Terry P. Lybrand

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BACKGROUND Heterokont algae form a monophyletic group within the stramenopile branch of the tree of life. These organisms display wide morphological diversity, ranging from minute unicells to massive, bladed forms. Surprisingly, chloroplast genome sequences are available only for diatoms, representing two (Coscinodiscophyceae and Bacillariophyceae) of(More)
In bee venom phospholipase A2, histidine-34 probably functions as a Brønsted base to deprotonate the attacking water. Aspartate-64 and tyrosine-87 form a hydrogen bonding network with histidine-34. We have prepared mutants at these positions and studied their kinetic properties. The mutant in which histidine-34 is changed to glutamine is catalytically(More)
Molecular dynamics simulations have been used to study the free energy of binding of an antiviral agent to the human rhinovirus HRV-14 and to a mutant in which a valine residue in the antiviral binding pocket is replaced by leucine. The simulations predict that the antiviral should bind to the two viruses with similar affinity, in apparent disagreement with(More)
Bacterial chemoreceptors signal across the membrane by conformational changes that traverse a four-helix transmembrane domain. High-resolution structures are available for the chemoreceptor periplasmic domain and part of the cytoplasmic domain but not for the transmembrane domain. Thus, we constructed molecular models of the transmembrane domains of(More)
We report a serious problem associated with a number of current implementations of Andersen and Langevin dynamics algorithms. When long simulations are run in many segments, it is sometimes possible to have a repeating sequence of pseudorandom numbers enter the calcuation. We show that, if the sequence repeats rapidly, the resulting artifacts can quickly(More)
Computer-aided model building techniques have been used to construct three-dimensional model structures for hamster beta 2 adrenergic receptor. Experimental data were used as constraints to guide the model building procedure, and a number of rather strict criteria were applied to assess the physical plausibility of model structures. We present details of(More)
A series of novel derivatives of the nonsteroidal anti-inflammatory drug (NSAID) sulindac sulfide were synthesized as potential agonists of the peroxisome proliferator-activated receptor gamma (PPARgamma). Nonpolar and aromatic substitutions on the benzylidene ring as well as retention of the carboxylic acid side chain were required for optimal activity.(More)
Numerous techniques have been used to elucidate the structural basis for interaction of cholecystokinin (CCK)-related peptides with their hormone-binding receptor, the CCK-A receptor (CCK-AR), including structure-activity relationship studies, site-directed mutagenesis, photoaffinity-labeling, and solution NMR analysis of both CCK peptide ligands and(More)
Computational tools are rapidly becoming an essential component of molecular biology research. However, there is as yet relatively little attention paid to computational biology in the standard curricula of most biology programs. We describe here some of the graduate computational biology courses we have developed in the Center for Bioengineering at the(More)