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Shoshana D Brown

Publications and source records attributed to Shoshana D Brown.

3 recordsLinked to original sources

Hydrolysis of alpha-alkyl-alpha-(methylthio)methylene Meldrum's acids. A kinetic and computational investigation of steric effects.

The rates of hydrolysis of alpha-R-alpha-(methylthio)methylene Meldrum's acids (8-R with R = H, Me, Et, s-Bu, and t-Bu) were determined in basic and acidic solution in 50% DMSO-50% water (v/v) at 20 degrees C. In basic solution (KOH), nucleophilic attack to form a tetrahedral intermediate (T(OH)-) is rate limiting for all substrates (k1(OH)). In acidic solution (HCl) and at intermediate pH values (acetate buffers), water attack (k1(H2O) is rate limiting for 8-Me, 8-Et, and 8-s-Bu; the same is presumably the case for 8-t-Bu, but rates were too slow for accurate measurements at low pH. For 8-H, water attack is rate limiting at intermediate pH but at pH < 4.5 MeS- departure from the tetrahedral intermediate becomes rate limiting. Our interpretation of these results is based on a reaction scheme that involves three pathways for the conversion of T(OH)- to products, two of which being unique to hydrolysis reactions and taking advantage of the acidic nature of the OH group in T(OH)-. This scheme provides an explanation why even at high [KOH] T(OH)- does not accumulate to detectable levels even though the equilibrium for OH- addition to 8-R is expected to favor T(OH)-, and why at low pH water attack is rate limiting for R = Me, Et, s-Bu, and t-Bu but leaving group departure becomes rate limiting with the sterically small R = H. The trend in the k1(OH) and k1(H2O) indicates increasing steric crowding at the transition state with increasing size of R, but this effect is partially offset by a sterically induced twisting of the C=C double bond in 8-R which leads to its elongation and makes the substrate less stable and hence more reactive. Our computational results suggest that this effect becomes particularly pronounced for R = t-Bu and explains why k1(OH) for 8-t-Bu is somewhat higher than for the less crowded 8-s-Bu.

Computer Simulation↗

Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database.

The study of mechanistically diverse enzyme superfamilies-collections of enzymes that perform different overall reactions but share both a common fold and a distinct mechanistic step performed by key conserved residues-helps elucidate the structure-function relationships of enzymes. We have developed a resource, the structure-function linkage database (SFLD), to analyze these structure-function relationships. Unique to the SFLD is its hierarchical classification scheme based on linking the specific partial reactions (or other chemical capabilities) that are conserved at the superfamily, subgroup, and family levels with the conserved structural elements that mediate them. We present the results of analyses using the SFLD in correcting misannotations, guiding protein engineering experiments, and elucidating the function of recently solved enzyme structures from the structural genomics initiative. The SFLD is freely accessible at http://sfld.rbvi.ucsf.edu.

Animals↗

A gold standard set of mechanistically diverse enzyme superfamilies.

Superfamily and family analyses provide an effective tool for the functional classification of proteins, but must be automated for use on large datasets. We describe a 'gold standard' set of enzyme superfamilies, clustered according to specific sequence, structure, and functional criteria, for use in the validation of family and superfamily clustering methods. The gold standard set represents four fold classes and differing clustering difficulties, and includes five superfamilies, 91 families, 4,887 sequences and 282 structures.

Conserved Sequence↗