JOSEPH LORIA

Summary

Affiliation: Yale University
Country: USA

Publications

  1. pmc Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex
    Michelle L Gill
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Nucleic Acids Res 34:4506-14. 2006
  2. doi request reprint Characterization of enzyme motions by solution NMR relaxation dispersion
    J Patrick Loria
    Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
    Acc Chem Res 41:214-21. 2008
  3. ncbi request reprint Value of a hydrogen bond in triosephosphate isomerase loop motion
    Rebecca B Berlow
    Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520, USA
    Biochemistry 46:6001-10. 2007
  4. pmc The effects of cosolutes on protein dynamics: the reversal of denaturant-induced protein fluctuations by trimethylamine N-oxide
    Vicky Doan-Nguyen
    Department of Chemistry, Yale University, New Haven, CT 06520, USA
    Protein Sci 16:20-9. 2007
  5. ncbi request reprint Evidence for flexibility in the function of ribonuclease A
    Roger Cole
    Department of Chemistry, Yale University, P O Box 208107, New Haven, Connecticut 06520, USA
    Biochemistry 41:6072-81. 2002
  6. ncbi request reprint Measurement of intermediate exchange phenomena
    James G Kempf
    Department of Chemistry, Yale University, New Haven, CT, USA
    Methods Mol Biol 278:185-231. 2004
  7. doi request reprint The crystal structure of ribonuclease A in complex with thymidine-3'-monophosphate provides further insight into ligand binding
    Nicolas Doucet
    Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
    Proteins 78:2459-68. 2010
  8. pmc The flexibility of a distant loop modulates active site motion and product release in ribonuclease A
    Nicolas Doucet
    Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
    Biochemistry 48:7160-8. 2009
  9. pmc Millisecond dynamics in the allosteric enzyme imidazole glycerol phosphate synthase (IGPS) from Thermotoga maritima
    James Lipchock
    Department of Chemistry, Yale University, New Haven, CT 06520, USA
    J Biomol NMR 45:73-84. 2009
  10. ncbi request reprint Temperature dependence of the backbone dynamics of ribonuclease A in the ground state and bound to the inhibitor 5'-phosphothymidine (3'-5')pyrophosphate adenosine 3'-phosphate
    Evgenii L Kovrigin
    Department of Chemistry, Yale University, P O Box 208107, New Haven, Connecticut 06520, USA
    Biochemistry 42:5279-91. 2003

Research Grants

Collaborators

  • S A Strobel
  • Evgenii L Kovrigin
  • James G Kempf
  • Nicolas Doucet
  • Roger Cole
  • Eric D Watt
  • Michelle L Gill
  • James Lipchock
  • James M Lipchock
  • Vicky Doan-Nguyen
  • Rebecca B Berlow
  • Heather Beach
  • Nicole S Sampson
  • Ju Yeon Jung
  • Miljan Simonovic
  • Thusitha B Jayasundera
  • Christina Ragain
  • Tatyana I Igumenova
  • Hiroko Shimada
  • Michael J Grey

Detail Information

Publications20

  1. pmc Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex
    Michelle L Gill
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Nucleic Acids Res 34:4506-14. 2006
    ..The assignment of these resonances provides evidence for the occurrence of conformational dynamics in the thymine loop region that is in slow exchange on the 205Tl timescale...
  2. doi request reprint Characterization of enzyme motions by solution NMR relaxation dispersion
    J 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...
  3. ncbi request reprint Value of a hydrogen bond in triosephosphate isomerase loop motion
    Rebecca B Berlow
    Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520, USA
    Biochemistry 46:6001-10. 2007
    ..The site-specific nature of these experiments leads to additional insight into loop 6 motion and the role of a conserved residue in modulating this motion...
  4. pmc The effects of cosolutes on protein dynamics: the reversal of denaturant-induced protein fluctuations by trimethylamine N-oxide
    Vicky Doan-Nguyen
    Department of Chemistry, Yale University, New Haven, CT 06520, USA
    Protein Sci 16:20-9. 2007
    ..These data suggest that TMAO restricts the bond vector motions on the protein energy landscape to resemble those motions that occur in the native protein and points to a relation between stability and dynamics in this enzyme...
  5. ncbi request reprint Evidence for flexibility in the function of ribonuclease A
    Roger Cole
    Department of Chemistry, Yale University, P O Box 208107, New Haven, Connecticut 06520, USA
    Biochemistry 41:6072-81. 2002
    ....
  6. ncbi request reprint Measurement of intermediate exchange phenomena
    James G Kempf
    Department of Chemistry, Yale University, New Haven, CT, USA
    Methods Mol Biol 278:185-231. 2004
    ..Here, we review the two most common experimental methods for characterizing conformational motions in proteins: the relaxation-compensated Carr-Purcell-Meiboom-Gill (rcCPMG) and off-resonance R1rho experiments...
  7. doi request reprint The crystal structure of ribonuclease A in complex with thymidine-3'-monophosphate provides further insight into ligand binding
    Nicolas Doucet
    Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
    Proteins 78:2459-68. 2010
    ..Accumulating evidence suggests that very subtle structural, chemical, and potentially motional variations contribute to ligand discrimination in this enzyme...
  8. pmc The flexibility of a distant loop modulates active site motion and product release in ribonuclease A
    Nicolas Doucet
    Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
    Biochemistry 48:7160-8. 2009
    ..Together, these NMR and biochemical experiments provide additional insight into the mechanism of millisecond motions in the RNase A catalytic cycle...
  9. pmc Millisecond dynamics in the allosteric enzyme imidazole glycerol phosphate synthase (IGPS) from Thermotoga maritima
    James Lipchock
    Department of Chemistry, Yale University, New Haven, CT 06520, USA
    J Biomol NMR 45:73-84. 2009
    ..Together, these data demonstrate a grouping of flexible residues that link the HisF active site with the protein interface to which HisH binds and provide a model for the path of communication between the IGPS active sites...
  10. ncbi request reprint Temperature dependence of the backbone dynamics of ribonuclease A in the ground state and bound to the inhibitor 5'-phosphothymidine (3'-5')pyrophosphate adenosine 3'-phosphate
    Evgenii L Kovrigin
    Department of Chemistry, Yale University, P O Box 208107, New Haven, Connecticut 06520, USA
    Biochemistry 42:5279-91. 2003
    ..Furthermore, experiment and semiempirical estimates suggest that a large negative DeltaC(p) should accompany binding of pTppAp, and we conclude that this contribution must arise from factors other than amide backbone dynamics...
  11. ncbi request reprint Off-resonance TROSY (R1 rho - R1) for quantitation of fast exchange processes in large proteins
    James G Kempf
    Department of Chemistry, Yale University, P O Box 208107, New Haven, Connecticut 06520, USA
    J Am Chem Soc 125:12064-5. 2003
    ..1 T). The TROSY (R1rho - R1) experiment should therefore be of general utility for investigation of fast conformational exchange events in large proteins...
  12. ncbi request reprint Characterization of the transition state of functional enzyme dynamics
    Evgenii L Kovrigin
    Department of Chemistry, Yale University, P O Box 208107, New Haven, Connecticut 06520, USA
    J Am Chem Soc 128:7724-5. 2006
    ..These results provide compelling evidence for close coupling between enzyme dynamics and function and demonstrate that characterization of the transition state for protein motion in atomic detail is experimentally accessible...
  13. ncbi request reprint Enzyme dynamics along the reaction coordinate: critical role of a conserved residue
    Evgenii L Kovrigin
    Yale University, Department of Chemistry, Post Office Box 208107, New Haven, Connecticut 06520, USA
    Biochemistry 45:2636-47. 2006
    ..These data suggest that one role of this conserved residue is to facilitate important millisecond protein dynamics...
  14. ncbi request reprint Faithful estimation of dynamics parameters from CPMG relaxation dispersion measurements
    Evgenii L Kovrigin
    Department of Chemistry, Yale University, P O Box 208107, New Haven, CT 06520, USA
    J Magn Reson 180:93-104. 2006
    ..The strong parameter inter-dependence can readily be overcome through acquisition of spin-relaxation data at more than one static magnetic field thereby allowing accurate assessment of conformational exchange properties...
  15. ncbi request reprint Conservation of mus-ms enzyme motions in the apo- and substrate-mimicked state
    Heather Beach
    Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
    J Am Chem Soc 127:9167-76. 2005
    ..These data suggest that ligand binding stabilizes the bound conformer but does not induce it...
  16. ncbi request reprint FAST-Modelfree: a program for rapid automated analysis of solution NMR spin-relaxation data
    Roger Cole
    Department of Chemistry, Yale University, P O Box 208107, New Haven, CT 06520, USA
    J Biomol NMR 26:203-13. 2003
    ..In all cases results obtained with FAST-Modelfree compared favorably with the original literature results...
  17. pmc Dynamic requirements for a functional protein hinge
    James G Kempf
    Department of Chemistry, Yale University, P O Box 208107, New Haven, CT 06520, USA
    J Mol Biol 368:131-49. 2007
    ..These experiments elucidate an important principle of catalytic hinge design in proteins: structural rigidity is essential for focused motional freedom of active-site loops...
  18. pmc The mechanism of rate-limiting motions in enzyme function
    Eric D Watt
    Department of Chemistry, Yale University, P O Box 208107, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 104:11981-6. 2007
    ..These studies have identified, of approximately 160 potential exchangeable protons, a single site that is integral in the rate-limiting step in RNase A enzyme function...
  19. ncbi request reprint Protein dynamics from solution NMR: theory and applications
    James G Kempf
    Department of Chemistry, Yale University, PO Box 208107, New Haven, CT 06520, USA
    Cell Biochem Biophys 37:187-211. 2003
    ..We review these advances as well as their recent application to the study of proteins...
  20. doi request reprint Monitoring molecular interactions by NMR
    James M Lipchock
    Department of Chemistry, Yale University, New Haven, CT, USA
    Methods Mol Biol 490:115-34. 2009
    ..Here we review the theory upon which this analysis is based, provide several illustrative examples, and highlight potential problems in the study of binding interactions by solution NMR...

Research Grants5

  1. Dynamics, Function, and Stability in Large Enzymes
    JOSEPH LORIA; Fiscal Year: 2009
    ..This combination of experiments will allow characterization of the dynamics of catalytically important residues and the active site loop. ..