Ligand-protein Thermodynamics

IV.2. Monte Carlo equilibrium simulations of ligand-protein thermodynamics... 

Homans SW (2007) Dynamics and Thermodynamics of Ligand-Protein Interactions. 272 51-82... 

The energy landscape approach can elucidate such general properties of molecular recognition as the nature of the thermodynamic phases and barriers on the ligand-protein association pathway [127,128]. This method evaluates equilibrium thermodynamic properties of the system from Monte Carlo simulations of the system at a broad temperature range with the aid of the optimized data analysis and the weighted histogram analysis technique [148-153],... 

Homans, S.W. (2007) Dynamics and thermodynamics of ligand—protein interactions, in Bioactive Corformation I, vol. 272, Topics in Current Chemistry (ed. T. Peters), Springer, Berlin, pp. 51-82. 

Gel pads of MAGIChips could serve as micro cuvettes, which would enable massive parallel or multiplex thermodynamical studies for any DNA duplexes, triplexes, DNA binding ligands, proteins, and so forth. Thousands of melting curves could be obtained simultaneously, which cannot be accomplished with the usual UV-VIS spectrophotometer. This fact demonstrates that all mismatch discrimination and mutation detection is based on the sohd theoretical foundation of classical DNA thermodynamics. 

The importance of the hydrophobic interaction has been emphasized in many biological systems, but the coulombic contribution has been shown to be small. However, negative values for all the thermodynamic parameters, AQO, AH , and AS°, have been observed frequently for many small ligand/protein interactions and the dimerization of dye molecules, 1 in which the reactions are entropically unfavorable. 

Shlmokhina, N., Bronowska, A., and Homans, S.W. (2006) Contribution of ligand desolvation to binding thermodynamics in a ligand-protein interaction. Angewandte Chemie International Edition in English, 45, 6374-6376. 

J.H., and Martin, S.F. (2011) Protein-ligand interactions thermodynamic effects associated with increasing nonpolar surfece area. Journal of the American Chemical Society, 133,18518-18521. 

Celey, M.S. Dassie, S.A. Freire, E. Bianconi, M.L. Fideho, G.D. (2005) Ligand induced thermostability in proteins Thermodynamic analysis of ANS-albumin interaction. 

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