NIH/NHLBI/LBC/CBS & FDA/CBER/OVRR/LB

Past seminars...

March 1999

Mar 25:	postponed
Mar 18:	Group meeting:	Tom Cheatham	REPLICA/PATH and estimation of the potential-of-mean-force along a given reaction coordinate; post-processing MD trajectories for crude (free) energy analysis; recent nucleic acid work
Mar 11:	Group meeting:	Gabriela Mustata	Ligand Traffic in Acetyl-choline Esterase
Mar 4:	postponed

February 1999

Feb 25:	Special seminar:	Paul Sherwood	QM/MM Methods and the QUASI Project
Feb 18:	Journal club	Pete Steinbach Tom Cheatham Fred Carson	``Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins'' by Ruben Abagyan and Maxim Totrov, J. Mol. Biol. 235, 983-1002 (1994) and connections to recent work within the MMIG will be presented. ``Ewald artifacts in computer simulations of ionic solvation and ion-ion interaction: A continuum electrostatics study'' by P. Hunenberger and J. McCammon, J. Chem. Phys. 110, 1856-1872 (1999). Issues related to including solvation in simulations and artifacts arising from applying cutoffs versus true periodicity will be introduced and discussed. ``Native Carboxypeptidase A in a New Crystal Environment Reveals a Different Conformation of the Important Tyrosine'' by J.T. Bukrinsky et al., Biochemistry 248:37, 16555-16564 (1998). Abstract

Supplemental Material

Carboxypeptidase A has served as a paradigm of enzyme structure and mechanism ever since Bill Lipscomb determined its crystal structure in 1965, when it became the first enzyme to have its structure determined. Lipscomb found that the free enzyme had the Tyr248 side chain poised away from the protein and exposed to solvent. However, when CPAalpha was co-crystallized with a slowly-hydrolyzed peptide, the side chain was seen to be situated 12 A away from that position, covering the hydrophobic side chain of the first residue of the peptide. This has been interpreted as powerful evidence supporting the induced fit theory of Dan Koshland (1958).
Now Kadziola and coworkers (Bukrinsky et al.) have found that a new crystal form of unliganded CPAbeta, which is CPAalpha truncated by 2 residues, crystallizes in space group P212121 and has the Tyr positioned exactly as in CPAalpha bound to a peptide. They conclude that the unusual position of Tyr248 in free CPAalpha is a consequence of crystal contacts with a neighboring enzyme molecule. Thus, the induced fit mechanism is not supported by this example after all, and arguments that Tyr248 acts as a "door," closing to trap the substrate at the active site, are wrong.