A comprehensive update of the sequence and structure classification of kinases
- Intrinsic disorder prediction from the analysis of multiple protein fold recognition models. // Bioinformatics;Aug2008, Vol. 24 Issue 16, p1798
Motivation: Intrinsic protein disorder is functionally implicated in numerous biological roles and is, therefore, ubiquitous in proteins from all three kingdoms of life. Determining the disordered regions in proteins presents a challenge for experimental methods and so recently there has been...
- Protein Folding. // Encyclopedic Reference of Molecular Pharmacology;2004, p757
An encyclopedia entry for protein folding is presented. It explains that proteins fold on a time scale from Âµseconds to seconds. Starting from a random coil conformation, proteins can find their stable fold quickly, although the number of possible conformation is astronomically high.
- Thinking outside the box: new insights into the mechanism of GroEL-mediated protein folding. Wang, Jue D.; Weissman, Jonathan S. // Nature Structural Biology;Jul99, Vol. 6 Issue 7, p597
GroEL is thought to assist protein folding in part by providing a passive 'box' in which folding can occur without danger of aggregation. Two new papers now suggest that GroEL can also play a more active role by promoting rearrangement and even unfolding of kinetic folding intermediates.
- The complete folding pathway of a protein from nanoseconds to microseconds. Mayor, Ugo; Guydosh, Nicholas R.; Johnson, Christopher M.; Grossmann, J. Günter; Sato, Satoshi; Jas, Gouri S.; Freund, Stefan M. V.; Alonso, Darwin O. V.; Daggett, Valerie; Fersht, Alan R. // Nature;2/20/2003, Vol. 421 Issue 6925, p863
Combining experimental and simulation data to describe all of the structures and the pathways involved in folding a protein is problematical. Transition states can be mapped experimentally by Ï† values, but the denatured state is very difficult to analyse under conditions that favour folding....
- Folding consensus? Baldwin, Robert L. // Nature Structural Biology;Feb2001, Vol. 8 Issue 2, p92
Deals with studies that address contradictions about the use of the hierarchic mechanism for the folding process in both two-state and three-state folding reactions. Discussion on the Î²-lactoglobulin foldingl Im7 folding; Folding simulations.
- Connecting statistical and optimized potentials in protein folding via a generalized foldability criterion. Saven, Jeffery G. // Journal of Chemical Physics;4/8/2003, Vol. 118 Issue 14, p6133
Developing a predictive understanding of protein folding requires quantitative measures of sequence-structure compatibility. A folding criterion is presented whose optimization over a training set of structures yields the commonly used statistical and optimized potentials as two limiting cases,...
- Investigation of the folding profiles of evolutionarily selected model proteins. Nelson, Erik; Grishin, Nick // Journal of Chemical Physics;2/15/2003, Vol. 118 Issue 7, p3342
Minimalist models of proteins, in which amino acid chains are represented by a necklace of beads that reconfigure the native fold on the sites of a cubic lattice, have been an important tool to infer early events in folding and to typify the energy landscapes of small globular proteins. In this...
- Heat shock factor 1 ameliorates proteotoxicity in cooperation with the transcription factor NFAT. Hayashida, Naoki; Fujimoto, Mitsuaki; Tan, Ke; Prakasam, Ramachandran; Shinkawa, Toyohide; Liangping Li; Ichikawa, Hitoshi; Takii, Ryosuke; Nakai, Akira // EMBO Journal;10/20/2010, Vol. 29 Issue 20, p3459
Heat shock transcription factor 1 (HSF1) is an important regulator of protein homeostasis (proteostasis) by controlling the expression of major heat shock proteins (Hsps) that facilitate protein folding. However, it is unclear whether other proteostasis pathways are mediated by HSF1. Here, we...
- Connectivity of Neutral Networks, Overdispersion, and Structural Conservation in Protein Evolution. Bastolla, Ugo; Porto, Markus; Roman, H. Eduardo; Vendruscolo, Michele H. // Journal of Molecular Evolution;Mar2003, Vol. 56 Issue 3, p243
Protein structures are much more conserved than sequences during evolution. Based on this observation, we investigate the consequences of structural conservation on protein evolution. We study seven of the most studied protein folds, determining that an extended neutral network in sequence space...