G Marius Clore

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation?
    G Marius Clore
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    J Am Chem Soc 126:2923-38. 2004
  2. ncbi Amplitudes of protein backbone dynamics and correlated motions in a small alpha/beta protein: correspondence of dipolar coupling and heteronuclear relaxation measurements
    G Marius Clore
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    Biochemistry 43:10678-91. 2004
  3. ncbi Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small alpha/beta protein: a unified picture of high probability, fast atomic motions in proteins
    G Marius Clore
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
    J Mol Biol 355:879-86. 2006
  4. ncbi Docking of protein-protein complexes on the basis of highly ambiguous intermolecular distance restraints derived from 1H/15N chemical shift mapping and backbone 15N-1H residual dipolar couplings using conjoined rigid body/torsion angle dynamics
    G Marius Clore
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0510, USA
    J Am Chem Soc 125:2902-12. 2003
  5. ncbi Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement
    G Marius Clore
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
    Curr Opin Struct Biol 17:603-16. 2007
  6. ncbi Exploring sparsely populated states of macromolecules by diamagnetic and paramagnetic NMR relaxation
    G Marius Clore
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    Protein Sci 20:229-46. 2011
  7. ncbi Solution structure of a post-transition state analog of the phosphotransfer reaction between the A and B cytoplasmic domains of the mannitol transporter IIMannitol of the Escherichia coli phosphotransferase system
    Jeong Yong Suh
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 281:8939-49. 2006
  8. ncbi Solution structure of the IIAChitobiose-IIBChitobiose complex of the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system
    Young Sang Jung
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 285:4173-84. 2010
  9. ncbi Solution NMR structures of productive and non-productive complexes between the A and B domains of the cytoplasmic subunit of the mannose transporter of the Escherichia coli phosphotransferase system
    Jun Hu
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 283:11024-37. 2008
  10. ncbi Three-dimensional solution structure of the cytoplasmic B domain of the mannitol transporter IImannitol of the Escherichia coli phosphotransferase system
    Patricia M Legler
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, USA
    J Biol Chem 279:39115-21. 2004

Collaborators

Detail Information

Publications78

  1. ncbi How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation?
    G Marius Clore
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    J Am Chem Soc 126:2923-38. 2004
    ..For most practical applications, however, refinement of NMR structures against dipolar couplings using a single structure representation is adequate and will not adversely impact coordinate accuracy within the limits of the NMR method...
  2. ncbi Amplitudes of protein backbone dynamics and correlated motions in a small alpha/beta protein: correspondence of dipolar coupling and heteronuclear relaxation measurements
    G Marius Clore
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    Biochemistry 43:10678-91. 2004
    ..In addition, direct evidence is obtained for ubiquitous crankshaft motions along the entire length of the polypeptide backbone manifested by the anticorrelation of the backbone torsion angles phi(i) and psi(i-1)...
  3. ncbi Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small alpha/beta protein: a unified picture of high probability, fast atomic motions in proteins
    G Marius Clore
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
    J Mol Biol 355:879-86. 2006
    ....
  4. ncbi Docking of protein-protein complexes on the basis of highly ambiguous intermolecular distance restraints derived from 1H/15N chemical shift mapping and backbone 15N-1H residual dipolar couplings using conjoined rigid body/torsion angle dynamics
    G Marius Clore
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0510, USA
    J Am Chem Soc 125:2902-12. 2003
    ..This methodology should be particularly useful for high throughput, NMR-based, structural proteomics...
  5. ncbi Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement
    G Marius Clore
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
    Curr Opin Struct Biol 17:603-16. 2007
    ....
  6. ncbi Exploring sparsely populated states of macromolecules by diamagnetic and paramagnetic NMR relaxation
    G Marius Clore
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    Protein Sci 20:229-46. 2011
    ..Examples of these various approaches are presented...
  7. ncbi Solution structure of a post-transition state analog of the phosphotransfer reaction between the A and B cytoplasmic domains of the mannitol transporter IIMannitol of the Escherichia coli phosphotransferase system
    Jeong Yong Suh
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 281:8939-49. 2006
    ....
  8. ncbi Solution structure of the IIAChitobiose-IIBChitobiose complex of the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system
    Young Sang Jung
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 285:4173-84. 2010
    ....
  9. ncbi Solution NMR structures of productive and non-productive complexes between the A and B domains of the cytoplasmic subunit of the mannose transporter of the Escherichia coli phosphotransferase system
    Jun Hu
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 283:11024-37. 2008
    ..The non-productive IIA(Man)-IIB(Man) complex may possibly be relevant to subsequent phosphoryl transfer from His-175 of IIB(Man) to the incoming sugar located on the transmembrane IIC(Man)-IID(Man) complex...
  10. ncbi Three-dimensional solution structure of the cytoplasmic B domain of the mannitol transporter IImannitol of the Escherichia coli phosphotransferase system
    Patricia M Legler
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, USA
    J Biol Chem 279:39115-21. 2004
    ..All three proteins utilize a cysteine residue in the nucleophilic attack of a phosphoryl group covalently bound to another protein...
  11. ncbi Solution structure of the IIAChitobiose-HPr complex of the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system
    Young Sang Jung
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 287:23819-29. 2012
    ....
  12. ncbi Visualization of the phosphorylated active site loop of the cytoplasmic B domain of the mannitol transporter II(Mannitol) of the Escherichia coli phosphotransferase system by NMR spectroscopy and residual dipolar couplings
    Jeong Yong Suh
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
    J Mol Biol 353:1129-36. 2005
    ....
  13. ncbi A simple and reliable approach to docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints
    Chun Tang
    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 36:37-44. 2006
    ....
  14. ncbi Visualization of transient encounter complexes in protein-protein association
    Chun Tang
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    Nature 444:383-6. 2006
    ..Qualitatively similar results are presented for two other protein-protein complexes...
  15. ncbi Impact of phosphorylation on structure and thermodynamics of the interaction between the N-terminal domain of enzyme I and the histidine phosphocarrier protein of the bacterial phosphotransferase system
    Jeong Yong Suh
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 283:18980-9. 2008
    ..This facilitates highly efficient phosphoryl transfer between EIN and HPr, which is estimated to occur at a rate of approximately 850 s(-1) from exchange spectroscopy...
  16. ncbi Solution NMR structure of the 48-kDa IIAMannose-HPr complex of the Escherichia coli mannose phosphotransferase system
    David C Williams
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 280:20775-84. 2005
    ....
  17. ncbi Global jumping and domain-specific intersegment transfer between DNA cognate sites of the multidomain transcription factor Oct-1
    Michaeleen Doucleff
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
    Proc Natl Acad Sci U S A 105:13871-6. 2008
    ....
  18. ncbi Solution NMR structure of the barrier-to-autointegration factor-Emerin complex
    Mengli Cai
    Laboratories of Chemical Physics and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892 0520, USA
    J Biol Chem 282:14525-35. 2007
    ..The relevance of the implications of the structural and biophysical data on the complex in the context of the interaction between the BAF(2) dimer and Em(LEM) at the nuclear envelope is discussed...
  19. ncbi Visualization of transient ultra-weak protein self-association in solution using paramagnetic relaxation enhancement
    Chun Tang
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    J Am Chem Soc 130:4048-56. 2008
    ....
  20. ncbi Molecular basis of sequence-specific single-stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single-stranded DNA
    Demetrios T Braddock
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0510, USA
    EMBO J 21:3476-85. 2002
    ....
  21. ncbi Intramolecular domain-domain association/dissociation and phosphoryl transfer in the mannitol transporter of Escherichia coli are not coupled
    Jeong Yong Suh
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
    Proc Natl Acad Sci U S A 104:3153-8. 2007
    ....
  22. ncbi Solution structure of the 128 kDa enzyme I dimer from Escherichia coli and its 146 kDa complex with HPr using residual dipolar couplings and small- and wide-angle X-ray scattering
    Charles D Schwieters
    Division of Computational Biosciences, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892 5624, USA
    J Am Chem Soc 132:13026-45. 2010
    ..These large-scale interdomain motions shed light on the structural transitions that accompany the catalytic cycle of EI...
  23. ncbi Crystal structures of the HIV-1 inhibitory cyanobacterial protein MVL free and bound to Man3GlcNAc2: structural basis for specificity and high-affinity binding to the core pentasaccharide from n-linked oligomannoside
    David C Williams
    Laboratory of Chemical Physics, National Institutes of Health, Bethesda, MD 20892, USA
    J Biol Chem 280:29269-76. 2005
    ..The structures of MVL and the MVL-Man3GlcNAc2 complex further our understanding of the molecular basis of high affinity and specificity in protein-carbohydrate recognition...
  24. ncbi Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm
    John J Kuszewski
    Imaging Sciences Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892 5624, USA
    J Biomol NMR 41:221-39. 2008
    ..We show that useful assignment information can be obtained even in the case in which a unique structure cannot be determined...
  25. ncbi Characterization of nonspecific protein-DNA interactions by 1H paramagnetic relaxation enhancement
    Junji Iwahara
    Contribution from the Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD 20892-0520, USA
    J Am Chem Soc 126:12800-8. 2004
    ..Combining the (1)H-PRE data with the crystal structure of the HMGB-1 A-box/cisplatin-modified DNA complex allows one to obtain a semiquantitative estimate of the equilibrium populations at the various sites...
  26. ncbi Molecular basis for synergistic transcriptional activation by Oct1 and Sox2 revealed from the solution structure of the 42-kDa Oct1.Sox2.Hoxb1-DNA ternary transcription factor complex
    David C Williams
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    J Biol Chem 279:1449-57. 2004
    ....
  27. ncbi Solution structure of enzyme IIA(Chitobiose) from the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system
    Chun Tang
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    J Biol Chem 280:11770-80. 2005
    ..This is associated with the presence of an unusually large (230-angstroms3) buried hydrophobic cavity at the trimer interface in IIA(Lac) that is reduced to only 45 angstroms3) in IIA(Chb)...
  28. ncbi Intra- and intermolecular translocation of the bi-domain transcription factor Oct1 characterized by liquid crystal and paramagnetic NMR
    Yuki Takayama
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
    Proc Natl Acad Sci U S A 108:E169-76. 2011
    ..Thus cross-talk between the POU(S) and POU(HD) domains, each fulfilling different and complementary components of the search process ensures efficient sampling of DNA, thereby facilitating the location of specific Oct1 target sites...
  29. ncbi Synergistic inhibition of HIV-1 envelope-mediated membrane fusion by inhibitors targeting the N and C-terminal heptad repeats of gp41
    Elena Gustchina
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
    J Mol Biol 364:283-9. 2006
    ..The mechanistic, as well as potential therapeutic, implications of these observations for HIV-Env-mediated membrane fusion are discussed...
  30. ncbi Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement
    G Marius Clore
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
    Mol Biosyst 4:1058-69. 2008
    ..The PRE offers unique opportunities to directly probe and explore in structural terms lowly-populated regions of the free energy landscape and promises to yield fundamental new insights into biophysical processes...
  31. ncbi Visualizing transient events in amino-terminal autoprocessing of HIV-1 protease
    Chun Tang
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    Nature 455:693-6. 2008
    ....
  32. ncbi Sequestering of the prehairpin intermediate of gp41 by peptide N36Mut(e,g) potentiates the human immunodeficiency virus type 1 neutralizing activity of monoclonal antibodies directed against the N-terminal helical repeat of gp41
    Elena Gustchina
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
    J Virol 82:10032-41. 2008
    ..The mechanistic implications of these findings are discussed...
  33. ncbi Differential inhibition of HIV-1 and SIV envelope-mediated cell fusion by C34 peptides derived from the C-terminal heptad repeat of gp41 from diverse strains of HIV-1, HIV-2, and SIV
    Elena Gustchina
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
    J Med Chem 48:3036-44. 2005
    ..This result suggests that C34 from HIV-2 EHO may present a potentially useful therapeutic agent against diverse and/or resistant strains of HIV-1...
  34. ncbi A monoclonal Fab derived from a human nonimmune phage library reveals a new epitope on gp41 and neutralizes diverse human immunodeficiency virus type 1 strains
    Elena Gustchina
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0820, USA
    J Virol 81:12946-53. 2007
    ....
  35. ncbi Combined use of residual dipolar couplings and solution X-ray scattering to rapidly probe rigid-body conformational transitions in a non-phosphorylatable active-site mutant of the 128 kDa enzyme I dimer
    Yuki Takayama
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, United States
    J Am Chem Soc 133:424-7. 2011
    ....
  36. ncbi No interaction of barrier-to-autointegration factor (BAF) with HIV-1 MA, cone-rod homeobox (Crx) or MAN1-C in absence of DNA
    Ying Huang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 6:e25123. 2011
    ..The absence of direct binding of BAF to MAN1-C eliminates disruption of this interaction as the cause of the premature aging phenotype...
  37. ncbi Heteronuclear NMR spectroscopy for lysine NH(3) groups in proteins: unique effect of water exchange on (15)N transverse relaxation
    Junji Iwahara
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    J Am Chem Soc 129:2971-80. 2007
    ..Finally, we consider the potential use of lysine NH3 groups as an alternative probe for larger systems as illustrated by data obtained on the 128-kDa enzyme I dimer...
  38. ncbi Structural basis of HIV-1 neutralization by affinity matured Fabs directed against the internal trimeric coiled-coil of gp41
    Elena Gustchina
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Pathog 6:e1001182. 2010
    ....
  39. ncbi Affinity maturation by targeted diversification of the CDR-H2 loop of a monoclonal Fab derived from a synthetic naïve human antibody library and directed against the internal trimeric coiled-coil of gp41 yields a set of Fabs with improved HIV-1 neutraliza
    Elena Gustchina
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
    Virology 393:112-9. 2009
    ....
  40. ncbi Conformational changes in HIV-1 gp41 in the course of HIV-1 envelope glycoprotein-mediated fusion and inactivation
    Antony S Dimitrov
    Center for Cancer Research, Nanobiology Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
    Biochemistry 44:12471-9. 2005
    ..This inactivation pathway may be important for the design of entry inhibitors and vaccine candidates...
  41. ncbi Probing exchange kinetics and atomic resolution dynamics in high-molecular-weight complexes using dark-state exchange saturation transfer NMR spectroscopy
    Nicolas L Fawzi
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
    Nat Protoc 7:1523-33. 2012
    ..Although the length of the experiments depends strongly on sample conditions, approximately 1 week of NMR spectrometer time was sufficient for full characterization of samples of amyloid-β (Aβ) at concentrations of ~100 μM...
  42. ncbi Coupling between internal dynamics and rotational diffusion in the presence of exchange between discrete molecular conformations
    Yaroslav Ryabov
    Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Building 12A, Bethesda, Maryland 20892 5624, USA
    J Chem Phys 136:034108. 2012
    ..We specialize the results for the computation of the frequency-domain correlation function associated with the NMR relaxation...
  43. ncbi Structural basis of the association of HIV-1 matrix protein with DNA
    Mengli Cai
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 5:e15675. 2010
    ..We show that MA interacts with DNA and this is likely sufficient to account for its association with the PIC...
  44. ncbi Ensemble approach for NMR structure refinement against (1)H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule
    Junji Iwahara
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
    J Am Chem Soc 126:5879-96. 2004
    ..This is particularly significant in the case of macromolecular complexes where intermolecular translational restraints derived from nuclear Overhauser enhancement data may be limited...
  45. ncbi Completely automated, highly error-tolerant macromolecular structure determination from multidimensional nuclear overhauser enhancement spectra and chemical shift assignments
    John Kuszewski
    Contribution from the Division of Computational Bioscience, Building 12A, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892-5624, USA
    J Am Chem Soc 126:6258-73. 2004
    ..The limits of the method are explored using simulated data on the 56-residue B1 domain of Streptococcal protein G...
  46. ncbi Using the experimentally determined components of the overall rotational diffusion tensor to restrain molecular shape and size in NMR structure determination of globular proteins and protein-protein complexes
    Yaroslav Ryabov
    Division of Computational Bioscience, Building 12A, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892 5624, USA
    J Am Chem Soc 131:9522-31. 2009
    ..In each case, the cluster containing the lowest-energy structure corresponds to the correct solution...
  47. ncbi Replica exchange simulations of transient encounter complexes in protein-protein association
    Young C Kim
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
    Proc Natl Acad Sci U S A 105:12855-60. 2008
    ..Nonspecific complexes may not only accelerate the binding kinetics by enhancing the rate of success of random diffusional encounters but also play a role in protein function as alternative binding modes...
  48. ncbi Characterization and HIV-1 fusion inhibitory properties of monoclonal Fabs obtained from a human non-immune phage library selected against diverse epitopes of the ectodomain of HIV-1 gp41
    John M Louis
    Laboratory of Chemical Physics National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room B1/30I, Bethesda, MD 20892, USA
    J Mol Biol 353:945-51. 2005
    ..The two most potent fusion inhibitors belonged to class B. This panel of Fabs provides a set of useful probes for studying HIV-1 envelope-mediated cell fusion and may serve as a basis for developing Fab-based anti-HIV-1 therapeutics...
  49. ncbi Detecting transient intermediates in macromolecular binding by paramagnetic NMR
    Junji Iwahara
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
    Nature 440:1227-30. 2006
    ..The intermolecular PRE method is general and can be readily applied to investigations of transient intermediates in many other macromolecular binding processes...
  50. ncbi Conformational selection and substrate binding regulate the monomer/dimer equilibrium of the C-terminal domain of Escherichia coli enzyme I
    Vincenzo Venditti
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    J Biol Chem 287:26989-98. 2012
    ..Upon PEP binding, the β3α3 turn is effectively locked in the closed state by the formation of salt bridges between the phosphate group of PEP and the side chains of Lys(340) and Arg(358), thereby stabilizing the dimer...
  51. ncbi NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA
    Junji Iwahara
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD 20892-0520, USA
    Proc Natl Acad Sci U S A 103:15062-7. 2006
    ....
  52. ncbi Solution structure of the phosphoryl transfer complex between the signal-transducing protein IIAGlucose and the cytoplasmic domain of the glucose transporter IICBGlucose of the Escherichia coli glucose phosphotransferase system
    Mengli Cai
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 278:25191-206. 2003
    ..IIBGlc and the two upstream complexes of the glucose phosphotransferase system (EI.HPr and IIAGlc.HPr) reveal a cascade in which highly overlapping binding sites on HPr and IIAGlc recognize structurally diverse proteins...
  53. ncbi Solution structure of the monovalent lectin microvirin in complex with Man(alpha)(1-2)Man provides a basis for anti-HIV activity with low toxicity
    Syed Shahzad-ul-hussan
    Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 286:20788-96. 2011
    ....
  54. ncbi Kinetics of amyloid beta monomer-to-oligomer exchange by NMR relaxation
    Nicolas L Fawzi
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    J Am Chem Soc 132:9948-51. 2010
    ..The fraction of peptide within the "dark" oligomeric state undergoing exchange with free monomer is calculated to be approximately 3%...
  55. ncbi Mechanistic details of a protein-protein association pathway revealed by paramagnetic relaxation enhancement titration measurements
    Nicolas L Fawzi
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
    Proc Natl Acad Sci U S A 107:1379-84. 2010
    ....
  56. ncbi 13C-detected HN(CA)C and HMCMC experiments using a single methyl-reprotonated sample for unambiguous methyl resonance assignment
    Kaifeng Hu
    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 36:259-66. 2006
    ..The applicability of these experiments for the assignment of methyl 1H and 13C resonances is demonstrated using the 18.6 kDa B domain of the Escherichia coli mannose transporter (IIBMannose)...
  57. ncbi Accurate determination of leucine and valine side-chain conformations using U-[15N/13C/2H]/[1H-(methine/methyl)-Leu/Val] isotope labeling, NOE pattern recognition, and methine Cgamma-Hgamma/Cbeta-Hbeta residual dipolar couplings: application to the 34-kDa
    Chun Tang
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5/B1-30I, Bethesda, MD 20892-0520, USA
    J Biomol NMR 33:105-21. 2005
    ..The impact of the method on protein structure determination is illustrated by application to enzyme IIA(Chitobiose), a 34 kDa homotrimeric phosphotransferase protein...
  58. ncbi Mapping the binding of the N-terminal extracellular tail of the CXCR4 receptor to stromal cell-derived factor-1alpha
    Elliott K Gozansky
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD 20892-0520, USA
    J Mol Biol 345:651-8. 2005
    ..This surface overlaps with but is not identical to that mapped on several other chemokines for the binding of equivalent peptides derived from their respective receptors...
  59. ncbi Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR
    Chun Tang
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    Nature 449:1078-82. 2007
    ..Using ensemble simulated annealing refinement against the PRE data we are able to determine a <r(-6)> ensemble average structure of the minor apo species and show that it is distinct from the sugar-bound state...
  60. ncbi Peptides from second extracellular loop of C-C chemokine receptor type 5 (CCR5) inhibit diverse strains of HIV-1
    Cajetan Dogo-Isonagie
    Laboratory of Bioorganic Chemistry, NIAID, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 287:15076-86. 2012
    ..These peptides may serve as a starting point for the design of inhibitors with broad spectrum anti-HIV activity...
  61. ncbi Exploring translocation of proteins on DNA by NMR
    G Marius Clore
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 02892 0520, USA
    J Biomol NMR 51:209-19. 2011
    ..These studies led to the first direct demonstration of rotation-coupled sliding of a protein along the DNA and the direct transfer of a protein from one DNA molecule to another without dissociating into free solution...
  62. ncbi Atomic-resolution dynamics on the surface of amyloid-β protofibrils probed by solution NMR
    Nicolas L Fawzi
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    Nature 480:268-72. 2011
    ..The values, however, are significantly larger for the C-terminal residues of Aβ42 than Aβ40, which might explain the former's higher propensity for rapid aggregation and fibril formation...
  63. ncbi Temperature-dependent intermediates in HIV-1 envelope glycoprotein-mediated fusion revealed by inhibitors that target N- and C-terminal helical regions of HIV-1 gp41
    Stephen A Gallo
    Laboratory of Experimental and Computational Biology, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
    Biochemistry 43:8230-3. 2004
    ..Priming experiments with Env-expressing cells indicate that the N-HR region but not the C-HR region is exposed by treatment with sCD4 at 31 degrees C, whereas both the N- and C-HR regions are exposed at 37 degrees C...
  64. ncbi Structure and dynamics of KH domains from FBP bound to single-stranded DNA
    Demetrios T Braddock
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Nature 415:1051-6. 2002
    ..Dynamics measurements show that the two KH domains bind as articulated modules to single-stranded DNA, providing a flexible framework with which to recognize transient, moving targets...
  65. ncbi Direct observation of enhanced translocation of a homeodomain between DNA cognate sites by NMR exchange spectroscopy
    Junji Iwahara
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
    J Am Chem Soc 128:404-5. 2006
    ..The relevance of this mechanism to the kinetics of protein-DNA interactions within the cell is discussed...
  66. ncbi EDTA-derivatized deoxythymidine as a tool for rapid determination of protein binding polarity to DNA by intermolecular paramagnetic relaxation enhancement
    Junji 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
    ....
  67. ncbi Spin-state selective carbon-detected HNCO with TROSY optimization in all dimensions and double echo-antiecho sensitivity enhancement in both indirect dimensions
    Kaifeng Hu
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    J Am Chem Soc 129:5484-91. 2007
    ..dEA offers sensitivity enhancement of in both indirect dimensions and is generally applicable to many multidimensional experiments...
  68. ncbi Sensitivity improvement for correlations involving arginine side-chain Nepsilon/Hepsilon resonances in multi-dimensional NMR experiments using broadband 15N 180 degrees pulses
    Junji Iwahara
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD, 20892-0520, USA
    J Biomol NMR 36:251-7. 2006
    ....
  69. ncbi Reweighted atomic densities to represent ensembles of NMR structures
    Charles D Schwieters
    Computational Bioscience and Engineering Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892 5624, USA
    J Biomol NMR 23:221-5. 2002
    ..The approach is illustrated using several examples...
  70. ncbi Solution structure of the phosphoryl transfer complex between the cytoplasmic A domain of the mannitol transporter IIMannitol and HPr of the Escherichia coli phosphotransferase system
    Gabriel Cornilescu
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 277:42289-98. 2002
    ....
  71. ncbi Chi(1) rotamer populations and angles of mobile surface side chains are accurately predicted by a torsion angle database potential of mean force
    G Marius Clore
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0510, USA
    J Am Chem Soc 124:2866-7. 2002
    ....
  72. ncbi A pseudopotential for improving the packing of ellipsoidal protein structures determined from NMR data
    Charles D Schwieters
    Imaging Sciences Laboratory, Center for Information Technology, National Institutes of Health, Building 12A, Bethesda, Maryland 20892 5624, USA
    J Phys Chem B 112:6070-3. 2008
    ..We demonstrate that this new gyration volume term improves structures both during the calculation of an initial unknown fold and during final refinement...
  73. ncbi A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large-angle X-ray scattering data
    Charles D Schwieters
    Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Building 12A, Bethesda, Maryland 20892 5624, USA
    Biochemistry 46:1152-66. 2007
    ....
  74. ncbi Using conjoined rigid body/torsion angle simulated annealing to determine the relative orientation of covalently linked protein domains from dipolar couplings
    G Marius Clore
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0510, USA
    J Magn Reson 154:329-35. 2002
    ..By this means translational information afforded by the presence of an intact linker is preserved. We illustrate this approach using the domain-swapped dimer of the HIV-inactivating protein cyanovirin-N as an example...
  75. ncbi Design of a novel peptide inhibitor of HIV fusion that disrupts the internal trimeric coiled-coil of gp41
    Carole A Bewley
    Laboratories of Bioorganic Chemistry, Chemical Physics, and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 277:14238-45. 2002
    ..Thus N36(Mut(e,g)) represents a novel third class of gp41-targeted HIV fusion inhibitor. A quantitative model describing the interaction of N36(Mut(e,g)) with the pre-hairpin intermediate is presented...
  76. ncbi Theoretical and computational advances in biomolecular NMR spectroscopy
    G Marius Clore
    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0510, USA
    Curr Opin Struct Biol 12:146-53. 2002
    ....
  77. ncbi Direct use of 15N relaxation rates as experimental restraints on molecular shape and orientation for docking of protein-protein complexes
    Yaroslav Ryabov
    Division of Computational Bioscience, Building 12A, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892 5624, USA
    J Am Chem Soc 132:5987-9. 2010
    ....
  78. ncbi Role of electrostatic interactions in transient encounter complexes in protein-protein association investigated by paramagnetic relaxation enhancement
    Jeong-Yong Suh
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
    J Am Chem Soc 129:12954-5. 2007