Genomes and Genes
Experts and Doctors on binding sites in College Station, Texas, United States
Locale: College Station, Texas, United States
Topic: binding sites
Publications117 found, 100 shown here
- Mariño Ramírez L, Campbell L, Hu J. Screening peptide/protein libraries fused to the lambda repressor DNA-binding domain in E. coli cells. Methods Mol Biol. 2003;205:235-50 pubmed
- Hill C, Li W, Thoden J, Holden H, Raushel F. Enhanced degradation of chemical warfare agents through molecular engineering of the phosphotriesterase active site. J Am Chem Soc. 2003;125:8990-1 pubmed..These studies demonstrate that substantial changes in substrate specificity can be achieved by relatively minor changes to the primary amino acid sequence. ..
- Sun Z, Martinez Lemus L, Trache A, Trzeciakowski J, Davis G, Pohl U, et al. Mechanical properties of the interaction between fibronectin and alpha5beta1-integrin on vascular smooth muscle cells studied using atomic force microscopy. Am J Physiol Heart Circ Physiol. 2005;289:H2526-35 pubmed..Our results indicate that the functional activity of alpha5beta1 and focal contact assembly can be rapidly regulated. ..
- Wilken L, Nikolov Z. Factors influencing recombinant human lysozyme extraction and cation exchange adsorption. Biotechnol Prog. 2006;22:745-52 pubmed..High purity was achieved with a single chromatography step by adjusting the pH 4.5 extract to pH 6 before adsorption. The disadvantage of this approach was the drastically lower saturation capacity compared to adsorption at pH 4.5...
- Ren S, Mandadi K, Boedeker A, Rathore K, McKnight T. Regulation of telomerase in Arabidopsis by BT2, an apparent target of TELOMERASE ACTIVATOR1. Plant Cell. 2007;19:23-31 pubmed
- Dey S, Hu Z, Xu X, Sacchettini J, Grant G. D-3-Phosphoglycerate dehydrogenase from Mycobacterium tuberculosis is a link between the Escherichia coli and mammalian enzymes. J Biol Chem. 2005;280:14884-91 pubmed..The differential sensitivity to serine inhibition by M. tuberculosis and human PGDH may open up interesting possibilities in the treatment of multidrug-resistant tuberculosis. ..
- Tsai C, Gokulan K, Sobrado P, Sacchettini J, Fitzpatrick P. Mechanistic and structural studies of H373Q flavocytochrome b2: effects of mutating the active site base. Biochemistry. 2007;46:7844-51 pubmed..The combination of an altered active site and the small kinetic isotope effects is consistent with the slowest step in turnover being a conformational change involving a conformation in which lactate is bound unproductively. ..
- Hostetler H, Lupas D, Tan Y, Dai J, Kelzer M, Martin G, et al. Acyl-CoA binding proteins interact with the acyl-CoA binding domain of mitochondrial carnitine palmitoyl transferase I. Mol Cell Biochem. 2011;355:135-48 pubmed publisher..These data suggest that both interactions with lipid binding proteins and the peptide itself are important for optimal enzyme activity. ..
- Kim J, Raushel F. Allosteric control of the oligomerization of carbamoyl phosphate synthetase from Escherichia coli. Biochemistry. 2001;40:11030-6 pubmed
- Draheim R, Bormans A, Lai R, Manson M. Tuning a bacterial chemoreceptor with protein-membrane interactions. Biochemistry. 2006;45:14655-64 pubmed..Aromatic residues analogous to Trp-209/Tyr-210 are present in other chemoreceptors and many transmembrane sensor kinases, where they may serve a similar function. ..
- Sharma V, Sharma S, Hoener zu Bentrup K, McKinney J, Russell D, Jacobs W, et al. Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis. Nat Struct Biol. 2000;7:663-8 pubmed publisher..The structure of a C191S mutant of the enzyme with the inhibitor 3-nitropropionate provides further insight into the reaction mechanism...
- Nilsson I, Kelleher D, Miao Y, Shao Y, Kreibich G, Gilmore R, et al. Photocross-linking of nascent chains to the STT3 subunit of the oligosaccharyltransferase complex. J Cell Biol. 2003;161:715-25 pubmed
- Paricharttanakul N, Ye S, Menefee A, Javid Majd F, Sacchettini J, Reinhart G. Kinetic and structural characterization of phosphofructokinase from Lactobacillus bulgaricus. Biochemistry. 2005;44:15280-6 pubmed publisher..The effector binding site, however, shows many differences that could explain the observed decreases in binding affinity for MgADP and PEP in LbPFK as compared to the other two enzymes...
- Rohde B, Zhu M, el Messiry S, Chiou G. Effects of some opiates and opioid peptide eyedrops on ocular melatonin regulation in rabbits. Ophthalmic Res. 1993;25:378-85 pubmed..v. raised levels in the ciliary body. No opiate binding sites could be detected in the rabbit iris or iris root-ciliary body for any class of receptor. Our data suggest opioids may be useful for treating glaucoma...
- Narayanan A, Lekven A. Biphasic wnt8a expression is achieved through interactions of multiple regulatory inputs. Dev Dyn. 2012;241:1062-75 pubmed publisher..Analysis of stickleback wnt8a suggests this mechanism of regulation may be conserved. The seemingly simple wnt8a expression pattern reflects complex interactions of multiple regulatory inputs. ..
- Wang F, Cassidy C, Sacchettini J. Crystal structure and activity studies of the Mycobacterium tuberculosis beta-lactamase reveal its critical role in resistance to beta-lactam antibiotics. Antimicrob Agents Chemother. 2006;50:2762-71 pubmed
- Frolov A, Cho T, Murphy E, Schroeder F. Isoforms of rat liver fatty acid binding protein differ in structure and affinity for fatty acids and fatty acyl CoAs. Biochemistry. 1997;36:6545-55 pubmed..Thus, rat L-FABP isoforms differ markedly in both structure and ligand binding function. ..
- Yang K, Ren Z, Raushel F, Zhang J. Structures of the Carbon-Phosphorus Lyase Complex Reveal the Binding Mode of the NBD-like PhnK. Structure. 2016;24:37-42 pubmed publisher..This structural information provides a basis for further deciphering of the reaction mechanism of the C-P lyase. ..
- Huang H, Ball J, Billheimer J, Schroeder F. The sterol carrier protein-2 amino terminus: a membrane interaction domain. Biochemistry. 1999;38:13231-43 pubmed..These data were consistent with the N-terminus of SCP2 providing a membrane interaction domain that preferentially bound to membranes rich in anionic phospholipid and cholesterol. ..
- Kimmel J, Reinhart G. Isolation of an individual allosteric interaction in tetrameric phosphofructokinase from Bacillus stearothermophilus. Biochemistry. 2001;40:11623-9 pubmed..48 +/- 0.15 kcal/mol compared to the 3.58 +/- 0.02 kcal/mol measured for the enzyme. ..
- Zhang W, Richardson R, Chamni S, Smith J, Romo D. Beta-lactam congeners of orlistat as inhibitors of fatty acid synthase. Bioorg Med Chem Lett. 2008;18:2491-4 pubmed publisher..While in general these derivatives showed lower potency compared to beta-lactones, a reasonably potent, lead compound (-)-9 (IC(50)=8.6microM) was discovered that suggests that this class of compounds should be evaluated further. ..
- Martin G, Hostetler H, McIntosh A, Tichy S, Williams B, Russell D, et al. Structure and function of the sterol carrier protein-2 N-terminal presequence. Biochemistry. 2008;47:5915-34 pubmed publisher..These data indicate the importance of the N-terminal presequence in regulating SCP-2 structure, cholesterol localization within the ligand binding site, membrane association, and, potentially, intracellular targeting. ..
- Dorsey C, Laarakker M, Humphries A, Weening E, B umler A. Salmonella enterica serotype Typhimurium MisL is an intestinal colonization factor that binds fibronectin. Mol Microbiol. 2005;57:196-211 pubmed publisher..These data identify MisL as an extracellular matrix adhesin involved in intestinal colonization...
- Martin G, McIntosh A, Huang H, Gupta S, Atshaves B, Landrock K, et al. The human liver fatty acid binding protein T94A variant alters the structure, stability, and interaction with fibrates. Biochemistry. 2013;52:9347-57 pubmed publisher..Thus, while the T94A substitution did not alter the affinity of the human L-FABP for PPAR? agonist ligands, it significantly altered the human L-FABP structure, stability, and conformational and functional response to fibrate. ..
- Frolov A, Miller K, Billheimer J, Cho T, Schroeder F. Lipid specificity and location of the sterol carrier protein-2 fatty acid-binding site: a fluorescence displacement and energy transfer study. Lipids. 1997;32:1201-9 pubmed..These findings not only contribute to our understanding of the SCP-2 ligand binding site but also provide evidence suggesting a potential role for SCP-2 and/or L-FABP in metabolism of branched-chain fatty acids and isoprenoids. ..
- Busenlehner L, Pennella M, Giedroc D. The SmtB/ArsR family of metalloregulatory transcriptional repressors: Structural insights into prokaryotic metal resistance. FEMS Microbiol Rev. 2003;27:131-43 pubmed..We hypothesize that distinct allosteric pathways for metal sensing have co-evolved with metal specificities of distinct alpha3N and alpha5 coordination complexes. ..
- Osborne E, Ward W, Ruehle M, DeRose V. The identity of the nucleophile substitution may influence metal interactions with the cleavage site of the minimal hammerhead ribozyme. Biochemistry. 2009;48:10654-64 pubmed publisher..These data suggest that metal ion association with the HHRz cleavage site may include an interaction with the 2'-OH nucleophile. ..
- Trache A, Trzeciakowski J, Gardiner L, Sun Z, Muthuchamy M, Guo M, et al. Histamine effects on endothelial cell fibronectin interaction studied by atomic force microscopy. Biophys J. 2005;89:2888-98 pubmed..These changes can be recorded as direct measurements on live endothelial cells by using atomic force microscopy. ..
- Wang L, Dean S, Shippen D. Oligomerization of the telomerase reverse transcriptase from Euplotes crassus. Nucleic Acids Res. 2002;30:4032-9 pubmed..crassus telomerase has the potential to assume different conformations in vivo. Together, these data indicate that oligomerization is a conserved feature of telomerase and that the minimal functional unit of the enzyme is a dimer...
- Kumar N, Bernstein L. Ten ERK-related proteins in three distinct classes associate with AP-1 proteins and/or AP-1 DNA. J Biol Chem. 2001;276:32362-72 pubmed..p97 is a class III ERP, related to ERK3, that associates with AP-1 DNA without AP-1 proteins. With the exception of ERK2, none of the 10 ERPs appear to be known mitogen-activated protein kinase superfamily members. ..
- Yang D, Shipman L, Roessner C, Scott A, Sacchettini J. Structure of the Methanococcus jannaschii mevalonate kinase, a member of the GHMP kinase superfamily. J Biol Chem. 2002;277:9462-7 pubmed publisher..Analysis of the MVK model in the context of the other members of the GHMP kinase family offers the opportunity to understand both the mechanism of these enzymes and the structural details that may lead to the design of novel drugs...
- Yang W, Gelles J, Musser S. Imaging of single-molecule translocation through nuclear pore complexes. Proc Natl Acad Sci U S A. 2004;101:12887-92 pubmed..Molecular tracking reveals that substrate molecules spend most of their transit time randomly moving in the central pore of the NPC and that the rate-limiting step is escape from the central pore. ..
- Vogt M, Lahiri S, Hoogstraten C, Britt R, DeRose V. Coordination environment of a site-bound metal ion in the hammerhead ribozyme determined by 15N and 2H ESEEM spectroscopy. J Am Chem Soc. 2006;128:16764-70 pubmed..Although it has a relatively high thermodynamic affinity, this ion remains partially hydrated and is chelated to the RNA by just two ligands. ..
- Qian Y, Tiffany Castiglioni E, Harris E. Sequence of a Menkes-type Cu-transporting ATPase from rat C6 glioma cells: comparison of the rat protein with other mammalian Cu-transporting ATPases. Mol Cell Biochem. 1998;181:49-61 pubmed
- Gardina P, Bormans A, Manson M. A mechanism for simultaneous sensing of aspartate and maltose by the Tar chemoreceptor of Escherichia coli. Mol Microbiol. 1998;29:1147-54 pubmed..In the wild-type Tar dimer, aspartate and MBP can bind in either the 'same' or the 'opposite' orientation, a freedom that can explain the partial additivity of the aspartate and maltose responses that is seen with tar+ cells...
- Ronning D, Klabunde T, Besra G, Vissa V, Belisle J, Sacchettini J. Crystal structure of the secreted form of antigen 85C reveals potential targets for mycobacterial drugs and vaccines. Nat Struct Biol. 2000;7:141-6 pubmed publisher..Also, a large region of conserved surface residues among ag85A, B and C is a probable site for the interaction of ag85 proteins with human fibronectin...
- Benedict C, Lu J, Pettigrew D, Liu J, Stipanovic R, Williams H. The cyclization of farnesyl diphosphate and nerolidyl diphosphate by a purified recombinant delta-cadinene synthase. Plant Physiol. 2001;125:1754-65 pubmed..The amino acids having catalytic roles in epi-aristochene synthase are substituted in the CDN synthase and may be related to differences in catalytic properties. ..
- Petrescu A, Huang H, Hostetler H, Schroeder F, Kier A. Structural and functional characterization of a new recombinant histidine-tagged acyl coenzyme A binding protein (ACBP) from mouse. Protein Expr Purif. 2008;58:184-93 pubmed publisher..Thus, C-terminal his-tagged-ACBP maintained very similar structural and functional features of the untagged native protein and can be used in further in vitro experiments that require pure recombinant ACBP. ..
- Ru Lee W, Chen C, Liu S, Safe S. 17beta-estradiol (E2) induces cdc25A gene expression in breast cancer cells by genomic and non-genomic pathways. J Cell Biochem. 2006;99:209-20 pubmed..Thus, both genomic and non-genomic pathways of estrogen action are involved in induction of cdc25A in breast cancer cells. ..
- Wei J, Wu C, Sachs M. The arginine attenuator peptide interferes with the ribosome peptidyl transferase center. Mol Cell Biol. 2012;32:2396-406 pubmed publisher..The mode of PTC inhibition appears unusual because neither specific amino acids nor a specific nascent peptide chain length was required for AAP to inhibit PTC function. ..
- Yang Y, Igumenova T. The C-terminal V5 domain of Protein Kinase C? is intrinsically disordered, with propensity to associate with a membrane mimetic. PLoS ONE. 2013;8:e65699 pubmed publisher..The ability of V5? to partition into the hydrophobic micellar environment suggests that it may serve as a membrane anchor during the PKC maturation process. ..
- Spencer J, Stolowich N, Roessner C, Scott A. The Escherichia coli cysG gene encodes the multifunctional protein, siroheme synthase. FEBS Lett. 1993;335:57-60 pubmed..Thus CysG is a multifunctional protein solely responsible for siroheme synthesis from uro'gen III in E. coli, and accordingly is renamed siroheme synthase. ..
- Wu X, Davis G, Meininger G, Wilson E, Davis M. Regulation of the L-type calcium channel by alpha 5beta 1 integrin requires signaling between focal adhesion proteins. J Biol Chem. 2001;276:30285-92 pubmed..This interaction may represent a novel mechanism for control of calcium influx in vascular smooth muscle and other cell types. ..
- Xu M, Arulandu A, Struck D, Swanson S, Sacchettini J, Young R. Disulfide isomerization after membrane release of its SAR domain activates P1 lysozyme. Science. 2005;307:113-7 pubmed publisher..Thus, the exported P1 endolysin is kept inactive by three levels of control-topological, conformational, and covalent-until its release from the membrane is triggered by the P1 holin...
- Shipman L, Li D, Roessner C, Scott A, Sacchettini J. Crystal structure of precorrin-8x methyl mutase. Structure. 2001;9:587-96 pubmed..Analysis of the structure with bound product suggests that the [1,5]-sigmatropic shift proceeds by protonation of the ring C nitrogen, leading to subsequent methyl migration...
- Dey S, Grant G, Sacchettini J. Crystal structure of Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase: extreme asymmetry in a tetramer of identical subunits. J Biol Chem. 2005;280:14892-9 pubmed..Significant asymmetry is also seen at the subunit level where different conformations exist at the NAD-binding site and the putative serine-binding site in the two unique subunits. ..
- Klabunde T, Petrassi H, Oza V, Raman P, Kelly J, Sacchettini J. Rational design of potent human transthyretin amyloid disease inhibitors. Nat Struct Biol. 2000;7:312-21 pubmed..This research provides a rationale for a chemotherapeutic approach for the treatment of TTR-associated amyloid diseases. ..
- Mir K, Parr R, Schroeder F, Ball J. Rotavirus NSP4 interacts with both the amino- and carboxyl-termini of caveolin-1. Virus Res. 2007;126:106-15 pubmed..However, NSP4 binding to one of the termini was sufficient for the interaction. ..
- Prabhakaran S, Liang X, Skare J, Potts J, Hook M. A novel fibronectin binding motif in MSCRAMMs targets F3 modules. PLoS ONE. 2009;4:e5412 pubmed publisher..The results of this study provide evidence for how bacteria can target host proteins to manipulate host cell activities. ..
- Zhao H, Gabbaï F. A bidentate Lewis acid with a telluronium ion as an anion-binding site. Nat Chem. 2010;2:984-90 pubmed publisher..These results, which illustrate the viability of heavier chalcogenium centres as anion-binding sites, allow us to introduce a novel strategy for the design of polydentate Lewis acids with enhanced anion affinities. ..
- Busenlehner L, Apuy J, Giedroc D. Characterization of a metalloregulatory bismuth(III) site in Staphylococcus aureus pI258 CadC repressor. J Biol Inorg Chem. 2002;7:551-9 pubmed publisher..Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0336-9...
- Gokulan K, Rupp B, Pavelka M, Jacobs W, Sacchettini J. Crystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesis. J Biol Chem. 2003;278:18588-96 pubmed
- White S, Taylor K, Abbey C, Gill C, Womack J. Haplotype variation in bovine Toll-like receptor 4 and computational prediction of a positively selected ligand-binding domain. Proc Natl Acad Sci U S A. 2003;100:10364-9 pubmed..These data provide a basic understanding of bovine TLR4 sequence variation and supply haplotype markers for disease association studies. ..
- Reddy M, Kuppan G, Shetty N, Owen J, Ioerger T, Sacchettini J. Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors. Protein Sci. 2008;17:2134-44 pubmed publisher..Differences in the entrance to this access channel between human and Mtb SAHH are identified...
- Wales M, Hoover T, Wild J. Site-specific substitutions of the Tyr-165 residue in the catalytic chain of aspartate transcarbamoylase promotes a T-state preference in the holoenzyme. J Biol Chem. 1988;263:6109-14 pubmed..coli aspartate transcarbamoylase, although other substitutions have been reported (Robey, E. H., and Schachman, H. K. (1984) J. Biol. Chem. 259, 11180-11183) which show more complex effects...
- Hsieh Y, Omarov R, Scholthof H. Diverse and newly recognized effects associated with short interfering RNA binding site modifications on the Tomato bushy stunt virus p19 silencing suppressor. J Virol. 2009;83:2188-200 pubmed publisher..benthamiana plants but not in spinach. In conclusion, even though siRNA binding by P19 is a key functional property, compromised siRNA sequestration can result in novel and diverse host-dependent properties...
- Ball J, Schroeder M, Williams C, Schroeder F, Parr R. Mutational analysis of the rotavirus NSP4 enterotoxic domain that binds to caveolin-1. Virol J. 2013;10:336 pubmed publisher..The integrity of the helical structure is important for both cav-1 binding and diarrhea induction implying a connection between NSP4 functional and binding activities...
- Pettigrew D, Yu G, Liu Y. Nucleotide regulation of Escherichia coli glycerol kinase: initial-velocity and substrate binding studies. Biochemistry. 1990;29:8620-7 pubmed..Several properties of the enzyme are consistent with negative cooperativity as the basis for the difference in affinities. The possible physiological importance of the regulatory behavior with respect to ATP is considered. ..
- Aravind L, Koonin E. Phosphoesterase domains associated with DNA polymerases of diverse origins. Nucleic Acids Res. 1998;26:3746-52 pubmed..In these cases, the pyrophosphate may be hydrolyzed by a stand-alone phosphatase, and candidates for such a role were identified among bacterial PHP superfamily members. ..
- Wood T, Bridwell Rabb J, Kim Y, Gao T, Chang Y, LiWang A, et al. The KaiA protein of the cyanobacterial circadian oscillator is modulated by a redox-active cofactor. Proc Natl Acad Sci U S A. 2010;107:5804-9 pubmed publisher..Our data suggest that KaiA directly senses environmental signals as changes in redox state and modulates the circadian clock. ..
- Fenwick M, Almabruk K, Ealick S, Begley T, Philmus B. Biochemical Characterization and Structural Basis of Reactivity and Regioselectivity Differences between Burkholderia thailandensis and Burkholderia glumae 1,6-Didesmethyltoxoflavin N-Methyltransferase. Biochemistry. 2017;56:3934-3944 pubmed publisher..Furthermore, in BthII1283, N1 is hydrogen bonded to a histidine residue whereas BgToxA does not supply an obvious basic residue for either N6 or N1 methylation...
- diSioudi B, Grimsley J, Lai K, Wild J. Modification of near active site residues in organophosphorus hydrolase reduces metal stoichiometry and alters substrate specificity. Biochemistry. 1999;38:2866-72 pubmed
- Gallegos A, Atshaves B, Storey S, Starodub O, Petrescu A, Huang H, et al. Gene structure, intracellular localization, and functional roles of sterol carrier protein-2. Prog Lipid Res. 2001;40:498-563 pubmed
- Chen X, Zhang B, Harmon P, Schaffner W, Peterson D, Giedroc D. A novel cysteine cluster in human metal-responsive transcription factor 1 is required for heavy metal-induced transcriptional activation in vivo. J Biol Chem. 2004;279:4515-22 pubmed
- Chifotides H, Koomen J, Kang M, Tichy S, Dunbar K, Russell D. Binding of DNA purine sites to dirhodium compounds probed by mass spectrometry. Inorg Chem. 2004;43:6177-87 pubmed..Ultimately, both MALDI and ESI MS proved to be complementary, valuable tools for probing the identity and stability of dinuclear metal-DNA adducts...
- Liu S, Bian X, Lockless S. Preferential binding of K+ ions in the selectivity filter at equilibrium explains high selectivity of K+ channels. J Gen Physiol. 2012;140:671-9 pubmed publisher..We hypothesize that the equilibrium preference for K(+) ions originates in part through the optimal spacing between sites to accommodate multiple K(+) ions within the selectivity filter...
- Odokonyero D, Ragumani S, Lopez M, Bonanno J, Ozerova N, Woodard D, et al. Divergent evolution of ligand binding in the o-succinylbenzoate synthase family. Biochemistry. 2013;52:7512-21 pubmed publisher..Instead, large deletions outside the active site were accompanied by alteration of active site size and electrostatic interactions, resulting in small but significant differences in ligand binding. ..
- Gardina P, Manson M. Attractant signaling by an aspartate chemoreceptor dimer with a single cytoplasmic domain. Science. 1996;274:425-6 pubmed..Thus, a Tar dimer containing only one cytoplasmic domain can initiate an attractant (inhibitory) signal, although it may not be able to stimulate kinase activity of CheA. ..
- Stolowich N, Frolov A, Atshaves B, Murphy E, Jolly C, Billheimer J, et al. The sterol carrier protein-2 fatty acid binding site: an NMR, circular dichroic, and fluorescence spectroscopic determination. Biochemistry. 1997;36:1719-29 pubmed..The pH-induced changes in SCP-2 secondary structure and ligand binding activity may be important to the mechanism whereby this protein interacts with membrane surfaces to enhance lipid binding/transfer. ..
- Zhu Salzman K, Hammen P, Salzman R, Koiwa H, Bressan R, Murdock L, et al. Calcium modulates protease resistance and carbohydrate binding of a plant defense legume lectin, Griffonia simplicifolia lectin II (GSII). Comp Biochem Physiol B Biochem Mol Biol. 2002;132:327-34 pubmed..Thus, both carbohydrate binding (presumably to targets in the insect gut) and biochemical stability to proteolytic degradation in situ indeed contribute to anti-insect activity, and these activities are Ca(2+)-dependent...
- Kim J, Howell S, Huang X, Raushel F. Structural defects within the carbamate tunnel of carbamoyl phosphate synthetase. Biochemistry. 2002;41:12575-81 pubmed..The partial reactions of CPS have not been significantly impaired by these mutations, and thus, the catalytic machinery at the individual active sites has not been functionally perturbed...
- Lee J, Kim K, Sacchettini J, Smith C, Safe S. DRIP150 coactivation of estrogen receptor alpha in ZR-75 breast cancer cells is independent of LXXLL motifs. J Biol Chem. 2005;280:8819-30 pubmed..These results demonstrate that coactivation of ERalpha by DRIP150 in ZR-75 cells is NR box-independent and requires a novel sequence with putative alpha-helical structure. ..
- Rerngsamran P, Murphy M, Doyle S, Ebbole D. Fluffy, the major regulator of conidiation in Neurospora crassa, directly activates a developmentally regulated hydrophobin gene. Mol Microbiol. 2005;56:282-97 pubmed publisher..In addition, yeast one hybrid experiments demonstrated that the C-terminal portion of FL functions in transcriptional activation. Transcriptional profiling was used to identify additional potential targets for regulation by fl...
- Marti Arbona R, Fresquet V, Thoden J, Davis M, Holden H, Raushel F. Mechanism of the reaction catalyzed by isoaspartyl dipeptidase from Escherichia coli. Biochemistry. 2005;44:7115-24 pubmed..Collapse of the tetrahedral intermediate and cleavage of the carbon-nitrogen bond occur with donation of a proton from the protonated form of Asp285. ..
- Pavon J, Fitzpatrick P. Insights into the catalytic mechanisms of phenylalanine and tryptophan hydroxylase from kinetic isotope effects on aromatic hydroxylation. Biochemistry. 2006;45:11030-7 pubmed
- Dey S, Burton R, Grant G, Sacchettini J. Structural analysis of substrate and effector binding in Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase. Biochemistry. 2008;47:8271-82 pubmed publisher..Furthermore, comparison to the structure of a truncated form of human d-3-phosphoglycerate dehydrogenase with cofactor and a substrate analog, provides insight into the conformational changes that occur during catalysis. ..
- Arockiasamy A, Aggarwal A, Savva C, Holzenburg A, Sacchettini J. Crystal structure of calcium dodecin (Rv0379), from Mycobacterium tuberculosis with a unique calcium-binding site. Protein Sci. 2011;20:827-33 pubmed publisher..Structure and sequence analysis were used to identify orthologs of Rv0379 with different ligand-binding specificity. ..
- Kim M, Peterson D. Oct-1 protein promotes functional transcription complex assembly on the mouse mammary tumor virus promoter. J Biol Chem. 1995;270:27823-8 pubmed
- Bernhardt T, Wang I, Struck D, Young R. A protein antibiotic in the phage Qbeta virion: diversity in lysis targets. Science. 2001;292:2326-9 pubmed..Thus, the two small phages characterized for their lysis strategy, Qbeta and the small DNA phage phiX174, effect host lysis by targeting different enzymes in the multistep, universally conserved pathway of cell wall biosynthesis...
- Kim J, Raushel F. Perforation of the tunnel wall in carbamoyl phosphate synthetase derails the passage of ammonia between sequential active sites. Biochemistry. 2004;43:5334-40 pubmed..Overall, the catalytic constants of the mutant were consistent with the model where the channeling of ammonia has been disrupted due to the leakage from the ammonia tunnel to the protein exterior...
- Choi S, Hema M, Gopinath K, Santos J, Kao C. Replicase-binding sites on plus- and minus-strand brome mosaic virus RNAs and their roles in RNA replication in plant cells. J Virol. 2004;78:13420-9 pubmed..These results identify the replicase-binding sites in all of the BMV RNAs and suggest that the recognition of RNA3 is different from that of RNA1 and RNA2...
- Li J, Fitzpatrick P. Characterization of metal ligand mutants of phenylalanine hydroxylase: Insights into the plasticity of a 2-histidine-1-carboxylate triad. Arch Biochem Biophys. 2008;475:164-8 pubmed publisher..The results complement previous results with tyrosine hydroxylase in establishing the plasticity of the individual iron ligands in this enzyme family. ..
- Wang Y, Kendall J, Cavet J, Giedroc D. Elucidation of the functional metal binding profile of a Cd(II)/Pb(II) sensor CmtR(Sc) from Streptomyces coelicolor. Biochemistry. 2010;49:6617-26 pubmed publisher..The implications of these findings on the ability to predict metal specificity and function from metal-site signatures in the primary structure of ArsR family proteins are discussed. ..
- Stewart M, Igumenova T. Reactive cysteine in the structural Zn(2+) site of the C1B domain from PKC?. Biochemistry. 2012;51:7263-77 pubmed publisher..Our data suggest that Cys151 serves as an entry point for the reactive oxygen species that activate PKC? in a process involving Zn(2+) release. ..
- Shende V, Neuendorff N, Earnest D. Role of miR-142-3p in the post-transcriptional regulation of the clock gene Bmal1 in the mouse SCN. PLoS ONE. 2013;8:e65300 pubmed publisher..Collectively, our results suggest that miR-142-3p may play a role in the post-transcriptional modulation of Bmal1 and its oscillatory regulation in molecular feedback loops mediating SCN circadian function. ..
- Czerwinski R, Mareya S, Raushel F. Regulatory changes in the control of carbamoyl phosphate synthetase induced by truncation and mutagenesis of the allosteric binding domain. Biochemistry. 1995;34:13920-7 pubmed..Six conserved amino acids within the allosteric domain were mutated.(ABSTRACT TRUNCATED AT 250 WORDS)..
- Allen B, Uhlmann F, Gaur L, Mulder B, Posey K, Jones L, et al. DNA recognition properties of the N-terminal DNA binding domain within the large subunit of replication factor C. Nucleic Acids Res. 1998;26:3877-82 pubmed..Combined with existing data, these DNA binding properties suggest a role for the N-terminal DNA binding domain in the recognition of phosphorylated DNA ends. ..
- Zhang Y, Gardina P, Kuebler A, Kang H, Christopher J, Manson M. Model of maltose-binding protein/chemoreceptor complex supports intrasubunit signaling mechanism. Proc Natl Acad Sci U S A. 1999;96:939-44 pubmed