TAILIEUCHUNG - Báo cáo khóa học: Numerical calculations of the pH of maximal protein stability

A large number of proteins, found experimentally to have different optimum pH of maximal stability, were studied to reveal the basic principles of their preferenence for a par-ticular pH. The pH-dependent free energy of folding was modeled numerically as a function of pH as well as the net charge of the protein. The optimum pH was determined in the numerical calculations as the pH of the minimum free energy of folding. The experimental data for the pH of maximal stability (experimental optimum pH) was repro-ducible (rmsd¼) | Eur. J. Biochem. 271 173-185 2004 FEBS 2003 doi Numerical calculations of the pH of maximal protein stability The effect of the sequence composition and three-dimensional structure Emil Alexov Howard Hughes Medical Institute and Columbia University Biochemistry Department New York USA A large number of proteins found experimentally to have different optimum pH of maximal stability were studied to reveal the basic principles of their preferenence for a particular pH. The pH-dependent free energy of folding was modeled numerically as a function of pH as well as the net charge of the protein. The optimum pH was determined in the numerical calculations as the pH of the minimum free energy of folding. The experimental data for the pH of maximal stability experimental optimum pH was reproducible rmsd . It was shown that the optimum pH results from two factors - amino acid composition and the organization of the titratable groups with the 3D structure. It was demonstrated that the optimum pH and isoelectric point could be quite different. In many cases the optimum pH was found at a pH corresponding to a large net charge of the protein. At the same time there was a tendency for proteins having acidic optimum pHs to have a base acid ratio smaller than one and vice versa. The correlation between the optimum pH and base acid ratio is significant if only buried groups are taken into account. It was shown that a protein that provides a favorable electrostatic environment for acids and disfavors the bases tends to have high optimum pH and vice versa. Keywords electrostatics pH stability pKa optimum pH. The concentration of hydrogen ions pH is an important factor that affects protein function and stability in different locations in the cell and in the body 1 . Physiological pH varies in different organs in human body the pH in the digestive tract ranges from to in the kidney it ranges from to and body liquids have a pH of .

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