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The assembly of signaling molecules surrounding the integrin family of adhesion receptors remains poorly understood. Recently, the membrane protein caveolin was found in complexes with beta1 integrins. Caveolin binds cholesterol and several signaling molecules potentially linked to integrin function, e.g., Src family kinases, although caveolin has not been(More)
A new monotonicity-constrained maximum likelihood approach, called Partial Order Optimum Likelihood (POOL), is presented and applied to the problem of functional site prediction in protein 3D structures, an important current challenge in genomics. The input consists of electrostatic and geometric properties derived from the 3D structure of the query protein(More)
he integrin ␣ 3 ␤ 1 mediates cellular adhesion to the matrix ligand laminin-5. A second integrin ligand, the urokinase receptor (uPAR), associates with ␣ 3 ␤ 1 via a surface loop within the ␣ 3 ␤-propeller (residues 242– 246) but outside the laminin binding region, suggesting that uPAR–integrin interactions could signal differently from matrix engagement.(More)
rokinase-type plasminogen activator receptors (uPARs), up-regulated during tumor progression, associate with ␤ 1 integrins, localizing urokinase to sites of cell attachment. Binding of uPAR to the ␤-propeller of ␣ 3 ␤ 1 empowers vitronectin adhesion by this integrin. How uPAR modifies other ␤ 1 integrins remains unknown. Using recombinant proteins, we found(More)
Genomics has posed the challenge of determination of protein function from sequence and/or 3-D structure. Functional assignment from sequence relationships can be misleading, and structural similarity does not necessarily imply functional similarity. Proteins in the DJ-1 family, many of which are of unknown function, are examples of proteins with both(More)
BACKGROUND Methods are now available for the prediction of interaction sites in protein 3D structures. While many of these methods report high success rates for site prediction, often these predictions are not very selective and have low precision. Precision in site prediction is addressed using Theoretical Microscopic Titration Curves (THEMATICS), a simple(More)
Previously, we have shown that the phosphoinositide-3-kinase (PI3K) mediated acute (24 h) post-conditioning neuroprotection induced by propofol. We also found that propofol post-conditioning produced long term neuroprotection and inhibited the internalization of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor GluR2 subunit up to 28 days(More)
Although the beneficial effects of acupuncture in asthma treatment have been well documented, little is known regarding the biological basis of this treatment. Changes in the lung proteome of acupuncture-treated rats with asthma onset were comparatively analyzed using a two-dimensional gel electrophoresis (2DE) and mass-spectrometry- (MS-) based proteomic(More)
Prediction of protein functional sites from 3D structure is an important problem, particularly as structural genomics projects produce hundreds of structures of unknown function, including novel folds and the structures of orphan sequences. The present paper shows how computed protonation properties provide unique and powerful capabilities for the(More)