Limiting assumptions in structure-based design: binding entropy.
In order to deal with the complexity of biological systems at the atomic level, limiting assumptions are often made which do not reflect the reality of the system under study. One example is the assumption that the entropy of binding of the macromolecule is not influenced significantly by the different ligands. Recent experimental data on ligands binding to HIV-1 protease challenge this assumption.
Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, MO, USA. garlandm@gmail.com
Garland R
GR
Marshall
D001665:Binding Sites; D020134:Catalytic Domain; D024882:Drug Resistance, Viral; D019277:Entropy; D017320:HIV Protease Inhibitors / Q000737:chemistry*; D015497:HIV-1 / Q000737:chemistry*; D006801:Humans; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D009154:Mutation; D010447:Peptide Hydrolases / Q000737:chemistry*; D011485:Protein Binding; D013113:Spin Labels; D049490:Systems Biology / Q000639:trends
D017320:HIV Protease Inhibitors; D008024:Ligands; D013113:Spin Labels; D010447:Peptide Hydrolases