Genomes and Genes
Experts and Doctors on protein conformation in Salt Lake City, Utah, United States
Locale: Salt Lake City, Utah, United States
Topic: protein conformation
- Schubert H, Phillips J, Hill C. Structures along the catalytic pathway of PrmC/HemK, an N5-glutamine AdoMet-dependent methyltransferase. Biochemistry. 2003;42:5592-9 pubmed publisher..These structures, therefore, represent intermediates along the catalytic pathway of PrmC and show how the (D/N)PPY motif can be used to select a wide variety substrates...
- Phillips J, Whitby F, Warby C, Labbe P, Yang C, Pflugrath J, et al. Crystal structure of the oxygen-dependant coproporphyrinogen oxidase (Hem13p) of Saccharomyces cerevisiae. J Biol Chem. 2004;279:38960-8 pubmed..The structure therefore suggests residues that likely play critical roles in catalysis and explains the deleterious effect of many of the mutations associated with the disease hereditary coproporphyria. ..
- Tu J, Park T, Morado D, Hughes K, Molineux I, Liu J. Dual host specificity of phage SP6 is facilitated by tailspike rotation. Virology. 2017;507:206-215 pubmed publisher..SP6 also infects S. Typhimurium strains lacking O antigen; in these infections tailspikes have no apparent specific role and the phage tail must therefore interact with a distinct host receptor to allow infection. ..
- McCullough L, Poe B, Connell Z, Xin H, Formosa T. The FACT histone chaperone guides histone H4 into its nucleosomal conformation in Saccharomyces cerevisiae. Genetics. 2013;195:101-13 pubmed publisher..FACT can therefore destabilize nucleosomes by favoring the reorganized state, but it can also promote assembly by tethering histones and DNA together and maintaining them in conformations that promote canonical nucleosome formation. ..
- Fetherolf M, Boyd S, Taylor A, Kim H, Wohlschlegel J, Blackburn N, et al. Copper-zinc superoxide dismutase is activated through a sulfenic acid intermediate at a copper ion entry site. J Biol Chem. 2017;292:12025-12040 pubmed publisher..Sod1 is the predominant disulfide bond-requiring enzyme in the cytoplasm, and this copper-induced mechanism of disulfide bond formation obviates the need for a thiol/disulfide oxidoreductase in that compartment. ..
- Imanishi Y, Yang L, Sokal I, Filipek S, Palczewski K, Baehr W. Diversity of guanylate cyclase-activating proteins (GCAPs) in teleost fish: characterization of three novel GCAPs (GCAP4, GCAP5, GCAP7) from zebrafish (Danio rerio) and prediction of eight GCAPs (GCAP1-8) in pufferfish (Fugu rubripes). J Mol Evol. 2004;59:204-217 pubmed publisher..Based on genome searches and EST analyses, the mouse and human genomes do not harbor GCAP4-8 or GCIP genes. ..
- Blagg B, Jarstfer M, Rogers D, Poulter C. Recombinant squalene synthase. A mechanism for the rearrangement of presqualene diphosphate to squalene. J Am Chem Soc. 2002;124:8846-53 pubmed
- Forster A, Whitby F, Hill C. The pore of activated 20S proteasomes has an ordered 7-fold symmetric conformation. EMBO J. 2003;22:4356-64 pubmed..Evolutionary considerations suggest that other activators might induce the same open proteasome conformation as seen with the 11S activator. ..
- Leavitt J, Gogokhia L, Gilcrease E, Bhardwaj A, Cingolani G, Casjens S. The tip of the tail needle affects the rate of DNA delivery by bacteriophage P22. PLoS ONE. 2013;8:e70936 pubmed publisher..These findings suggest that the needle plays a role in phage P22 DNA delivery by controlling the kinetics of DNA ejection into the host. ..
- Singer J, Hermann G, Shaw J. Suppressors of mdm20 in yeast identify new alleles of ACT1 and TPM1 predicted to enhance actin-tropomyosin interactions. Genetics. 2000;156:523-34 pubmed..The characteristics of the mutant ACT1 and TPM1 alleles and their potential effects on protein structure and binding are discussed. ..
- Decher N, Pirard B, Bundis F, Peukert S, Baringhaus K, Busch A, et al. Molecular basis for Kv1.5 channel block: conservation of drug binding sites among voltage-gated K+ channels. J Biol Chem. 2004;279:394-400 pubmed..Based on the homology models, the positions of the five amino acids identified to interact with S0100176 face toward the central cavity and overlap with putative binding sites for other blockers and voltage-gated potassium channels. ..
- Wimberly B, Guymon R, McCutcheon J, White S, Ramakrishnan V. A detailed view of a ribosomal active site: the structure of the L11-RNA complex. Cell. 1999;97:491-502 pubmed..These antibiotics are proposed to bind in this cleft, locking the putative switch and interfering with the function of elongation factors...
- Paul K, Harmon J, Blair D. Mutational analysis of the flagellar rotor protein FliN: identification of surfaces important for flagellar assembly and switching. J Bacteriol. 2006;188:5240-8 pubmed..The results indicate that FliN is more closely involved in switching than has been supposed, possibly contributing to the binding site for CheY on the switch. ..
- Ames P, Parkinson J. Phenotypic suppression methods for analyzing intra- and inter-molecular signaling interactions of chemoreceptors. Methods Enzymol. 2007;423:436-57 pubmed..The suppression patterns exhibit allele-specificity with respect to the compensatory residue positions and amino acid side chains, a hallmark of stereospecific protein-protein interactions. ..
- Higa M, Alam S, Sundquist W, Ullman K. Molecular characterization of the Ran-binding zinc finger domain of Nup153. J Biol Chem. 2007;282:17090-100 pubmed..Taken together, these studies elucidate the Ran-binding interface on Nup153 and, more broadly, provide insight into the versatility of this zinc finger binding module. ..
- Davis Kaplan S, Compton M, Flannery A, Ward D, Kaplan J, Stevens T, et al. PKR1 encodes an assembly factor for the yeast V-type ATPase. J Biol Chem. 2006;281:32025-35 pubmed..Our data indicate that Pkr1p functions together with the other V-ATPase assembly factors in the ER to efficiently assemble the V-ATPase membrane sector. ..
- Martins L, Jensen L, Simon J, Keller G, Winge D, Simons J. Metalloregulation of FRE1 and FRE2 homologs in Saccharomyces cerevisiae. J Biol Chem. 1998;273:23716-21 pubmed..From the three Mac1-responsive elements in FRE7, a new consensus sequence for Mac1 binding can be established as TTTGC(T/G)C(A/G). ..
- Ajioka R, Phillips J, Kushner J. Biosynthesis of heme in mammals. Biochim Biophys Acta. 2006;1763:723-36 pubmed..The biochemistry, structural biology and the mechanisms of tissue-specific regulation are presented in this review along with the key features of the porphyric disorders. ..
- Horng Y, Leary S, Cobine P, Young F, George G, Shoubridge E, et al. Human Sco1 and Sco2 function as copper-binding proteins. J Biol Chem. 2005;280:34113-22 pubmed..Both the mutant yeast and human proteins were nonfunctional, suggesting the importance of this aspartate for normal function. Taken together, these data suggest that both Cu(I) and Cu(II) binding are critical for normal Sco function. ..
- Topham M, Epand R. Mammalian diacylglycerol kinases: molecular interactions and biological functions of selected isoforms. Biochim Biophys Acta. 2009;1790:416-24 pubmed publisher..It is localized in several subcellular organelles, including the nucleus. The current state of our understanding of the properties and functions of these proteins is reviewed. ..
- Karren M, Coonrod E, Anderson T, Shaw J. The role of Fis1p-Mdv1p interactions in mitochondrial fission complex assembly. J Cell Biol. 2005;171:291-301 pubmed..These studies suggest that the concave binding surface of the Fis1p TPR-like fold interacts with Mdv1p during mitochondrial fission and that Mdv1p facilitates Dnm1p recruitment into functional fission complexes. ..
- Paul K, Gonzalez Bonet G, Bilwes A, Crane B, Blair D. Architecture of the flagellar rotor. EMBO J. 2011;30:2962-71 pubmed publisher..Recently proposed alternative models of rotor assembly, based on a subunit contact observed in crystals, are not supported by experiment. ..
- Shahrokh K, Cheatham T, Yost G. Conformational dynamics of CYP3A4 demonstrate the important role of Arg212 coupled with the opening of ingress, egress and solvent channels to dehydrogenation of 4-hydroxy-tamoxifen. Biochim Biophys Acta. 2012;1820:1605-17 pubmed publisher..Thus adequate sampling of the conformational space of these drug-metabolizing promiscuous enzymes is important for substrates that may bind in malleable regions of the enzyme active-site. ..
- Makise M, Mackay D, Elgort S, Shankaran S, Adam S, Ullman K. The Nup153-Nup50 protein interface and its role in nuclear import. J Biol Chem. 2012;287:38515-22 pubmed publisher..Consistent with this, disruption of the Nup153-Nup50 interface decreases efficiency of nuclear import. ..
- Braun D, Rao J, Mollet G, Schapiro D, Daugeron M, Tan W, et al. Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly. Nat Genet. 2017;49:1529-1538 pubmed publisher..We thus identified four new monogenic causes of GAMOS, describe a link between KEOPS function and human disease, and delineate potential pathogenic mechanisms. ..
- Olson T, Michels V, Thibodeau S, Tai Y, Keating M. Actin mutations in dilated cardiomyopathy, a heritable form of heart failure. Science. 1998;280:750-2 pubmed..Coupled with previous data showing that dystrophin mutations also cause dilated cardiomyopathy, these results raise the possibility that defective transmission of force in cardiac myocytes is a mechanism underlying heart failure. ..
- Howard B, Vajdos F, Li S, Sundquist W, Hill C. Structural insights into the catalytic mechanism of cyclophilin A. Nat Struct Biol. 2003;10:475-81 pubmed..CypA Arg55 guanidinium group probably facilitates catalysis by anchoring the substrate proline oxygen and stabilizing sp3 hybridization of the proline nitrogen in the transition state. ..
- Jairajpuri M, Lu A, Desai U, Olson S, Bjork I, Bock S. Antithrombin III phenylalanines 122 and 121 contribute to its high affinity for heparin and its conformational activation. J Biol Chem. 2003;278:15941-50 pubmed
- Braun T, Blair D. Targeted disulfide cross-linking of the MotB protein of Escherichia coli: evidence for two H(+) channels in the stator Complex. Biochemistry. 2001;40:13051-9 pubmed..Positions near the middle of the segment were inaccessible to sulhydryl reagents. Positions within 6-8 residues of either end, which includes residues around Asp32, were accessible. ..
- Messick T, Chmiel N, Golinelli M, Langer M, Joshua Tor L, David S. Noncysteinyl coordination to the [4Fe-4S]2+ cluster of the DNA repair adenine glycosylase MutY introduced via site-directed mutagenesis. Structural characterization of an unusual histidinyl-coordinated cluster. Biochemistry. 2002;41:3931-42 pubmed..The relative resistance of the [4Fe-4S]2+ cluster toward oxidation, as well as the retention of activity of the [3Fe-4S]1+ form, may be an important aspect of the role of MutY in repair of DNA damage resulting from oxidative stress. ..
- Mozdy A, McCaffery J, Shaw J. Dnm1p GTPase-mediated mitochondrial fission is a multi-step process requiring the novel integral membrane component Fis1p. J Cell Biol. 2000;151:367-80 pubmed..We propose that mitochondrial fission in yeast is a multi-step process, and that membrane-bound Fis1p is required for the proper assembly, membrane distribution, and function of Dnm1p-containing complexes during fission. ..
- Knowlton J, Johnston S, Whitby F, Realini C, Zhang Z, Rechsteiner M, et al. Structure of the proteasome activator REGalpha (PA28alpha). Nature. 1997;390:639-43 pubmed..The binding of REG probably causes conformational changes that open a pore in the proteasome alpha-subunits through which substrates and products can pass. ..
- Bibikov S, Barnes L, Gitin Y, Parkinson J. Domain organization and flavin adenine dinucleotide-binding determinants in the aerotaxis signal transducer Aer of Escherichia coli. Proc Natl Acad Sci U S A. 2000;97:5830-5 pubmed..One or both regions probably also play important roles in transmitting stimulus-induced conformational changes to the C-terminal flagellar signaling domain to trigger aerotactic behavioral responses. ..
- Kim E, Panushka J, Meyer T, Ide N, Carlisle R, Baker S, et al. Biogenesis of the Flagellar Switch Complex in Escherichia coli: Formation of Sub-Complexes Independently of the Basal-Body MS-Ring. J Mol Biol. 2017;429:2353-2359 pubmed publisher..FliM does not multimerize efficiently by itself but does so in the presence of FliG. Thus, pre-assemblies of the switch-complex proteins can form in the cytosol and might function as intermediates in assembly. ..
- Jairajpuri M, Lu A, Bock S. Elimination of P1 arginine 393 interaction with underlying glutamic acid 255 partially activates antithrombin III for thrombin inhibition but not factor Xa inhibition. J Biol Chem. 2002;277:24460-5 pubmed
- Ames P, Parkinson J. Conformational suppression of inter-receptor signaling defects. Proc Natl Acad Sci U S A. 2006;103:9292-7 pubmed..These collaborative teams may be responsible for the high-gain signaling properties of bacterial chemoreceptors. ..
- Brown P, Mathews M, Joss L, Hill C, Blair D. Crystal structure of the flagellar rotor protein FliN from Thermotoga maritima. J Bacteriol. 2005;187:2890-902 pubmed publisher..On the basis of the present data and available electron microscopic images, we propose a model for the organization of FliN subunits in the C ring...
- Saha A, Wittmeyer J, Cairns B. Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev. 2002;16:2120-34 pubmed..Nucleosomes bearing nicks are remodeled less efficiently than intact nucleosomes. These results suggest that RSC and Sth1 are DNA translocases that use both DNA translocation and twist to remodel nucleosomes efficiently. ..
- Kojima S, Blair D. Solubilization and purification of the MotA/MotB complex of Escherichia coli. Biochemistry. 2004;43:26-34 pubmed..35)S-radiolabeling showed that MotA and MotB are present in a 2:1 ratio in the complex. Purified MotA/MotB complexes should enable in vitro study of the proton-induced conformational change and other aspects of stator function. ..
- Stray J, Lindsley J. Biochemical analysis of the yeast condensin Smc2/4 complex: an ATPase that promotes knotting of circular DNA. J Biol Chem. 2003;278:26238-48 pubmed..Based on these models, we propose a DNA displacement mechanism to explain how differences in geometry could affect the competitive potential of DNA. ..
- Lloyd S, Whitby F, Blair D, Hill C. Structure of the C-terminal domain of FliG, a component of the rotor in the bacterial flagellar motor. Nature. 1999;400:472-5 pubmed publisher..On the basis of the disposition of these residues, we present a hypothesis for the orientation of FliG-C domains in the flagellar motor, and propose a structural model for the part of the rotor that interacts with the stator...
- Green S, Coyne H, McIntosh L, Graves B. DNA binding by the ETS protein TEL (ETV6) is regulated by autoinhibition and self-association. J Biol Chem. 2010;285:18496-504 pubmed publisher..We speculate that TEL compensates for the low affinity, which is caused by autoinhibition, by binding to DNA as a cooperative polymer. ..
- Pufall M, Lee G, Nelson M, Kang H, Velyvis A, Kay L, et al. Variable control of Ets-1 DNA binding by multiple phosphates in an unstructured region. Science. 2005;309:142-5 pubmed..Variable phosphorylation thus serves as a "rheostat" for cell signaling to fine-tune transcription at the level of DNA binding. ..
- Sadre Bazzaz K, Whitby F, Robinson H, Formosa T, Hill C. Structure of a Blm10 complex reveals common mechanisms for proteasome binding and gate opening. Mol Cell. 2010;37:728-35 pubmed publisher..We also demonstrate that Blm10 acts to maintain mitochondrial function. Consistent with the structural data, the C-terminal residues of Blm10 are needed for this activity. ..
- Pfaendtner J, Voth G. Molecular dynamics simulation and coarse-grained analysis of the Arp2/3 complex. Biophys J. 2008;95:5324-33 pubmed publisher..Finally, nucleotide-dependent coarse-grained models for Arp3 are developed that serve to further highlight the structural differences induced in Arp3 by nucleotide hydrolysis. ..
- Han T, Teichert R, Olivera B, Bulaj G. Conus venoms - a rich source of peptide-based therapeutics. Curr Pharm Des. 2008;14:2462-79 pubmed..This review summarizes recent efforts in the discovery of conopeptides, and their preclinical and clinical development. ..
- Paul K, Blair D. Organization of FliN subunits in the flagellar motor of Escherichia coli. J Bacteriol. 2006;188:2502-11 pubmed..Electron microscopic reconstructions show a bulge at the bottom of the C-ring whose size and shape are a close match for the hypothesized FliN tetramer. ..
- Dameron C, Winge D, George G, Sansone M, Hu S, Hamer D. A copper-thiolate polynuclear cluster in the ACE1 transcription factor. Proc Natl Acad Sci U S A. 1991;88:6127-31 pubmed..The Cu cluster organizes and stabilizes the conformation of the N-terminal domain of ACE1 for specific DNA binding. ..
- Hugo S, Schlegel A. A Genetic Model to Study Increased Hexosamine Biosynthetic Flux. Endocrinology. 2017;158:2420-2426 pubmed publisher..This animal model will provide a platform for dissecting how O-GlcNAc modification alters insulin responsiveness in multiple tissues. ..
- Smith T, Rutter J. Regulation of glucose partitioning by PAS kinase and Ugp1 phosphorylation. Mol Cell. 2007;26:491-9 pubmed..We propose that regulation of glucose partitioning by altered enzyme and substrate localization is a rapid and potent response to metabolic deficiency. ..
- Carr H, George G, Winge D. Yeast Cox11, a protein essential for cytochrome c oxidase assembly, is a Cu(I)-binding protein. J Biol Chem. 2002;277:31237-42 pubmed..Cytochrome c oxidase activity is reduced in these mutants. Thus, the residues important for Cu(I) binding correlate with in vivo function, suggesting that Cu(I) binding is important in Cox11 function. ..
- Clemons W, Davies C, White S, Ramakrishnan V. Conformational variability of the N-terminal helix in the structure of ribosomal protein S15. Structure. 1998;6:429-38 pubmed..A large, conserved basic patch at one end of S15 and a cluster of conserved but exposed aromatic residues at the other end provide two possible RNA-binding sites on S15...
- Whitby F, Xia G, Pickart C, Hill C. Crystal structure of the human ubiquitin-like protein NEDD8 and interactions with ubiquitin pathway enzymes. J Biol Chem. 1998;273:34983-91 pubmed..One such residue, Ala-72 (Arg in ubiquitin), is shown to perform a key role in selecting against reaction with the ubiquitin E1 enzyme, thereby acting to prevent the inappropriate diversion of NEDD8 into ubiquitin-specific pathways. ..
- Monroe N, Han H, Gonciarz M, Eckert D, Karren M, Whitby F, et al. The oligomeric state of the active Vps4 AAA ATPase. J Mol Biol. 2014;426:510-25 pubmed publisher..cerevisiae. These data challenge the prevailing model that active Vps4 is a double-ring dodecamer, and argue that, like other type I AAA ATPases, Vps4 functions as a single ring with six subunits. ..
- Zhou Q, Ames P, Parkinson J. Biphasic control logic of HAMP domain signalling in the Escherichia coli serine chemoreceptor. Mol Microbiol. 2011;80:596-611 pubmed publisher..The findings of this study provide strong support for a three-state dynamic bundle model of HAMP signalling in Tsr, and possibly in other bacterial transducers as well. ..
- Vajdos F, Yoo S, Houseweart M, Sundquist W, Hill C. Crystal structure of cyclophilin A complexed with a binding site peptide from the HIV-1 capsid protein. Protein Sci. 1997;6:2297-307 pubmed
- Walker J, Poulter C. Synthesis and evaluation of 1-deoxy-D-xylulose 5-phosphate analogues as chelation-based inhibitors of methylerythritol phosphate synthase. J Org Chem. 2005;70:9955-9 pubmed..The carboxylate (1), methyl ester (3), amide (4), and alcohol (5) analogues were inhibitors with IC50's ranging from 0.25 to 1.0 mM. The hydroxamic acid (2) and amino (6) analogues did not inhibit the enzyme. ..
- Sadler I, Crawford A, Michelsen J, Beckerle M. Zyxin and cCRP: two interactive LIM domain proteins associated with the cytoskeleton. J Cell Biol. 1992;119:1573-87 pubmed
- Harper B, Beckerle M, Pomies P. Fine mapping of the alpha-actinin binding site within cysteine-rich protein. Biochem J. 2000;350 Pt 1:269-74 pubmed..The critical lysine residue localizes within a short alpha-helix, raising the possibility that mutagenesis-induced alterations in alpha-actinin-binding capacity might be attributed to the disruption of a key structural element. ..
- Karow M, Georgopoulos C. Isolation and characterization of the Escherichia coli msbB gene, a multicopy suppressor of null mutations in the high-temperature requirement gene htrB. J Bacteriol. 1992;174:702-10 pubmed..These results suggest that MsbB and HtrB play an important role in outer membrane structure and/or function...
- Deveraux Q, Jensen C, Rechsteiner M. Molecular cloning and expression of a 26 S protease subunit enriched in dileucine repeats. J Biol Chem. 1995;270:23726-9 pubmed..Thus, the 26 S protease contains at least two distinct subunits with apparent molecular masses of 50 kDa. ..
- Koirala S, Guo Q, Kalia R, Bui H, Eckert D, Frost A, et al. Interchangeable adaptors regulate mitochondrial dynamin assembly for membrane scission. Proc Natl Acad Sci U S A. 2013;110:E1342-51 pubmed publisher..This result demonstrates that an adaptor protein alters the architecture of a mitochondrial dynamin GTPase polymer in a manner that could facilitate membrane constriction and severing activity. ..
- Casjens S, Molineux I. Short noncontractile tail machines: adsorption and DNA delivery by podoviruses. Adv Exp Med Biol. 2012;726:143-79 pubmed publisher..On the other hand, phages like P22 probably deliver their DNA more rapidly so that it can be circularized before the cascade of gene expression begins...
- Koirala S, Bui H, Schubert H, Eckert D, Hill C, Kay M, et al. Molecular architecture of a dynamin adaptor: implications for assembly of mitochondrial fission complexes. J Cell Biol. 2010;191:1127-39 pubmed publisher..Our results provide a framework for understanding how adaptors act as scaffolds to orient and stabilize the assembly of dynamins on membranes...
- Zhai Q, Fisher R, Chung H, Myszka D, Sundquist W, Hill C. Structural and functional studies of ALIX interactions with YPX(n)L late domains of HIV-1 and EIAV. Nat Struct Mol Biol. 2008;15:43-9 pubmed..These results reveal how YPX(n)L late domains recruit ALIX to facilitate virus budding and how ALIX can bind YPX(n)L sequences with both n = 1 and n = 3. ..
- Ilan B, Tajkhorshid E, Schulten K, Voth G. The mechanism of proton exclusion in aquaporin channels. Proteins. 2004;55:223-8 pubmed..A second and lower barrier is observed at the selectivity filter near the periplasmic outlet where the channel is narrowest. This secondary barrier may be essential in filtering other large solutes and cations. ..
- Porello S, Cannon M, David S. A substrate recognition role for the [4Fe-4S]2+ cluster of the DNA repair glycosylase MutY. Biochemistry. 1998;37:6465-75 pubmed..More importantly, these results provide evidence that the presence of the [4Fe-4S]2+ cluster is critical for the specific recognition of substrate DNA necessary for the adenine glycosylase activity of MutY. ..
- Phillips C, Thrower J, Pickart C, Hill C. Structure of a new crystal form of tetraubiquitin. Acta Crystallogr D Biol Crystallogr. 2001;57:341-4 pubmed..1994), J. Mol. Biol. 236, 601--609]. The new structure suggests that polyubiquitin chains may possess a substantially greater degree of conformational flexibility than has previously been appreciated. ..
- Olson T, Kishimoto N, Whitby F, Michels V. Mutations that alter the surface charge of alpha-tropomyosin are associated with dilated cardiomyopathy. J Mol Cell Cardiol. 2001;33:723-32 pubmed..Therefore, substitution of different amino acid residues in the same thin filament proteins is associated with the distinct phenotypes of cardiac hypertrophy or congestive heart failure. ..