Protein Interactions and Mass Prediction Automation

The study investigates how localized geometric constraints affect the conformations adopted by the amino acid side-chain dihedral angles in proteins. Without knowledge of the fundamental principles upon which protein structure rests, no protein can be designed, nor mutations in natural proteins analyzed. The specific aim is to establish the importance of geometry and physicochemical properties toward dihedral angle combinations by amino acid side chains in peptides and proteins. Some progress has been made in site-directed structural biology, but it is still not clear why certain combinations of side chain dihedral angles are so much more frequent than others. With the help of computational methodologies and analyzing protein structures, we aim to resolve this complex relationship of local geometry and side chain conformations. This study complements the other activities being undertaken to increase protein structure knowledge for protein function, which may be useful for the future protein engineering and drug design activity.