Member Publications

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68 Member Publications for July 2012

A quick guide to software licensing for the scientist-programmer.
1. PLoS Comput Biol - published July 31, 2012
2. Morin A, Urban J, Sliz P
The metal ion-dependent adhesion site motif of the Enterococcus faecalis EbpA pilin mediates pilus function in catheter-associated urinary tract infection.
1. MBio - published July 26, 2012
2. Nielsen HV, Guiton PS, Kline KA, Port GC, Pinkner JS, Neiers F, Normark S, Henriques-Normark B, Caparon MG, Hultgren SJ
Application of confocal single-molecule FRET to intrinsically disordered proteins.
1. Methods Mol Biol - published July 24, 2012
2. Schuler B, Müller-Späth S, Soranno A, Nettels D
Denaturant-induced conformational transitions in intrinsically disordered proteins.
1. Methods Mol Biol - published July 24, 2012
2. Neyroz P, Ciurli S, Uversky VN
Respiratory syncytial virus assembles into structured filamentous virion particles independently of host cytoskeleton and related proteins.
1. PLoS One - published July 19, 2012
2. Shaikh FY, Utley TJ, Craven RE, Rogers MC, Lapierre LA, Goldenring JR, Crowe JE Jr
Moonlighting peptides with emerging function.
1. PLoS One - published July 19, 2012
2. Rodríguez Plaza JG, Villalón Rojas A, Herrera S, Garza-Ramos G, Torres Larios A, Amero C, Zarraga Granados G, Gutiérrez Aguilar M, Lara Ortiz MT, Polanco Gonzalez C, Uribe Carvajal S, Coria R, Peña Díaz A, Bredesen DE, Castro-Obregon S, del Rio G
The lectin pathway of complement activation is a critical component of the innate immune response to pneumococcal infection.
1. PLoS Pathog - published July 14, 2012
2. Ali YM, Lynch NJ, Haleem KS, Fujita T, Endo Y, Hansen S, Holmskov U, Takahashi K, Stahl GL, Dudler T, Girija UV, Wallis R, Kadioglu A, Stover CM, Andrew PW, Schwaeble WJ
A Lon-like protease with no ATP-powered unfolding activity.
1. PLoS One - published July 14, 2012
2. Liao JH, Kuo CI, Huang YY, Lin YC, Lin YC, Yang CY, Wu WL, Chang WH, Liaw YC, Lin LH, Chang CI, Wu SH
Molecular insights into the function of RING finger (RNF)-containing proteins hRNF8 and hRNF168 in Ubc13/Mms2-dependent ubiquitylation.
1. J Biol Chem - published July 6, 2012
2. Campbell SJ, Edwards RA, Leung CC, Neculai D, Hodge CD, Dhe-Paganon S, Glover JN
Structure of the cytoplasmic region of PelD, a degenerate diguanylate cyclase receptor that regulates exopolysaccharide production in Pseudomonas aeruginosa.
1. J Biol Chem - published July 6, 2012
2. Whitney JC, Colvin KM, Marmont LS, Robinson H, Parsek MR, Howell PL
Role of reversible dimerization in reactions of amphoteric aziridine aldehydes.
1. J Org Chem - published July 6, 2012
2. Assem N, Hili R, He Z, Kasahara T, Inman BL, Decker S, Yudin AK
The structure of human argonaute-2 in complex with miR-20a.
1. Cell - published July 6, 2012
2. Elkayam E, Kuhn CD, Tocilj A, Haase AD, Greene EM, Hannon GJ, Joshua-Tor L
Intrinsic fluorescence of intrinsically disordered proteins.
1. Methods Mol Biol - published July 5, 2012
2. Neyroz P, Ciurli S
The changing face of HIV vaccine research.
1. J Int AIDS Soc - published July 5, 2012
2. Kwong PD, Mascola JR, Nabel GJ
WITHDRAWN: Epigallocatechin-3-gallate up-regulates tumor suppressor gene expression via a reactive oxygen species-dependent down-regulation of UHRF1.
1. Biochem Biophys Res Commun - published July 4, 2012
2. Achour M, Mousli M, Alhosin M, Ibrahim A, Peluso J, Muller CD, Schini-Kerth VB, Hamiche A, Dhe-Paganon S, Christian Bronner
Adaptor protein self-assembly drives the control of a cullin-RING ubiquitin ligase.
1. Structure - published July 3, 2012
2. Errington WJ, Khan MQ, Bueler SA, Rubinstein JL, Chakrabartty A, Privé GG
Conformational selection or induced fit? A critical appraisal of the kinetic mechanism.
1. Biochemistry - published July 3, 2012
2. Vogt AD, Di Cera E
E-cadherin is under constitutive actomyosin-generated tension that is increased at cell-cell contacts upon externally applied stretch.
1. Proc Natl Acad Sci U S A - published July 3, 2012
2. Borghi N, Sorokina M, Shcherbakova OG, Weis WI, Pruitt BL, Nelson WJ, Dunn AR
Supramolecular structure of membrane-associated polypeptides by combining solid-state NMR and molecular dynamics simulations.
1. Biophys J - published July 3, 2012
2. Weingarth M, Ader C, Melquiond AS, Nand D, Pongs O, Becker S, Bonvin AM, Baldus M
Structures of KlenTaq DNA polymerase caught while incorporating C5-modified pyrimidine and C7-modified 7-deazapurine nucleoside triphosphates.
1. J Am Chem Soc - published July 2, 2012
2. Bergen K, Steck AL, Strütt S, Baccaro A, Welte W, Diederichs K, Marx A
Fission yeast Dma1 requires RING domain dimerization for its ubiquitin ligase activity and mitotic checkpoint function.
1. J Biol Chem - published July 2, 2012
2. Johnson AE, Collier SE, Ohi MD, Gould KL
Characterization of a novel activated Ran GTPase mutant and its ability to induce cellular transformation.
1. J Biol Chem - published July 2, 2012
2. Milano SK, Kwon W, Pereira R, Antonyak MA, Cerione RA
Design, synthesis, calorimetry, and crystallographic analysis of 2-alkylaminoethyl-1,1-bisphosphonates as inhibitors of Trypanosoma cruzi farnesyl diphosphate synthase.
1. J Med Chem - published July 2, 2012
2. Aripirala S, Szajnman SH, Jakoncic J, Rodriguez JB, Docampo R, Gabelli SB, Amzel LM
Allyl m-trifluoromethyldiazirine mephobarbital: an unusually potent enantioselective and photoreactive barbiturate general anesthetic.
1. J Med Chem - published July 2, 2012
2. Savechenkov PY, Zhang X, Chiara DC, Stewart DS, Ge R, Zhou X, Raines DE, Cohen JB, Forman SA, Miller KW, Bruzik KS
Structural basis for germ-line gene usage of a potent class of antibodies targeting the CD4-binding site of HIV-1 gp120.
1. Proc Natl Acad Sci U S A - published July 2, 2012
2. West AP Jr, Diskin R, Nussenzweig MC, Bjorkman PJ
HIV-1 envelope trimer elicits more potent neutralizing antibody responses than monomeric gp120.
1. Proc Natl Acad Sci U S A - published July 2, 2012
2. Kovacs JM, Nkolola JP, Peng H, Cheung A, Perry J, Miller CA, Seaman MS, Barouch DH, Chen B
Structural and energetic basis of ALS-causing mutations in the atypical proline-tyrosine nuclear localization signal of the Fused in Sarcoma protein (FUS).
1. Proc Natl Acad Sci U S A - published July 2, 2012
2. Zhang ZC, Chook YM
Systematic functional prioritization of protein posttranslational modifications.
1. Cell - published July 2, 2012
2. Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ
Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains.
1. Nat Commun - published July 2, 2012
2. Cong L, Zhou R, Kuo YC, Cunniff M, Zhang F
An unusual role for a mobile flavin in StaC-like indolocarbazole biosynthetic enzymes.
1. Chem Biol - published July 2, 2012
2. Goldman PJ, Ryan KS, Hamill MJ, Howard-Jones AR, Walsh CT, Elliott SJ, Drennan CL
Clofarabine targets the large subunit (α) of human ribonucleotide reductase in live cells by assembly into persistent hexamers.
1. Chem Biol - published July 2, 2012
2. Aye Y, Brignole EJ, Long MJ, Chittuluru J, Drennan CL, Asturias FJ, Stubbe J
The RNA worlds in context.
1. Cold Spring Harb Perspect Biol - published July 1, 2012
2. Cech TR
Solution structure of the N-terminal dsRBD of Drosophila ADAR and interaction studies with RNA.
1. Biochimie - published July 1, 2012
2. Barraud P, Heale BS, O'Connell MA, Allain FH
Nuclear localization of Klotho in brain: an anti-aging protein.
1. Neurobiol Aging - published July 1, 2012
2. German DC, Khobahy I, Pastor J, Kuro-O M, Liu X
The chemical complexity of cellular microtubules: tubulin post-translational modification enzymes and their roles in tuning microtubule functions.
1. Cytoskeleton (Hoboken) - published July 1, 2012
2. Garnham CP, Roll-Mecak A
Density-cluster NMA: A new protein decomposition technique for coarse-grained normal mode analysis.
1. Proteins - published July 1, 2012
2. Demerdash ON, Mitchell JC
Insights into CRAC channel gating and ion permeation.
1. Cell Res - published July 1, 2012
2. Hogan PG
Clustering biomolecular complexes by residue contacts similarity.
1. Proteins - published July 1, 2012
2. Rodrigues JP, Trellet M, Schmitz C, Kastritis P, Karaca E, Melquiond AS, Bonvin AM
Sequence and structure relationships within von Willebrand factor.
1. Blood - published July 1, 2012
2. Zhou YF, Eng ET, Zhu J, Lu C, Walz T, Springer TA
Balancing antiviral potency and host toxicity: identifying a nucleotide inhibitor with an optimal kinetic phenotype for HIV-1 reverse transcriptase.
1. Mol Pharmacol - published July 1, 2012
2. Sohl CD, Kasiviswanathan R, Kim J, Pradere U, Schinazi RF, Copeland WC, Mitsuya H, Baba M, Anderson KS
Structure-based optimization of designed Armadillo-repeat proteins.
1. Protein Sci - published July 1, 2012
2. Madhurantakam C, Varadamsetty G, Grütter MG, Plückthun A, Mittl PR
Evidence for a genetic and physical interaction between nonstructural proteins NS1 and NS4B that modulates replication of West Nile virus.
1. J Virol - published July 1, 2012
2. Youn S, Li T, McCune BT, Edeling MA, Fremont DH, Cristea IM, Diamond MS
A Bayesian adaptive basis algorithm for single particle reconstruction.
1. J Struct Biol - published July 1, 2012
2. Kucukelbir A, Sigworth FJ, Tagare HD
Electron tomography of late stages of FcRn-mediated antibody transcytosis in neonatal rat small intestine.
1. Mol Biol Cell - published July 1, 2012
2. Ladinsky MS, Huey-Tubman KE, Bjorkman PJ
Activity and inhibition of prostasin and matriptase on apical and basolateral surfaces of human airway epithelial cells.
1. Am J Physiol Lung Cell Mol Physiol - published July 1, 2012
2. Nimishakavi S, Besprozvannaya M, Raymond WW, Craik CS, Gruenert DC, Caughey GH
Targeting the Notch pathway: twists and turns on the road to rational therapeutics.
1. J Clin Oncol - published July 1, 2012
2. Aster JC, Blacklow SC
Sensing the messenger: the diverse ways that bacteria signal through c-di-GMP.
1. Protein Sci - published July 1, 2012
2. Krasteva PV, Giglio KM, Sondermann H
Human B-cell ontogeny in humanized NOD/SCID γc(null) mice generates a diverse yet auto/poly- and HIV-1-reactive antibody repertoire.
1. Genes Immun - published July 1, 2012
2. Chang H, Biswas S, Tallarico AS, Sarkis PT, Geng S, Panditrao MM, Zhu Q, Marasco WA
Divergence of multimodular polyketide synthases revealed by a didomain structure.
1. Nat Chem Biol - published July 1, 2012
2. Zheng J, Gay DC, Demeler B, White MA, Keatinge-Clay AT
KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.
1. Nat Chem Biol - published July 1, 2012
2. Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A
A model of GAG/MIP-2/CXCR2 interfaces and its functional effects.
1. Biochemistry - published July 1, 2012
2. Rajasekaran D, Keeler C, Syed MA, Jones MC, Harrison JK, Wu D, Bhandari V, Hodsdon ME, Lolis EJ
Tailoring of membrane proteins by alternative splicing of pre-mRNA.
1. Biochemistry - published July 1, 2012
2. Mittendorf KF, Deatherage CL, Ohi MD, Sanders CR
Conformational modulation of in vitro activity of cyclic RGD peptides via aziridine aldehyde-driven macrocyclization chemistry.
1. Bioconjug Chem - published July 1, 2012
2. Roxin Á, Chen J, Scully CC, Rotstein BH, Yudin AK, Zheng G
Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy.
1. Nature - published July 1, 2012
2. Bharat TA, Davey NE, Ulbrich P, Riches JD, de Marco A, Rumlova M, Sachse C, Ruml T, Briggs JA
Are N-heterocyclic carbenes "better" ligands than phosphines in main group chemistry? A theoretical case study of ligand-stabilized E2 molecules, L-E-E-L (L = NHC, phosphine; E = C, Si, Ge, Sn, Pb, N, P, As, Sb, Bi).
1. Inorg Chem - published July 1, 2012
2. Wilson DJ, Couchman SA, Dutton JL
Three-dimensional structure and determinants of stability of the iron-sulfur cluster scaffold protein IscU from Escherichia coli.
1. Biochemistry - published July 1, 2012
2. Kim JH, Tonelli M, Kim T, Markley JL
The structure of a GH10 xylanase from Fusarium oxysporum reveals the presence of an extended loop on top of the catalytic cleft.
1. Acta Crystallogr D Biol Crystallogr - published July 1, 2012
2. Dimarogona M, Topakas E, Christakopoulos P, Chrysina ED
Combining in situ proteolysis and mass spectrometry to crystallize Escherichia coli PgaB.
1. Acta Crystallogr Sect F Struct Biol Cryst Commun - published July 1, 2012
2. Little DJ, Whitney JC, Robinson H, Yip P, Nitz M, Howell PL
Scc1 sumoylation by Mms21 promotes sister chromatid recombination through counteracting Wapl.
1. Genes Dev - published July 1, 2012
2. Wu N, Kong X, Ji Z, Zeng W, Potts PR, Yokomori K, Yu H
Molecular mechanism of proton transport in CLC Cl-/H+ exchange transporters.
1. Proc Natl Acad Sci U S A - published July 1, 2012
2. Feng L, Campbell EB, MacKinnon R
Structure-based design of potent Bcl-2/Bcl-xL inhibitors with strong in vivo antitumor activity.
1. J Med Chem - published July 1, 2012
2. Zhou H, Aguilar A, Chen J, Bai L, Liu L, Meagher JL, Yang CY, McEachern D, Cong X, Stuckey JA, Wang S
Purification, crystallization and preliminary X-ray diffraction analysis of a hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT) from Coffea canephora involved in chlorogenic acid biosynthesis.
1. Acta Crystallogr Sect F Struct Biol Cryst Commun - published July 1, 2012
2. Lallemand LA, McCarthy JG, McSweeney S, McCarthy AA
HIV-1 assembly, budding, and maturation.
1. Cold Spring Harb Perspect Med - published July 1, 2012
2. Sundquist WI, Kräusslich HG
Biochemistry. Nature's intricate clockwork.
1. Science - published July 1, 2012
2. Crane BR
Aquaporin 4-specific T cells in neuromyelitis optica exhibit a Th17 bias and recognize Clostridium ABC transporter.
1. Ann Neurol - published July 1, 2012
2. Varrin-Doyer M, Spencer CM, Schulze-Topphoff U, Nelson PA, Stroud RM, Cree BA, Zamvil SS
Regulation of ligand-independent Notch signal through intracellular trafficking.
1. Commun Integr Biol - published July 1, 2012
2. Hori K, Sen A, Kirchhausen T, Artavanis-Tsakonas S
Cullin-3 and the endocytic system: New functions of ubiquitination for endosome maturation.
1. Cell Logist - published July 1, 2012
2. Hubner M, Peter M
Scalable Anisotropic Shape and Electrostatic Models for Biological Bromine Halogen Bonds.
1. J Chem Theory Comput - published July 1, 2012
2. Carter M, Rappé AK, Ho PS