Paul E. Smith

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Initial simulated values of the surface tension for the SPC/E water model have indicated excellent agreement with experiment. More recently, differing values have been obtained which are significantly lower than previous estimates. Here, we attempt to explain the differences between the previous studies and show that a variety of simulation conditions can(More)
The illumination of oxygen-evolving PSII core complexes at very low temperatures in spectral regions not expected to excite P680 leads to charge separation in a majority of centers. The fraction of centers photoconverted as a function of the number of absorbed photons per PSII core is determined by quantification of electrochromic shifts on Pheo(D1). These(More)
LigD 3'-phosphoesterase (PE) is a component of the bacterial NHEJ apparatus that performs 3'-end-healing reactions at DNA breaks. The tertiary structure, active site and substrate specificity of bacterial PE are unique vis-à-vis other end-healing enzymes. PE homologs are present in archaea, but their properties are uncharted. Here, we demonstrate the(More)
LigD 3 0-phosphoesterase (PE) is a component of the bacterial NHEJ apparatus that performs 3 0-end-healing reactions at DNA breaks. The tertiary structure, active site and substrate specifi-city of bacterial PE are unique vis–a `-vis other end-healing enzymes. PE homologs are present in archaea, but their properties are uncharted. Here, we demonstrate the(More)
A model for the human delta opioid receptor has been generated via sequence alignment, structure building using the crystal structure of bovine rhodopsin as a template, and refinement by molecular dynamics simulation. The model building suggested that, in addition to the previously postulated interaction between D128 and Y308, an internal salt bridge also(More)
Many economically important oceanic fishes travel in large schools, but the foraging behaviors of these schools and the life history consequences of these behaviors have rarely been addressed. The availability of extensive information on bioenergetics of the northern anchovy (Engraulis mordax) allows us to use this species as a case study. We modeled two(More)
Yeast Prp28 is a DEAD-box pre-mRNA splicing factor implicated in displacing U1 snRNP from the 5' splice site. Here we report that the 588-aa Prp28 protein consists of a trypsin-sensitive 126-aa N-terminal segment (of which aa 1-89 are dispensable for Prp28 function in vivo) fused to a trypsin-resistant C-terminal catalytic domain. Purified recombinant Prp28(More)
Clostridium thermocellum polynucleotide kinase (CthPnk), the 5' end-healing module of a bacterial RNA repair system, catalyzes reversible phosphoryl transfer from an NTP donor to a 5'-OH polynucleotide acceptor. Here we report the crystal structures of CthPnk-D38N in a Michaelis complex with GTP•Mg(2+) and a 5'-OH oligonucleotide and a product complex with(More)
LigD 3'-phosphoesterase (PE) enzymes perform end-healing reactions at DNA breaks. Here we characterize the 3'-ribonucleoside-resecting activity of Candidatus Korarchaeum PE. CkoPE prefers a single-stranded substrate versus a primer-template. Activity is abolished by vanadate (10 mM), but is less sensitive to phosphate (IC(50) 50 mM) or chloride (IC(50) 150(More)
Aromatic/aliphatic copolyesters containing hydrophilic moieties in the main chain or side chain were synthesized by bulk polycondensation of aromatic monomers without or with solubilizing substituents and aliphatic monomers. Hydrolytic and enzymatic degradation studies were carried out in vitro at 37 degrees C in pH 7.4 phosphate buffer and in Tris-HCl(More)