Solvent and biomolecular interactions guiding assembly and recognition

Hydrophobic property of proteins drives it to form sub-nanometer organized structures such as alpha-helix, beta-strand. In biology this protein structural unit makes important class of functional macromolecules. Enzymatic activity, cellular signaling, ability to bind other molecules, and molecular transport are some of the important functions of protein assembly. Functional consequences of the physical interactions such as van der Waal's forces or electrostatic interaction, at play can be modulated by protein engineering techniques for applications in advanced biomaterial arenas. In addition, proteins folding to higher order structures in appropriate environment, and unfolding by removing those conditions underlie the importance of solvent interaction. Role of solvent activity is crucial and understanding of solvent interaction can be employed to commonly encountered chemical engineering problems as in evaluation of solute solubility.;This dissertation focuses on evaluation of solvation free energy of non-polar solute in organic solvent using molecular scaled particle theory. Molecular simulations of variety of organic solvents are performed and revised version of Reiss's scaled particle theory is utilized for predicting accurate solvation free energy. Next we investigate molecular mechanisms for specific recognition of organo-metallic ligand complexes by engineered antibodies. In addition, the technique to functionalize protein with polymer for structure stabilization has been scrutinized to elucidate the underlying mechanism. Molecular dynamic simulations were conducted on the hybrid protein-polymers and antibody systems, complementing and corroborating the experimental results observed.;In the first chapter organic solvent with varying topology such as linear alkanes, branched alkanes, cyclic alkanes and aromatic compound are simulated. The solvation free energy of cavity solute in solvent is determined by the probability of observing cavity of given size. This probability is systematically related to excess chemical potential using Reiss's scaled particle theory which treats multi-atomic molecule as a single spherical site. Reiss's revised version of scaled particle theory (MSPT) is presented recently which accurately evaluated the excluded volume of a multi-atomic molecule without resorting to single spherical site approximation. Systematic changes in the contact density for homologous aliphatic hydrocarbons observed from simulation are compared with MSPT. Accurate cavity solvation free energy for all the solvents is obtained from MSPT.;In the second chapter experimentally raised antibody 5B2 for specific binding of organo-metallic (or metal-ligand complex) - PbDTPA is modeled. The anionic organometallic ligand complex can bind to antibody pocket amino acids by variety of mechanisms such as hydrogen bonding, electrostatic interaction, or hydrophobic stacking. Efficient identification of these mechanisms aids in the timely response and optimization of novel biosensors. Simulations were performed for observation of binding between metal-ligand complex and antibody 5B2. The strong interaction of positively charged arginine, lysine and polar amino acids serine, tyrosine with oxygen sites on ligand-metal complex is responsible for efficient binding. Primary (cationic R95, K58 and polar S98, Y56) and secondary binding sites (cationic R50, polar Y97, Y33, S30c and non-polar W91) are identified from investigation of simulation results. Single site mutational simulations led to escape of the metal-ligand complex from antibody pocket, when binding sites were mutated to anionic or non-polar amino acids.;In the final chapter the simulation of protein 1CW and protein 1CW conjugated with poly(ethylene oxide) is performed to see enhancement of protein helical structure due to polymer presence to corroborate experimental results. This hybrid protein-polymer system possesses a more stable structure, compared to native protein systems, which makes it appealing for applications in peptide based drug therapies, hydrogel for tissue engineering, and controlled drug release. Quantification of individual amino acid interaction with ethylene oxide allowed us to generate hypothesis of helix-stabilization. Ethylene oxide preferentially interacts with cationic lysine and thereby stabilize hydrogen-bonding with neighboring amino acids. Side chain interference of cationic lysine with its neighbors is reduced as ethylene oxide acts as solvent to take away that interaction with a consequential increase in helicity. Polyalanine and lysine and arginine mutant polyalanine were conjugated with polymer and simulation results were quantified. Resultant enhanced helicity for cases of lysine and arginine mutants again proved role of destabilizing nature of cationic amino acids and subsequent solvent role of polymer in decreasing this destabilizing nature. We therefore conclude the interaction of lysine with ethylene oxide contributes to helix stability in original peptide 1CW.