title: Simulation Studies of Protein and Small Molecule Interactions and Reaction.
abstract: Computational studies of protein and small molecule (protein-ligand/enzyme-substrate) interactions become more and more important in biological science and drug discovery. Computer modeling can provide molecular details of the processes such as conformational change, binding, and transportation of small molecules/proteins, which are not easily to be captured in experiments. In this chapter, we discussed simulation studies of both protein and small molecules from three aspects: conformation sampling, transportations of small molecules in enzymes, and enzymatic reactions involving small molecules. Both methodology developments and examples of simulation studies in this field were presented.
authors: College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, PR China; Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, PR China.
authors: L
authors: L
authors: Yang
authors: College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, PR China; Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, PR China.
authors: J
authors: J
authors: Zhang
authors: College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, PR China; Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, PR China.
authors: X
authors: X
authors: Che
authors: College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, PR China; Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, PR China. Electronic address: gaoyq@pku.edu.cn.
authors: Y Q
authors: YQ
authors: Gao
mesh_terms: D001419:Bacteria / Q000737:chemistry / Q000201:enzymology; D001920:Bradykinin / Q000737:chemistry; D002118:Calcium / Q000737:chemistry; D002147:Calmodulin / Q000737:chemistry; D002222:Carbamoyl-Phosphate Synthase (Ammonia) / Q000737:chemistry; D002826:Chorismate Mutase / Q000737:chemistry; D004791:Enzyme Inhibitors / Q000737:chemistry*; D006801:Humans; D007700:Kinetics; D008024:Ligands; D008565:Membrane Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009712:Nucleotides, Cyclic / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D054852:Small Molecule Libraries / Q000737:chemistry*; D013816:Thermodynamics; D000099197:STING Protein
chemical_list: D001920:Bradykinin; D002118:Calcium; D002147:Calmodulin; D002222:Carbamoyl-Phosphate Synthase (Ammonia); D002826:Chorismate Mutase; D004791:Enzyme Inhibitors; D008024:Ligands; D008565:Membrane Proteins; D009712:Nucleotides, Cyclic; D054852:Small Molecule Libraries; C532857:STING1 protein, human; D000099197:STING Protein
keywords: Conformational change; Enhanced sampling; Enzymatic reaction; Ligand binding; Ligand transportation; Molecular simulation