and Christov, Christo Z.},journal={Inorganic Chemistry},volume={63},number={23},pages={10737--10755},year={2024},doi={10.1021/acs.inorgchem.4c01365},}
2023
Revealing the Catalytic Strategy of FTO
Ann Varghese, Sodiq O. Waheed, Shobhit S. Chaturvedi, and 7 more authors
@article{varghese2023fto,title={Revealing the Catalytic Strategy of FTO},author={Varghese, Ann and Waheed, Sodiq O. and Chaturvedi, Shobhit S. and DiCastri, Isabella and LaRouche, Ciara and Kaski, Brendan and Lehnert, Nicolai and Li, Deyu and Christov, Christo Z. and Karabencheva-Christova, Tatyana G.},journal={Chem Catalysis},volume={3},number={9},pages={100732},year={2023},doi={10.1016/j.checat.2023.100732},}
From Random to Rational: Improving Enzyme Design Through Electric Fields, Second Coordination Sphere Interactions, and Conformational Dynamics
@article{chaturvedi2023chemsci,title={From Random to Rational: Improving Enzyme Design Through Electric Fields, Second Coordination Sphere Interactions, and Conformational Dynamics},author={Chaturvedi, Shobhit S. and B{\'\i}m, Daniel and Christov, Christo Z. and Alexandrova, Anastassia N.},journal={Chemical Science},volume={14},number={40},pages={10997--11011},year={2023},doi={10.1039/D3SC02982D},}
Catalysis by KDM6 Histone Demethylases – A Synergy between the Non-Heme Iron(II) Center, Second Coordination Sphere, and Long-Range Interactions
Simahudeen Bathir Jaber Sathik Rifayee, Shobhit S. Chaturvedi, Cait Warner, and 5 more authors
@article{rifayee2023kdm6,title={Catalysis by KDM6 Histone Demethylases -- A Synergy between the Non-Heme Iron(II) Center, Second Coordination Sphere, and Long-Range Interactions},author={Rifayee, Simahudeen Bathir Jaber Sathik and Chaturvedi, Shobhit S. and Warner, Cait and Wildey, Jon and White, Walter and Thompson, Martin and Schofield, Christopher J. and Christov, Christo Z.},journal={Chemistry -- A European Journal},volume={29},number={51},pages={e202301305},year={2023},doi={10.1002/chem.202301305},}
Can an External Electric Field Switch Between Ethylene Formation and L-Arginine Hydroxylation in the Ethylene Forming Enzyme?
Shobhit S. Chaturvedi, Simahudeen Bathir Jaber Sathik Rifayee, Rajeev Ramanan, and 4 more authors
@article{chaturvedi2023pccp,title={Can an External Electric Field Switch Between Ethylene Formation and L-Arginine Hydroxylation in the Ethylene Forming Enzyme?},author={Chaturvedi, Shobhit S. and Jaber Sathik Rifayee, Simahudeen Bathir and Ramanan, Rajeev and Rankin, Joel A. and Hu, Jian and Hausinger, Robert P. and Christov, Christo Z.},journal={Physical Chemistry Chemical Physics},volume={25},number={19},pages={13772--13783},year={2023},doi={10.1039/D3CP01899G},}
Dioxygen Binding Is Controlled by the Protein Environment in Non-heme Fe(II) and 2-Oxoglutarate Oxygenases: A Study on Histone Demethylase PHF8 and an Ethylene-Forming Enzyme
Shobhit S. Chaturvedi, Midhun George Thomas, Simahudeen Bathir Jaber Sathik Rifayee, and 8 more authors
@article{chaturvedi2023chemeurj,title={Dioxygen Binding Is Controlled by the Protein Environment in Non-heme Fe(II) and 2-Oxoglutarate Oxygenases: A Study on Histone Demethylase PHF8 and an Ethylene-Forming Enzyme},author={Chaturvedi, Shobhit S. and Thomas, Midhun George and Rifayee, Simahudeen Bathir Jaber Sathik and White, Walter and Wildey, Jon and Warner, Cait and Schofield, Christopher J. and Hu, Jian and Hausinger, Robert P. and Karabencheva-Christova, Tatyana G. and Christov, Christo Z.},journal={Chemistry -- A European Journal},volume={29},number={24},pages={e202300138},year={2023},doi={10.1002/chem.202300138},}
2022
Can Second Coordination Sphere and Long-Range Interactions Modulate Hydrogen Atom Transfer in a Non-Heme Fe(II)-Dependent Histone Demethylase?
Shobhit S. Chaturvedi, Simahudeen Bathir Jaber Sathik Rifayee, Sodiq O. Waheed, and 5 more authors
@article{chaturvedi2022jacsau,title={Can Second Coordination Sphere and Long-Range Interactions Modulate Hydrogen Atom Transfer in a Non-Heme Fe(II)-Dependent Histone Demethylase?},author={Chaturvedi, Shobhit S. and Jaber Sathik Rifayee, Simahudeen Bathir and Waheed, Sodiq O. and Wildey, Jon and Warner, Cait and Schofield, Christopher J. and Karabencheva-Christova, Tatyana G. and Christov, Christo Z.},journal={JACS Au},volume={2},number={9},pages={2169--2186},year={2022},doi={10.1021/jacsau.2c00345},}
How Human TET2 Enzyme Catalyzes the Oxidation of Unnatural Cytosine Modifications in Double-Stranded DNA
Sodiq O. Waheed, Ann Varghese, Shobhit S. Chaturvedi, and 2 more authors
@article{waheed2022tet2,title={How Human TET2 Enzyme Catalyzes the Oxidation of Unnatural Cytosine Modifications in Double-Stranded DNA},author={Waheed, Sodiq O. and Varghese, Ann and Chaturvedi, Shobhit S. and Karabencheva-Christova, Tatyana G. and Christov, Christo Z.},journal={ACS Catalysis},volume={12},number={9},pages={5327--5344},year={2022},doi={10.1021/acscatal.2c00024},}
Effects of the Nature of Metal Ion, Protein and Substrate on the Catalytic Center in Matrix Metalloproteinase-1: Insights from Multilevel MD, QM/MM and QM Studies
Ann Varghese, Shobhit S. Chaturvedi, Bella DiCastri, and 3 more authors
@article{varghese2022mmp1,title={Effects of the Nature of Metal Ion, Protein and Substrate on the Catalytic Center in Matrix Metalloproteinase-1: Insights from Multilevel MD, QM/MM and QM Studies},author={Varghese, Ann and Chaturvedi, Shobhit S. and DiCastri, Bella and Mehler, Emerald and Fields, Gregg B. and Karabencheva-Christova, Tatyana G.},journal={ChemPhysChem},volume={23},number={4},pages={e202100680},year={2022},doi={10.1002/cphc.202100680},}
Multilevel Computational Investigation into the Dynamics and Reaction Mechanisms of Non-Heme Iron and 2-Oxoglutarate Dependent Enzymes
@phdthesis{chaturvedi2022thesis,title={Multilevel Computational Investigation into the Dynamics and Reaction Mechanisms of Non-Heme Iron and 2-Oxoglutarate Dependent Enzymes},author={Chaturvedi, Shobhit Sanjeev},school={Michigan Technological University},year={2022},doi={10.37099/mtu.dc.etdr/1519},}
2021
A Synergy Between the Catalytic and Structural Zn(II) Ions and the Enzyme and Substrate Dynamics Underlies the Structure-Function Relationships of Matrix Metalloproteinase Collagenolysis
Ann Varghese, Shobhit S. Chaturvedi, Gregg B. Fields, and 1 more author
@article{varghese2021jbic,title={A Synergy Between the Catalytic and Structural Zn(II) Ions and the Enzyme and Substrate Dynamics Underlies the Structure-Function Relationships of Matrix Metalloproteinase Collagenolysis},author={Varghese, Ann and Chaturvedi, Shobhit S. and Fields, Gregg B. and Karabencheva-Christova, Tatyana G.},journal={Journal of Biological Inorganic Chemistry},volume={26},number={5},pages={583--597},year={2021},}
Catalytic Mechanism of Human Ten-Eleven Translocation-2 (TET2) Enzyme: Effects of Conformational Changes, Electric Field, and Mutations
@article{waheed2021tet2mech,title={Catalytic Mechanism of Human Ten-Eleven Translocation-2 (TET2) Enzyme: Effects of Conformational Changes, Electric Field, and Mutations},author={Waheed, Sodiq O. and Chaturvedi, Shobhit S. and Karabencheva-Christova, Tatyana G. and Christov, Christo Z.},journal={ACS Catalysis},volume={11},number={7},pages={3877--3890},year={2021},doi={10.1021/acscatal.0c05034},}
Atomic and Electronic Structure Determinants Distinguish Between Ethylene Formation and L-Arginine Hydroxylation Reaction Mechanisms in the Ethylene-Forming Enzyme
Shobhit S. Chaturvedi, Rajeev Ramanan, Jian Hu, and 2 more authors
@article{chaturvedi2021efe,title={Atomic and Electronic Structure Determinants Distinguish Between Ethylene Formation and L-Arginine Hydroxylation Reaction Mechanisms in the Ethylene-Forming Enzyme},author={Chaturvedi, Shobhit S. and Ramanan, Rajeev and Hu, Jian and Hausinger, Robert P. and Christov, Christo Z.},journal={ACS Catalysis},volume={11},number={3},pages={1578--1592},year={2021},doi={10.1021/acscatal.0c03349},}
2020
Role of Structural Dynamics in Selectivity and Mechanism of Non-heme Fe(II) and 2-Oxoglutarate-Dependent Oxygenases Involved in DNA Repair
Sodiq O. Waheed, Rajeev Ramanan, Shobhit S. Chaturvedi, and 4 more authors
@article{waheed2020acscentsci,title={Role of Structural Dynamics in Selectivity and Mechanism of Non-heme Fe(II) and 2-Oxoglutarate-Dependent Oxygenases Involved in DNA Repair},author={Waheed, Sodiq O. and Ramanan, Rajeev and Chaturvedi, Shobhit S. and Lehnert, Nicolai and Schofield, Christopher J. and Christov, Christo Z. and Karabencheva-Christova, Tatyana G.},journal={ACS Central Science},volume={6},number={5},pages={795--814},year={2020},doi={10.1021/acscentsci.0c00312},}
Catalysis by the Non-Heme Iron(II) Histone Demethylase PHF8 Involves Iron Center Rearrangement and Conformational Modulation of Substrate Orientation
Shobhit S. Chaturvedi, Rajeev Ramanan, Nicolai Lehnert, and 3 more authors
@article{chaturvedi2020phf8,title={Catalysis by the Non-Heme Iron(II) Histone Demethylase PHF8 Involves Iron Center Rearrangement and Conformational Modulation of Substrate Orientation},author={Chaturvedi, Shobhit S. and Ramanan, Rajeev and Lehnert, Nicolai and Schofield, Christopher J. and Karabencheva-Christova, Tatyana G. and Christov, Christo Z.},journal={ACS Catalysis},volume={10},number={2},pages={1195--1209},year={2020},doi={10.1021/acscatal.9b04907},}
Catalysis by the JmjC Histone Demethylase KDM4A Integrates Substrate Dynamics, Correlated Motions, and Molecular Orbital Control
Rajeev Ramanan, Shobhit S. Chaturvedi, Nicolai Lehnert, and 3 more authors
@article{ramanan2020kdm4a,title={Catalysis by the JmjC Histone Demethylase KDM4A Integrates Substrate Dynamics, Correlated Motions, and Molecular Orbital Control},author={Ramanan, Rajeev and Chaturvedi, Shobhit S. and Lehnert, Nicolai and Schofield, Christopher J. and Karabencheva-Christova, Tatyana G. and Christov, Christo Z.},journal={Chemical Science},volume={11},number={36},pages={9950--9961},year={2020},doi={10.1039/D0SC03713C},}
2019
Conformational Dynamics Underlies Different Functions of Human KDM7 Histone Demethylases
Shobhit S. Chaturvedi, Rajeev Ramanan, Sodiq O. Waheed, and 6 more authors
@article{chaturvedi2019kdm7,title={Conformational Dynamics Underlies Different Functions of Human KDM7 Histone Demethylases},author={Chaturvedi, Shobhit S. and Ramanan, Rajeev and Waheed, Sodiq O. and Ainsley, Jon and Evison, Martin and Ames, Jennifer M. and Schofield, Christopher J. and Karabencheva-Christova, Tatyana G. and Christov, Christo Z.},journal={Chemistry -- A European Journal},volume={25},number={21},pages={5422--5426},year={2019},doi={10.1002/chem.201900492},}
Structure-Function Relationships in KDM7 Histone Demethylases
Shobhit S. Chaturvedi, Rajeev Ramanan, Sodiq O. Waheed, and 2 more authors
@inbook{chaturvedi2019apcsb,title={Structure-Function Relationships in KDM7 Histone Demethylases},author={Chaturvedi, Shobhit S. and Ramanan, Rajeev and Waheed, Sodiq O. and Karabencheva-Christova, Tatyana G. and Christov, Christo Z.},booktitle={Advances in Protein Chemistry and Structural Biology},volume={117},pages={113--125},year={2019},publisher={Elsevier},doi={10.1016/bs.apcsb.2019.08.005},}
Conformational Flexibility Influences Structure-Function Relationships in Nucleic Acid N-Methyl Demethylases
Sodiq O. Waheed, Rajeev Ramanan, Shobhit S. Chaturvedi, and 6 more authors
@article{waheed2019obc,title={Conformational Flexibility Influences Structure-Function Relationships in Nucleic Acid N-Methyl Demethylases},author={Waheed, Sodiq O. and Ramanan, Rajeev and Chaturvedi, Shobhit S. and Ainsley, Jon and Evison, Martin and Ames, Jennifer M. and Schofield, Christopher J. and Christov, Christo Z. and Karabencheva-Christova, Tatyana G.},journal={Organic \& Biomolecular Chemistry},volume={17},number={8},pages={2223--2231},year={2019},doi={10.1039/C9OB00162J},}
2018
Integrating Molecular Probes and Molecular Dynamics to Reveal Binding Modes of GLUT5 Activatory and Inhibitory Ligands
@article{ainsley2018glut5,title={Integrating Molecular Probes and Molecular Dynamics to Reveal Binding Modes of GLUT5 Activatory and Inhibitory Ligands},author={Ainsley, Jon and Chaturvedi, Shobhit S. and Karabencheva-Christova, Tatyana G. and Tanasova, Marina and Christov, Christo Z.},journal={Chemical Communications},volume={54},number={71},pages={9917--9920},year={2018},doi={10.1039/C8CC04843F},}