Julie Penzotti

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TCR engagement of peptide-MHC class II ligands involves specific contacts between the TCR and residues on both the MHC and peptide molecules. We have used molecular modeling and assays of peptide binding and T cell function to characterize these interactions for a CD4+ Th1 cell clone, ESL4.34, which recognizes a peptide epitope of the herpes simplex type 2(More)
P-glycoprotein (P-gp) functions as a drug efflux pump, mediating multidrug resistance and limiting the efficacy of many drugs. Clearly, identification of potential P-gp substrate liability early in the drug discovery process would be advantageous. We describe a multiple-pharmacophore model that can discriminate between substrates and nonsubstrates of P-gp(More)
In order to develop robust machine-learning or statistical models for predicting biological activity, descriptors that capture the essence of the protein-ligand interaction are required. In the absence of structural information from X-ray or NMR experiments, deriving informative descriptors can be difficult. We have developed feature-map vectors (FMVs), a(More)
The streptavidin–biotin system has provided a unique opportunity to investigate the molecular details of ligand dissociation pathways. An underlying mechanistic question is whether ligand dissociation proceeds with a relatively ordered process of bond breaking and ligand escape. Here we report a joint computational and crystallographic study of the earliest(More)
Computational methods are increasingly used to streamline and enhance the lead discovery and optimization process. However, accurate prediction of absorption, distribution, metabolism and excretion (ADME) and adverse drug reactions (ADR) is often difficult, due to the complexity of underlying physiological mechanisms. Modeling approaches have been hampered(More)
It is currently unclear whether small molecules dissociate from a protein binding site along a defined pathway or through a collection of dissociation pathways. We report herein a joint crystallographic, computational, and biophysical study that suggests the Asp-128 --> Ala (D128A) streptavidin mutant closely mimics an intermediate on a well-defined(More)
HLA molecules associated with rheumatoid arthritis (RA) contain a discrete structural element known as the shared epitope, a set of conserved amino acid residues located on the alpha helical portion of the class II beta chain. Each of the different HLA molecules associated with RA contain the same shared epitope sequence, although they may vary markedly in(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)
The high affinity energetics in the streptavidin-biotin system provide an excellent model system for studying how proteins balance enthalpic and entropic components to generate an impressive overall free energy for ligand binding. We review here concerted site-directed mutagenesis, biophysical, and computational studies of aromatic and hydrogen bonding(More)
This review discusses the current challenges facing researchers developing computational models to predict absorption, distribution, metabolism, excretion and toxicity (ADMET) for early drug discovery. The strengths and weaknesses of different modeling approaches are reviewed and a survey of recent strategies to model several key ADMET parameters, including(More)