Genomes and Genes
Experts and Doctors on amino acid sequence in Ames, Iowa, United States
Locale: Ames, Iowa, United States
Topic: amino acid sequence
- Mallis R, Brazin K, Fulton D, Andreotti A. Structural characterization of a proline-driven conformational switch within the Itk SH2 domain. Nat Struct Biol. 2002;9:900-5 pubmed..The structures indicate that the heterogeneous Pro residue acts as a hinge that modulates ligand recognition by controlling the relative orientation of protein-binding surfaces. ..
- Halling S. On the presence and organization of open reading frames of the nonmotile pathogen Brucella abortus similar to class II, III, and IV flagellar genes and to LcrD virulence superfamily. Microb Comp Genomics. 1998;3:21-9 pubmed..A homolog of the LcrD virulence superfamily was also found. This superfamily is involved in type III protein secretion. B. abortus has the potential for motility and type III secretion. ..
- Bergmann D, Zahn J, DiSpirito A. High-molecular-mass multi-c-heme cytochromes from Methylococcus capsulatus bath. J Bacteriol. 1999;181:991-7 pubmed..The subunit molecular masses, arrangement and number of hemes, and amino acid sequences demonstrate that cytochrome c553O and the gene products of ORF1 and ORF3 constitute a new class of c-type cytochrome. ..
- Kleiboeker S. Sequence analysis of the fiber genomic region of a porcine adenovirus predicts a novel fiber protein. Virus Res. 1995;39:299-309 pubmed..Thus the predicted amino acid sequence of the NADC-1 fiber head is unique among adenoviruses for which the sequence of the fiber protein is known. ..
- Stanton T, Humphrey S, Bayles D, Zuerner R. Identification of a divided genome for VSH-1, the prophage-like gene transfer agent of Brachyspira hyodysenteriae. J Bacteriol. 2009;191:1719-21 pubmed publisher..6-kb cluster. The location and transcription direction of these genes relative to those of the previously described VSH-1 16.3-kb gene operon indicate that the gene transfer agent VSH-1 has a noncontiguous, divided genome. ..
- Wang Q, Hillwig M, Wu Y, Peters R. CYP701A8: a rice ent-kaurene oxidase paralog diverted to more specialized diterpenoid metabolism. Plant Physiol. 2012;158:1418-25 pubmed publisher..This further expands the range of enzymes recruited from the ancestral GA primary pathway to the more complex and specialized labdane-related diterpenoid metabolic network found in rice. ..
- Brar H, Swaminathan S, Bhattacharyya M. The Fusarium virguliforme toxin FvTox1 causes foliar sudden death syndrome-like symptoms in soybean. Mol Plant Microbe Interact. 2011;24:1179-88 pubmed publisher..The requirement of light for foliar SDS-like symptom development indicates that FvTox1 induces foliar SDS in soybean, most likely through production of free radicals by interrupting photosynthesis. ..
- Stickney J, Buss J. Murine guanylate-binding protein: incomplete geranylgeranyl isoprenoid modification of an interferon-gamma-inducible guanosine triphosphate-binding protein. Mol Biol Cell. 2000;11:2191-200 pubmed..The C20-selective impairment in prenylation also identifies mGBP1 as an important model for the study of substrate/geranylgeranyl transferase I interactions. ..
- Cantu D, Chen Y, Lemons M, Reilly P. ThYme: a database for thioester-active enzymes. Nucleic Acids Res. 2011;39:D342-6 pubmed publisher..ThYme is continually updated as sequences and tertiary structures become available. ..
- Choe J, Nelson S, Arienti K, Axe F, Collins T, Jones T, et al. Inhibition of fructose-1,6-bisphosphatase by a new class of allosteric effectors. J Biol Chem. 2003;278:51176-83 pubmed..Moreover, the inhibitor could mimic an unknown natural effector of fructose-1,6-bisphosphatase, as it interacts strongly with a conserved residue of undetermined functional significance. ..
- Humphries J, Kimber M, Barton Y, Hsu W, Marks N, Greer B, et al. Structure and bioactivity of neuropeptide F from the human parasites Schistosoma mansoni and Schistosoma japonicum. J Biol Chem. 2004;279:39880-5 pubmed
- Dinges J, Colleoni C, James M, Myers A. Mutational analysis of the pullulanase-type debranching enzyme of maize indicates multiple functions in starch metabolism. Plant Cell. 2003;15:666-80 pubmed..Therefore, pullulanase-type DBE partially compensates for the defect in isoamylase-type DBE, suggesting a function during starch synthesis as well as degradation. ..
- Mousley A, Novozhilova E, Kimber M, Day T. Neuropeptide physiology in helminths. Adv Exp Med Biol. 2010;692:78-97 pubmed
- Wang W, Gorrell A, Honzatko R, Fromm H. A study of Escherichia coli adenylosuccinate synthetase association states and the interface residues of the homodimer. J Biol Chem. 1997;272:7078-84 pubmed..Our results suggest that IMP binding induces enzyme dimerization and that two residues in the interface region, Arg143 and Asp231, play significant roles in IMP and GTP binding. ..
- Zhou L, Lacroute F, Thornburg R. Cloning, expression in Escherichia coli, and characterization of Arabidopsis thaliana UMP/CMP kinase. Plant Physiol. 1998;117:245-54 pubmed..The optimal pH for the enzyme is 6.5. P1, P5-di(adenosine-5') pentaphosphate was found to be a competitive inhibitor of both ATP and UMP. ..
- Gao Y, Shen L, Honzatko R. Central cavity of fructose-1,6-bisphosphatase and the evolution of AMP/fructose 2,6-bisphosphate synergism in eukaryotic organisms. J Biol Chem. 2014;289:8450-61 pubmed publisher..Taken together, these observations suggest the evolution of AMP/Fru-2,6-P2 synergism in eukaryotic FBPases from an ancestral FBPase having a central aqueous cavity and exhibiting synergistic feedback inhibition by AMP and Fru-6-P. ..
- El Manzalawy Y, Dobbs D, Honavar V. On evaluating MHC-II binding peptide prediction methods. PLoS ONE. 2008;3:e3268 pubmed publisher..These results underscore the importance of using similarity-reduced datasets in rigorously comparing the performance of alternative MHC-II peptide prediction methods. ..
- Townsend J, Wright D, Winfrey R, Fu F, Maeder M, Joung J, et al. High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature. 2009;459:442-5 pubmed publisher..More than 40% of recombinant plants had modifications in multiple SuR alleles. The observed high frequency of gene targeting indicates that it is now possible to efficiently make targeted sequence changes in endogenous plant genes. ..
- Xiao C, Giménez Lirola L, Jiang Y, Halbur P, Opriessnig T. Characterization of a novel porcine parvovirus tentatively designated PPV5. PLoS ONE. 2013;8:e65312 pubmed publisher..The high similarity to PPV4 and the lack of ORF3 may suggest PPV5 is an intermediate of PPV4 during the evolution of parvoviruses in pigs. ..
- Borza T, Iancu C, Pike E, Honzatko R, Fromm H. Variations in the response of mouse isozymes of adenylosuccinate synthetase to inhibitors of physiological relevance. J Biol Chem. 2003;278:6673-9 pubmed..Fructose 1,6-bisphosphate and IMP together may be dynamic regulators of the basic isozyme in muscle, causing potent inhibition of the synthetase under conditions of high AMP deaminase activity. ..
- Ellingson J, Bolin C, Stabel J. Identification of a gene unique to Mycobacterium avium subspecies paratuberculosis and application to diagnosis of paratuberculosis. Mol Cell Probes. 1998;12:133-42 pubmed publisher..paratuberculosis. The dOH method could be a good alternative to existing assays and will be adapted for specific identification of M. paratuberculosis from faecal samples, mixed bacteriologic cultures, tissue specimens and whole blood...
- Jing F, Cantu D, Tvaruzkova J, Chipman J, Nikolau B, Yandeau Nelson M, et al. Phylogenetic and experimental characterization of an acyl-ACP thioesterase family reveals significant diversity in enzymatic specificity and activity. BMC Biochem. 2011;12:44 pubmed publisher..These acyl-ACP TEs can potentially be used to diversify the fatty acid biosynthesis pathway to produce novel fatty acids. ..
- Sahin O, Plummer P, Jordan D, Sulaj K, Pereira S, Robbe Austerman S, et al. Emergence of a tetracycline-resistant Campylobacter jejuni clone associated with outbreaks of ovine abortion in the United States. J Clin Microbiol. 2008;46:1663-71 pubmed publisher..Together, these results indicate that a single tetracycline-resistant C. jejuni clone has emerged as the major cause of Campylobacter-associated sheep abortion in the United States...
- DiSpirito A, Semrau J, Murrell J, Gallagher W, Dennison C, Vuilleumier S. Methanobactin and the Link between Copper and Bacterial Methane Oxidation. Microbiol Mol Biol Rev. 2016;80:387-409 pubmed publisher..We also explore its potential applications, how mbs may alter the bioavailability of multiple metals, and the many roles mbs may play in the physiology of methanotrophs. ..
- Xu M, Brar H, Grosic S, Palmer R, Bhattacharyya M. Excision of an active CACTA-like transposable element from DFR2 causes variegated flowers in soybean [Glycine max (L.) Merr.]. Genetics. 2010;184:53-63 pubmed publisher..The highly active endogenous transposon, Tgm9, should facilitate genomics studies specifically that relate to legume biology. ..
- Sturms R, Kakar S, Trent J, Hargrove M. Trema and parasponia hemoglobins reveal convergent evolution of oxygen transport in plants. Biochemistry. 2010;49:4085-93 pubmed publisher..These results demonstrate distinct mechanisms for convergent evolution of oxygen transport in different phylogenetic classes of plant hemoglobins...
- Liu S, Chougule N, Vijayendran D, Bonning B. Deep sequencing of the transcriptomes of soybean aphid and associated endosymbionts. PLoS ONE. 2012;7:e45161 pubmed publisher..The soybean aphid has significantly impacted soybean production in the U.S. Transcriptomic analyses were conducted for further insight into leads for potential novel management strategies...
- Zamanian M, Agbedanu P, Wheeler N, McVeigh P, Kimber M, Day T. Novel RNAi-mediated approach to G protein-coupled receptor deorphanization: proof of principle and characterization of a planarian 5-HT receptor. PLoS ONE. 2012;7:e40787 pubmed publisher..Future work can help optimize and adapt this protocol for higher-throughput platforms as well as other phyla...
- Hou Z, Wang W, Fromm H, Honzatko R. IMP Alone Organizes the Active Site of Adenylosuccinate Synthetase from Escherichia coli. J Biol Chem. 2002;277:5970-6 pubmed
- Gao X, Vander Velden K, Voytas D, Gu X. SplitTester: software to identify domains responsible for functional divergence in protein family. BMC Bioinformatics. 2005;6:137 pubmed..From the analysis of retroelements reverse transcriptase family, we successfully identified the regions splitting this family according to the primer specificity, implying their functions in the specific primer selection. ..
- Chang C, Yoon K, Zimmerman J, Harmon K, Dixon P, Dvorak C, et al. Evolution of porcine reproductive and respiratory syndrome virus during sequential passages in pigs. J Virol. 2002;76:4750-63 pubmed..Although no epitopic changes were detected under the conditions of this experiment, PRRS virus was shown to evolve continuously in infected pigs, with different genes of the viral genome undergoing various degrees of change. ..
- Iancu C, Borza T, Choe J, Fromm H, Honzatko R. Recombinant mouse muscle adenylosuccinate synthetase: overexpression, kinetics, and crystal structure. J Biol Chem. 2001;276:42146-52 pubmed..Observed differences in ligand recognition among adenylosuccinate synthetases may be due in part to conformational variations in the IMP pocket of the ligand-free enzymes. ..
- Coats S, Booden M, Buss J. Transient palmitoylation supports H-Ras membrane binding but only partial biological activity. Biochemistry. 1999;38:12926-34 pubmed..Farnesyl may be important for signaling, especially transformation, while palmitates may provide potentially dynamic regulation of membrane binding. ..
- Wu D, Wright D, Wetzel C, Voytas D, Rodermel S. The IMMUTANS variegation locus of Arabidopsis defines a mitochondrial alternative oxidase homolog that functions during early chloroplast biogenesis. Plant Cell. 1999;11:43-55 pubmed
- Bannantine J, Lingle C, Stabel J, Ramyar K, Garcia B, Raeber A, et al. MAP1272c encodes an NlpC/P60 protein, an antigen detected in cattle with Johne's disease. Clin Vaccine Immunol. 2012;19:1083-92 pubmed publisher..These tools provide additional means to study a strong antigen of M. avium subsp. paratuberculosis. ..
- Meyer M, Lichti C, Townsend R, Rao A. Identification of in vitro autophosphorylation sites and effects of phosphorylation on the Arabidopsis CRINKLY4 (ACR4) receptor-like kinase intracellular domain: insights into conformation, oligomerization, and activity. Biochemistry. 2011;50:2170-86 pubmed publisher..Sedimentation velocity and gel filtration experiments indicate that the ICD has a propensity to oligomerize and that this property is lost upon autophosphorylation. ..
- De la Rosa M, Nelson S. An interaction between the Walker A and D-loop motifs is critical to ATP hydrolysis and cooperativity in bacteriophage T4 Rad50. J Biol Chem. 2011;286:26258-66 pubmed publisher..Additionally, we propose that the asparagine acts as a ?-phosphate sensor and, through its interaction with the conserved D-loop aspartate, transmits conformational changes across the dimer interface to the second ATP binding site...
- Shen H, Halbur P, Opriessnig T. Prevalence and phylogenetic analysis of the current porcine circovirus 2 genotypes after implementation of widespread vaccination programmes in the USA. J Gen Virol. 2012;93:1345-55 pubmed publisher..The data generated in this study provide novel information on the distribution of PCV2 genotypes in vaccinated pig populations...
- Zhang W, Wang Y, Long J, Girton J, Johansen J, Johansen K. A developmentally regulated splice variant from the complex lola locus encoding multiple different zinc finger domain proteins interacts with the chromosomal kinase JIL-1. J Biol Chem. 2003;278:11696-704 pubmed..Thus, genetic interaction assays provide direct evidence that gene products from the lola locus function within the same pathway as the chromosomal kinase JIL-1. ..
- Chen H, Rosin F, Prat S, Hannapel D. Interacting transcription factors from the three-amino acid loop extension superclass regulate tuber formation. Plant Physiol. 2003;132:1391-404 pubmed..Our results demonstrate an interaction between KNOX and BEL1-like transcription factors of potato that may potentially regulate processes of development...
- Baccam P, Thompson R, Li Y, Sparks W, Belshan M, Dorman K, et al. Subpopulations of equine infectious anemia virus Rev coexist in vivo and differ in phenotype. J Virol. 2003;77:12122-31 pubmed..A quasispecies model with multiple subpopulations may provide additional insight into the nature of lentivirus reservoirs and the evolution of antigenic and drug-resistant variants...
- Meng Y, Moscou M, Wise R. Blufensin1 negatively impacts basal defense in response to barley powdery mildew. Plant Physiol. 2009;149:271-85 pubmed publisher..Collectively, these data suggest that the grass-specific Bln1 negatively impacts basal defense against Bgh...
- Rath U, Wang D, Ding Y, Xu Y, Qi H, Blacketer M, et al. Chromator, a novel and essential chromodomain protein interacts directly with the putative spindle matrix protein skeletor. J Cell Biochem. 2004;93:1033-47 pubmed..These findings suggest that Chromator is a nuclear protein that plays a role in proper spindle dynamics during mitosis. ..
- Joseph R, Norris F. Substrate specificity and recognition is conferred by the pleckstrin homology domain of the Dbl family guanine nucleotide exchange factor P-Rex2. J Biol Chem. 2005;280:27508-12 pubmed..Thus substrate recognition can now be added to the growing list of functions that are being attributed to the PH domain of Dbl family GEFs. ..
- Bergmann D, Zahn J, Hooper A, DiSpirito A. Cytochrome P460 genes from the methanotroph Methylococcus capsulatus bath. J Bacteriol. 1998;180:6440-5 pubmed..capsulatus Bath indicated that the expression level of cytochrome P460 was not affected either by expression of the two different methane monooxygenases or by addition of ammonia to the culture medium...
- Iancu C, Zhou Y, Borza T, Fromm H, Honzatko R. Cavitation as a mechanism of substrate discrimination by adenylosuccinate synthetases. Biochemistry. 2006;45:11703-11 pubmed..At an approximate energy cost of 2.2 kcal/mol, the unfavorable thermodynamics of cavity formation may be the major factor in destabilizing ligands at the L-aspartate pocket. ..
- Kappes M, Miller C, Faaberg K. Highly divergent strains of porcine reproductive and respiratory syndrome virus incorporate multiple isoforms of nonstructural protein 2 into virions. J Virol. 2013;87:13456-65 pubmed publisher..Together, these data identify nsp2 as a virion-associated structural PRRSV protein and reveal that nsp2 exists in or on viral particles as multiple isoforms. ..
- Kitikoon P, Vincent A, Gauger P, Schlink S, Bayles D, Gramer M, et al. Pathogenicity and transmission in pigs of the novel A(H3N2)v influenza virus isolated from humans and characterization of swine H3N2 viruses isolated in 2010-2011. J Virol. 2012;86:6804-14 pubmed publisher..Continued monitoring of these H3N2 viruses is necessary to evaluate the evolution and potential loss of population immunity in swine and humans...
- Zhang C, Bradshaw J, Whitham S, Hill J. The development of an efficient multipurpose bean pod mottle virus viral vector set for foreign gene expression and RNA silencing. Plant Physiol. 2010;153:52-65 pubmed publisher..These results demonstrate the utility of this BPMV vector set for a wide range of applications in soybean and common bean, and they have implications for improvement of other plant virus-based vector systems...
- Srivastava R, Deng Y, Shah S, Rao A, Howell S. BINDING PROTEIN is a master regulator of the endoplasmic reticulum stress sensor/transducer bZIP28 in Arabidopsis. Plant Cell. 2013;25:1416-29 pubmed publisher..Thus, the dissociation of BiP from the C-terminal tail of bZIP28 is a major switch that activates one arm of the unfolded protein response signaling pathway in plants. ..
- Gao M, Wanat J, Stinard P, James M, Myers A. Characterization of dull1, a maize gene coding for a novel starch synthase. Plant Cell. 1998;10:399-412 pubmed..We conclude that Du1 codes for a starch synthase, most likely SSII, and that secondary effects of du1- mutations, such as reduction of SBEIIa, result from the primary deficiency in this starch synthase. ..
- Suarez D, Whetstone C. Identification of hypervariable and conserved regions in the surface envelope gene in the bovine lentivirus. Virology. 1995;212:728-33 pubmed..The four field isolates sequenced for this study had SU genes larger than R29-127. R29-derived isolates may not be representative of BIV currently present in United States cattle...
- Gao H, Narayanan N, Ellison L, Bhattacharyya M. Two classes of highly similar coiled coil-nucleotide binding-leucine rich repeat genes isolated from the Rps1-k locus encode Phytophthora resistance in soybean. Mol Plant Microbe Interact. 2005;18:1035-45 pubmed..Analyses of independent R0, R1, R2, and R3 progeny populations suggested that both gene classes confer Phytophthora resistance in soybean. A possible evolutionary mechanism for the Class I gene family is proposed. ..
- Graham M, Marek L, Shoemaker R. Organization, expression and evolution of a disease resistance gene cluster in soybean. Genetics. 2002;162:1961-77 pubmed..Three genes appeared to be constitutively expressed, while three were differentially expressed. Analyses of the R-genes within this BAC suggest that R-gene evolution in soybean is a complex and dynamic process. ..
- Valenzuela N. Multivariate expression analysis of the gene network underlying sexual development in turtle embryos with temperature-dependent and genotypic sex determination. Sex Dev. 2010;4:39-49 pubmed publisher..mutica, consistent with the hypothesis that sexual development is a more canalized process in A. mutica, as would be expected if GSD evolved in this lineage through directional selection from its TSD ancestor...
- Hennen Bierwagen T, Lin Q, Grimaud F, Planchot V, Keeling P, James M, et al. Proteins from multiple metabolic pathways associate with starch biosynthetic enzymes in high molecular weight complexes: a model for regulation of carbon allocation in maize amyloplasts. Plant Physiol. 2009;149:1541-59 pubmed publisher..PPDK and SUS-SH1 required SSIII, SSIIa, SBEIIa, and SBEIIb for assembly into the 670-kD complex. These complexes may function in global regulation of carbon partitioning between metabolic pathways in developing seeds. ..
- Terribilini M, Sander J, Lee J, Zaback P, Jernigan R, Honavar V, et al. RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucleic Acids Res. 2007;35:W578-84 pubmed..RNABindR automatically displays 'high specificity' and 'high sensitivity' predictions of RNA-binding residues. RNABindR is freely available at http://bindr.gdcb.iastate.edu/RNABindR. ..
- Kirthi N, Roy Chaudhuri B, Kelley T, Culver G. A novel single amino acid change in small subunit ribosomal protein S5 has profound effects on translational fidelity. RNA. 2006;12:2080-91 pubmed..This study highlights the importance of S5 in ribosome function and cell physiology, and suggests that translational fidelity can be regulated in multiple ways. ..
- Terribilini M, Lee J, Yan C, Jernigan R, Honavar V, Dobbs D. Prediction of RNA binding sites in proteins from amino acid sequence. RNA. 2006;12:1450-62 pubmed..RNABindR is available as a Web tool from http://bindr.gdcb.iastate.edu.). ..
- Zhang Y, Shin Y. Transmembrane organization of yeast syntaxin-analogue Sso1p. Biochemistry. 2006;45:4173-81 pubmed..Thus, hyperfine splitting may be used as an additional parameter to measure bilayer immersion depths of nitroxide. ..
- Wang B, Brendel V. Molecular characterization and phylogeny of U2AF35 homologs in plants. Plant Physiol. 2006;140:624-36 pubmed..A C-terminal motif (named SERE) is highly conserved in all seed plant protein homologs, suggesting it may have an important function specific to higher plants. ..
- Laederach A, Cradic K, Brazin K, Zamoon J, Fulton D, Huang X, et al. Competing modes of self-association in the regulatory domains of Bruton's tyrosine kinase: intramolecular contact versus asymmetric homodimerization. Protein Sci. 2002;11:36-45 pubmed
- Trent J, Hargrove M. A ubiquitously expressed human hexacoordinate hemoglobin. J Biol Chem. 2002;277:19538-45 pubmed..The discovery of histoglobin demonstrates that humans, like plants, differentially express multiple hexacoordinate hemoglobins. ..
- Walker D, Wang D, Jin Y, Rath U, Wang Y, Johansen J, et al. Skeletor, a novel chromosomal protein that redistributes during mitosis provides evidence for the formation of a spindle matrix. J Cell Biol. 2000;151:1401-12 pubmed..Thus, the identification and characterization of skeletor represents the first direct molecular evidence for the existence of a complete spindle matrix that forms within the nucleus before microtubule spindle formation. ..
- Waters W, Nonnecke B, Palmer M, Robbe Austermann S, Bannantine J, Stabel J, et al. Use of recombinant ESAT-6:CFP-10 fusion protein for differentiation of infections of cattle by Mycobacterium bovis and by M. avium subsp. avium and M. avium subsp. paratuberculosis. Clin Diagn Lab Immunol. 2004;11:729-35 pubmed..avium subsp. paratuberculosis, it appears that use of the rESAT-6:CFP-10 fusion protein will be useful for the detection of tuberculous cattle in herds with pre-existing sensitization to M. avium and/or M. avium subsp. paratuberculosis. ..
- Ji Y, Rath U, Girton J, Johansen K, Johansen J. D-Hillarin, a novel W180-domain protein, affects cytokinesis through interaction with the septin family member Pnut. J Neurobiol. 2005;64:157-69 pubmed..Based on these results we propose that D-hil may function as a regulator of septin function during cytokinesis in the developing nervous system. ..
- Shen C, Shao Z, Powell Coffman J. The Caenorhabditis elegans rhy-1 gene inhibits HIF-1 hypoxia-inducible factor activity in a negative feedback loop that does not include vhl-1. Genetics. 2006;174:1205-14 pubmed..Collectively, these data support models in which RHY-1 and EGL-9 function in VHL-1-independent pathway(s) to repress HIF-1 transcriptional activity. ..
- Hemken P, Bellin R, Sernett S, Becker B, Huiatt T, Robson R. Molecular characteristics of the novel intermediate filament protein paranemin. Sequence reveals EAP-300 and IFAPa-400 are highly homologous to paranemin. J Biol Chem. 1997;272:32489-99 pubmed..Antibody labeling of these cells suggests that paranemin does not form IFs by itself, but rather is incorporated into heteropolymeric IFs with vimentin. ..