J Org Chem 2002 Mar;67(6):1827-37
Department of Pharmaceutical Chemistry, University of California, San Francisco 94143, USA.
Proteins 1993 Jul;16(3):226-45
Department of Pharmaceutical Chemistry, University of California, San Francisco 94143.
We present calculations of the absolute and relative binding free energies of complexation of streptavidin with biotin and its analogs by means of a thermodynamic free energy perturbation method implemented with molecular dynamics. Using the recently solved crystal structure of the streptavidin-biotin complex, biotin was mutated into a dummy molecule as well as thiobiotin and iminobiotin both in the protein and in solution. The calculated absolute binding free energy was dependent on the simulation model used. Read More
J Phys Chem B 2009 Jul;113(29):9958-67
National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada.
We studied the electronic structure of the binding site of the streptavidin-biotin complex by using the ONIOM method at the HF/STO-3G:UFF level and obtained the solvation structure of the complex by using the statistical-mechanical, three-dimensional molecular theory of solvation (aka three-dimensional reference interaction site model, 3D-RISM-KH). All the streptavidin residues located within 3 A of the biotin residue were included in the quantum mechanical (QM) layer. In total, 16 residues including biotin with 274 atoms were in the QM layer, in which five residues are responsible for the hydrophobic interactions and nine residues for the hydrogen-bonding/electrostatic interaction with biotin. Read More
Proteins 1999 Feb;34(3):395-402
Graduate Group in Biophysics, University of California, San Francisco 94143, USA.
Recently a semiempirical method has been proposed by Aqvist et al. to calculate absolute and relative binding free energies. In this method, the absolute binding free energy of a ligand is estimated as deltaGbind = alpha
Acta Crystallogr D Biol Crystallogr 2006 Jun 12;62(Pt 6):576-81. Epub 2006 May 12.
Departments of Biological Structure and Biochemistry, Biomolecular Structure Center, University of Washington, Seattle, WA 98195, USA.
(+)-Epi-biotin differs from (+)-biotin in the configuration of the chiral center at atom C2. This could lead to a difference in the mode of binding of (+)-epi-biotin to streptavidin, a natural protein receptor for (+)-biotin. Diffraction data were collected to a maximum of 0. Read More