Author ORCID Identifier:
Date of Graduation
5-2026
Document Type
Dissertation
Degree Name
Doctor of Philosophy in Chemistry (PhD)
Degree Level
Graduate
Department
Chemistry & Biochemistry
Advisor/Mentor
Moradi, Mahmoud
Committee Member
Fan, Chenguang
Second Committee Member
Adams, Paul
Third Committee Member
Thallapuranam, Suresh
Keywords
Chemomechanical Couplings; Molecular Dynamics; Mitochondrial Localization Peptide (MLP) Enhanced Sampling Techniques
Abstract
Proteins function through a complex interplay between chemical interactions and mechanical motions across multiple spatial and temporal scales. Understanding how ligand binding, conformational dynamics, and structural flexibility collectively regulate protein function remains one of the central challenges in molecular biophysics. This dissertation presents a computational investigation into chemomechanical coupling in three distinct classes of biomolecular systems using all-atom molecular dynamics (MD) simulations and enhanced sampling methods, with particular emphasis on free-energy calculations and long-timescale conformational analysis. The first part of this work focuses on ligand binding in hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, which regulate rhythmic electrical activity in the heart and brain. Using free-energy perturbation (FEP) simulations, the absolute binding free energies of cyclic AMP (cAMP) were quantified for the cyclic nucleotide-binding domains (CNBDs) of HCN1–4 isoforms. Comparative analysis revealed isoform-dependent differences in binding energetics and highlighted the role of conserved residues in stabilizing ligand interactions. These results provide molecular-level insight into the origin of differential channel sensitivities and suggest mechanistic features relevant to isoform-selective drug design. The second part investigates energy transduction in the peptidase-containing ATP-binding cassette (ABC) transporter PCAT1. Through microsecond-scale MD simulations and alchemical freeenergy calculations, this work characterizes nucleotide binding preferences across multiple conformational states and biochemical conditions. The results reveal that nucleotide specificity depends strongly on conformational state, substrate presence, and magnesium coordination, suggesting a regulatory mechanism that prevents futile ATP hydrolysis and promotes productive transport cycles. Per-residue energetic analyses further identify key structural motifs that modulate nucleotide recognition and conformational stability. The final part examines the conformational behavior of an intrinsically disordered localization sequence, dubbed Mitochondrial Localization Peptide (MLP), emphasizing how structural heterogeneity and transient interactions shape functional dynamics. Simulations reveal a rich conformational landscape governed by local interactions and environmental context, highlighting the importance of disorder in mediating flexible molecular recognition. Taken together, this dissertation demonstrates how atomistic simulations and free-energy methods can be used to bridge structure, dynamics, and function across diverse protein systems. By integrating binding thermodynamics, conformational transitions, and disorder-driven flexibility, this work advances our understanding of the chemomechanical principles underlying protein regulation and provides a computational framework for studying complex biomolecular mechanisms.
Citation
Brownd, M. (2026). Deciphering Chemomechanical Couplings in Proteins Using Molecular Dynamics and Enhanced Sampling Techniques. Graduate Theses and Dissertations Retrieved from https://scholarworks.uark.edu/etd/6170
