Molecular Recognition and Conformational Dynamics in Macromolecules

Abstract: Computational methods gained a widespread use in drug discovery. Understanding conformational dynamics of protein and mechanisms of protein-ligand binding are two major areas in drug discovery. Molecular dynamics (MD) simulation have been routinely used to study conformational dynamics of protein and mechanisms of protein-ligand binding. In classical MD simulation, the system often remains stuck in a local free energy minimum for a long time. Hence, conformational changes associated with long timescales (e.g. loop motion, ligand binding/unbinding etc.) are beyond reach of classical MD simulation. Metadynamics is an enhanced sampling method which deposits bias along some chosen reaction coordinate and forces the system to escape local minimum thus, allows better sampling of the conformational space. In this thesis, I have used MD and metadynamics to study protein-ligand binding andconformational dynamics of globular proteins. We found that the presence of trapped water in the binding site of the protein plays a key role ligand binding. Further, we found that the side-chains of binding site residues and flexibility ofligands play a key role in the protein-ligand binding. We also studied how rotation of tyrosine dictates conformational dynamics in a class of protein known as pepsin-like aspartic protease. We found that apo protease remains in adynamic equilibrium between normal and flipped states due to rotation of tyrosine side-chain. Conformational dynamics also plays a crucial role in hydrogen exchange via solvent penetration. Local fluctuations in protein breaks the hydrogen bond interactions involving backbone amides which allows solvent penetration. We defined this metastable state as broken state. In the broken state, the backbone amide forms hydrogen bond interaction with water molecule. Using molecular dynamics and metadynamics we predicted free energy difference between the broken and ground state (backbone amide remains hydrogen bonded with neighboring residue) in a small globular protein.