The interaction of ligands to macromolecules is a key element in all biological processes. Ligand interactions are important for molecular recognition, protein engineering, drug design, cellular regulating systems, cell signaling, drug formulation and discovery of novel ligands. Ligands can be small molecules such as metabolites, ions such as Fe (II) or large molecules such as nucleic acid and other protein partners. Some of my recent researches in this subject are as below: Fundamental research The interaction between human serum albumin (HSA) and two drugs indicated that amlodipine causes an increase, and that propranolol leads to a decrease in - helix content of HSA [1]. The presence of quercetin (QUER) increased binding constant of propranolol (PROP) with HSA [2]. The binding sites of SDS on carbonic anhydrase and thiourea (TOU) to cobra cardio toxin A3 (CTX A3) evaluated by MD simulation [3]. Protein engineering The structures of the native (Amyl-C) and truncated Taka amylase were compared by molecular modeling methods. Using in silico enzyme engineering approach, 50 (Amyl-S1) and 100 (Amyl-S2) amino acids were eliminated from Amyl-C to produce the truncated forms [4].

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