Publications

Group highlights

(For a full list see below or go to Google Scholar.)

Full List

2025

• E Khodadadi, E Khodadadi,P Chaturvedi and M Moradi, Molecular Dynamics Simulations of Liposomes: Structure, Dynamics, and Applications Membranes, 15 (9), 259, 2025
• A Fakharzadeh, M Moradi, C Sagui and C Roland, Comparative Study of the Bending Free Energies of C- and G‑Based DNA: A‑, B‑, and Z‑DNA and Associated Mismatched Trinucleotide Repeats, Journal of Chemical Information and Modeling, 65 (5672–5689), 2025
• S Thangapandian, A Fakharzadeh, M Moradi and E Tajkhorshid, Conformational free energy landscape of a glutamate transporter and microscopic details of its transport mechanism. Proceedings of the National Academy of Sciences, 122 (10), 2025
• E Khodadadi, E Khodadadi,P Chaturvedi and M Moradi, Comprehensive Insights into the Cholesterol-Mediated Modulation of Membrane Function through Molecular Dynamics Simulations Membranes, 15 (6), 173, 2025

Preprint

• R Dastvan, B Abd Emami, A Shubbar, H Woods, and M Moradi, Structural Dynamics of Sphingosine Kinase 1 Regulation and Inhibition Research Square
• E Khodadadi, E Khodadadi,P Chaturvedi and M Moradi, Molecular Insights into Cholesterol Concentration Effects on Planar and Curved Lipid Bilayers for Liposomal Drug Delivery bioRxiv
• E Khodadadi, S Badiee, E Khodadadi and M Moradi, Lipid-Mediated Modulation of mGluR2 Embedded in Micelle and Bilayer Environments: Insights from Molecular Dynamics bioRxiv
• S Badiee, J Hettige and M Moradi, Lipid-dependent conformational dynamics of bacterial ATP-binding cassette transporter Sav1866 bioRxiv
• U Isu, S Badiee, A Polasa, S H Tabari, M Derakhshani-Molayousefi and M Moradi, Cholesterol Dependence of the Conformational Changes in Metabotropic Glutamate Receptor 1 bioRxiv
• D Ogden and M Moradi, Atomic-level characterization of the conformational transition pathways in SARS-CoV-1 and SARS-CoV-2 spike proteins bioRxiv
• D Ogden, K Immadisetty, S Sauve, M Moradi, Conformational Transition Pathways in Major Facilitator Superfamily Transporters bioRxiv
• J-L Losey, M Jauch,A Cortes-Cubero, H Wu, A Polasa, S Sauve, R Rivera, D-S Matteson, M Moradi, Simulating freely-diffusing single-molecule FRET data with consideration of protein conformational dynamics bioRxiv
• C Goolsby, A Fakharzadeh, M Moradi, Thermodynamic and Kinetic Characterization of Protein Conformational Dynamics within a Riemannian Framework bioRxiv

2024

• M Furr, S A Badiee, S Basha, S Agrawal, Z Alraawi, S Heng, C L Stacy, Y Ahmed, M Moradi, T K S Kumar, R M Ceballos Structural stability comparisons between natural and engineered group II chaperonins: Are crenarchaeal heat shock proteins also pH shock resistant? Microorganisms, 12:2348, 2024.
• S Badiee, V Govind Kumar and M Moradi, Molecular dynamics investigation of the influenza hemagglutinin conformational changes in acidic pH The Journal of Physical Chemistry B, 128:11151, 2024.
• R Zhang , K Jagessar , M Brownd , A Polasa , R Stein , M Moradi ,E Karakas and H Mchaourab. Conformational cycle of a protease-containing ABC transporter in lipid nanodiscs reveals the mechanism of cargo-protein coupling Nature Communications, 15:9055, 2024.
• A Polasa, S Badiee and M Moradi. Deciphering the Inter-domain Coupling in a Gram-negative Bacterial Membrane Insertase The Journal of Physical Chemistry B, 128:9734, 2024.
• U Isu, A Polasa and M Moradi. Differential Behavior of Conformational Dynamics in Active and Inactive States of Cannabinoid Receptor 1 The Journal of Physical Chemistry B, 128:8437, 2024.
• Y Ao, J R Grover, L Gifford, Y Han, G Zhong, R Katte, W Li, R Bhattacharjee, B Zhang, S Sauve, W Qin, D Ghimire, M A Haque, J Arthos, M Moradi, W Mothes, E A Lemke, P D Kwong, G B Melikyan, and M Lu. Bioorthogonal click labeling of an amber-free HIV-1 provirus for in-virus single molecule imaging Cell Chemical Biology, 31:487, 2024.

2023

• A Polasa and M Moradi, Towards A Purely Physics-based Computational Binding Affinity Estimation Nature Computational Science, 3:11, 2023.
• U Isu, S Badiee, E Khodadadi, M Moradi, Cholesterol in Class C GPCRs: Role, Relevance, and Localization Membranes, 13:301, 2023.
• S Sauve, J Williamson, A Polasa, M Moradi, Ins and Outs of Rocker Switch Mechanism in Major Facilitator Superfamilty of Transporters Membranes, 13:462, 2023.
• S Badiee, U Isu, E Khodadadi, M Moradi, The Alternating Access Mechanism in Mammalian Multidrug Resistance Transporters and Their Bacterial Homologs Membranes, 13:568, 2023.
• V Govind Kumar, A Polasa, S Agrawal, T K S Kumar, M Moradi, Binding Affinity Estimation from Restrained Umbrella Sampling Simulations Nature Computational Science, 3:59, 2023.
• M Benton, M Furr, V Govind Kumar, A Polasa, F Gao, C-D Heyes, T-K Suresh Kumar, M Moradi cpSRP43 is both highly flexible and stable: Structural insights using a combined experimental and computational approach Journal of Chemical Information and Modeling, 63 :4137, 2023.
• C Goolsby, J Losey, A Fakharzadeh, Y Xu, M Düker, M Getmansky Sherman, D Matteson, M Morad. Addressing the Embeddability Problem in Transition Rate Estimation The Journal of Physical Chemistry A, 127:5759, 2023.

2022

• A Polasa, J Hettige, K Immadisetty, M Moradi, An investigation of the YidC-mediated membrane insertion of Pf3 coat protein using molecular dynamics simulations Front. Mol. Biosci., 9 :15, 2022
• A Polasa, I Mosleh, J Losey, A Abbaspourrad, R Beitle, M Moradi, Developing a Rational Approach to Designing Recombinant Proteins for Peptide-Directed Nanoparticle Synthesis Nanoscale Adv., 4:3171, 2022
• K Immadisetty, A Polasa, R Shelton, and M Moradi, Elucidating the Molecular Basis of Spontaneous Activation in an Engineered Mechanosensitive Channel. Comput. Struct. Biotechnol. J., 20:2539, 2022.
• V Govind Kumar, D-S Ogden, U-H Isu, A Polasa, J-L Losey, and M Moradi, Prefusion Spike Protein Conformational Changes Are Slower in SARS-CoV-2 than in SARS-CoV-1. J. Biol. Chem, 298:101814, 2022.
• H Chen, D Ogden, S Pant, W Cai, E Tajkhorshid, M Moradi, B Roux, and C Chipot, A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls J. Chem. Theory Comput., 18:1406–1422, 2022.

2021

• V Govind Kumar, S Agrawal, T-K Suresh Kumar, M Moradi, Mechanistic Picture for Monomeric Human Fibroblast Growth Factor 1 Stabilization by Heparin Binding. J. Phys. Chem. B, 125:12690-12697, 2021.
• D-R Baucom, M Furr, V Govind Kumar, P Okoto, J-L Losey, R-L Henry, M Moradi, T-K Suresh Kumar, C-D Heyes Transient local secondary structure in the intrinsically disordered C-term of the Albino3 insertase Biophys. J, 120:4992-5004, 2021.
• K Immadisetty and M Moradi Mechanistic Picture for Chemomechanical Coupling in a Bacterial Proton-Coupled Oligopeptide Transporter from Streptococcus Thermophilus J. Phys. Chem. B, 125:9738–9750, 2021.
• D Ogden, M Moradi, Molecular Dynamics–Based Thermodynamic and Kinetic Characterization of Membrane Protein Conformational Transitions Structure and Function of Membrane Proteins. Methods in Molecular Biology, 2302:309, 2021.
• S Agrawal, V Govind Kumar, R-K Gundampati, M Moradi & T-K Suresh Kumar, Characterization of the structural forces governing the reversibility of the thermal unfolding of the human acidic fbroblast growth factor Sci. Rep., 11:15579, 2021.

2019

• 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.

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 Practice. Biochem. Mol. Biol. Educ, 46:230-236, 2018.
• 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.

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 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.

2016

• A Fakharzadeh and M Moradi, Effective Riemannian Diffusion Model for Conformational Dynamics of Biomolecular Systems. J. Phys. Chem. Lett., 7:4980-4987, 2016.

2015

• 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.

2014

• 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.

2013

• 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.

2009-2012

• 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.
• 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 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, Are long-range structural correlations behind the aggregation phenomena of polyglutamine diseases? PLoS Comput. Biol., 8:e1002501, 2012.