Genomes and Genes
biomolecular nuclear magnetic resonance
Summary: 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.
Publications295 found, 100 shown here
- 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...
- Evaluating protein structures determined by structural genomics consortiaAneerban Bhattacharya
Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers University and Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
Proteins 66:778-95. 2007..Potential reasons for this "structure quality score gap" between NMR and X-ray crystal structures are discussed...
- 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...
- 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...
- NMR characterization of the dynamics of biomacromoleculesArthur G Palmer
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
Chem Rev 104:3623-40. 2004
- Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactionsFrank H Schumann
Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
J Biomol NMR 39:275-89. 2007..As we show combined chemical shifts can also be applied for a more reliable quantitative evaluation of titration data...
- 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....
- High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNASenada Nozinovic
Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University Frankfurt, Max von Laue Strasse 7, 60438 Frankfurt am Main, Germany
Nucleic Acids Res 38:683-94. 2010..Here, we discuss the impact of various NMR restraints on structure quality and discuss in detail the dynamics of this system as previously determined...
- 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...
- 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...
- Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse modelFrancois Pierre J Martin
Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, London, UK
Mol Syst Biol 4:157. 2008....
- Solution structure of the Reps1 EH domain and characterization of its binding to NPF target sequencesS Kim
Department of Biochemistry, Tufts University School of Medicine, 136 Harrison Avenue, Boston, Massachusetts 02111, USA
Biochemistry 40:6776-85. 2001..In addition, we characterized binding to a peptide containing a DPF sequence (Kd = 0.5 +/- 0.2 mM). The characterization of binding between the Reps1 EH domain and its target proteins provides information about their role in endocytosis...
- NMR analysis of a 900K GroEL GroES complexJocelyne Fiaux
Institut fur Molekularbiologie und Biophysik, Eidgenossische Technische Hochschule Zurich, CH 8093 Zurich, Switzerland
Nature 418:207-11. 2002..This establishes the utility of these techniques for solution NMR studies that should permit the exploration of structure, dynamics and interactions in large macromolecular complexes...
- Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequencesVirginia A Jarymowycz
Department of Chemistry and Interdisciplinary Biochemistry Program, Indiana University, Bloomington, Indiana 47405 0001, USA
Chem Rev 106:1624-71. 2006
- Probing the conformational heterogeneity of the acetylaminofluorene-modified 2'-deoxyguanosine and DNA by 19F NMR spectroscopyB P Cho
Department of Biomedical Sciences, College of Pharmacy, University of Rhode Island, Kingston 02881, USA
Biochemistry 38:7572-83. 1999..et al. (1997) J. Am. Chem. Soc. 119, 5384-5389]. The exclusive stacked nature of the AAF adducts may provide insight into why AAF adducts are more mutagenic and prone to repair than the nonacetylated AF adducts...
- 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 ...
- Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extractsOlaf Beckonert
Department of Biomolecular Medicine, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London, UK
Nat Protoc 2:2692-703. 2007....
- 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...
- 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...
- Correlation between the occurrence of 1H-MRS lipid signal, necrosis and lipid droplets during C6 rat glioma developmentSonja Zoula
Laboratoire mixte INSERM U438 Université Joseph Fourier, Laboratoire de Recherche Correspondant du CEA, Centre Hospitalier Universitaire, Grenoble, France
NMR Biomed 16:199-212. 2003..These necrotic areas contained large amounts of lipid droplets. All these results suggest that mobile lipids detected in vivo by 1H MRS (136 ms echo time) in C6 rat brain glioma arise mainly from lipid droplets located in necrosis...
- 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....
- Inhibitors of amyloid toxicity based on beta-sheet packing of Abeta40 and Abeta42Takeshi Sato
Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794 5215, USA
Biochemistry 45:5503-16. 2006..Importantly, the designed peptide inhibitors significantly reduce the toxicity induced by Abeta42 on cultured rat cortical neurons...
- 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...
- 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...
- Helix movement is coupled to displacement of the second extracellular loop in rhodopsin activationShivani Ahuja
Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794 5215, USA
Nat Struct Mol Biol 16:168-75. 2009..These results provide a comprehensive view of how retinal isomerization triggers helix motion and activation in this prototypical G protein-coupled receptor...
- Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANATorsten Herrmann
Institut fur Molekularbiologie und Biophysik, Eidgenossische Technische Hochschule Honggerberg, CH 8093 Zurich, Switzerland
J Mol Biol 319:209-27. 2002....
- NMR and biochemical characterization of recombinant human tRNA(Lys)3 expressed in Escherichia coli: identification of posttranscriptional nucleotide modifications required for efficient initiation of HIV-1 reverse transcriptionC Tisne
Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Faculte de Pharmacie, Centre National de la Recherche Scientifique Equipe Postulante 2075, Paris, France
RNA 6:1403-12. 2000..coli (m2G10, psi27, m5C48, m5C49, and m1A58) as well as the mnm5 group at position 34 are dispensable for initiation of reverse transcription. In contrast, the 2-thio group at position 34 seems to play an important part in this process...
- Quantitative dynamics and binding studies of the 20S proteasome by NMRRemco Sprangers
Department of Biochemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
Nature 445:618-22. 2007..Our results establish that NMR spectroscopy can provide detailed insight into supra-molecular structures over an order of magnitude larger than those routinely studied using methodology that is generally applicable...
- Structure of Bax: coregulation of dimer formation and intracellular localizationM Suzuki
Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
Cell 103:645-54. 2000..The Bax structure shows that the orientation of helix alpha 9 provides simultaneous control over its mitochondrial targeting and dimer formation...
- Metabonomic and microbiological analysis of the dynamic effect of vancomycin-induced gut microbiota modification in the mouseIvan K S Yap
Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom
J Proteome Res 7:3718-28. 2008....
- 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...
- Conformational averaging in structural biology: issues, challenges and computational solutionsDaniela Kruschel
Laboratory of Computational Biophysics, Mediterranean Institute for Life Sciences, Mestrovicevo setaliste bb, Split, HR 21000, Croatia
Mol Biosyst 5:1606-16. 2009....
- Characterization of conformational and dynamic properties of natively unfolded human and mouse alpha-synuclein ensembles by NMR: implication for aggregationKuen Phon Wu
Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, USA
J Mol Biol 378:1104-15. 2008..These transient interchain interactions coupled with a non-A beta amyloid component (NAC) region that is both more exposed and has a higher propensity to beta structure may accelerate the rate of fibril formation of aS...
- Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer predictionMichael Andrec
Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854 8087, USA
J Struct Funct Genomics 2:103-11. 2002....
- A phase cycle scheme that significantly suppresses offset-dependent artifacts in the R2-CPMG 15N relaxation experimentGrover N B Yip
Department of Chemistry, University of Michigan Biophysics Research Division 930 N University Ave, Ann Arbor, MI 48109, USA
J Magn Reson 171:25-36. 2004....
- Probing the sequence effects on NarI-induced -2 frameshift mutagenesis by dynamic 19F NMR, UV, and CD spectroscopyNidhi Jain
Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, USA
Biochemistry 46:13310-21. 2007..We also provide evidence for AF/FAF conformational compatibility in the NarI sequences...
- Experimental and analytical variation in human urine in 1H NMR spectroscopy-based metabolic phenotyping studiesAnthony D Maher
Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics SORA, Faculty of Medicine, Imperial College London, South Kensington SW7 2AZ, United Kingdom
Anal Chem 79:5204-11. 2007....
- Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysisDan McElheny
Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Proc Natl Acad Sci U S A 102:5032-7. 2005....
- 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....
- Solid-state NMR spectroscopy reveals that E. coli inclusion bodies of HET-s(218-289) are amyloidsChristian Wasmer
Laboratorium fur Physikalische Chemie, ETH Zurich, 8093 Zurich, Switzerland
Angew Chem Int Ed Engl 48:4858-60. 2009..coli IBs of the prion-forming domain from the fungal prion HET-s is the same as that previously determined for fibrils assembled in vitro, and show prion infectivity. These results demonstrate that the IBs of HET-s(218-289) are amyloids...
- 1H NMR metabonomics can differentiate the early atherogenic effect of dairy products in hyperlipidemic hamstersJean Charles Martin
Institut National de la Recherche Agronomique, UMR1260 Nutriments Lipidiques et Prevention des Maladies Metaboliques, Marseille, France
Atherosclerosis 206:127-33. 2009..This proof-of-principle study demonstrates the first use of plasma metabonomics for improving the prognosis of diet-induced atherogenesis, revealing novel potential disease biomarkers...
- 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....
- Locked nucleic acid (LNA) recognition of RNA: NMR solution structures of LNA:RNA hybridsMichael Petersen
Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Odense University, DK 5230 Odense M, Denmark
J Am Chem Soc 124:5974-82. 2002....
- An intramolecular G-quadruplex structure with mixed parallel/antiparallel G-strands formed in the human BCL-2 promoter region in solutionJixun Dai
College of Pharmacy, University of Arizona, Tucson, 85721, USA
J Am Chem Soc 128:1096-8. 2006..This predominant bcl-2 G-quadruplex represents an attractive novel target for the design of new anticancer drugs that specifically modulate bcl-2 gene expression...
- NMR structure of the full-length linear dimer of stem-loop-1 RNA in the HIV-1 dimer initiation siteNikolai B Ulyanov
Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
J Biol Chem 281:16168-77. 2006..These guanines may be recognized by the nucleocapsid protein, which binds tightly to the G-bulge in vitro...
- Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solutionTatyana I Igumenova
Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104 6059, USA
Chem Rev 106:1672-99. 2006
- The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolutionF Mueller
Max Planck Institut fur Molekulare Genetik, Ihnestrasse 73, Berlin, 14195, Germany
J Mol Biol 298:35-59. 2000....
- Structural basis of site-specific histone recognition by the bromodomains of human coactivators PCAF and CBP/p300Lei Zeng
Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York University, New York, NY 10029, USA
Structure 16:643-52. 2008....
- Conformation of alamethicin in oriented phospholipid bilayers determined by (15)N solid-state nuclear magnetic resonanceM Bak
Laboratory for Biomolecular NMR Spectroscopy, Department of Molecular and Structural Biology, Science Park, University of Aarhus, DK-8000 Aarhus C, Denmark
Biophys J 81:1684-98. 2001..300:325-330, 1982). The solid-state NMR-compatible structures may support the formation of a left-handed and parallel multimeric ion channel...
- 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....
- Nuclear magnetic resonance solution structure of the Escherichia coli DNA polymerase III theta subunitGeoffrey A Mueller
Laboratory of Structural Biology, MR 01, National Institute of Environmental Health Sciences, 111 Alexander Drive, Research Triangle Park, North Carolina 27709, USA
J Bacteriol 187:7081-9. 2005..The new theta structure is expected to provide additional insight into its physiological role and its effect on the epsilon proofreading subunit...
- 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...
- 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...
- 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...
- The apical stem-loop of the hepatitis B virus encapsidation signal folds into a stable tri-loop with two underlying pyrimidine bulgesSara Flodell
Department of Medical Biochemistry and Biophysics, Umea University, S 901 87 Umea, Sweden
Nucleic Acids Res 30:4803-11. 2002..In particular, the residues essential for this fold are either totally conserved or show rare non-disruptive mutations. These data strongly indicate that this fold is essential for recognition by the reverse transcriptase...
- Automated NMR structure calculation with CYANAPeter Güntert
RIKEN Genomic Sciences Center, Yokohama, Japan
Methods Mol Biol 278:353-78. 2004....
- MUNIN: a new approach to multi-dimensional NMR spectra interpretationV Y Orekhov
Swedish NMR Centre at Göteborg University
J Biomol NMR 20:49-60. 2001..As a result, the extraction of structural information simply consists of one-dimensional peak picking of the shape along the NOE-axis obtained for each amide group...
- Solution structure and lipid membrane partitioning of VSTx1, an inhibitor of the KvAP potassium channelHoi Jong Jung
Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500 712, Korea
Biochemistry 44:6015-23. 2005....
- SOFAST-HMQC experiments for recording two-dimensional heteronuclear correlation spectra of proteins within a few secondsPaul Schanda
Institut de Biologie Structurale Jean Pierre Ebel, UMR5075 CNRS CEA UJF, 41, rue Jules Horowitz, 38027, Grenoble Cedex, France
J Biomol NMR 33:199-211. 2005....
- i-motif solution structure and dynamics of the d(AACCCC) and d(CCCCAA) tetrahymena telomeric repeatsNarcisse Esmaili
Laboratoire de RMN à Haut Champ, Institut de Chimie des Substances Naturelles Gif sur Yvette, F 91198, France
Nucleic Acids Res 33:213-24. 2005..In both topologies, the adenosine bases are fairly well stacked to the adjacent C*C+ pairs. They are not paired but form symmetrical pseudo-pairs with their H6cis amino proton and N1 nitrogen pointing towards each other...
- Interaction between trichosanthin, a ribosome-inactivating protein, and the ribosomal stalk protein P2 by chemical shift perturbation and mutagenesis analysesDenise S B Chan
Department of Biochemistry, Centre for Protein Science and Crystallography and Molecular Biotechnology Programme, The Chinese University of Hong Kong, Shatin, Hong Kong, China
Nucleic Acids Res 35:1660-72. 2007..In an analogy to the role of stalk proteins in binding elongation factors, we propose that interaction with acidic ribosomal stalk proteins help TCS to locate its RNA substrate...
- HMDB: the Human Metabolome DatabaseDavid S Wishart
Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
Nucleic Acids Res 35:D521-6. 2007..The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. The HMDB is available at: www.hmdb.ca...
- The formation pathway of i-motif tetramersJean Louis Leroy
Laboratoire de Chimie et Biologie Structurale, Institut de Chimie des Substances Naturelles, Gif sur Yvette 91190, France
Nucleic Acids Res 37:4127-34. 2009....
- Conserved structure for single-stranded telomeric DNA recognitionRachel M Mitton-Fry
Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
Science 296:145-7. 2002..The common usage of an OB fold for telomeric DNA interaction demonstrates conservation of end-protection mechanisms among eukaryotes...
- How the human telomeric proteins TRF1 and TRF2 recognize telomeric DNA: a view from high-resolution crystal structuresRobert Court
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
EMBO Rep 6:39-45. 2005..The binding of the TRF2-Dbd to the DNA double helix shows no distortions that would account for the promotion of t-loops in which TRF2 has been implicated...
- [5mCCTCTCTCC]4: an i-motif tetramer with intercalated T*T pairsMuriel Canalia
Laboratoire de Chimie et Biologie Structurale, Institut de Chimie des Substances Naturelles, Gif sur Yvette, France 91190
J Am Chem Soc 131:12870-1. 2009..This observation provides indications of the origin of the conflict that usually hinders T*T intercalation into i-motif structures and more generally of the constraints influencing i-motif formation...
- Structural and dynamic characterization of an unfolded state of poplar apo-plastocyanin formed under nondenaturing conditionsY Bai
Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
Protein Sci 10:1056-66. 2001....
- NMR structures of loop B RNAs from the stem-loop IV domain of the enterovirus internal ribosome entry site: a single C to U substitution drastically changes the shape and flexibility of RNAZhihua Du
Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143 2280, USA
Biochemistry 43:5757-71. 2004....
- Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complexRinaldo W Montalvao
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
J Am Chem Soc 130:15990-6. 2008..The results that we report thus indicate that chemical shifts can be used as structural restraints for the determination of the conformations of protein complexes that are difficult to obtain by more standard NMR approaches...
- 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....
- 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....
- 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...
- 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...
- 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...
- 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....
- 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...
- 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...
- 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...
- 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....
- 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...
- Using NMRView to visualize and analyze the NMR spectra of macromoleculesBruce A Johnson
Molecular Systems, Merck Research Labs, Rahway, NJ, USA
Methods Mol Biol 278:313-52. 2004..NMR spectral peaks can be analyzed and assigned. A suite of tools exists within NMRView for assigning the data from triple-resonance experiments...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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....
- 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...
- 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....
- 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...
- 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...
- 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...
- 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...
- Molecular basis for temperature sensing by an RNA thermometerSaheli Chowdhury
Institute of Molecular Biology and Biophysics, ETH Zurich, 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...
- 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...
- 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...
- 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...
Research Grants132 found, 100 shown here
- 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....