Terry P. Lybrand

Learn 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)
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)
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)
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)
Myasthenia gravis (MG) is characterized by muscle weakness due to autoimmunity against the nicotinic acetylcholine receptor (nAChR). MG is associated with polymorphisms in HLA-DQ genes and the aim of the present study was to characterize structural differences in the peptide binding groove of HLA-DQ molecules positively and negatively associated with MG.(More)
Myelin oligodendrocyte glycoprotein (MOG) is a protein on the surface of myelin sheaths. It is a putative target of the autoimmune attack in the inflammatory and demyelinating CNS disease multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis. MOG belongs to the immunoglobulin superfamily (IgSF), and its extracellular N-terminal(More)
The cyclooxygenase enzymes (COX-1 and COX-2) are the therapeutic targets of nonsteroidal anti-inflammatory drugs (NSAIDs). Neutralization of the carboxylic acid moiety of the NSAID indomethacin to an ester or amide functionality confers COX-2 selectivity, but the molecular basis for this selectivity has not been completely revealed through mutagenesis(More)
Ion mobility-mass spectrometry (IM-MS) allows the separation of ionized molecules based on their charge-to-surface area (IM) and mass-to-charge ratio (MS), respectively. The IM drift time data that is obtained is used to calculate the ion-neutral collision cross section (CCS) of the ionized molecule with the neutral drift gas, which is directly related to(More)