Research Topics
| ARTHUR PALMERSummaryAffiliation: Columbia University Country: USA Publications
Research Grants
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Detail Information
Publications
Probing molecular motion by NMRA G Palmer
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
Curr Opin Struct Biol 7:732-7. 1997..Theoretical interpretations of the relaxation data provide insights into the biophysical and functional properties of proteins...- Nmr probes of molecular dynamics: overview and comparison with other techniquesA G Palmer
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA
Annu Rev Biophys Biomol Struct 30:129-55. 2001..Insights into the dynamical properties of proteins obtained from NMR spin relaxation spectroscopy are compared with results derived from other experimental and theoretical techniques... - 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 - Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopyArthur G Palmer
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, New York 10032, USA
Chem Rev 106:1700-19. 2006 - Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomeraseFrancesca Massi
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, New York 10032, USA
Biochemistry 45:10787-94. 2006..The results of the joint NMR and MD study provide global insight into the role of conformational dynamic processes in the function of TIM... - Microsecond-to-millisecond conformational dynamics demarcate the GluR2 glutamate receptor bound to agonists glutamate, quisqualate, and AMPAElizabeth R Valentine
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, New York 10032, USA
Biochemistry 44:3410-7. 2005..The sites of conformational mobility in GluR2 S1S2 imply that subtle differences exist between the agonists glutamate, quisqualate, and AMPA in modulating glutamate receptor function... 
TROSY-selected ZZ-exchange experiment for characterizing slow chemical exchange in large proteinsYing Li
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
J Biomol NMR 45:357-60. 2009..J Am Chem Soc 129: 13232-13237, 2007), by preserving the TROSY effect during the mixing period as well as the frequency encoding periods...- Partially folded equilibrium intermediate of the villin headpiece HP67 defined by 13C relaxation dispersionNichole E O'Connell
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
J Biomol NMR 45:85-98. 2009..In addition, a second faster process was detected that appears to represent local dynamics within the folded state of the molecule and is largely confined to the hydrophobic interface between the N- and C-terminal subdomains... - R(1rho) relaxation for two-site chemical exchange: general approximations and some exact solutionsVesselin Z Miloushev
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
J Magn Reson 177:221-7. 2005..The solutions are exact when the R1 and R2 relaxation rate constants are identical, and nearly exact under realistic experimental conditions... - Phi-value analysis for ultrafast folding proteins by NMR relaxation dispersionJae Hyun Cho
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, New York 10032, USA
J Am Chem Soc 132:450-1. 2010..The transition and intermediate states of the villin headpiece domain, HP67, are characterized in varying solvent conditions to validate the method... - Temperature dependence of NMR order parameters and protein dynamicsFrancesca Massi
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
J Am Chem Soc 125:11158-9. 2003..The results provide a linkage between experimental and theoretical measures of the temperature dependence of protein motions... - Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherinsVesselin Z Miloushev
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
Structure 16:1195-205. 2008..The results suggest possible kinetic mechanisms for EC1 dimerization... - Protein conformational flexibility prediction using machine learningOleg Trott
Department of Biochemistry and Molecular Biophysics, The Columbia University College of Physicians and Surgeons, Columbia University, Box 36, 630 West 168th Street, New York, NY 10032, USA
J Magn Reson 192:37-47. 2008..70. Predicted order parameters for non-terminal amino acid residues depends most strongly on the local packing density and the probability that the residue is located in regular secondary structure... - Off-resonance TROSY-selected R 1rho experiment with improved sensitivity for medium- and high-molecular-weight proteinsTatyana I Igumenova
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
J Am Chem Soc 128:8110-1. 2006..The method is validated using [90%-15N, 70%-2H] ubiquitin at 280 K. The TROSY-selected R1rho experiment enables characterization of backbone dynamics on the microsecond time scale in large proteins... - Protein side-chain dynamics and residual conformational entropyNikola Trbovic
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
J Am Chem Soc 131:615-22. 2009..Dynamic decoupling thus may represent a general biophysical strategy for minimizing the entropic penalties of folding and binding... - Characterization of chemical exchange using residual dipolar couplingTatyana I Igumenova
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
J Am Chem Soc 129:13396-7. 2007 - Structural analysis of protein dynamics by MD simulations and NMR spin-relaxationNikola Trbovic
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
Proteins 71:684-94. 2008..Structural analysis reveals that relative imbalance between the description of hydrogen bonding and other terms of modern force fields may be responsible for disagreement... - Conformational dynamics in loop swap mutants of homologous fibronectin type III domainsKeri Siggers
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
Biophys J 93:2447-56. 2007..The results suggest that changes in conformational dynamics of mutant proteins must be considered in both theoretical studies and protein design efforts... - Disulfide bond isomerization in basic pancreatic trypsin inhibitor: multisite chemical exchange quantified by CPMG relaxation dispersion and chemical shift modelingMichael J Grey
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
J Am Chem Soc 125:14324-35. 2003..A comparison of the kinetics and thermodynamics for the transitions between the two alternative Cys 14-Cys 38 conformations highlights the factors that affect the contribution of disulfide bonds to protein stability... - Kurt Wüthrich and NMR of biological macromoleculesArthur G Palmer
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10025, USA
Structure 10:1603-4. 2002..Wüthrich shared the prize with John B. Fenn and Koichi Tanaka, who were recognized for the development of ionization methods for the analysis of proteins using mass spectrometry... - Theoretical study of R(1rho) rotating-frame and R2 free-precession relaxation in the presence of n-site chemical exchangeOleg Trott
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
J Magn Reson 170:104-12. 2004..The perturbation treatment is valid whenever the population of one site is dominant. The new results are generally applicable to investigations of kinetic processes by NMR spectroscopy... - Characterizing a partially folded intermediate of the villin headpiece domain under non-denaturing conditions: contribution of His41 to the pH-dependent stability of the N-terminal subdomainMichael J Grey
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
J Mol Biol 355:1078-94. 2006.... - Solution structure of the NaV1.2 C-terminal EF-hand domainVesselin Z Miloushev
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032 3702, USA
J Biol Chem 284:6446-54. 2009..Clinically significant mutations identified in the C-terminal region of NaV1 sodium channels cluster in the helix I-IV interface and the helix II-III interhelical segment or in helices III and IV of the NaV1.2 (1777-1882) structure... - Continuum secondary structure captures protein flexibilityClaus A F Andersen
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
Structure 10:175-84. 2002..Thus, continuous assignments of secondary structure may affect future protein structure analysis, comparison, and prediction... - Joint composite-rotation adiabatic-sweep isotope filtrationElizabeth R Valentine
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
J Biomol NMR 38:11-22. 2007.... - Narrowing of protein NMR spectral lines broadened by chemical exchangeYing Li
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
J Am Chem Soc 132:8856-7. 2010.... - The N-terminus is unstructured, but not dynamically disordered, in the complex between HK022 Nun protein and lambda-phage BoxB RNA hairpinAshley C Stuart
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
FEBS Lett 553:95-8. 2003..Restriction of conformation flexibility in the N-terminal extension of Nun may be important for binding to other target molecules involved in transcription termination... - Mapping chemical exchange in proteins with MW > 50 kDChunyu Wang
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
J Am Chem Soc 125:8968-9. 2003..The success of our method is demonstrated in triosephosphate isomerase (TIM, MW = 54 kD)... - Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1rho relaxation experimentsFrancesca Massi
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
Protein Sci 14:735-42. 2005..These residues are located near or at the regions known to interact with various enzymes of the ubiquitin-dependent protein degradation pathway... - Solution structure of the Vts1 SAM domain in the presence of RNAThomas A Edwards
Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA
J Mol Biol 356:1065-72. 2006..These results provide a structural basis for the versatility of the SAM domain in protein and RNA-recognition... - Solution NMR spin relaxation methods for characterizing chemical exchange in high-molecular-weight systemsArthur G Palmer
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
Methods Enzymol 394:430-65. 2005.... - Dynamics of ATP-binding cassette contribute to allosteric control, nucleotide binding and energy transduction in ABC transportersChunyu Wang
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 W. 168th St, New York, NY 10032, USA
J Mol Biol 342:525-37. 2004..The restriction of correlated protein motions is likely a central mechanism for allosteric communications. Comparison between dynamics data from NMR and X-ray crystallography reveals their overall consistency and complementarity... - Multiple time scale backbone dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymesJoel A Butterwick
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, Box 36, New York, NY 10032-3702, USA
J Mol Biol 339:855-71. 2004..Increased activation barriers, coupled with motion between alpha-helices B and C not present in ecRNH, may be associated with the reduced catalytic activity of the thermophilic enzyme at 310 K... - NMR R1 rho rotating-frame relaxation with weak radio frequency fieldsFrancesca Massi
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, New York 10032, USA
J Am Chem Soc 126:2247-56. 2004..The new experiments also extend the capability of the R(1 rho) technique to study exchange processes outside the fast exchange limit... - Differential multiple quantum relaxation caused by chemical exchange outside the fast exchange limitChunyu Wang
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 W. 168th Street, New York, NY 10032, USA
J Biomol NMR 24:263-8. 2002..The new theoretical expression is valuable for identification and characterization of exchange processes in proteins using differential relaxation of multiple quantum coherences... - Crystal structures of beta-neurexin 1 and beta-neurexin 2 ectodomains and dynamics of splice insertion sequence 4Jesko Koehnke
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
Structure 16:410-21. 2008..These results raise the possibility that beta-NRX insertion sequence 4 may function in roles independent of neuroligin binding... - An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases HJoel A Butterwick
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
Protein Sci 15:2697-707. 2006.... - R1rho relaxation outside of the fast-exchange limitOleg Trott
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, New York 10032, USA
J Magn Reson 154:157-60. 2002..The new expressions for R1rho will be particularly useful in analyzing experimental data when exchange is not fast and site populations are unequal... - Titration and exchange studies of liver fatty acid-binding protein with 13C-labeled long-chain fatty acidsHsin Wang
Department of Chemistry, CUNY Graduate Center and College of Staten Island, Staten Island, New York 10314, USA
Biochemistry 41:5453-61. 2002..In light of these NMR measurements, possible molecular mechanisms for the ligand-exchange process are evaluated and implications for the anomalous fatty acid transport mechanism of LFABP are discussed... - Approximate solutions of the Bloch-McConnell equations for two-site chemical exchangeDaniel Abergel
Laboratoire de Chimie, Ecole Normale Supérieure 24, rue Lhomond, 75005 Paris, France
Chemphyschem 5:787-93. 2004..These expressions are useful for interpretation of chemical exchange processes in NMR spectroscopy... - Temperature dependence of the NMR generalized order parameterEric Johnson
Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, Ohio 45267 0524, USA
Proteins 66:796-803. 2007..The analysis also provides evidence for variations in the potential of mean force for different secondary structural elements... - Biophysics: proteins hunt and gatherDavid Eliezer
Nature 447:920-1. 2007 - Temperature-dependent dynamics of the villin headpiece helical subdomain, an unusually small thermostable proteinLiliya Vugmeyster
Department of Chemistry, SUNY Stony Brook, Stony Brook, NY 11794-3400, USA
J Mol Biol 320:841-54. 2002..The results suggest that backbone dynamics, as probed by relaxation measurements, make very little contribution to the heat capacity difference between folded and unfolded states for HP36... - Beyond the decoupling approximation in the model free approach for the interpretation of NMR relaxation of macromolecules in solutionLiliya Vugmeyster
Department of Chemistry, SUNY Stony Brook, Stony Brook, NY 11794-3400, USA
J Am Chem Soc 125:8400-4. 2003..The parameters of the spectral density function provide insight into the effects on the MF parameters that result from violation of the decoupling approximation... - Multistate folding of the villin headpiece domainYuefeng Tang
Department of Chemistry, State University of New York at Stony Brook, Stony Brook, NY 11790 3400, USA
J Mol Biol 355:1066-77. 2006..The mutation stabilizes both domains, but folding is still multistate, indicating that His41 is not solely responsible for the unusual equilibrium unfolding behavior of villin headpiece domain... - A Markov model for relaxation and exchange in NMR spectroscopyDaniel Abergel
Departement de Chimie, Ecole Normale Superieure, 24, rue Lhomond, 75231 Paris Cedex 05
J Phys Chem B 109:4837-44. 2005..Time-scale separation emerges as an essential feature from the lowest-order perturbation expansion of the average resolvent in the Laplace domain... - Disorder breathes life into a DEAD motorLorraine F Cavanaugh
Nat Struct Mol Biol 13:566-9. 2006 - 1H, 15N and 13C backbone assignment of MJ1267, an ATP-binding cassetteChunyu Wang
J Biomol NMR 24:167-8. 2002
Research Grants
- PROTEIN MOTIONS IN RECOGNITION, REGULATION AND CATALYSISARTHUR PALMER; Fiscal Year: 2005..Successful completion of these goals will enable the application of the techniques developed to a wide range of additional protein systems of biological interest. ..
- TRAINING PROGRAM IN MOLECULAR BIOPHYSICSARTHUR PALMER; Fiscal Year: 2007..abstract_text> ..
- PROTEIN MOTIONS IN RECOGNITION, REGULATION AND CATALYSISARTHUR PALMER; Fiscal Year: 2009..The proposed research will measure these changes for three model protein systems involved in cellular structure, nerve transmission, and basic metabolism. ..
- NMR Studies of Structures and Dynamics of ProteinsArthur G Palmer; Fiscal Year: 2010....
- Nuclear Magnetic Resonance Studies of Structures and Dynamics of ProteinsARTHUR PALMER; Fiscal Year: 2009..ABC MJ1267 represents an example of selected-fit molecular recognition and allosteric transmission of conformational changes between remote sites in proteins. ..
- NMR Studeis of Structures and Dynamics of ProteinsARTHUR PALMER; Fiscal Year: 2004..abstract_text> ..
- Student Travel Stipends for Experimental NMR ConferenceARTHUR PALMER; Fiscal Year: 2004..This would permit an increased number of deserving students to attend the conference. ..
- STRUCTURE AND DYNAMICS OF RIBONUCLEASE HARTHUR PALMER; Fiscal Year: 2000....
- Cryoprobe Accesory for Bruker DRX 600 NMR SpectrometerARTHUR PALMER; Fiscal Year: 2002..In each of these cases, sufficient sensitivity cannot be obtained simply by increasing acquisition times, due to practical limitations on total experimental durations. ..
- Protein motions in recognition, regulation, and catalysisArthur G Palmer; Fiscal Year: 2010..Elaboration of the roles of conformational dynamics in actuating and regulating these processes is essential for understanding the fundamental functions of proteins in human health and disease. ..