Member Publications

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75 Member Publications for July 2011

Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis.
1. Nat Genet - published July 31, 2011
2. MG Vander Heiden, LC Cantley, JS Brugge, JM Asara, G Wagner, L Chin, AL Richardson, M Meyerson, AH Ligon, G Stephanopoulos, R Beroukhim, M Sasaki, NI Vokes, E Mullarky, D Anastasiou, AT Sasaki, H Sharfi, T Muranen, CM Metallo, G Heffron, AJ Bass, KR Mattaini, CA Lyssiotis, T Melman, AR Grassian, JW Locasale
Substrate Preferences and Catalytic Parameters Determined by Structural Characteristics of Sterol 14{alpha}-Demethylase (CYP51) from Leishmania infantum.
1. J Biol Chem - published July 29, 2011
2. GI Lepesheva, MR Waterman, WD Nes, J Liu, Z Wawrzak, TY Hargrove
Initiation complex structure and promoter proofreading.
1. Science - published July 29, 2011
2. RD Kornberg, X Huang, DA Silva, DA Bushnell, X Liu
The metalloprotease of Listeria monocytogenes is regulated by pH.
1. J Bacteriol - published July 29, 2011
2. H Marquis, H Sondermann, KJ Kota, ER Slepkov, AP Bitar, BM Forster
The Phenix software for automated determination of macromolecular structures.
1. Methods - published July 29, 2011
2. PH Zwart, TC Terwilliger, JS Richardson, DC Richardson, RJ Read, RD Oeffner, NW Moriarty, AJ McCoy, RW Grosse Kunstleve, GJ Kapral, S Jain, LW Hung, JJ Headd, N Echols, VB Chen, G Bunkóczi, PV Afonine, PD Adams
Applications of Non-Uniform Sampling and Processing.
1. Top Curr Chem - published July 28, 2011
2. G Wagner, H Arthanari, SG Hyberts
Structural basis of regiospecificity of a mononuclear iron enzyme in antibiotic fosfomycin biosynthesis.
1. J Am Chem Soc - published July 27, 2011
2. CL Drennan, HW Liu, F Yan, LJ Higgins, M Dey, D Yun
Structure of FcRY, an avian immunoglobulin receptor related to mammalian mannose receptors, and its complex with IgY.
1. Proc Natl Acad Sci U S A - published July 26, 2011
2. PJ Bjorkman, Y He
Hyperconjugation contributes to the bimodal distribution of glycine conformations observed in protein three-dimensional structures.
1. Chembiochem - published July 25, 2011
2. Z Jia, DA Pratt, B Wathen
Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching.
1. Nature - published July 24, 2011
2. JJ Chou, SC Harrison, WM Shih, MJ Berardi
A conformational switch in complexin is required for synaptotagmin to trigger synaptic fusion.
1. Nat Struct Mol Biol - published July 24, 2011
2. JE Rothman, F Pincet, KM Reinisch, J Coleman, SW Baguley, L Khandan, F Li, CG Giraudo, D Kümmel, DT Radoff, SS Krishnakumar
Complexin cross-links prefusion SNAREs into a zigzag array.
1. Nat Struct Mol Biol - published July 24, 2011
2. CG Giraudo, F Li, DT Radoff, SS Krishnakumar, D Kümmel, KM Reinisch, JE Rothman, F Pincet
Dynamics of Preferential Substrate Recognition in HIV-1 Protease: Redefining the Substrate Envelope.
1. J Mol Biol - published July 22, 2011
2. CA Schiffer, T Haliloğlu, A Ozen
PHD Finger Recognition of Unmodified Histone H3R2 Links UHRF1 to Regulation of Euchromatic Gene Expression.
1. Mol Cell - published July 22, 2011
2. Y Shi, DJ Patel, Y Xu, YG Shi, F Lan, H Li, F Wu, R Guo, Y Lin, H Chen, L Hu, H Ma, Z Wang, E Rajakumara
Transpeptidase-mediated incorporation of D-amino acids into bacterial peptidoglycan.
1. J Am Chem Soc - published July 20, 2011
2. D Kahne, S Walker, TS Wang, EH Doud, H Tsukamoto, TJ Lupoli
In vitro system capable of differentiating fast Ca2+-triggered content mixing from lipid exchange for mechanistic studies of neurotransmitter release.
1. Proc Natl Acad Sci U S A - published July 19, 2011
2. A Srivastava, M Kyoung, AT Brunger, S Chu, E Nogales, P Grob, M Vrljic, J Diao, Y Zhang
The challenge of developing robust drugs to overcome resistance.
1. Drug Discov Today - published July 19, 2011
2. NP Peet, CA Schiffer, MP Pollastri, AC Anderson
γ-Hydroxy-1,N(2)-propano-2'-deoxyguanosine DNA Adduct Conjugates the N-Terminal Amine of the KWKK Peptide via a Carbinolamine Linkage.
1. Chem Res Toxicol - published July 18, 2011
2. MP Stone, RS Lloyd, AK McCullough, CJ Rizzo, A Kozekova, MW Voehler, H Wang, H Huang
1,N(2)-Etheno-2'-deoxyguanosine Adopts the syn Conformation about the Glycosyl Bond When Mismatched with Deoxyadenosine.
1. Chem Res Toxicol - published July 18, 2011
2. MP Stone, CJ Rizzo, FP Guengerich, ID Kozekov, G Shanmugam
Crenarchaeal CdvA forms double-helical filaments containing DNA and interacts with ESCRT-III-like CdvB.
1. PLoS One - published July 16, 2011
2. Moriscot C, Gribaldo S, Jault JM, Krupovic M, Arnaud J, Jamin M, Schoehn G, Forterre P, Weissenhorn W, Renesto P
Characterization of the structure and function of Klebsiella pneumoniae allantoin racemase.
1. J Mol Biol - published July 15, 2011
2. SE Ealick, DB Neau, JB French
Structural and thermodynamic signatures of DNA recognition by Mycobacterium tuberculosis DnaA.
1. J Mol Biol - published July 15, 2011
2. T Biswas, OV Tsodikov
Nedd4-1 binds and ubiquitylates activated FGFR1 to control its endocytosis and function.
1. EMBO J - published July 15, 2011
2. D Rotin, B Ciruna, P Dirks, F Sicheri, I Clarke, S Guettler, M Hayes, P Alberts, A Persaud
Structure of the FANCI-FANCD2 complex: insights into the Fanconi anemia DNA repair pathway.
1. Science - published July 15, 2011
2. NP Pavletich, SJ Elledge, O Buzovetsky, DG Rudge, A Smogorzewska, NS Persky, G Xu, W Joo
Resistance of bulky DNA lesions to nucleotide excision repair can result from extensive aromatic lesion-base stacking interactions.
1. Nucleic Acids Res - published July 15, 2011
2. Y Cai, K Kropachev, H Mu, DA Reeves, NE Geacintov, S Broyde, DJ Patel, S Amin, J Krzeminski, Y Chen, M Kolbanovskiy, A Kolbanovskiy, S Ding
Ex vivo characterization and isolation of rare memory B cells with antigen tetramers.
1. Blood - published July 14, 2011
2. K Wucherpfennig, G Dranoff, Jr May KF, B Franz
Fragment-based phase extension for three-dimensional structure determination of membrane proteins by electron crystallography.
1. Structure - published July 13, 2011
2. T Gonen, G Wisedchaisri
Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1.
1. Structure - published July 13, 2011
2. DJ Patel, RB Darnell, SK Burley, A Teplov, K Musunuru, R Abagyan, M Lu, J Song, JC Darnell, L Malinina, M Teplova
Vaccine design reaches the atomic level.
1. Sci Transl Med - published July 13, 2011
2. L Shapiro, PD Kwong
Dephosphorylation of the nuclear factor of activated T cells (NFAT) transcription factor is regulated by an RNA-protein scaffold complex.
1. Proc Natl Acad Sci U S A - published July 12, 2011
2. A Rao, DB Sacks, PG Hogan, V Schmidt, Z Li, B Baust, S Oberdoerffer, HS Bandukwala, GM Findlay, S Sharma
The crystal structure of a voltage-gated sodium channel.
1. Nature - published July 10, 2011
2. WA Catterall, N Zheng, T Scheuer, J Payandeh
Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein.
1. J Biol Chem - published July 8, 2011
2. Nady N, Lemak A, Walker JR, Avvakumov GV, Kareta MS, Achour M, Xue S, Duan S, Allali-Hassani A, Zuo X, Wang YX, Bronner C, Chédin F, Arrowsmith CH, Dhe-Paganon S
Introduction to the series on novel aspects of cardiovascular G-protein-coupled receptor signaling.
1. Circ Res - published July 8, 2011
2. Rockman HA, Lefkowitz RJ
Pyridoxal phosphate: Biosynthesis and catabolism.
1. Biochim Biophys Acta - published July 8, 2011
2. TP Begley, SE Ealick, I Tews, J Hanes, T Mukherjee
ADAR proteins: double-stranded RNA and Z-DNA binding domains.
1. Curr Top Microbiol Immunol - published July 6, 2011
2. Barraud P, Allain FH
Structural and functional basis for RNA cleavage by Ire1.
1. BMC Biol - published July 6, 2011
2. Korennykh AV, Korostelev AA, Egea PF, Finer-Moore J, Stroud RM, Zhang C, Shokat KM, Walter P
Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1.
1. BMC Biol - published July 6, 2011
2. Korennykh AV, Egea PF, Korostelev AA, Finer-Moore J, Stroud RM, Zhang C, Shokat KM, Walter P
Combined structural and functional investigation of a C-3''-ketoreductase involved in the biosynthesis of dTDP-L-digitoxose.
1. Biochemistry - published July 5, 2011
2. Kubiak RL, Holden HM
Learning from directed evolution: Thermus aquaticus DNA polymerase mutants with translesion synthesis activity.
1. Chembiochem - published July 4, 2011
2. Obeid S, Schnur A, Gloeckner C, Blatter N, Welte W, Diederichs K, Marx A
Selective removal of promoter nucleosomes by the RSC chromatin-remodeling complex.
1. Nat Struct Mol Biol - published July 3, 2011
2. RD Kornberg, B Maier-Davis, H Boeger, J Griesenbeck, Y Lorch
Model structures of Helicobacter pylori UreD(H) domains: a putative molecular recognition platform.
1. J Chem Inf Model - published July 2, 2011
2. Musiani F, Bellucci M, Ciurli S
Molecular recognition of leucine-aspartate repeat (LD) motifs by the focal adhesion targeting homology domain of cerebral cavernous malformation 3 (CCM3).
1. J Biol Chem - published July 2, 2011
2. Li X, Ji W, Zhang R, Folta-Stogniew E, Min W, Boggon TJ
Actin filament bundling by fimbrin is important for endocytosis, cytokinesis, and polarization in fission yeast.
1. J Biol Chem - published July 2, 2011
2. Skau CT, Courson DS, Bestul AJ, Winkelman JD, Rock RS, Sirotkin V, Kovar DR
Studies of the mechanistic details of the pH-dependent association of botulinum neurotoxin with membranes.
1. J Biol Chem - published July 2, 2011
2. Mushrush DJ, Koteiche HA, Sammons MA, Link AJ, McHaourab HS, Lacy DB
Structural insights to how mammalian capping enzyme reads the CTD code.
1. Mol Cell - published July 2, 2011
2. Ghosh A, Shuman S, Lima CD
Crystallographic and kinetic evidence of allostery in a trypsin-like protease.
1. Biochemistry - published July 2, 2011
2. Niu W, Chen Z, Gandhi PS, Vogt AD, Pozzi N, Pelc LA, Zapata F, Di Cera E
Voltage-gated sodium channel (NaV) protein dissection creates a set of functional pore-only proteins.
1. Proc Natl Acad Sci U S A - published July 2, 2011
2. Shaya D, Kreir M, Robbins RA, Wong S, Hammon J, Brüggemann A, Minor DL Jr
GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data.
1. BMC Bioinformatics - published July 2, 2011
2. Fahey ME, Bennett MJ, Mahon C, Jäger S, Pache L, Kumar D, Shapiro A, Rao K, Chanda SK, Craik CS, Frankel AD, Krogan NJ
Transforming binding affinities from three dimensions to two with application to cadherin clustering.
1. Nature - published July 2, 2011
2. Wu Y, Vendome J, Shapiro L, Ben-Shaul A, Honig B
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.
1. J Struct Funct Genomics - published July 1, 2011
2. Gabanyi MJ, Adams PD, Arnold K, Bordoli L, Carter LG, Flippen-Andersen J, Gifford L, Haas J, Kouranov A, McLaughlin WA, Micallef DI, Minor W, Shah R, Schwede T, Tao YP, Westbrook JD, Zimmerman M, Berman HM
The Nudix hydrolase CDP-chase, a CDP-choline pyrophosphatase, is an asymmetric dimer with two distinct enzymatic activities.
1. J Bacteriol - published July 1, 2011
2. Duong-Ly KC, Gabelli SB, Xu W, Dunn CA, Schoeffield AJ, Bessman MJ, Amzel LM
Structural characterization of the mitomycin 7-O-methyltransferase.
1. Proteins - published July 1, 2011
2. Singh S, Chang A, Goff RD, Bingman CA, Grüschow S, Sherman DH, Phillips GN Jr, Thorson JS
Chemistry of Ni2+ in urease: sensing, trafficking, and catalysis.
1. Acc Chem Res - published July 1, 2011
2. Zambelli B, Musiani F, Benini S, Ciurli S
Neutralizing monoclonal antibodies against hepatitis C virus E2 protein bind discontinuous epitopes and inhibit infection at a postattachment step.
1. J Virol - published July 1, 2011
2. Sabo MC, Luca VC, Prentoe J, Hopcraft SE, Blight KJ, Yi M, Lemon SM, Ball JK, Bukh J, Evans MJ, Fremont DH, Diamond MS
Structure-function analysis of core STRIPAK Proteins: a signaling complex implicated in Golgi polarization.
1. J Biol Chem - published July 1, 2011
2. Kean MJ, Ceccarelli DF, Goudreault M, Sanches M, Tate S, Larsen B, Gibson LC, Derry WB, Scott IC, Pelletier L, Baillie GS, Sicheri F, Gingras AC
CCM3/PDCD10 heterodimerizes with germinal center kinase III (GCKIII) proteins using a mechanism analogous to CCM3 homodimerization.
1. J Biol Chem - published July 1, 2011
2. Ceccarelli DF, Laister RC, Mulligan VK, Kean MJ, Goudreault M, Scott IC, Derry WB, Chakrabartty A, Gingras AC, Sicheri F
Structural and functional analysis of C2-type ketoreductases from modular polyketide synthases.
1. J Mol Biol - published July 1, 2011
2. Zheng J, Keatinge-Clay AT
Rae1: A new clue for nucleoporin leukemias.
1. Cell Cycle - published July 1, 2011
2. A Hoelz, T Stuwe
PredUs: a web server for predicting protein interfaces using structural neighbors.
1. Nucleic Acids Res - published July 1, 2011
2. Zhang QC, Deng L, Fisher M, Guan J, Honig B, Petrey D
Protein-protein HADDocking using exclusively pseudocontact shifts.
1. J Biomol NMR - published July 1, 2011
2. Schmitz C, Bonvin AM
The LRF transcription factor regulates mature B cell development and the germinal center response in mice.
1. J Clin Invest - published July 1, 2011
2. Sakurai N, Maeda M, Lee SU, Ishikawa Y, Li M, Williams JC, Wang L, Su L, Suzuki M, Saito TI, Chiba S, Casola S, Yagita H, Teruya-Feldstein J, Tsuzuki S, Bhatia R, Maeda T
CsgE is a curli secretion specificity factor that prevents amyloid fibre aggregation.
1. Mol Microbiol - published July 1, 2011
2. Nenninger AA, Robinson LS, Hammer ND, Epstein EA, Badtke MP, Hultgren SJ, Chapman MR
MarkUs: a server to navigate sequence-structure-function space.
1. Nucleic Acids Res - published July 1, 2011
2. Fischer M, Zhang QC, Dey F, Chen BY, Honig B, Petrey D
Novel nanomolar imidazo[4,5-b]pyridines as selective nitric oxide synthase (iNOS) inhibitors: SAR and structural insights.
1. Bioorg Med Chem Lett - published July 1, 2011
2. Grädler U, Fuchss T, Ulrich WR, Boer R, Strub A, Hesslinger C, Anézo C, Diederichs K, Zaliani A
Mechanism of activation gating in the full-length KcsA K+ channel.
1. Proc Natl Acad Sci U S A - published July 1, 2011
2. Uysal S, Cuello LG, Cortes DM, Koide S, Kossiakoff AA, Perozo E
A regulatory gene induces trichome formation and embryo lethality in tomato.
1. Proc Natl Acad Sci U S A - published July 1, 2011
2. Yang C, Li H, Zhang J, Luo Z, Gong P, Zhang C, Li J, Wang T, Zhang Y, Lu Y, Ye Z
Evolution of the V, D, and J gene segments used in the primate gammadelta T-cell receptor reveals a dichotomy of conservation and diversity.
1. Proc Natl Acad Sci U S A - published July 1, 2011
2. Kazen AR, Adams EJ
Physiological adaptation of the bacterium Lactococcus lactis in response to the production of human CFTR.
1. Mol Cell Proteomics - published July 1, 2011
2. Steen A, Wiederhold E, Gandhi T, Breitling R, Slotboom DJ
A distributed multi-GPU system for high speed electron microscopic tomographic reconstruction.
1. Ultramicroscopy - published July 1, 2011
2. Zheng SQ, Branlund E, Kesthelyi B, Braunfeld MB, Cheng Y, Sedat JW, Agard DA
Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF.
1. Nature - published July 1, 2011
2. Mackereth CD, Madl T, Bonnal S, Simon B, Zanier K, Gasch A, Rybin V, Valcárcel J, Sattler M
Multiple modalities converge on a common gate to control K2P channel function.
1. EMBO J - published July 1, 2011
2. Bagriantsev SN, Peyronnet R, Clark KA, Honoré E, Minor DL Jr
A structural model for binding of the serine-rich repeat adhesin GspB to host carbohydrate receptors.
1. PLoS Pathog - published July 1, 2011
2. Pyburn TM, Bensing BA, Xiong YQ, Melancon BJ, Tomasiak TM, Ward NJ, Yankovskaya V, Oliver KM, Cecchini G, Sulikowski GA, Tyska MJ, Sullam PM, Iverson TM
The crystal structure of GXGD membrane protease FlaK.
1. Nature - published July 1, 2011
2. Hu J, Xue Y, Lee S, Ha Y
Chronicles of the GTPase switch.
1. Nat Chem Biol - published July 1, 2011
2. Cherfils J, Zeghouf M
Crystal structure of the β2 adrenergic receptor-Gs protein complex.
1. Nature - published July 1, 2011
2. Rasmussen SG, DeVree BT, Zou Y, Kruse AC, Chung KY, Kobilka TS, Thian FS, Chae PS, Pardon E, Calinski D, Mathiesen JM, Shah ST, Lyons JA, Caffrey M, Gellman SH, Steyaert J, Skiniotis G, Weis WI, Sunahara RK, Kobilka BK