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.


Thanks for stopping in! We hope you'll be back!

Ads make the world go around. Help us out!

2007 week 05: Articles of Related Interest

ENTIRE CATALOG OF FERRET PROTEINS TO DATE


Chopping Off Protein Puts Immune Cells Into High Gear
The complex task of launching a well-organized, effective immune system attack on specific targets is thrown into high gear when either of two specific enzymes chop a protein called LAG-3 off the immune cells leading that battle, according to investigators at St. Jude Children's Research Hospital.

Role For Proteomics In Identifying Hematologic Malignancies
Scientists have identified a set of biomarkers that could help clinicians identify a group of hematologic malignancies known as myelodysplastic syndromes (MDS), which affect approximately 300,000 individuals worldwide and often progress to acute myeloid leukemia.

Motor protein plays key role in connecting neurons
A motor protein called myosin X runs the main road of a developing neuron, delivering to its tip a receptor that enables it to communicate with other neurons, scientists say. In another piece of the puzzle of how neurons form connections, researchers have found myosin X travels a portion of a neuron's backbone called the actin filament, a sort of two-way highway in the cell's highest traffic area, says Dr. Wen-Cheng Xiong, developmental neurobiologist at the Medical College of Georgia.

'Quiet Revolution' May Herald New RNA Therapeutics
Scientists at the University of Oxford have identified a surprising way of switching off a gene involved in cell division. The mechanism involves a form of RNA, a chemical found in cell nuclei, whose role was previously unknown, and could have implications for preventing the growth of tumour cells.
RNA plays an important and direct role in the synthesis of proteins, the building blocks of our bodies. However, scientists have known for some time that not all types of RNA are directly involved in protein synthesis. Now, in research funded by the Wellcome Trust and the Medical Research Council, a team of scientists has shown that one particular type of RNA plays a key role in regulating the gene implicated in control of tumour growth. The research is published online today in Nature.

Chemical Switch Triggers Critical Cell Activities
The freeze-frame image of a molecular relay race, in which one enzyme passes off a protein like a baton to another enzyme, has solved a key mystery to how cells control some vital functions, according to investigators at St. Jude Children's Research Hospital. A report on this work appears in the January 14 advanced online publication issue of Nature.

Buckyballs used as 'passkey' into cancer cells
Rice University chemists and Baylor College of Medicine pediatric scientists have discovered how to use buckyballs as passkeys that allows drugs to enter cancer cells. Research in the January 21 issue of the journal Organic and Biomolecular Chemistry, describes how the researchers mimicked the techniques used by some viruses to introduce non-toxic bits of buckyball-containing protein into both neuroblastoma and liver cancer cells.

Filamins Tether Cystic Fibrosis Protein To Cell Surface
Cystic fibrosis (CF) is caused by mutations in a gene that encodes a protein known as CFTR. More than 1000 different disease-causing mutations in CFTR have been identified, and although the overall effect of each mutation is to decrease CFTR expression at the cell surface, it is not known for every one of these mutations what the molecular defect is that causes the decreased cell surface expression of CFTR.
From the article itself: "Our data demonstrate what we believe to be a previously unrecognized role for the CFTR N terminus in the regulation of the plasma membrane stability and metabolic stability of CFTR. In addition, we elucidate the molecular defect associated with the S13F mutation."

Breakthrough Could Prevent Multiple Fibrotic Diseases: Tests Find Protein Stops Fibrosis In Lung, Heart, Other Tissues Science Daily
A scientific breakthrough at Rice University could lead to the first treatment that prevents the build-up of deadly scar tissue in a broad class of diseases that account for an estimated 45 percent of U.S. deaths each year.
"Fibrotic diseases kill so many people because they can crop up in almost any part of the body, and cardiac fibrosis is a particular problem for anyone who's had a heart attack," said Richard Gomer, professor of biochemistry and cell biology at Rice. "We've discovered a naturally occurring blood protein that prevents dangerous scar tissue from forming."

Brown team finds crucial protein role in deadly prion spread
Brown University biologists have made another major advance toward understanding the deadly work of prions, the culprits behind fatal brain diseases such as mad cow and their human counterparts. In new work published online in PLoS Biology, researchers show that the protein Hsp104 must be present and active for prions to multiply and cause disease.

Scripps Research study reveals new function of protein kinase pathway in tumor suppression
Scientists at the Scripps Research Institute have discovered a surprising new function of a well-known signaling pathway that, when activated, can inhibit tumor development. This finding may lead to the development of drugs that can serve as an effective cancer therapy by artificially activating this pathway in cancer cells.

Disabling key protein may give physicians time to treat pneumonic plague
The deadly attack of the bacterium that causes pneumonic plague is significantly slowed when it can't make use of a key protein, scientists at Washington University School of Medicine in St. Louis report in this week's issue of Science.

Thanks for stopping in! We hope you'll be back!

Ads make the world go around. Help us out!