If you would like to submit feedback regarding any Health Tags direct all correspondence to:

Retroviruses are the worst sort of guest. Over eons, these molecular parasites have insinuated themselves into their hosts? DNA and caused a ruckus. The poor hosts can?t even be rid of the intruders by killing them, because they stubbornly remain after death., delicious.com

Journal of Computational Chemistry, Vol. 9999, No. 9999. (2007), NA.Computational protein design will continue to improve as new implementations and parameterizations are explored. An automated protein design procedure is implemented and applied to the full redesign of 16 globular proteins. We combine established but simple ingredients: a molecular mechanics description of the protein where nonpolar hydrogens are implicit, a simple solvent model, a folded state where the backbone is fixed, and a tripeptide model of the unfolded state. Sequences are selected to optimize the folding free energy, using a simple heuristic algorithm to explore sequence and conformational space. We show that a balanced parametrization, obtained here and in our previous work, makes this procedure effective, despite the simplicity of the ingredients. Calculations were done using our Proteins @ Home distributed computing platform, with the help of several thousand volunteers. We describe the software implementation, the optimization of selected terms in the energy function, and the performance of the method. We allowed all amino acids to mutate except glycines, prolines, and cysteines. For 15 of the 16 test proteins, the scores of the computed sequences were comparable to those of natural homologues. Using the low energy computed sequences in a BLAST search of the SWISSPROT database, we could retrieve natural sequences for all protein families considered, with no high-ranking false-positives. The good stability of the designed sequences was supported by molecular dynamics simulations of selected sequences, which gave structures close to the experimental native structure. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007Marcel, Anne Lopes, David Mignon, Thomas Simonson, citeulike.org

J Am Chem Soc, Vol. 126, No. 49. (15 December 2004), pp. 15948-15949.PJ Bond, JM Cuthbertson, SS Deol, MS Sansom, citeulike.org

A protein which helps a baby's gut develop in the womb could hold the key to treating bowel disorders, according to scientists. Edinburgh University tests suggest flaws in the GLI1 protein could cause inflammatory bowel diseases like Crohn's and ulcerative colitis., delicious.com

Nat Struct Mol Biol, Vol. 2, No. 10. (October 1995), pp. 852-855.George Makhatadze, Marius Clore, Angela Gronenborn, citeulike.org

J. Phys. Chem. B, Vol. 102, No. 10. (5 March 1998), pp. 1797-1805.Abstract: Water molecules buried inside a protein are often considered as an integral part of the structure and are increasingly used as NMR probes to study the dynamics of proteins (Denisov, V.; Peters, J.; Horlein, H. D.; Halle, B. Nat. Struct. Biol. 1996, 3, 505). The present calculations give new insights into the mobility of such structural water. Reaction path calculations using conjugate peak refinement (Fischer, S.; Karplus, M. Chem. Phys. Lett. 1992, 194, 252) are carried out to compute the transition state and activation energy (9.7 kcal mol-1) for the rotation of a water molecule buried in the protein bovine pancreatic trypsin inhibitor. These are compared to the values calculated (10-12.3 kcal mol-1) for the same process in ice, for which the experimental value has been determined (12.8 ± 0.9 kcal mol-1). The process, which results in the interchange of the two water hydrogens, is similar in both systems. It is not a simple C2-flip of the buried water, but a complex motion involving two successive rotations around orthogonal axes. A normal-mode analysis performed on the ground and transition states of the protein enables the correction for the vibrational entropy to be included in the derivation of the rotational correlation time (45 ns) of the buried water. Vibrational frequencies up to 620 cm-1 are found to contribute, thus requiring the inclusion of quantum effects. A fluctuation frequency of 20-50 cm-1 along the curvilinear reaction path is derived, which leads to a vibrational entropy of activation of 8.6 cal mol-1 K-1.S Fischer, CS Verma, RE Hubbard, citeulike.org