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タグ: allostery [173 articles]

Recent papers classified by the tag allostery.
  • Evolutionarily conserved networks of residues mediate allosteric communication in proteins.
    Nat Struct Biol, Vol. 10, No. 1. (January 2003), pp. 59-69.
    by GM Süel, SW Lockless, MA Wall, R Ranganathan
    posted to allostery by yalexeev on 2008-03-21 17:21:12 as ** along with 15 people and 3 groups lna dimka marcius eckart_bindewald gbart analogAI nirfriedman dgront caporaso choonpeng efge carlescorbi mingzhi weisblum ca3295 biomedical-nlp BioinfoCIPF SGU-CIPF
  • Allostery without conformational change
    European Biophysics Journal, Vol. 11, No. 2. (1 October 1984), pp. 103-109.
    by A Cooper, DTF Dryden
    posted to allostery by viktor21614 on 2007-08-21 20:36:30 as ****
  • A Computational Investigation of Allostery in the Catabolite Activator Protein
    J. Am. Chem. Soc., Vol. 129, No. 50. (19 December 2007), pp. 15668-15676.
    by L Li, VN Uversky, AK Dunker, SO Meroueh
    posted to allostery electrostatics molecular_simulation solvation by sobolevnrm on 2007-12-27 12:44:54 as read along with 1 person and 1 group ruvido baker-group
  • Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play.
    J Mol Biol (29 February 2008)
    by Chung-Jung J Tsai, Antonio Del Sol, Ruth Nussinov
    posted to allostery by sobolevnrm on 2008-03-31 12:10:12 as read along with 6 people and 3 groups barry choonpeng cactus CameronNeylon higueruelo cchang structural_bioinformatics McCammon group
  • Ordered water molecules as key allosteric mediators in a cooperative dimeric hemoglobin
    Proceedings of the National Academy of Sciences, Vol. 93, No. 25. (10 December 1996), pp. 14526-14531.
    by William e Royer, Animesh Pardanani, Quentin h Gibson, Eric s Peterson, Joel m Friedman
    posted to allostery solvation by sobolevnrm on 2008-02-15 12:43:24 as read along with 1 group baker-group
  • Conformational Switching upon Phosphorylation: A Predictive Framework Based on Energy Landscape Principles
    Biochemistry (17 January 2008)
    by J Latzer, T Shen, PG Wolynes
    posted to allostery molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2008-01-17 12:32:48 as read along with 2 people and 1 group neils paulschlesinger baker-group
  • Intrinsic motions along an enzymatic reaction trajectory
    Nature (18 November 2007)
    by Katherine A Henzler-Wildman, Vu Thai, Ming Lei, Maria Ott, Magnus Wolf-Watz, Tim Fenn, Ed Pozharski, Mark A Wilson, Gregory A Petsko, Martin Karplus, Christian G Hübner, Dorothee Kern
    posted to allostery molecular_dynamics quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-12-20 12:39:49 as read along with 6 people and 1 group aqeel ebeutler cactus paulschlesinger jlh64 yalexeev baker-group
  • How Directional Translocation is Regulated in a DNA Helicase Motor
    Biophys. J. (17 August 2007), biophysj.107.109546.
    by Jin Yu, Taekjip Ha, Klaus Schulten
    posted to allostery helicase quasiharmonic-models_elastic-network_gnm_nma_pca_etc correlatedmutations by sobolevnrm on 2007-08-26 19:58:10 as read along with 1 group baker-group
  • Molecular Dynamics of Apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations
    J. Phys. Chem. B, Vol. 110, No. 47. (30 November 2006), pp. 24121-24137.
    by H Lou, RI Cukier
    posted to allostery enhanced_sampling molecular_simulation by sobolevnrm on 2007-12-05 12:35:49 as read along with 1 person and 1 group allmensch baker-group
  • Contact rearrangements form coupled networks from local motions in allosteric proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Michael D Daily, Tarak J Upadhyaya, Jeffrey J Gray
    posted to allostery molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc correlatedmutations by sobolevnrm on 2007-11-08 12:54:28 as read along with 1 group baker-group
  • Hamiltonian and Distance Replica Exchange Method Studies of Met-Enkephalin
    J. Phys. Chem. B, Vol. 111, No. 42. (25 October 2007), pp. 12310-12321.
    by L Su, RI Cukier
    posted to allostery enhanced_sampling molecular_simulation by sobolevnrm on 2007-12-05 12:35:23 as ** along with 1 group baker-group
  • Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design
    Proceedings of the National Academy of Sciences, Vol. 105, No. 3. (22 January 2008), pp. 901-906.
    by Jin Liu, Ruth Nussinov
    posted to allostery molecular_dynamics by sobolevnrm on 2008-02-21 12:30:30 as read along with 1 person and 1 group cactus baker-group
  • Signal Propagation in Proteins and Relation to Equilibrium Fluctuations
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e172.
    by Chakra Chennubhotla, Ivet Bahar
    posted to allostery quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-10-04 12:39:43 as read along with 1 group baker-group
  • Allosteric cooperativity in protein kinase A
    Proceedings of the National Academy of Sciences, Vol. 105, No. 2. (15 January 2008), pp. 506-511.
    by Larry R Masterson, Alessandro Mascioni, Nathaniel J Traaseth, Susan S Taylor, Gianluigi Veglia
    posted to allostery nmr by sobolevnrm on 2008-02-19 12:21:06 as read along with 2 people and 1 group ruvido cactus baker-group
  • Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
    Proceedings of the National Academy of Sciences (13 November 2007), 0706443104.
    by Karunesh Arora, Charles L Brooks
    posted to allostery molecular_simulation by sobolevnrm on 2007-11-21 12:45:51 as read along with 5 people and 2 groups barry allmensch cactus jlh64 karunesh structural_bioinformatics baker-group
  • A Coupled Equilibrium Shift Mechanism in Calmodulin-Mediated Signal Transduction
    Structure, Vol. 16, No. 5. (7 May 2008), pp. 736-746.
    by Jörg Gsponer, John Christodoulou, Andrea Cavalli, Jennifer M Bui, Barbara Richter, Christopher M Dobson, Michele Vendruscolo
    posted to allostery quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2008-06-20 11:32:37 as read along with 1 group baker-group
  • Molecular Dynamics Simulation of the Escherichia coli NikR Protein: Equilibrium Conformational Fluctuations Reveal Interdomain Allosteric Communication Pathways
    Journal of Molecular Biology, Vol. In Press, Corrected Proof
    by Michael J Bradley, Peter T Chivers, Nathan A Baker
    posted to allostery metalloregulation molecular_dynamics by sobolevnrm on 2008-04-26 14:52:57 as read along with 2 people and 2 groups skoddet barry baker-group structural_bioinformatics
  • Reassessing a sparse energetic network within a single protein domain
    Proceedings of the National Academy of Sciences (13 March 2008), 0711732105.
    by Celestine N Chi, Lisa Elfstrom, Yao Shi, Tord Snall, Ake Engstrom, Per Jemth
    posted to allostery correlatedmutations by sobolevnrm on 2008-04-30 11:02:56 as read along with 4 people and 1 group apaydin cjeans cactus sunhwan baker-group
  • The signaling pathway of rhodopsin.
    Structure, Vol. 15, No. 5. (May 2007), pp. 611-623.
    by Y Kong, M Karplus
    posted to allostery quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2008-07-11 12:18:57 as read along with 2 people and 1 group vahmurk dimka baker-group
  • Engineering Protein Allostery: 1.05 Å Resolution Structure and Enzymatic Properties of a Na+-activated Trypsin
    Journal of Molecular Biology, Vol. 378, No. 3. (2 May 2008), pp. 666-672.
    by Michael J Page, Christopher J Carrell, Enrico Di Cera
    posted to allostery protein_engineering protein-ligand_interactions thrombin by sobolevnrm on 2008-05-03 12:32:51 as read along with 1 group baker-group
  • Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
    Current Opinion in Structural Biology, Vol. 17, No. 6. (December 2007), pp. 633-640.
    by Ivet Bahar, Chakra Chennubhotla, Dror Tobi
    posted to allostery quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-12-04 16:45:11 as read along with 8 people and 4 groups barry aqeel ruvido cactus jennifermbui higueruelo LamBras jmccammon structural_bioinformatics Bioinformatics baker-group McCammon
  • Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling
    Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 2. (2006), pp. 347-361.
    by Kim Sharp, John J Skinner
    posted to allostery molecular_simulation by sobolevnrm on 2007-10-01 12:56:11 as read along with 3 people and 3 groups barry lna choonpeng structural_bioinformatics Bioinformatics baker-group
  • Illuminating the mechanistic roles of enzyme conformational dynamics
    Proceedings of the National Academy of Sciences, Vol. 104, No. 46. (13 November 2007), pp. 18055-18060.
    by Jeffrey A Hanson, Karl Duderstadt, Lucas P Watkins, Sucharita Bhattacharyya, Jason Brokaw, Jhih-Wei Chu, Haw Yang
    posted to allostery by sobolevnrm on 2007-12-10 12:36:26 as read along with 1 person and 1 group biehl baker-group
  • Transition networks for modeling the kinetics of conformational change in macromolecules
    Current Opinion in Structural Biology, Vol. 18, No. 2. (April 2008), pp. 154-162.
    by Frank Noé, Stefan Fischer
    posted to allostery diffusion kinetics molecular_simulation by sobolevnrm on 2008-04-18 11:47:00 as read along with 4 people and 3 groups aqeel barry paulschlesinger toerst structural_bioinformatics baker-group McCammon
  • Dynamics of Recognition between tRNA and Elongation Factor Tu
    Journal of Molecular Biology, Vol. 377, No. 5. (11 April 2008), pp. 1382-1405.
    by John Eargle, Alexis A Black, Anurag Sethi, Leonardo G Trabuco, Zaida Luthey-Schulten
    posted to allostery electrostatics nucleic_acids protein-nucleic_acid_interactions by sobolevnrm on 2008-03-25 11:14:57 as read along with 1 group baker-group
  • Predicting Allosteric Communication in Myosin via a Pathway ofConserved Residues
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Susan Tang, Jung-Chi Liao, Alexander R Dunn, Russ B Altman, James A Spudich, Jeanette P Schmidt
    posted to allostery bioinformatics correlatedmutations by sobolevnrm on 2007-09-04 12:46:29 as read along with 5 people and 2 groups barry choonpeng cactus jlh64 melting structural_bioinformatics baker-group
  • Allosteric communication in Dihydrofolate Reductase: Signaling network and pathways for closed to occluded transition and back
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Jie Chen, Ruxandra I Dima, D Thirumalai
    posted to allostery by sobolevnrm on 2007-08-28 12:10:10 as read along with 1 group baker-group
  • Principles underlying energetic coupling along an allosteric communication trajectory of a voltage-activated K+ channel
    Proceedings of the National Academy of Sciences (5 December 2007), 0708120104.
    by Evgeniya Sadovsky, Ofer Yifrach
    posted to allostery biomembranes ion_channels by sobolevnrm on 2008-01-21 12:41:39 as read along with 1 person and 1 group cjeans baker-group
  • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    Nature (18 November 2007)
    by Katherine A Henzler-Wildman, Ming Lei, Vu Thai, Jordan S Kerns, Martin Karplus, Dorothee Kern
    posted to allostery molecular_dynamics quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-12-20 12:39:26 as read along with 7 people and 1 group tmmurali allmensch cactus jlh64 RamuAnandakrishnan dmobley chenway baker-group
  • A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis
    Proceedings of the National Academy of Sciences, Vol. 104, No. 40. (2 October 2007), pp. 15711-15716.
    by Amit Ghosh, Saraswathi Vishveshwara
    posted to allostery quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-10-08 12:57:46 as read along with 3 people and 1 group zwang cactus phoenixzxl baker-group
  • A Proposed Time-Resolved X-Ray Scattering Approach to Track Local and Global Conformational Changes in Membrane Transport Proteins
    Structure, Vol. 16, No. 1. (8 January 2008), pp. 21-28.
    by Magnus Andersson, Jonathan Vincent, David van der Spoel, Jan Davidsson, Richard Neutze
    posted to allostery experimental_methodology molecular_dynamics by sobolevnrm on 2008-02-13 12:52:10 as read along with 1 person and 1 group r2s2 baker-group
  • Evidence for Subdomain Flexibility in Drosophila melanogaster Acetylcholinesterase
    Biochemistry, Vol. 47, No. 20. (20 May 2008), pp. 5599-5607.
    by Jure Stojan, Caroline Ladurantie, Omid R Siadat, Laurent Paquereau, Didier Fournier
    posted to acetylcholinesterase allostery by sobolevnrm on 2008-06-30 11:35:00 as read along with 1 group baker-group
  • Structural identification of the pathway of long-range communication in an allosteric enzyme
    Proceedings of the National Academy of Sciences, Vol. 105, No. 6. (12 February 2008), pp. 1832-1837.
    by Prafull S Gandhi, Zhiwei Chen, Scott F Mathews, Enrico Di Cera
    posted to allostery structure thrombin by sobolevnrm on 2008-03-04 12:37:52 as read along with 2 people and 1 group lna cactus baker-group
  • The origin of protein interactions and allostery in colocalization
    Nature, Vol. 450, No. 7172. (12 December 2007), pp. 983-990.
    by John Kuriyan, David Eisenberg
    posted to allostery bioinformatics protein-protein_interactions structure by sobolevnrm on 2008-01-22 12:31:35 as read along with 4 people and 1 group cjeans mingzhi phoenixzxl higueruelo baker-group
  • Dynamic personalities of proteins
    Nature, Vol. 450, No. 7172. (12 December 2007), pp. 964-972.
    by Katherine Henzler-Wildman, Dorothee Kern
    posted to allostery experimental_methodology molecular_dynamics protein_folding protein-ligand_interactions by sobolevnrm on 2008-01-22 12:33:20 as read along with 12 people and 1 group pavanghatty chad_davis allmensch choonpeng rsantana cjeans wilbur mijam kjell phoenixzxl higueruelo GeeSharpMinor baker-group
  • Coarse-Grained Free Energy Functions for Studying Protein Conformational Changes: A Double-Well Network Model
    Biophys. J., Vol. 93, No. 11. (1 December 2007), pp. 3860-3871.
    by Jhih-Wei Chu, Gregory A Voth
    posted to allostery molecular_simulation multiscale quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-11-16 00:47:06 as read along with 1 person and 1 group jlh64 baker-group
  • The Allosteric Mechanism of Yeast Chorismate Mutase: A Dynamic Analysis
    Journal of Molecular Biology, Vol. 356, No. 1. (10 February 2006), pp. 237-247.
    by Yifei Kong, Jianpeng Ma, Martin Karplus, William N Lipscomb
    posted to allostery tmd by ruvido on 2008-02-22 12:05:19 as ** along with 2 people and 2 groups barry higueruelo structural_bioinformatics Bioinformatics
  • Networks for the allosteric control of protein kinases
    Current Opinion in Structural Biology, Vol. 16, No. 6. (December 2006), pp. 686-692.
    by Zhengshuang Shi, Katheryn A Resing, Natalie G Ahn
    posted to kinases allostery by ruvido on 2008-09-02 09:07:48 as ** along with 2 people lna choonpeng
  • Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 A resolution.
    J Mol Biol, Vol. 304, No. 5. (15 December 2000), pp. 847-859.
    by JM Passner, SC Schultz, TA Steitz
    posted to allostery cap xray by ruvido on 2008-02-18 10:21:49 as read
  • Role of residue 138 in the interdomain hinge region in transmitting allosteric signals for DNA binding in Escherichia coli cAMP receptor protein.
    Biochemistry, Vol. 43, No. 16. (27 April 2004), pp. 4662-4669.
    by S Yu, JC Lee
    posted to allostery cap dynamics mutations by ruvido on 2008-02-22 10:03:43 as **
  • Communications between the high-affinity cyclic nucleotide binding sites in E. coli cyclic AMP receptor protein: effect of single site mutations.
    Biochemistry, Vol. 41, No. 39. (1 October 2002), pp. 11857-11867.
    by SH Lin, JC Lee
    posted to allostery cap kinetics by ruvido on 2008-02-22 09:33:56 as **
  • Allostery and cooperativity revisited
    Protein Sci, Vol. 17, No. 8. (1 August 2008), pp. 1295-1307.
    by Qiang Cui, Martin Karplus
    posted to protein dynamics allostery by ruvido on 2008-09-12 11:20:02 as ** along with 2 people agrossfield tny
  • Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble.
    Proc Natl Acad Sci U S A, Vol. 97, No. 22. (24 October 2000), pp. 12020-12025.
    by H Pan, JC Lee, VJ Hilser
    posted to allostery dhfr by ruvido on 2007-05-08 18:11:55 as ** along with 2 people lna dgront
  • Structural Understanding of the Allosteric Conformational Change of Cyclic AMP Receptor Protein by Cyclic AMP Binding
    Biochemistry, Vol. 39, No. 45. (14 November 2000), pp. 13953-13962.
    by HS Won, T Yamazaki, TW Lee, MK Yoon, SH Park, Y Kyogoku, BJ Lee
    posted to allostery cap by ruvido on 2008-02-22 08:23:38 as **
  • A tertiary two-state allosteric model for hemoglobin
    Biophysical Chemistry, Vol. 98, No. 1-2. (10 July 2002), pp. 149-164.
    by Eric R Henry, Stefano Bettati, James Hofrichter, William A Eaton
    posted to allostery hemoglobin mwc population_shifts by ruvido on 2007-05-08 17:48:36 as **
  • Structural Model of the R State of Escherichia coli Aspartate Transcarbamoylase with Substrates Bound
    Journal of Molecular Biology, Vol. 371, No. 5. (31 August 2007), pp. 1261-1273.
    by Jie Wang, Joby Eldo, Evan R Kantrowitz
    posted to allostery catalysis enzyme by ruvido on 2007-08-09 14:39:45 as **
  • Is allostery an intrinsic property of all dynamic proteins?
    Proteins, Vol. 57, No. 3. (15 November 2004), pp. 433-443.
    by K Gunasekaran, B Ma, R Nussinov
    posted to allostery population_shifts by ruvido on 2007-05-04 15:15:25 as ** along with 5 people lna gbart leemary4 choonpeng cactus
  • Structure of the CAP-DNA Complex at 2.5 Å Resolution: A Complete Picture of the Protein-DNA Interface
    Journal of Molecular Biology, Vol. 260, No. 3. (19 July 1996), pp. 395-408.
    by Gary Parkinson, Christopher Wilson, Angelo Gunasekera, Yon W Ebright, Richard E Ebright, Helen M Berman
    posted to protein cap_dna cap allostery by ruvido on 2008-09-15 10:54:00 as **
  • The changing landscape of protein allostery.
    Curr Opin Struct Biol, Vol. 16, No. 1. (February 2006), pp. 102-108.
    by JF Swain, LM Gierasch
    posted to allostery population_shifts by ruvido on 2007-05-04 15:12:46 as ** along with 4 people nigham lna choonpeng mottonen
  • New insights into allosteric mechanisms from trapping unstable protein conformations in silica gels
    PNAS, Vol. 101, No. 40. (5 October 2004), pp. 14414-14419.
    by Cristiano Viappiani, Stefano Bettati, Stefano Bruno, Luca Ronda, Stefania Abbruzzetti, Andrea Mozzarelli, William A Eaton
    posted to allostery hemoglobin mwc population_shifts by ruvido on 2007-05-08 17:54:16 as **
    • 注: このページを引用する時は次のURLでどうぞ: http://www.citeulike.org/tag/allostery

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