Question

5.DISEASE AND PATHWAYS: Most drugs target proteins involved in signaling pathways in the cell. Describe two examples by which a protein can be chemically altered and thereby act as a logic switch in a signaling pathway in the cell.

6.MOLECULAR DRUG DOCKING: Why is molecular docking (e.g. autodock vina) take less time to run than molecular dynamics? What aspect of molecular reality regarding the target protein is sacrificed during simulation to obtain computational speed?

Answer 1

5, chemistry and movement that gives protein extraordinary capabilities that process in the living cells..protein molecules depend on its physical interaction with other molecules.. Antibiotics attach to viruses or bacteria for destruction, the enzyme hexokinase binds glucose and ATP to catalyse a reaction between them..the substance bound by the protein may be ion,small molecules or macromolecules in protein have ability to bind high affinity to a ligand depends on bonds, formed simultaneously..protein have chemical capabilities due to interaction in ways by chemical reactivity of amino acids side chains and clustering of neighbouring polar aminoacids side chains can alter their activity..

6, new drug targets emerging from genomic and proteomic initiatives, now computer- aided drug design techniques effective in reducing costs and speedup drug discovery..Both the structure of the protein receptors and the binding site are known..computational approach can be applied at different stages of drug design process..incorporation of protein flexibility in the docking process, extensive exploration of the ligand conformation with in the binding site, refinement and stability evaluation of the final complexes and estimation of the free binding energy..molecules dynamic simulation play a another role to improve this docking procedure..MD is slow conformational changes and stability to obtain time- averaged properties of the biomolecular system..