2007 week 05: Articles in Proteins

ENTIRE CATALOG OF FERRET PROTEINS TO DATE


Getting one's protein in a bunch -- When quality control fails in cells
Over time, a relatively minor mistake in protein production at the cellular level may lead to serious neurological diseases. But exactly how the cell avoids such mistakes has remained unclear until now. Researchers at Ohio State University found the mechanism that prevents such errors, and explain their findings in the Proceedings of the National Academy of Sciences.

Quantum biology -- Powerful computer models reveal key biological mechanism
Troy, N.Y. -- Using powerful computers to model the intricate dance of atoms and molecules, researchers at Rensselaer Polytechnic Institute have revealed the mechanism behind an important biological reaction. In collaboration with scientists from the Wadsworth Center of the New York State Department of Health, the team is working to harness the reaction to develop a "nanoswitch" for a variety of applications, from targeted drug delivery to genomics and proteomics to sensors.
The research is part of a burgeoning discipline called "quantum biology," which taps the skyrocketing power of today's high-performance computers to precisely model complex biological processes. The secret is quantum mechanics -- the much-touted theory from physics that explains the inherent "weirdness" of the atomic realm.

Microtubule protein interactions visualized en masse
In a new study published online in the open access journal PLoS Biology, Philipp Niethammer, Eric Karsenti, and colleagues investigate the regulation of microtubule dynamics via application of their new method, called visual immunoprecipitation (VIP), which enables simultaneous visualization of multiple protein interactions in cell extracts.

Assignment of polar states for protein amino acid residues using a interaction cluster decomposition algorithm and its application to high resolution protein structure modeling
We have developed a new method (Independent Cluster Decomposition Algorithm, ICDA) for creating all-atom models of proteins given the heavy-atom coordinates, provided by X-ray crystallography, and the pH. In our method the ionization states of titratable residues, the crystallographic mis-assignment of amide orientations in Asn/Gln, and the orientations of OH/SH groups are addressed under the unified framework of polar states assignment. To address the large number of combinatorial possibilities for the polar hydrogen states of the protein, we have devised a novel algorithm to decompose the system into independent interacting clusters, based on the observation of the crucial interdependence between the short range hydrogen bonding network and polar residue states, thus significantly reducing the computational complexity of the problem and making our algorithm tractable using relatively modest computational resources. We utilize an all atom protein force field (OPLS) and a Generalized Born continuum solvation model, in contrast to the various empirical force fields adopted in most previous studies. We have compared our prediction results with a few well-documented methods in the literature (WHATIF, REDUCE). In addition, as a preliminary attempt to couple our polar state assignment method with real structure predictions, we further validate our method using single side chain prediction, which has been demonstrated to be an effective way of validating structure prediction methods without incurring sampling problems. Comparisons of single side chain prediction results after the application of our polar state prediction method with previous results with default polar state assignments indicate a significant improvement in the single side chain predictions for polar residues. Proteins 2007. © 2006 Wiley-Liss, Inc.

Understanding the regulation mechanisms of PAF receptor by agonists and antagonists: Molecular modeling and molecular dynamics simulation studies
Platelet-activating factor receptor (PAFR) is a member of G-protein coupled receptor (GPCR) superfamily. Understanding the regulation mechanisms of PAFR by its agonists and antagonists at the atomic level is essential for designing PAFR antagonists as drug candidates for treating PAF-mediated diseases. In this study, a 3D model of PAFR was constructed by a hierarchical approach integrating homology modeling, molecular docking and molecular dynamics (MD) simulations. Based on the 3D model, regulation mechanisms of PAFR by agonists and antagonists were investigated via three 8-ns MD simulations on the systems of apo-PAFR, PAFR-PAF and PAFR-GB. The simulations revealed that binding of PAF to PAFR triggers the straightening process of the kinked helix VI, leading to its activated state. In contrast, binding of GB to PAFR locks PAFR in its inactive state. Proteins 2007. © 2007 Wiley-Liss, Inc.


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