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| biomolecular nuclear magnetic resonanceSummarySummary: NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope. Top Publications
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Publications
Structure of PTB bound to RNA: specific binding and implications for splicing regulationFlorian C Oberstrass
Institute for Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology, Zurich, ETH Honggerberg, CH 8093 Zurich, Switzerland
Science 309:2054-7. 2005..Thus, PTB will induce RNA looping when bound to two separated pyrimidine tracts within the same RNA. This leads to structural models for how PTB functions as an alternative-splicing repressor...- Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomicsFrank Dieterle
F. Hoffman-La Roche Ltd, Pharmaceuticals Division, PRBD-E, Building 065/512, 4070 Basel, Switzerland
Anal Chem 78:4281-90. 2006.... - Comparison of multiple Amber force fields and development of improved protein backbone parametersViktor Hornak
Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794, USA
Proteins 65:712-25. 2006..It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides and better accord with experimental NMR relaxation data of test protein systems... - Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pairMagnus Wolf-Watz
Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, USA
Nat Struct Mol Biol 11:945-9. 2004..This comparative and quantitative study of activity, structure and dynamics revealed a close link between protein dynamics and catalytic turnover... - Automated NMR structure calculation with CYANAPeter Güntert
RIKEN Genomic Sciences Center, Yokohama, Japan
Methods Mol Biol 278:353-78. 2004.... - PRIMe: a Web site that assembles tools for metabolomics and transcriptomicsKenji Akiyama
RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
In Silico Biol 8:339-45. 2008.... - A site-specific low-enrichment (15)N,(13)C isotope-labeling approach to unambiguous NMR spectral assignments in nucleic acidsAnh Tuân Phan
Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center New York, New York 10021, USA
J Am Chem Soc 124:1160-1. 2002..This simple and cost-effective methodology is demonstrated on the d(GGGTTCAGG) DNA sequence, which forms a dimeric G-quadruplex containing G.G.G.G tetrads sandwiched between G.(C-A) triads... 
SCOR: a Structural Classification of RNA databasePeter S Klosterman
Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
Nucleic Acids Res 30:392-4. 2002..A classification of the well-characterized tertiary interactions found in the larger RNA structures is also included along with examples. The SCOR database is accessible at http://scor.lbl.gov...- Toward a unified representation of protein structural dynamics in solutionPhineus R L Markwick
Protein Dynamics and Flexibility, Institute de Biologie Structurale Jean Pierre Ebel, CNRS CEA UJF UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble Cedex, France
J Am Chem Soc 131:16968-75. 2009..This constraint-free approach thereby provides an atomic resolution free-energy weighted Boltzmann description of protein dynamics occurring on time scales over many orders of magnitude in the protein ubiquitin... - The Xplor-NIH NMR molecular structure determination packageCharles D Schwieters
Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Building 12A, 20892-5624, Bethesda, MD, USA
J Magn Reson 160:65-73. 2003..Support for these scripting languages also facilitates interaction with existing external programs for structure analysis, structure manipulation, visualization, and spectral analysis... - Competitive Na(+) and Rb(+) binding in the minor groove of DNAFlaminia Cesare Marincola
Department of Biophysical Chemistry, Lund University, SE-22100 Lund, Sweden
J Am Chem Soc 126:6739-50. 2004..At 4 degrees C, the mean residence time of groove-bound ions is 0.2 +/- 0.1 micros for Rb(+) and 10 ns to 100 micros for Na(+). A shorter correlation time of 2 ns is attributed to counterions bridging cross-strand phosphate groups... - Structure and mechanism of the M2 proton channel of influenza A virusJason R Schnell
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
Nature 451:591-5. 2008..Drug-resistance mutations are predicted to counter the effect of drug binding by either increasing the hydrophilicity of the pore or weakening helix-helix packing, thus facilitating channel opening... - Scaffold-independent analysis of RNA-protein interactions: the Nova-1 KH3-RNA complexBarbara Beuth
Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, U K
J Am Chem Soc 129:10205-10. 2007..Our NMR binding assays using the third KH domain of the Nova-1 protein provide a proof-of-principle for the method and novel information on the specificity of this domain for its RNA targets... 
Structural insight into the recognition of the H3K4me3 mark by the TFIID subunit TAF3Hugo van Ingen
Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
Structure 16:1245-56. 2008..Interference by asymmetric dimethylation of arginine 2 suggests that a H3R2/K4 "methyl-methyl" switch in the histone code dynamically regulates TFIID-promoter association...- A method for efficient isotopic labeling of recombinant proteinsJ Marley
Department of Biochemistry, Weill Medical College of Cornell University, New York, NY 10021, USA
J Biomol NMR 20:71-5. 2001..Following a short period for growth recovery and unlabeled metabolite clearance, the cells are induced. The expression yields obtained provide a fourfold to eightfold reduction in isotope costs using simple shake flask growths... - Structural insights into activation of phosphatidylinositol 4-kinase (Pik1) by yeast frequenin (Frq1)Thomas Strahl
Department of Molecular and Cell Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, California 94720 3202, USA
J Biol Chem 282:30949-59. 2007..Frq1 may activate Pik1 by facilitating membrane targeting via the exposed N-myristoyl group and by imposing a structural transition that promotes association of the lipid kinase unique motif with the kinase domain... - Structural basis of integrin activation by talinKate L Wegener
Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, UK
Cell 128:171-82. 2007.... - Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURFHaitao Li
Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
Nature 442:91-5. 2006..Our findings call attention to the PHD finger as a previously uncharacterized chromatin-binding module found in a large number of chromatin-associated proteins... - Protein alignment by a coexpressed lanthanide-binding tag for the measurement of residual dipolar couplingsJens Wöhnert
Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe Universitat Frankfurt, Marie Curie Strasse 11, 60439 Frankfurt M, Germany
J Am Chem Soc 125:13338-9. 2003..6 to 6.1 Hz for Dy3+, while an opposite alignment tensor is observed for Tm3+ (4.5 to -2.9 Hz) at 800 MHz. Experimental RDCs are in excellent agreement with those predicted on the basis of the X-ray structure of the protein... - Characterization of enzyme motions by solution NMR relaxation dispersionJ Patrick Loria
Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
Acc Chem Res 41:214-21. 2008..Solution NMR relaxation dispersion experiments are powerful experimental tools that can elucidate protein motions with atomic resolution and can provide insight into the role of these motions in biological function... - A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computationsLin Liu
Department of Computational Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, Pittsburgh, Pennsylvania 15213, USA
Proteins 77:927-39. 2009.... - Structural basis for recognition of the AGNN tetraloop RNA fold by the double-stranded RNA-binding domain of Rnt1p RNase IIIHaihong Wu
Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, CA 90095-1569, USA
Proc Natl Acad Sci U S A 101:8307-12. 2004..These results show how a single dsRBD can convey specificity for particular RNA targets, by structure specific recognition of a conserved tetraloop fold... - Differential responses of the backbone and side-chain conformational dynamics in FKBP12 upon binding the transition-state analog FK506: implications for transition-state stabilization and target protein recognitionUlrika Brath
Division of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, Lund, Sweden
J Mol Biol 387:233-44. 2009.... - Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognitionAaron T Frank
Department of Chemistry, University of California Irvine, 1102 Natural Sciences 2, Irvine, CA 92697, USA
Nucleic Acids Res 37:3670-9. 2009.... - Structure of the Hybrid-2 type intramolecular human telomeric G-quadruplex in K+ solution: insights into structure polymorphism of the human telomeric sequenceJixun Dai
College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA
Nucleic Acids Res 35:4927-40. 2007.... - NMR structure of the active conformation of the Varkud satellite ribozyme cleavage siteBernd Hoffmann
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
Proc Natl Acad Sci U S A 100:7003-8. 2003..The combination of NMR and bioinformatic approaches presented here has identified a novel RNA fold and provides insights into the structural basis of catalytic function in the Neurospora VS ribozyme... - Molecular structure of amyloid fibrils: insights from solid-state NMRRobert Tycko
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
Q Rev Biophys 39:1-55. 2006.... - Recognition of pre-formed and flexible elements of an RNA stem-loop by nucleolinP Bouvet
Laboratoire de Pharmacologie et de Biologie Structurale, 205 route de Narbonne, Toulouse Cedex, 31077, France
J Mol Biol 309:763-75. 2001..The loop E motif also has specific interactions with the protein. Implications of these findings for the mechanism of recognition of RNA structures by modular proteins are discussed... - EDTA-derivatized deoxythymidine as a tool for rapid determination of protein binding polarity to DNA by intermolecular paramagnetic relaxation enhancementJunji Iwahara
Laboratories of Chemical Physics and Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases/NIH, Bethesda, MD 20892-0510, USA
J Am Chem Soc 125:6634-5. 2003.... - Design of a novel globular protein fold with atomic-level accuracyBrian Kuhlman
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Science 302:1364-8. 2003..2 angstroms) to the design model. The ability to design a new protein fold makes possible the exploration of the large regions of the protein universe not yet observed in nature... - Solution structure of a TBP-TAF(II)230 complex: protein mimicry of the minor groove surface of the TATA box unwound by TBPD Liu
Department of Medical Biophysics, University of Toronto, Ontario, Canada
Cell 94:573-83. 1998..This protein mimicry of the TATA element surface provides the structural basis of the mechanism by which dTAF(II)230 negatively controls the TATA box-binding activity within the TFIID complex... - NMR analysis of a Tau phosphorylation patternIsabelle Landrieu
CNRS UMR 8525, Institut Pasteur de Lille, 59019 Lille Cedex, France
J Am Chem Soc 128:3575-83. 2006..We finally demonstrate that the NMR approach can equally be used to evaluate potential kinase inhibitors in a straightforward manner... - Thermodynamics and kinetics for base-pair opening in the P1 duplex of the Tetrahymena group I ribozymeJoon Hwa Lee
Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309 0215, USA
Nucleic Acids Res 35:2965-74. 2007.... - A novel chair-type G-quadruplex formed by a Bombyx mori telomeric sequenceSamir Amrane
Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
Nucleic Acids Res 37:931-8. 2009..Our result highlights the effect of G-tract length on the folding topology of G-quadruplexes, but also poses the question of whether a similar chair-type G-quadruplex fold exists in the human telomeric sequences... - De novo protein structure generation from incomplete chemical shift assignmentsYang Shen
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
J Biomol NMR 43:63-78. 2009..This strategy, which uses traditional Rosetta for pre-filtering of the fragment selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift assignments... - Structural basis for the enhancement of eIF4A helicase activity by eIF4GMonika Oberer
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
Genes Dev 19:2212-23. 2005..This model can explain the cooperativity between all binding partners of eIF4A (eIF4G, RNA, ATP) and stimulation of eIF4A activity in the eIF4F complex... - Rapid preparation of RNA samples for NMR spectroscopy and X-ray crystallographyHae-Kap Cheong
Magnetic Resonance Team, Korea Basic Science Institute, Eoun-Dong 52, Yuseong-gu, Daejeon 305-333, Korea
Nucleic Acids Res 32:e84. 2004..The 3' end tag is then removed by sequence-specific cleavage using trans-acting DNAzyme, the arm lengths of which are optimized for turnover number. This purification method is simpler and faster than the conventional method... - Single protein production in living cells facilitated by an mRNA interferaseMotoo Suzuki
Department of Biochemistry, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, New Jersey 08854, USA
Mol Cell 18:253-61. 2005..This expression system enables unparalleled signal to noise ratios that should dramatically simplify structural and functional studies of previously intractable but biologically important proteins... - A novel RNA pentaloop fold involved in targeting ADAR2Richard Stefl
Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology Zurich, , , Switzerland
RNA 11:592-7. 2005..The fold is stabilized by a complex interplay of hydrogen bonds and stacking interactions. We propose that this new pentaloop structure is an important determinant of the R/G site recognition by ADAR2... - NMR solution structure of a parallel LNA quadruplexAntonio Randazzo
Dipartimento di Chimica delle Sostanze Naturali, , Via D. Montesano 49, I-80131 Napoli, Italy
Nucleic Acids Res 32:3083-92. 2004..The structural features of the LNA quadruplex reported here may open new perspectives for the biological application of LNAs as novel versatile tools to design aptamer or catalyst oligonucleotides... - Unusual intercalation of acridin-9-ylthiourea into the 5'-GA/TC DNA base step from the minor groove: implications for the covalent DNA adduct profile of a novel platinum-intercalator conjugateHemanta Baruah
Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109-7486, USA
Nucleic Acids Res 31:4138-46. 2003..The unusual tolerance of the GA/TC intercalation site and the pronounced groove specificity of ACRAMTU play a significant role in the molecular recognition between the corresponding platinum conjugate, Pt-ACRAMTU, and DNA... - Structural and thermodynamic studies on mutant RNA motifs that impair the specificity between a viral replicase and its promoterC H Kim
Department of Chemistry, University of California Berkeley, CA, 94720-1460, USA
J Mol Biol 307:827-39. 2001..Based on this study, we conclude that the key structural motif in the triloop recognized by the replicase is a solution-exposed, 5'-adenine base in the triloop that is clamped to the stem helix, which is called a clamped adenine motif... - The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entriesJurgen F Doreleijers
Radboud University Medical Centre Nijmegen, Geert Grooteplein 26 28, HB, Nijmegen, The Netherlands
J Biomol NMR 45:389-96. 2009..Continuous efforts in automating the parsing of both old, and newly deposited files is steadily decreasing this fraction. The cleaned data files are available from the NMR restraints grid at http://restraintsgrid.bmrb.wisc.edu ... - Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homologyYang Shen
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
J Biomol NMR 38:289-302. 2007..52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for (15)N, (1)H(N), (1)H(alpha), (13)C(alpha), (13)C(beta) and (13)C', respectively, including outliers... - A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its familyGregory D Friedland
Graduate Group in Biophysics, University of California San Francisco, San Francisco, California, United States of America
PLoS Comput Biol 5:e1000393. 2009..More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics... - A novel family of RNA tetraloop structure forms the recognition site for Saccharomyces cerevisiae RNase IIIH Wu
Department of Chemistry and Biochemistry, 405 Hilgard Avenue, PO Box 951569, University of California, Los Angeles, CA 90095-1569, USA
EMBO J 20:7240-9. 2001.... - On the effect of covalently appended quinolones on termini of DNA duplexesJennifer Tuma
Department of Chemistry, University of Constance, Fach M 709, D-78457 Konstanz, Germany
J Am Chem Soc 124:4236-46. 2002..The structure of the "molecular cap" with its disrupted terminal base pair may also be helpful for modeling how quinolones block re-ligation of DNA strands in the active site of gyrases... - Crystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfacesShivender M D Shandilya
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
Structure 18:28-38. 2010..NMR solution data provides evidence that another interface, which coordinates a novel zinc site, also exists. Thus, the observed crystallographic interfaces of APOBEC3G may be important for both oligomerization and function... - Molecular basis for temperature sensing by an RNA thermometerSaheli Chowdhury
Institute of Molecular Biology and Biophysics, ETH Zurich, , Switzerland
EMBO J 25:2487-97. 2006..Our results indicate that RNA thermometers are able to sense temperature changes without the aid of accessory factors... - NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalisYuan Chao Lou
Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
Nucleic Acids Res 37:2381-94. 2009..The tvMyb1(35-141)/DNA complex model furthers our understanding of DNA recognition by Myb proteins and this approach could be applied in determining the complex structures involving proteins with multiple domains... - Metal-ion binding and metal-ion induced folding of the adenine-sensing riboswitch aptamer domainJonas Noeske
Department of Biochemistry, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
Nucleic Acids Res 35:5262-73. 2007..Compared to the highly similar guanine-sensing riboswitch, the folding pathway for the adenine-sensing riboswitch aptamer domain is more complex and the influence of Mg2+ is more pronounced... - Discrepancies between the NMR and X-ray structures of uncomplexed barstar: analysis suggests that packing densities of protein structures determined by NMR are unreliableG S Ratnaparkhi
Molecular Biophysics Unit, Indian Institute of Science, Bangalore
Biochemistry 37:6958-66. 1998.... - Insight into the structural basis of pro- and antiapoptotic p53 modulation by ASPP proteinsJinwoo Ahn
Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
J Biol Chem 284:13812-22. 2009..Our detailed structural analyses of the ASPP-p53 interactions provide insight into the structural basis of the differential behavior of pro- and antiapoptotic ASPP family members... - NMR structure of the amino-terminal domain of the lambda integrase protein in complex with DNA: immobilization of a flexible tail facilitates beta-sheet recognition of the major grooveEvgeny A Fadeev
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 1570, USA
J Mol Biol 388:682-90. 2009..This finding reveals the structural basis for the observation that the "unstructured" amino terminus is required for recombination... - BioMagResBankEldon L Ulrich
Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706, USA
Nucleic Acids Res 36:D402-8. 2008..protein.osaka-u.ac.jp) and the other at CERM, University of Florence, Florence, Italy (bmrb.postgenomicnmr.net/). The site at Osaka also accepts and processes data depositions... - Influence of the fluctuations of the alignment tensor on the analysis of the structure and dynamics of proteins using residual dipolar couplingsX Salvatella
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
J Biomol NMR 40:71-81. 2008.... - Probing the flexibility of the DsbA oxidoreductase from Vibrio cholerae--a 15N - 1H heteronuclear NMR relaxation analysis of oxidized and reduced forms of DsbAJames Horne
Department of Medicinal Chemistry, Victorian College of Pharmacy, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
J Mol Biol 371:703-16. 2007..Taken together, these data provide compelling evidence of a role for dynamics in the catalytic cycle of DsbA... - (1)H, (15)N, and (13)C chemical shift assignments of mouse HOXA13 DNA binding domainYonghong Zhang
Department of Chemistry, University of California, Davis, CA 95616, USA
Biomol NMR Assign 3:199-201. 2009..We report complete NMR chemical shift assignments of the mouse HOXA13 DNA binding domain (A13DBD; BMRB no. 16252)... - Relationship between chemical shift value and accessible surface area for all amino acid atomsWim F Vranken
European Bioinformatics Institute, Cambridge, UK
BMC Struct Biol 9:20. 2009..However, it is not trivial to link this information to available coordinate data from the PDB for non-backbone atoms due to atom and chain naming differences, as well as sequence numbering changes... - Dynamics and stability of individual base pairs in two homologous RNA-DNA hybridsYuegao Huang
Department of Chemistry and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, USA
Biochemistry 48:3988-97. 2009..These results provide the first demonstration that, for RNA-DNA hybrid structures with the same base sequence, the opening dynamics and the stability of individual base pairs are strongly influenced by the chemical nature of each strand... - Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopyPramodh Vallurupalli
Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
Proc Natl Acad Sci U S A 105:11766-71. 2008..The methodology described opens up the possibility for detailed structural studies of invisible protein conformers at a level of detail that has heretofore been restricted to applications involving visible ground states of proteins... - Slow dynamics in folded and unfolded states of an SH3 domainM Tollinger
Structural Biology and Biochemistry Program, Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
J Am Chem Soc 123:11341-52. 2001..The results illustrate that relaxation dispersion experiments provide an extremely sensitive tool to probe conformational exchange processes in unfolded states and to obtain information on the free energy landscape of such systems... - Amyloid fibrils of the HET-s(218-289) prion form a beta solenoid with a triangular hydrophobic coreChristian Wasmer
Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
Science 319:1523-6. 2008..The structure is likely to have broad implications for understanding the infectious amyloid state... - Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR methodMitsuhiro Takeda
Graduate School of Science, Nagoya University, Furo cho, Chikusa ku, Nagoya 464 8602, Japan
J Mol Biol 380:608-22. 2008.... - Structure of the BH3 domains from the p53-inducible BH3-only proteins Noxa and Puma in complex with Mcl-1Catherine L Day
Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
J Mol Biol 380:958-71. 2008..Our studies show that unstructured peptides, such as the BH3 domains, behave like their structured counterparts and can bind tightly and selectively in an enthalpically driven process... - Two distinct modes of ESCRT-III recognition are required for VPS4 functions in lysosomal protein targeting and HIV-1 buddingCollin Kieffer
Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112 5650, USA
Dev Cell 15:62-73. 2008.... - Crystal structure of the RIM1alpha C2B domain at 1.7 A resolutionRong Guan
Department of Biochemistry, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, Texas 75390, USA
Biochemistry 46:8988-98. 2007..Our results provide a structural basis to understand the function of RIM C2B domains and suggest that dimerization may be a crucial aspect of RIM function... - Solvent-exposed residues located in the beta-sheet modulate the stability of the tetramerization domain of p53--a structural and combinatorial approachPuig Mora
Department of Medicinal Chemistry, Centro de Investigacion Principe Felipe, E 46013 Valencia, Spain
Proteins 71:1670-85. 2008..We propose that stabilization through hydrophobic interactions of key secondary structure elements might be the underlying mechanism for the strong influence of solvent-exposed residues in the stability of p53TD... - The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracisElodie Laine
Unite de Bioinformatique Structurale, CNRS URA 2185 Institut Pasteur, 25 28, rue du Dr Roux, Paris 75 724, France
Proteins 71:1813-29. 2008..By contrast, the C-terminal domain is strongly locked in the open conformation by EF, and the removal of calcium induces a collapse of EF catalytic site (EF-(Apo-CaM))... - Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environmentTsutomu Yamane
International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, Japan
Proteins 71:1970-83. 2008..The hydration structures observed for the refined structures contained most of the crystal waters as a subset. We observed that various water-mediated PhoB-DNA interactions contributed to the molecular recognition between PhoB and DNA... - Solution structure of the region 51-160 of human KIN17 reveals an atypical winged helix domainLudovic Carlier
Equipe de Chimie Organique et Biologie Structurale, IFRMP 23, CNRS UMR 6014, Universite de Rouen, 76821 Mont Saint Aignan, France
Protein Sci 16:2750-5. 2007..Thus, human KIN17 region 51-160 might rather be involved in protein-protein interaction through its conserved surface centered on the 3(10)-helix... - Complex assembly mechanism and an RNA-binding mode of the human p14-SF3b155 spliceosomal protein complex identified by NMR solution structure and functional analysesKanako Kuwasako
Protein Research Group, RIKEN Genomic Sciences Center, Yokohama 230 0045, Japan
Proteins 71:1617-36. 2008..Collectively, this study provides details for the protein-recognition mode of p14 and insight into the branch site recognition... - Improved segmental isotope labeling methods for the NMR study of multidomain or large proteins: application to the RRMs of Npl3p and hnRNP LLenka Skrisovska
Institute of Molecular Biology and Biophysics, ETH Zurich, CH 8093 Zurich, Switzerland
J Mol Biol 375:151-64. 2008..Subsequently, the structures of the two RRMs of Npl3p were determined on the basis of samples in which each RRM was expressed individually. The two Npl3p RRMs adopt the expected beta alpha beta beta alpha beta fold... - NMR solution structure of subunit F of the methanogenic A1AO adenosine triphosphate synthase and its interaction with the nucleotide-binding subunit BShovanlal Gayen
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
Biochemistry 46:11684-94. 2007..Finally, the arrangement of subunit F within the complex is presented... - Conserved themes in target recognition by the PAH1 and PAH2 domains of the Sin3 transcriptional corepressorSarata C Sahu
Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, IL 60208 3500, USA
J Mol Biol 375:1444-56. 2008..These studies reveal that even conservative replacements of PAH2 residues with equivalent PAH1 residues are sufficient to alter the affinity and specificity of these protein-protein interactions dramatically... - Obestatin conformational features: a strategy to unveil obestatin's biological role?Mario Scrima
Department of Pharmaceutical Sciences, University of Salerno, I 84084 Fisciano, Italy
Biochem Biophys Res Commun 363:500-5. 2007..Conversely sequence and conformational specificity point to a new farmacoforic structure, on which innovative derivatives with a potential role in the treatment of obesity can be designed and synthetized... - Supramodular nature of GRIP1 revealed by the structure of its PDZ12 tandem in complex with the carboxyl tail of Fras1Jiafu Long
Department of Biochemistry, Molecular Neuroscience Center, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
J Mol Biol 375:1457-68. 2008.... - Interdomain cooperativity of calmodulin bound to melittin preferentially increases calcium affinity of sites I and IIRhonda A Newman
Department of Biochemistry, Roy J and Lucille A Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242 1109, USA
Proteins 71:1792-812. 2008.... - The solution structure of the outer membrane lipoprotein OmlA from Xanthomonas axonopodis pv. citri reveals a protein fold implicated in protein-protein interactionMarina Marques Teixeira Vanini
Center for Molecular and Structural Biology, Brazilian Synchrotron Light Laboratory, Campinas, SP, 13083 970, Brazil
Proteins 71:2051-64. 2008..In conclusion, the structure of OmlA does suggest that this protein may be implicated in protein-protein interactions required during X. citri infection... - The solution structure of the adhesion protein Bd37 from Babesia divergens reveals structural homology with eukaryotic proteins involved in membrane traffickingStephane Delbecq
DIMNP, Université Montpellier 1 et 2, CNRS, Laboratoire de Biologie Cellulaire et Moleculaire, ERT 1038, Faculté de Pharmacie BP 14491, Universite de Montpellier I, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
J Mol Biol 375:409-24. 2008..This strongly suggests that Apicomplexa have developed in parallel molecular machines similar in structure and function to the ones used for endo- and exocytosis in eukaryotic cells... - Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) from Escherichia coli: evidence for conformational dynamics in the single-stranded RNA-binding siteW Feng
Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854 5638, USA
Biochemistry 37:10881-96. 1998..88 +/- 0.04 ns and provide evidence for fast time scale (taue < 500 ps) dynamics in surface loops and motions on the microsecond to millisecond time scale within the proposed nucleic acid-binding epitope... - Solution structure and ligand recognition of the WW domain pair of the yeast splicing factor Prp40Silke Wiesner
Structural Biology Programme, EMBL Heidelberg, Meyerhofstr 1, 69117 Heidelberg, Germany
J Mol Biol 324:807-22. 2002..In contrast, no interaction was observed between the Prp40 WW domains and the CTD repeats used in this work... - Calcium-dependent homoassociation of E-cadherin by NMR spectroscopy: changes in mobility, conformation and mapping of contact regionsDaniel Haussinger
Division of Structural Biology and Division of Biophysical Chemistry, Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
J Mol Biol 324:823-39. 2002..According to weak alignment and relaxation data, the symmetry of a predominantly dimeric solution aggregate at 0.6 mM ECAD12 differs from the approximate C2-symmetry of the crystalline dimer... - H-NS oligomerization domain structure reveals the mechanism for high order self-association of the intact proteinDiego Esposito
Department of Biochemistry and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
J Mol Biol 324:841-50. 2002..A model is presented for the structural basis for DNA packaging in bacterial cells... - Structure determination and conformational change induced by tyrosine phosphorylation of the N-terminal domain of the alpha-chain of pig gastric H+/K+-ATPaseNaoki Fujitani
Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
Biochem Biophys Res Commun 300:223-9. 2003..This conformational change induced by the phosphorylation of Tyr 10 might be an advantageous reaction for sequential phosphorylation and may be important for regulating the function of H(+)/K(+)-ATPase... - Solution structure of the coiled-coil trimerization domain from lung surfactant protein DHelena Kovacs
Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
J Biomol NMR 24:89-102. 2002..This residue is completely symmetric in the solution structure, and markedly asymmetric in the crystalline phase. This difference may be functionally important, as it affects the orientation of the antigenic surface presented by SP-D... - NMR structure of the DNA-binding domain of the cell cycle protein Mbp1 from Saccharomyces cerevisiaeMargie Nair
Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
Biochemistry 42:1266-73. 2003..The fold-back structure extends the region of positive electrostatic potential, and this may enhance the nonspecific contribution to binding by favorable electrostatic interactions with the DNA backbone... - Solution structure of the cytotoxic RNase 4 from oocytes of bullfrog Rana catesbeianaChun-Hua Hsu
Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
J Mol Biol 326:1189-201. 2003..Furthermore, the differences of side-chain conformations of subsite residues among RNase A, ONC and rRNase 4 are related to their distinct catalytic activities and base preferences... - Global structure and dynamics of human apolipoprotein CII in complex with micelles: evidence for increased mobility of the helix involved in the activation of lipoprotein lipaseJ Zdunek
Department of Medical Biochemistry and Biophysics and Medical Biosciences, Physiological Chemistry, Umea University, SE 901 87 Umea, Sweden
Biochemistry 42:1872-89. 2003..The overall structure and the internal dynamics, combined with previous mutation data, give important clues toward a possible mechanism for the activation of LPL by apoCII... - A new zinc-protein coordination site in intracellular metal trafficking: solution structure of the Apo and Zn(II) forms of ZntA(46-118)Lucia Banci
Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
J Mol Biol 323:883-97. 2002.... - Structural and nucleotide-binding properties of YajQ and YnaF, two Escherichia coli proteins of unknown functionCosmin Saveanu
Laboratoire de Chimie Structurale des Macromolecules, CNRS URA 2185 Institut Pasteur, 75724 Paris Cedex 15, France
Protein Sci 11:2551-60. 2002..NMR studies, corroborated with local sequence conservation among YajQ homologs in various bacteria, indicate that one of the beta-sheets is mostly involved in biological activity... - NMR solution structure and dynamics of the peptidyl-prolyl cis-trans isomerase domain of the trigger factor from Mycoplasma genitalium compared to FK506-binding proteinMartin Vogtherr
Institut für Organische Chemie der Universität Frankfurt, Marie Curie Str 11, 60439 Frankfurt, Germany
J Mol Biol 318:1097-115. 2002..Our data indicate, however, that this strand may be partially structured as "nascent" beta strand. This makes the trigger factor PPIase domain the most minimal representative of the FKBP like protein family of PPIases... - Solution structure of the catalytic domain of human stromelysin-1 complexed to a potent, nonpeptidic inhibitorY C Li
Novartis Pharmaceuticals Corporation, Summit, New Jersey 07901, USA
Biochemistry 37:14048-56. 1998.... - An autoinhibitory mechanism for nonsyntaxin SNARE proteins revealed by the structure of Ykt6pH Tochio
Department of Biochemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, People s Republic of China
Science 293:698-702. 2001..The NH2-terminal domain plays an important biological role in the function of Ykt6p, which in vitro studies revealed to include influencing the kinetics and proper assembly of SNARE complexes... - The membrane-proximal tryptophan-rich region of the HIV glycoprotein, gp41, forms a well-defined helix in dodecylphosphocholine micellesD J Schibli
Department of Biological Sciences, University of Calgary, Alberta, Canada
Biochemistry 40:9570-8. 2001..This work shows that the Trp-rich membrane-proximal region of HIV and related viruses can bind to the surfaces of zwitterioninc membranes in a "Velcro-like" manner... - Structural basis for recognition of the intron branch site RNA by splicing factor 1Z Liu
European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
Science 294:1098-102. 2001..The branch point adenosine acting as the nucleophile in the first biochemical step of splicing is deeply buried. BPS RNA recognition suggests how SF1 may facilitate subsequent formation of the prespliceosomal complex A... - Structure of the type III secretion and substrate-binding domain of Yersinia YopH phosphataseC L Smith
Department of Biological Chemistry, University of Michigan, 930 N University Ave, Ann Arbor, MI 48109 1055, USA
Mol Microbiol 42:967-79. 2001..Phosphopeptide-induced perturbations in NMR chemical shifts define a substrate-binding surface on YopH(1-129) that includes residues previously shown by mutagenesis to be essential for YopH function... - The rhesus rotavirus VP4 sialic acid binding domain has a galectin fold with a novel carbohydrate binding sitePhilip R Dormitzer
Laboratory of Molecular Medicine, Enders 673, Children s Hospital, 320 Longwood Avenue, Boston, MA 02115, USA
EMBO J 21:885-97. 2002..From the fit of the VP8* core into the virion spikes, we propose that VP4 arose from the insertion of a host carbohydrate binding domain into a viral membrane interaction protein... - Folding and conformational consequences of glycine to alanine replacements at different positions in a collagen model peptideManjiri Bhate
Department of Biochemistry, UMDNJ-Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, New Jersey 08854, USA
Biochemistry 41:6539-47. 2002.... - Functional and structural characterization of a synthetic peptide representing the N-terminal domain of prokaryotic pyruvate dehydrogenaseAnnechien F Hengeveld
Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
Biochemistry 41:7490-500. 2002..Moreover, the flexibility might be essential in sustaining the allosteric properties of the enzyme bound in the complex... - Structural basis for recognition by an in vitro evolved affibodyMartin Högbom
Department of Biochemistry and Biophysics, Stockholm University, Roslagstullsbacken 15, AlbaNova University Center, SE 10691 Stockholm, Sweden
Proc Natl Acad Sci U S A 100:3191-6. 2003..The implications of the selected affibody binding-mode for its application as a universal binding protein are discussed...
Research Grants
- Structural Studies of Metabolic Membrane ProteinsJoanne Yeh; Fiscal Year: 2006..Our specific aims are to obtain atomic resolution structures of both membrane proteins, both of which are likely to be novel targets for antibiotic design and therapy. ..
- Molecular Target Focused Discovery of Anticancer DrugsGEORGE PETTIT; Fiscal Year: 2007..In summary, the proposed research will be sharply aimed at the discovery and very rapid development of new anticancer drugs for the NCI programs direct at improving human cancer treatments. ..
- Molecular Target Focused Discovery of Anticancer DrugsGEORGE PETTIT; Fiscal Year: 2005..In summary, the proposed research will be sharply aimed at the discovery and very rapid development of new anticancer drugs for the NCI programs directed at improving human cancer treatments. ..
- Molecular Target Focused Discovery of Anticancer DrugsGeorge R Pettit; Fiscal Year: 2010....
- Solid-state NMR studies of antimicrobial peptidesMei Hong; Fiscal Year: 2007..Moreover, the proposed research will fill our knowledge gap of how beta-sheet peptides interact with lipid bilayers in general. ..
- NMR SPECTROSCOPY OF IRON-SULFUR PROTEINSJohn Markley; Fiscal Year: 2007..To achieve these aims, we will make use of state-of-the-art approaches to protein production and isotopic labeling, NMR data collection and analysis, modeling of structures and complexes, and quantum chemical calculations. ..
- The sweet protein brazzein and its interaction with the human taste receptorFariba Assadi Porter; Fiscal Year: 2009..Explanation of molecular features that are essential for the brazzein-sweet receptor interaction may result in design of superior tasting non-caloric sweetener as an approach to help addressing diabetes and related disorders. ..
- 900 MHz NMR Spectrometer Biomolecular InvestigationsJohn Markley; Fiscal Year: 2006..Web-based software will be used to pair users with local collaborator(s), assess specific needs, design and schedule data collection, and share results. ..
- NMR SPECTROSCOPY OF IRON-SULFUR PROTEINSJohn Markley; Fiscal Year: 2006..Effort will also be expended toward developing new methodology for paramagnetic NMR, in particular, for systems that are not amenable to established approaches. ..
- Center for Eukaryotic Structural GenomicsJohn Markley; Fiscal Year: 2004..thaliana to be funded separately. The methods developed by the Center will be applicable to other eukaryotic genomes, including the human genome. ..
- NMR SPECTROSCOPY OF IRON-SULFUR PROTEINSJohn Markley; Fiscal Year: 2009..To achieve these aims, we will make use of state-of-the-art approaches to protein production and isotopic labeling, NMR data collection and analysis, modeling of structures and complexes, and quantum chemical calculations. ..
- NATIONAL BIOMEDICAL NMR RESOURCE AT MADISONJohn Markley; Fiscal Year: 2007..Our goal is to develop methods for making these investigations faster and less costly, as well as applicable to larger classes of proteins and nucleic acids of importance in human disease. ..
- Solid-state NMR of antimicrobial and cationic membrane peptidesMei Hong; Fiscal Year: 2010..It will also benefit the development of more effective drug-delivery compounds that cross the cell membrane without damaging its integrity. ..
- The sweet protein brazzein and its interaction with the human taste receptorFariba M Assadi Porter; Fiscal Year: 2010..Explanation of molecular features that are essential for the brazzein-sweet receptor interaction may result in design of superior tasting non-caloric sweetener as an approach to help addressing diabetes and related disorders. ..
- 900 MHZ NMR SPECTROMETERJohn Markley; Fiscal Year: 2001..abstract_text> ..
- Solid-state NMR of antimicrobial and cationic membrane peptidesMei Hong; Fiscal Year: 2009..It will also benefit the development of more effective drug-delivery compounds that cross the cell membrane without damaging its integrity. ..
- Solid-state NMR of influenza M2 protein in lipid bilayersMei Hong; Fiscal Year: 2010..The high-resolution structural information will be crucial for the design of new antiviral drugs to target the drug-resistant mutant proton channel, S31N-M2 in influenza A viruses. ..
- NMR SPECTROSCOPY OF IRON-SULFUR PROTEINSJohn L Markley; Fiscal Year: 2010..abstract_text> ..
- STRUCTURE & FUNCTION RELATIONSHIP: PROSTANOID RECEPTORSKe He Ruan; Fiscal Year: 2007..Determine the solution conformation of segments comprising the intracellular domains. ..
- Prostaglandin I synthase, Thromboxane A synthase & Prostaglandin E synthaseKe He Ruan; Fiscal Year: 2007....
- Prostaglandin I synthase, Thromboxane A synthase & Prostaglandin E synthaseKe He Ruan; Fiscal Year: 2009....
- CONFERENCE ON MAGNETIC RESONANCE IN BIOLOGICAL SYSTEMSJohn Markley; Fiscal Year: 2002..Those receiving travel support will be selected by a committee composed of the U.S. members of the International Organizing Committee for the meeting. ..
- NMR SPECTROSCOPY OF IRON-SULFUR PROTEINSJohn Markley; Fiscal Year: 2003..Effort will also be expended toward developing new methodology for paramagnetic NMR, in particular, for systems that are not amenable to established approaches. ..
- NMR SPECTROSCOPY OF IRON-SULFUR PROTEINSJohn Markley; Fiscal Year: 2007..abstract_text> ..
- NMR SPECTROSCOPY OF IRON-SULFUR PROTEINSJohn Markley; Fiscal Year: 2002....
- NMR SPECTROSCOPY OF IRON-SULFUR PROTEINSJohn L Markley; Fiscal Year: 2010..To achieve these aims, we will make use of state-of-the-art approaches to protein production and isotopic labeling, NMR data collection and analysis, modeling of structures and complexes, and quantum chemical calculations. ..
- Structural Basis of Dilated CardiomyopathyGianluigi Veglia; Fiscal Year: 2007..To the best of our knowledge, these are the first biophysical studies of protein-protein interactions between integral membrane proteins and soluble proteins ever carried out using NMR spectroseopy. ..
- Structural Basis of Dilated CardiomyopathyGianluigi Veglia; Fiscal Year: 2010..To the best of our knowledge, these are the first biophysical studies of protein-protein interactions between integral membrane proteins and soluble proteins ever carried out using NMR spectroscopy. ..
- KALLIKREINS AS DIAGNOSTIC MARKERS OF OVARIAN CARCINOMAEleftherios Diamandis; Fiscal Year: 2007..Relevance of this research to public health: By achieving early ovarian cancer diagnosis, it will be possible to reduce the burden of the disease by administration of effective treatment as early as possible. ..
- NMR Structural Analysis of Calcium Regulation in MuscleGianluigi Veglia; Fiscal Year: 2006..abstract_text> ..
- Structural Basis of Dilated CardiomyopathyGianluigi Veglia; Fiscal Year: 2007..To the best of our knowledge, these are the first biophysical studies of protein-protein interactions between integral membrane proteins and soluble proteins ever carried out using NMR spectroscopy. ..
- Human Kallikrein 4 (hK4): A New Prostatic Biomarker?Eleftherios Diamandis; Fiscal Year: 2003..If successful, our research will contribute to the development of new prostatic biomarkers and possibly, to better diagnosis which may lead to better clinical outcomes and reduced healthcare costs. ..
- NMR Structural Analysis of Calcium Regulation in MuscleGianluigi Veglia; Fiscal Year: 2010..Therefore, understanding SERCA regulation by both SLN and PLN is central to the development of non-conventional drug therapy such as gene therapy. ..
- SYNTHESIS OF TEDANOLIDES CYTOTOXIC POLYPROPIONATESMichael Jung; Fiscal Year: 1999....
- A New Biomarker for Ovarian Cancer DetectionEleftherios Diamandis; Fiscal Year: 2003..In this grant proposal, we describe further studies, which will examine in greater detail, the ability of a test for the amount of this protein in blood to correctly diagnose the presence of ovarian cancer. ..
- SYNTHESIS OF THE TEDANOLIDES, CYTOTOXIC POLYPROPIONATESMichael Jung; Fiscal Year: 2003....