Research Topics
Genomes and Genes | J F HuntSummaryAffiliation: Columbia University Country: USA Publications
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Publications
Structure and dynamics of the P7 protein from the bacteriophage phi 12Ertan Eryilmaz
Department of Chemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
J Mol Biol 382:402-22. 2008..Given the requirement of P7 in maintaining genome packaging efficiency and transcriptional fidelity, our data suggest a central biological role for P7-RNA interactions...
Ping-pong cross-validation in real space: a method for increasing the phasing power of a partial model without risk of model biasJohn F Hunt
Howard Hughes Medical Institute and Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9050, USA
Acta Crystallogr D Biol Crystallogr 59:214-24. 2003..Real-space cross-validation can be applied to reduce the risk of model bias associated with partial model phasing, streamlining this approach and expanding its range of applicability...- Spontaneous, pH-dependent membrane insertion of a transbilayer alpha-helixJ F Hunt
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
Biochemistry 36:15177-92. 1997..With a pKa of 6.0, the peptide inserts into the bilayer as a transbilayer alpha-helix. The insertion reaction proceeds rapidly at room temperature and is fully reversible... - Nucleotide control of interdomain interactions in the conformational reaction cycle of SecAJohn F Hunt
Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA
Science 297:2018-26. 2002.... - Crystal structures of the MJ1267 ATP binding cassette reveal an induced-fit effect at the ATPase active site of an ABC transporterN Karpowich
Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA
Structure 9:571-86. 2001..Previous structures have defined the fold of the ABC and established the flexibility of its alpha-helical subdomain. But the nature of the mechanical changes that occur at each step of the chemical ATPase cycle have not been defined... - Protein solubility and folding monitored in vivo by structural complementation of a genetic marker proteinW C Wigley
Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas TX 75235, USA
Nat Biotechnol 19:131-6. 2001..Thus, structural complementation provides a means of monitoring protein solubility/misfolding in vivo, and should find utility in the screening for compounds that influence the pathological consequences of these processes... - The crystal structure of the MJ0796 ATP-binding cassette. Implications for the structural consequences of ATP hydrolysis in the active site of an ABC transporterY R Yuan
Department of Biological Sciences, Columbia University, New York, New York 10027, USA
J Biol Chem 276:32313-21. 2001.... - Structural adaptations in the specialized bacteriophage T4 co-chaperonin Gp31 expand the size of the Anfinsen cageJ F Hunt
Howard Hughes Medical Institute and Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas 75235 9050, USA
Cell 90:361-71. 1997.... - Glycophorin A dimerization is driven by specific interactions between transmembrane alpha-helicesM A Lemmon
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
J Biol Chem 267:7683-9. 1992..This approach allows the interface between interacting helices to be defined... - Cell biology: shape-shifting protein channelJordi Benach
Nature 427:24-6. 2004 - Nucleotide exchange from the high-affinity ATP-binding site in SecA is the rate-limiting step in the ATPase cycle of the soluble enzyme and occurs through a specialized conformational stateJohn J Fak
Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, New York 10027, USA
Biochemistry 43:7307-27. 2004.... - 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... - The SufE sulfur-acceptor protein contains a conserved core structure that mediates interdomain interactions in a variety of redox protein complexesSharon Goldsmith-Fischman
Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
J Mol Biol 344:549-65. 2004..Therefore, the core fold of SufE/IscU has been adapted to mediate interdomain interactions in diverse redox protein systems in the course of evolution... - Impact of the deltaF508 mutation in first nucleotide-binding domain of human cystic fibrosis transmembrane conductance regulator on domain folding and structureHal A Lewis
Structural GenomiX, Inc, San Diego, California 92121, USA
J Biol Chem 280:1346-53. 2005.... - Role of a conserved glutamate residue in the Escherichia coli SecA ATPase mechanismChristopher R Zito
Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, Connecticut 06459, USA
J Biol Chem 280:14611-9. 2005.... - Crystal structures of two bacterial 3-hydroxy-3-methylglutaryl-CoA lyases suggest a common catalytic mechanism among a family of TIM barrel metalloenzymes cleaving carbon-carbon bondsFarhad Forouhar
Department of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA
J Biol Chem 281:7533-45. 2006..2006) J. Biol. Chem. 281, 7526-7532). Our model is consistent with extensive mutagenesis results and can guide subsequent studies directed at definitive experimental elucidation of this enzyme's reaction mechanism... - Crystal structure of human 3-hydroxy-3-methylglutaryl-CoA Lyase: insights into catalysis and the molecular basis for hydroxymethylglutaric aciduriaZhuji Fu
Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
J Biol Chem 281:7526-32. 2006..The structure provides a rationale for the decrease in enzyme activity due to clinical mutations, including H233R, R41Q, D42H, and D204N, that compromise active site function or enzyme stability... - Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkBBomina Yu
Department of Biological Sciences and Northeast Structural Genomics Consortium, 702A Fairchild Center, MC2434, Columbia University, New York, New York 10027, USA
Nature 439:879-84. 2006..These observations suggest that protein dynamics modulate redox chemistry and that a hypothesized migration of the reactive oxy-ferryl ligand on the catalytic Fe ion may be impeded when the protein is constrained in the crystal lattice... - Disorder breathes life into a DEAD motorLorraine F Cavanaugh
Nat Struct Mol Biol 13:566-9. 2006 - The structural basis of cyclic diguanylate signal transduction by PilZ domainsJordi Benach
Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA
EMBO J 26:5153-66. 2007..The very small size of the N-terminal conformational switch is likely to explain the facile evolutionary diversification of the PilZ domain... - Structure of nucleotide-binding domain 1 of the cystic fibrosis transmembrane conductance regulatorHal A Lewis
Structural GenomiX Inc, San Diego, CA, USA
EMBO J 23:282-93. 2004..Our results are consistent with a CFTR mechanism, whereby channel gating occurs through ATP binding in an NBD1-NBD2 nucleotide sandwich that forms upon displacement of NBD1 regulatory segments... - Bacillus subtilis SecA ATPase exists as an antiparallel dimer in solutionHaiyuan Ding
Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459, USA
Biochemistry 42:8729-38. 2003.... - The 2.3-A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenaseJordi Benach
Department of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, USA
J Biol Chem 278:19176-82. 2003..The nature and disposition of the active site residues suggest a novel reaction mechanism in which an aspartate acts as the general acid/base catalyst during the hydride transfer reaction... - Cooperative, ATP-dependent association of the nucleotide binding cassettes during the catalytic cycle of ATP-binding cassette transportersJonathan E Moody
Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA
J Biol Chem 277:21111-4. 2002..Thus, upon hydrolysis of bound ATP and the release of product, both electrostatic and conformational changes drive the cassettes apart, providing a second opportunity to couple free energy changes to the transport reaction... - The crystal structure of the olfactory marker protein at 2.3 A resolutionPaul C Smith
Department of Biological Sciences, 702A Fairchild Center, MC 2434, Columbia University, New York, NY 10027, USA
J Mol Biol 319:807-21. 2002.... - ATP binding to the motor domain from an ABC transporter drives formation of a nucleotide sandwich dimerPaul C Smith
Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, New York 10027, USA
Mol Cell 10:139-49. 2002..These results establish the stereochemical basis of the power stroke of ABC transporter pumps... - Phospholipid-induced monomerization and signal-peptide-induced oligomerization of SecAJordi Benach
Department of Biological Sciences, Columbia University, New York, New York 10027, USA
J Biol Chem 278:3628-38. 2003..Cycles of SecA subunit recruitment and dissociation could potentially be employed to achieve processivity in polypeptide transport... - The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferaseJacob P Keller
Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA
Structure 10:1475-87. 2002..Therefore, MT0146/CbiT probably functions as a precorrin methyltransferase and represents the first enzyme identified with this activity that does not have the canonical precorrin methyltransferase fold... - Crystal structures of the BtuF periplasmic-binding protein for vitamin B12 suggest a functionally important reduction in protein mobility upon ligand bindingNathan K Karpowich
Department of Biological Sciences, Columbia University, New York, New York 10027, USA
J Biol Chem 278:8429-34. 2003..Furthermore, the high mobility of this domain in free BtuF could provide an entropic driving force for the subsequent release of BtuF required to complete the transport cycle... - Structural characterization of an MJ1267 ATP-binding cassette crystal with a complex pattern of twinning caused by promiscuous fiber packingYu Ren Yuan
Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA
Acta Crystallogr D Biol Crystallogr 59:225-38. 2003.... - Assessment of protein folding/solubility in live cellsRhesa D Stidham
Department of Physiology, Graduate Program in Molecular Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
Methods Mol Biol 205:155-69. 2003 - The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolismJordi Benach
Department of Biological Sciences and Northeast Structural Genomics Consortium, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA
Acta Crystallogr D Biol Crystallogr 61:589-98. 2005..Therefore, the crystal structure of PF1337 supports the hypothesis that TenA homologs have an indirect effect in altering gene-expression patterns and function instead as enzymes involved in thiamine metabolism... - 1H, 15N and 13C backbone assignment of MJ1267, an ATP-binding cassetteChunyu Wang
J Biomol NMR 24:167-8. 2002 - The perplexing challenges of a pump turned channelJohn F Hunt
Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA
J Physiol 539:331. 2002 - Mutations that change the position of the putative gamma-phosphate linker in the nucleotide binding domains of CFTR alter channel gatingAllan L Berger
Howard Hughes Medical Institute, Departments of Internal Medicine and Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, Iowa 52242, USA
J Biol Chem 277:2125-31. 2002..Our results extend models of nucleotide-induced structural changes from bacterial NBDs to a functional mammalian ATP-binding cassette transporter... - Concentration-dependent effects of endogenous S-nitrosoglutathione on gene regulation by specificity proteins Sp3 and Sp1Khalequz Zaman
Division of Pulmonary Medicine, Department of Pediatrics, University of Virginia School of Medicine, P O Box 800356, Charlottesville, VA 22908, USA
Biochem J 380:67-74. 2004.... - A protein sequence that can encode native structure by disfavoring alternate conformationsW Christian Wigley
Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9040, USA
Nat Struct Biol 9:381-8. 2002....