TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets.

The TRAnsient Pockets in Proteins (TRAPP) webserver provides an automated workflow that allows users to explore the dynamics of a protein binding site and to detect pockets or sub-pockets that may transiently open due to protein internal motion. These transient or cryptic sub-pockets may be of interest in the design and optimization of small molecular inhibitors for a protein target of interest. The TRAPP workflow consists of the following three modules: (i) TRAPP structure- generation of an ensemble of structures using one or more of four possible molecular simulation methods; (ii) TRAPP analysis-superposition and clustering of the binding site conformations either in an ensemble of structures generated in step (i) or in PDB structures or trajectories uploaded by the user; and (iii) TRAPP pocket-detection, analysis, and visualization of the binding pocket dynamics and characteristics, such as volume, solvent-exposed area or properties of surrounding residues. A standard sequence conservation score per residue or a differential score per residue, for comparing on- and off-targets, can be calculated and displayed on the binding pocket for an uploaded multiple sequence alignment file, and known protein sequence annotations can be displayed simultaneously. The TRAPP webserver is freely available at http://trapp.h-its.org.

Evaluation and operationalization of commercial serum indices quality control material in the clinical laboratory.

BACKGROUND: Evaluation of specimen suitability for downstream analytical testing and identification of potential interferents in the clinical laboratory is critical for the generation of actionable clinical results. Within the clinical laboratory, hemolysis, icterus, and lipemia are commonly assessed spectrophotometrically. While clinical laboratories rely on analyte-specific quality control (QC) materials to monitor test or instrument performance, QC materials evaluating specimen integrity checks are infrequently implemented. METHODS: Using commercially available specimen integrity materials, we evaluated the Bio-Rad Liquichek™ Serum Indices product on Roche cobas® c701 analyzers at a large academic medical center. Target arbitrary values for the hemolysis, icterus, and lipemia QC materials were 200, 20, and 500, respectively. Means, standard deviations (SD), and coefficients of variation (%CV) were established for hemolysis, icterus, lipemia, and non-interfered QCs, and performance was monitored over a 60-day period. RESULTS: Across four c701 instruments, all QC materials performed well, with %CVs ≤ 1.76%, 4.51%, and 3.46% for hemolysis, icterus, and lipemia QC, respectively. CONCLUSIONS: The Bio-Rad Liquichek Serum Indices product can serve as an effective means of monitoring specimen integrity checks in a manner congruous with existing QC programs.

Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2.

There is increasing evidence of a significant correlation between prolonged drug-target residence time and increased drug efficacy. Here, we report a structural rationale for kinetic selectivity between two closely related kinases: focal adhesion kinase (FAK) and proline-rich tyrosine kinase 2 (PYK2). We found that slowly dissociating FAK inhibitors induce helical structure at the DFG motif of FAK but not PYK2. Binding kinetic data, high-resolution structures and mutagenesis data support the role of hydrophobic interactions of inhibitors with the DFG-helical region, providing a structural rationale for slow dissociation rates from FAK and kinetic selectivity over PYK2. Our experimental data correlate well with computed relative residence times from molecular simulations, supporting a feasible strategy for rationally optimizing ligand residence times. We suggest that the interplay between the protein structural mobility and ligand-induced effects is a key regulator of the kinetic selectivity of inhibitors of FAK versus PYK2.