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Mahmoud Moradi

Mahmoud Moradi

Assistant Professor

J. William Fulbright College of Arts & Sciences

(CHBC)-Chemistry & Biochemistry

Phone: 479-575-6459

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Physical Chemistry and Biochemistry

Office: CHEM 129; Lab: CHEM 104

Research in Moradi Lab (Biomolecular Simulations Group) is centered around two inter-related questions: (i) how do proteins function by changing their conformation and undergoing concerted motions? and (ii) how can we simulate these functionally important conformational changes at an atomic level? We develop and employ Molecular Dynamics (MD) based enhanced sampling techniques to tackle both problems. Answering these questions would shed light on the structure-function relationships in proteins, and could improve our understanding of disease at a molecular level. We attempt to narrow the gap between the state-of-the-art computational methodologies and biologically/biomedically relevant applications. We are particularly interested in the study of large-scale conformational changes of proteins such as those involved in membrane transport. A novel combination of nonequilibrium and equilibrium MD based techniques are employed to reconstruct the slow biomolecular processes such as inward- to outward-facing structural transition of membrane transporters at an atomic level.

CHEM 1123 University Chemistry II, Summer 2018, Spring 2019, Summer 2019

CHEM 3453 Elements of Physical Chemistry, Fall 2018, Fall 2019

CHEM 3504 Physical Chemistry I, Fall 2017

CHEM 5453 Quantum Chemistry I, Fall 2016

CHEM 5473 Chemical Kinetics, Spring 2016, 2017

CHEM 5573 Statistical Thermodynamics, Spring 2018

Ph.D., North Carolina State University (Physics)

M.Sc., Sharif University of Technology, Iran (Physics)

B.Sc., Sharif University of Technology, Iran (Physics)

  • T Harkey, V Govind Kumar, J Hettige, S H Tabari, K Immadisetty, and M Moradi, The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2. Sci. Rep., 9:14451, 2019.
  • R Al Faouri, E Krueger, V Kumar, D Fologea, D Straub, H Alismail, Q Alfaori, A Kight, J Ray, R Henry, M Moradi, and G Salamo, An Effective Electric Dipole Model for Voltage-induced Gating Mechanism of Lysenin. Sci. Rep., 9:11440, 2019.
  • K Immadisetty, J Hettige, and M Moradi, Lipid-Dependent Alternating Access Mechanism of a Bacterial Multidrug ABC Exporter. ACS Cent. Sci., 5:43-56, 2019.
  • M Kiaei, M Balasubramaniam, V Govind Kumar, R J Shmookler Reis, M Moradi, and K I Varughese, ALS-causing mutations in profilin-1 alter its conformational dynamics: A computational approach to explain propensity for aggregation. Sci. Rep., 2018 8:13102, 2018.
  • S Burgin, J Oramous, M Kaminski, L Stocker, and M Moradi, High School Biology Students Use of VMD as an Authentic Tool for Learning about Modeling as a Professional Scientific PracticeBiochem. Mol. Biol. Educ, 46:230-236, 2018.

  • A Singharoy, C Chipot, M Moradi, and K Schulten, Chemomechanical coupling in hexameric protein–protein interfaces harness energy within V–type ATPases. J. Am. Chem. Soc., 139:293-310, 2017.

  • K Immadisetty, J Hettige, and M Moradi, What Can and Cannot Be Learned from Molecular Dynamics Simulations of Bacterial Proton-Coupled Oligopeptide Transporter GkPOT?  J. Phys. Chem. B, 121:3644-3656, 2017.
  • A Fakharzadeh and M Moradi, Effective Riemannian Diffusion Model for Conformational Dynamics of Biomolecular Systems. J. Phys. Chem. Lett., 7:4980-4987, 2016.
  • M Moradi, G Enkavi, and E Tajkhorshid, Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate:phosphate antiporter. Nat. Commun., 6:8393, 2015.
  • J Li, P-C Wen, M Moradi, and E Tajkhorshid Computational Characterization of Structural Dynamics Underlying Function in Active Membrane Transporters. Curr. Opin. Struct. Biol., 31:96, 2015.
  • M Moradi, V Babin, C Roland, and C Sagui, The Adaptively Biased Molecular Dynamics method revisited: New capabilities and an application. J. Phys. Conf. Ser. 640:012020, 2015.
  • M Moradi, C Sagui, and C Roland, Calculating transition and reaction rates with nonequilibrium work measurements. J. Phys. Conf. Ser. 640:012014, 2015.
  • M Moradi, C Sagui, and C Roland, Investigating rare events with nonequilibrium work measurements: I. nonequilibrium transition path probabilities. J. Chem. Phys., 140:034114, 2014.
  • M Moradi, C Sagui, and C Roland, Investigating rare events with nonequilibrium work measurements: II. transition and reaction rates. J. Chem. Phys., 140:034115, 2014.
  • R E Hulse, J Sachleben, P-C Wen, M Moradi, E Tajkhorshid, E Perozo, Conformational dynamics at the inner gate of KcsA during activation. Biochemistry (Rapid Report), 53:2557, 2014.
  • M Moradi, and E Tajkhorshid, Computational recipe for efficient description of large-scale conformational changes in biomolecular systems. J. Chem. Theory Comput., 10:2866, 2014.
  • G Enkavi, J Li, P-C Wen, S Thangapandian, M Moradi, T Jiang, W Han, and E Tajkhorshid, A microscopic view of the mechanisms of active transport across the cellular membrane. Annual Reviews in Computational Chemistry, 10:77, 2014.
  • M Moradi, and E Tajkhorshid, Mechanistic picture for conformational transition of a membrane transporter at atomic resolution. Proc. Natl. Aca. Sci. USA, 110:18916, 2013. 
  • M Moradi, and E Tajkhorshid, Driven metadynamics: Reconstructing equilibrium free energies from driven adaptive-bias simulations. J. Phys. Chem. Lett., 4:1882, 2013.
  • M Moradi, V Babin, C Roland, and C Sagui, Reaction path ensemble of B-Z-DNA transition: A Comprehensive atomistic study. Nucleic Acids Res., 41:33, 2013.
  • M Moradi, V Babin, C Sagui, and C Roland, Recipes for free energy calculations in biomolecular systems. In Biomolecular simulations: methods and protocols. Humana Press (Springer),Methods Mol. Biol., 924:313-37, 2013.
  • M Moradi, V Babin, C Roland, and C Sagui, Free energies, structural characteristics, and transition mechanisms of proline-rich peptides. In Proline: Biosynthesis, Regulation and Health Benefits, Nova Publishers, ISBN: 978-1-62257-745-3, 2013.
  • M Kalani, A Moradi, M Moradi, E Tajkhorshid, Characterizing a histidine switch controlling pH-dependent conformational changes of the influenza virus hemagglutinin. Biophys. J., 105:993, 2013.
  • M Moradi, V Babin, C Roland, and C Sagui, Are long-range structural correlations behind the aggregation phenomena of polyglutamine diseases? PLoS Comput. Biol., 8:e1002501, 2012. 
  • M Moradi, V Babin, C Sagui, and C Roland, A statistical analysis of the PPII propensity of amino acid guests in proline-rich peptides. Biophys. J., 100:1083, 2011.
  • M Moradi, V Babin, C Sagui, and C Roland, PPII propensity of multiple-guest amino acids in a proline-rich environment. J. Phys. Chem. B, 115:8645, 2011. 
  • M Moradi, C Sagui, and C Roland, Calculating relative transition rates with driven nonequilibrium simulations. Chem. Phys. Lett., 518:109, 2011.
  • M Moradi, V Babin, C Roland, and C Sagui, A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers. J. Chem. Phys., 133:125104, 2010.
  • M Moradi, J-G Lee, V Babin, C Roland, and C Sagui, Free energy and structure of polyproline peptides: an ab initio and classical molecular dynamics investigation. Int. J. Quant. Chem., 110:2865, 2010.
  • M Moradi, V Babin, C Roland, T Darden, and C Sagui, Conformations and free energy landscapes of polyproline peptides. Proc. Natl. Aca. Sci. USA, 106:20746, 2009.
  • V Babin, V Karpusenka, M Moradi, C Roland, and C Sagui, Adaptively biased molecualr dynamics: An umbrella sampling method with a time-dependent potential. Int. J. Quant. Chem., 109:3666, 2009.

Education/Training:

Postdoctoral Associate, 2011-2015, Beckman Institute and Department of Biochemistry, University of Illinois at Urbana-Champaign (UIUC)

Ph.D., Physics, 2011, NC State University (NCSU), Raleigh

M.Sc., Physics, 2005, Sharif University of Technology (SUT), Tehran

B.Sc., Physics, 2002, Sharif University of Technology (SUT), Tehran

Editorial Service:

Editorial Board Member, Scientific Reports (Nature Publishing Group), 2014-present

Former Mentors:

Emad Tajkhorshid (UIUC), Christopher Roland (NCSU), Celeste Sagui (NCSU), and Shahin Rouhani (SUT)