Understanding the roles of chalcogen and van der Waals dispersion interaction in biomolecules

Abstract

Non-covalent interactions such as hydrogen bonds, hydrophobic, and van der Waals interactions are crucial for the stability and function of biomolecules and are well-researched. The essentiality of other weak interactions, such as C-H···O, cation/anion-π, and n→π* interactions, in sculpting protein structures is also being discovered. In this thesis, I have investigated the significance of the two aspects of weak interactions viz 1. understanding the role of sulfur-mediated chalcogen (Ch-) and hydrogen (H-) bond in proteins; 2. the role of van der Waals dispersion interaction in base-specific protein-DNA recognition. Divalent sulfur forms a Ch-bond via its σ–holes and H-bond via its lone pairs. The relevance of these interactions and their interplay in protein structure and function is unclear. Based on structural and computational analysis, the reciprocity of the substituent-dependent strength of the σ–holes and lone pairs was correlated with the formation of either Ch-bond or H-bond. In proteins, this has implications for the positioning of divalent sulfur and its role in structure and function. Computational analyses reveal that the S-mediated interactions stabilize protein secondary structures by mechanisms such as helix capping, protecting free β-sheet edges by negative-design, and augmenting the stability of β-turns. Furthermore, we experimentally demonstrate that the disruption of a Ch-bond between the enzyme methionyl-tRNA synthetase and its substrate methionine affects substrate binding. The role of van der Waals dispersion interaction in biomolecular recognition is investigated using McrBC endonuclease as a model system. McrB subunit of McrBC recognizes a two base pair DNA target sequence 5’-R(5mC)-3’, where R is a purine and 5mC is 5-methylcytosine. Mutation of the McrB-Leu68 in the binding pocket of the flipped 5mC and the intercalating residue McrB-Tyr41 results in broadening and modulating the base specificity. High-resolution crystal structures of these mutants bound to DNA and computationally calculated interaction energies reveal the essentiality of van der Waals interaction in establishing base specificity. Additionally, the crystal structures and molecular dynamics simulations reveal the role of an engineered H-bond between the proteins and flipped base and water-mediated interactions in modulating the specificity.