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61.
Robert M. Stroud Senyon Choe James Holton H. Ronald Kaback Witek Kwiatkowski Daniel L. Minor Roland Riek Andrej Sali Henning Stahlberg William Harries 《Journal of structural and functional genomics》2009,10(2):193-208
A synopsis of the 2007 annual progress report for the Center for Structures of Membrane Proteins, a specialized center of
the Protein Structure Initiative. 相似文献
62.
Berman HM Burley SK Chiu W Sali A Adzhubei A Bourne PE Bryant SH Dunbrack RL Fidelis K Frank J Godzik A Henrick K Joachimiak A Heymann B Jones D Markley JL Moult J Montelione GT Orengo C Rossmann MG Rost B Saibil H Schwede T Standley DM Westbrook JD 《Structure (London, England : 1993)》2006,14(8):1211-1217
63.
Parthasarathy Sampathkumar Frances Lu Xun Zhao Zhenzhen Li Jeremiah Gilmore Kevin Bain Marc E. Rutter Tarun Gheyi Kenneth D. Schwinn Jeffrey B. Bonanno Ursula Pieper J. Eduardo Fajardo Andras Fiser Steven C. Almo Subramanyam Swaminathan Mark R. Chance David Baker Shane Atwell Devon A. Thompson J. Spencer Emtage Stephen R. Wasserman Andrej Sali J. Michael Sauder Stephen K. Burley 《Proteins》2010,78(14):3056-3062
64.
Parthasarathy Sampathkumar Sinem A. Ozyurt Johnny Do Kevin T. Bain Mark Dickey Logan A. Rodgers Tarun Gheyi Andrej Sali Seung Joong Kim Jeremy Phillips Ursula Pieper Javier Fernandez‐Martinez Josef D. Franke Anne Martel Hiro Tsuruta Shane Atwell Devon A. Thompson J. Spencer Emtage Stephen R. Wasserman Michael P. Rout J. Michael Sauder Stephen K. Burley 《Proteins》2010,78(8):1992-1998
65.
66.
Comparative protein structure modeling by iterative alignment,model building and model assessment 总被引:2,自引:0,他引:2
Comparative or homology protein structure modeling is severely limited by errors in the alignment of a modeled sequence with related proteins of known three-dimensional structure. To ameliorate this problem, we have developed an automated method that optimizes both the alignment and the model implied by it. This task is achieved by a genetic algorithm protocol that starts with a set of initial alignments and then iterates through re-alignment, model building and model assessment to optimize a model assessment score. During this iterative process: (i) new alignments are constructed by application of a number of operators, such as alignment mutations and cross-overs; (ii) comparative models corresponding to these alignments are built by satisfaction of spatial restraints, as implemented in our program MODELLER; (iii) the models are assessed by a variety of criteria, partly depending on an atomic statistical potential. When testing the procedure on a very difficult set of 19 modeling targets sharing only 4–27% sequence identity with their template structures, the average final alignment accuracy increased from 37 to 45% relative to the initial alignment (the alignment accuracy was measured as the percentage of positions in the tested alignment that were identical to the reference structure-based alignment). Correspondingly, the average model accuracy increased from 43 to 54% (the model accuracy was measured as the percentage of the Cα atoms of the model that were within 5 Å of the corresponding Cα atoms in the superposed native structure). The present method also compares favorably with two of the most successful previously described methods, PSI-BLAST and SAM. The accuracy of the final models would be increased further if a better method for ranking of the models were available. 相似文献
67.
de Lorimier RM Smith JJ Dwyer MA Looger LL Sali KM Paavola CD Rizk SS Sadigov S Conrad DW Loew L Hellinga HW 《Protein science : a publication of the Protein Society》2002,11(11):2655-2675
Bacterial periplasmic binding proteins (bPBPs) are specific for a wide variety of small molecule ligands. bPBPs undergo a large, ligand-mediated conformational change that can be linked to reporter functions to monitor ligand concentrations. This mechanism provides the basis of a general system for engineering families of reagentless biosensors that share a common physical signal transduction functionality and detect many different analytes. We demonstrate the facility of designing optical biosensors based on fluorophore conjugates using 8 environmentally sensitive fluorophores and 11 bPBPs specific for diverse ligands, including sugars, amino acids, anions, cations, and dipeptides. Construction of reagentless fluorescent biosensors relies on identification of sites that undergo a local conformational change in concert with the global, ligand-mediated hinge-bending motion. Construction of cysteine mutations at these locations then permits site-specific coupling of environmentally sensitive fluorophores that report ligand binding as changes in fluorescence intensity. For 10 of the bPBPs presented in this study, the three-dimensional receptor structure was used to predict the location of reporter sites. In one case, a bPBP sensor specific for glutamic and aspartic acid was designed starting from genome sequence information and illustrates the potential for discovering novel binding functions in the microbial genosphere using bioinformatics. 相似文献
68.
Structural genomics: a pipeline for providing structures for the biologist 总被引:7,自引:0,他引:7 下载免费PDF全文
69.
Overexpression of 15-lipoxygenase-1 induces growth arrest through phosphorylation of p53 in human colorectal cancer cells 总被引:3,自引:0,他引:3
To investigate the function of 15-lipoxygenase-1 (15-LOX-1) in human colorectal cancer, we overexpressed 15-LOX-1 in HCT-116 human colorectal cancer cells. Clones expressing the highest levels of 15-LOX-1 displayed reduced viability compared with the HCT-116-Vector control cells. Further, by cell cycle gene array analyses, the cyclin-dependent kinase inhibitor p21WAF1/CIP1 and MDM2 genes were up-regulated in 15-LOX-1-overexpressing cells. The induction of p21(WAF1/CIP1) and MDM2 were linked to activation of p53 by 15-LOX-1, as there was a dramatic induction of phosphorylated p53 (Ser15) in 15-LOX-1-overesxpressing cells. However, the 15-LOX-1 metabolites 13(S)-hydroxyoctadecadienoic acid and 15(S)-hydroxyeicosatetraenoic acid failed to induce phosphorylation of p53 at Ser15, and the 15-LOX-1 inhibitor PD146176 did not inhibit the phosphorylation of p53 at Ser15 in 15-LOX-1-overexpressing cells. Nonetheless, the growth-inhibitory effects of 15-LOX-1 were p53 dependent, as 15-LOX-1 overexpression had no effect on cell growth in p53 (-/-) HCT-116 cells. Finally, treatment of HCT-116-15-LOX-1 cells with different kinase inhibitors suggested that the effects of 15-LOX-1 on p53 phosphorylation and activation were due to effects on DNA-dependent protein kinase. Collectively, these findings suggest a new mechanism to explain the biological activity of 15-LOX-1, where 15-LOX plays a stoichiometric role in activating a DNA-dependent protein kinase-dependent pathway that leads to p53-dependent growth arrest. 相似文献
70.
A structural perspective on protein-protein interactions 总被引:1,自引:0,他引:1
Russell RB Alber F Aloy P Davis FP Korkin D Pichaud M Topf M Sali A 《Current opinion in structural biology》2004,14(3):313-324