Experts and Doctors on sequence alignment in Ann Arbor, Michigan, United States

Summary

Locale: Ann Arbor, Michigan, United States
Topic: sequence alignment

Top Publications

  1. Vincenz C, Dixit V. Fas-associated death domain protein interleukin-1beta-converting enzyme 2 (FLICE2), an ICE/Ced-3 homologue, is proximally involved in CD95- and p55-mediated death signaling. J Biol Chem. 1997;272:6578-83 pubmed
    ..A functional role for FLICE2 is suggested by the finding that an active site mutant of FLICE2 inhibits CD95 and tumor necrosis factor receptor-mediated apoptosis. FLICE2 is therefore involved in CD95 and p55 signal transduction. ..
  2. Muzio M, Ni J, Feng P, Dixit V. IRAK (Pelle) family member IRAK-2 and MyD88 as proximal mediators of IL-1 signaling. Science. 1997;278:1612-5 pubmed
    ..Dominant negative forms of either attenuate IL-1R-mediated NF-kappaB activation. Therefore, IRAK-2 and MyD88 may provide additional therapeutic targets for inhibiting IL-1-induced inflammation. ..
  3. Pan G, Ni J, Yu G, Wei Y, Dixit V. TRUNDD, a new member of the TRAIL receptor family that antagonizes TRAIL signalling. FEBS Lett. 1998;424:41-5 pubmed
    ..Consistent with an inhibitory role, ectopic expression of TRUNDD attenuated TRAIL-induced apoptosis in mammalian cells. ..
  4. Lumeng C, Phelps S, Crawford G, Walden P, Barald K, Chamberlain J. Interactions between beta 2-syntrophin and a family of microtubule-associated serine/threonine kinases. Nat Neurosci. 1999;2:611-7 pubmed
    ..Our data suggest that MAST205 and SAST link the dystrophin/utrophin network with microtubule filaments via the syntrophins. ..
  5. Campbell H, Kent C. The CTP:phosphocholine cytidylyltransferase encoded by the licC gene of Streptococcus pneumoniae: cloning, expression, purification, and characterization. Biochim Biophys Acta. 2001;1534:85-95 pubmed
    ..The enzyme is also inhibited by all other tested divalent cations, including Mg(2+) at high concentrations. The cloning and expression of this enzyme sets the stage for design of inhibitors as possible antipneumococcal drugs...
  6. Puig S, Lee J, Lau M, Thiele D. Biochemical and genetic analyses of yeast and human high affinity copper transporters suggest a conserved mechanism for copper uptake. J Biol Chem. 2002;277:26021-30 pubmed
    ..Together, these results support a fundamentally conserved mechanism for high affinity copper uptake through the Ctr proteins in yeast and humans. ..
  7. Zhang J, Webb D. Rapid evolution of primate antiviral enzyme APOBEC3G. Hum Mol Genet. 2004;13:1785-91 pubmed
    ..The identification of pervasive positive selection for charge-altering amino acid substitutions supports the hypothesis of electrostatic interactions between APOBEC3G and vif or its functional equivalents. ..
  8. Fowler C, Pogozheva I, LeVine H, Mosberg H. Refinement of a homology model of the mu-opioid receptor using distance constraints from intrinsic and engineered zinc-binding sites. Biochemistry. 2004;43:8700-10 pubmed
    ..Subsequent distance geometry refinement of the MOR model indicates that the rhodopsin-like alpha aneurism is likely absent in TM2 but present in TM5. ..
  9. Das D, Shah R, Imperiale M. Detection and expression of human BK virus sequences in neoplastic prostate tissues. Oncogene. 2004;23:7031-46 pubmed
    ..Although BKV DNA was found in benign and atrophic lesions, TAg and p53 coexpression was observed only in atrophic lesions. ..

More Information

Publications115 found, 100 shown here

  1. Williams T, Williams M, Innis J. Range of HOX/TALE superclass associations and protein domain requirements for HOXA13:MEIS interaction. Dev Biol. 2005;277:457-71 pubmed
  2. Michael L, Swantek J, Robinson M. Cloning and expression of human mitogen-activated protein kinase kinase 7gamma1. Biochem Biophys Res Commun. 2006;341:679-83 pubmed
    ..Recombinant hMKK7gamma1 can be phosphorylated and activated by MEKK1. Further studies will provide insight into the role for hMKK7gamma1 versus other MKK7 isoforms. ..
  3. Winer I, Bommer G, Gonik N, Fearon E. Lysine residues Lys-19 and Lys-49 of beta-catenin regulate its levels and function in T cell factor transcriptional activation and neoplastic transformation. J Biol Chem. 2006;281:26181-7 pubmed
    ..Moreover, our results inform understanding of why single amino acid substitutions at lysine 19 or 49 have not been reported in human cancer. ..
  4. Lapinski P, Oliver J, Kamen L, Hughes E, Saunders T, King P. Genetic analysis of SH2D4A, a novel adapter protein related to T cell-specific adapter and adapter protein in lymphocytes of unknown function, reveals a redundant function in T cells. J Immunol. 2008;181:2019-27 pubmed
    ..Furthermore, knockdown of SH2D4A expression in human T cells did not impact upon their function. We conclude that in contrast to TSAd and ALX proteins, SH2D4A is dispensable for TCR signal transduction in T cells. ..
  5. Wang B, Xue J, Li L, Liu Y, Qiu Y. The complete mitochondrial genome sequence of the liverwort Pleurozia purpurea reveals extremely conservative mitochondrial genome evolution in liverworts. Curr Genet. 2009;55:601-9 pubmed publisher
  6. Oscherwitz J, Gribbin T, Cease K. A CD20 tandem-epitope immunogen elicits antibody in mice that binds murine cell surface CD20 and depletes splenic B cells in vivo. Mol Immunol. 2010;47:1484-91 pubmed publisher
    ..The tandem-epitope immunogen represents a promising tool for eliciting and studying active autoimmunity to CD20, as a basis for potential development of new immunotherapeutics for cancer and autoimmune diseases. ..
  7. Foit L, George J, Zhang B, Brooks C, Bardwell J. Chaperone activation by unfolding. Proc Natl Acad Sci U S A. 2013;110:E1254-62 pubmed publisher
    ..These results provide convincing evidence for direct activation of a protein by partial unfolding. ..
  8. Sambrotta M, Strautnieks S, Papouli E, Rushton P, Clark B, Parry D, et al. Mutations in TJP2 cause progressive cholestatic liver disease. Nat Genet. 2014;46:326-8 pubmed publisher
    ..These findings contrast with those in the embryonic-lethal knockout mouse, highlighting differences in redundancy in junctional complexes between organs and species. ..
  9. Oliner J, Kinzler K, Meltzer P, George D, Vogelstein B. Amplification of a gene encoding a p53-associated protein in human sarcomas. Nature. 1992;358:80-3 pubmed
    ..This mechanism of tumorigenesis parallels that for virally-induced tumours, in which viral oncogene products bind to and functionally inactivate p53. ..
  10. Maddock J, Bhatt A, Koch M, Skidmore J. Identification of an essential Caulobacter crescentus gene encoding a member of the Obg family of GTP-binding proteins. J Bacteriol. 1997;179:6426-31 pubmed
    ..Disruption of the cgtA gene was lethal, demonstrating that this gene is essential for cell growth. Immunoblot analysis revealed that CgtA protein levels remained constant throughout the C. crescentus cell cycle...
  11. Brown N, Kanekar S, Vetter M, Tucker P, Gemza D, Glaser T. Math5 encodes a murine basic helix-loop-helix transcription factor expressed during early stages of retinal neurogenesis. Development. 1998;125:4821-33 pubmed
    ..We propose that Math5 acts as a proneural gene, but has properties different from its most closely related vertebrate family member, Xath5. ..
  12. Russell M, Raeker M, Korytkowski K, Sonneman K. Identification, tissue expression and chromosomal localization of human Obscurin-MLCK, a member of the titin and Dbl families of myosin light chain kinases. Gene. 2002;282:237-46 pubmed
    ..The modular nature of the Obscurin-MLCK isoforms indicates that it may have an array of functions important to cardiac and skeletal muscle physiology. ..
  13. Buchner D, Meisler M. TSRC1, a widely expressed gene containing seven thrombospondin type I repeats. Gene. 2003;307:23-30 pubmed
    ..Human TSRC1 is located on chromosome 1q21 within an 11.7 Mb segment of conserved synteny. TSRC1 and the closely linked gene ADAM15 appear to be derived by a chromosomal inversion that interrupted an ancestral ADAMTS gene. ..
  14. Zhang J, Zhang Y. Pseudogenization of the tumor-growth promoter angiogenin in a leaf-eating monkey. Gene. 2003;308:95-101 pubmed
    ..Our findings also provide a strong case for the importance of evolutionary analysis in biomedical studies of gene functions. ..
  15. Grus W, Shi P, Zhang Y, Zhang J. Dramatic variation of the vomeronasal pheromone receptor gene repertoire among five orders of placental and marsupial mammals. Proc Natl Acad Sci U S A. 2005;102:5767-72 pubmed
    ..In sum, our results demonstrate tremendous diversity and rapid evolution of mammalian V1R gene inventories and caution the generalization of VNO biology from rodents to all mammals. ..
  16. Pogozheva I, Chai B, Lomize A, Fong T, Weinberg D, Nargund R, et al. Interactions of human melanocortin 4 receptor with nonpeptide and peptide agonists. Biochemistry. 2005;44:11329-41 pubmed
  17. Liu X, Korde N, Jakob U, Leichert L. CoSMoS: Conserved Sequence Motif Search in the proteome. BMC Bioinformatics. 2006;7:37 pubmed
    ..CoSMoS is a valuable tool to identify highly conserved sequence motifs, to find regions suitable for mutational studies in functional analyses and to predict important structural features in E. coli proteins. ..
  18. Sun J, Yu E, Yang Y, Confer L, Sun S, Wan K, et al. Stn1-Ten1 is an Rpa2-Rpa3-like complex at telomeres. Genes Dev. 2009;23:2900-14 pubmed publisher
  19. Carlson J, Fortman J, Anzai Y, Li S, Burr D, Sherman D. Identification of the tirandamycin biosynthetic gene cluster from Streptomyces sp. 307-9. Chembiochem. 2010;11:564-72 pubmed publisher
  20. Veeneman B, Iyer M, Chinnaiyan A. Oculus: faster sequence alignment by streaming read compression. BMC Bioinformatics. 2012;13:297 pubmed publisher
    ..The platform-independent C++ source code is freely available online, at http://code.google.com/p/oculus-bio. ..
  21. Nance M, Kreutz B, Tesmer V, Sterne Marr R, Kozasa T, Tesmer J. Structural and functional analysis of the regulator of G protein signaling 2-g?q complex. Structure. 2013;21:438-48 pubmed publisher
    ..RGS subfamilies that do not serve as GAPs for G?q are unlikely to form analogous stabilizing interactions. ..
  22. Lundquist M, Storaska A, Liu T, Larsen S, Evans T, Neubig R, et al. Redox modification of nuclear actin by MICAL-2 regulates SRF signaling. Cell. 2014;156:563-76 pubmed publisher
    ..These data identify redox modification of nuclear actin as a regulatory switch that mediates SRF/MRTF-A-dependent gene transcription. ..
  23. Richards A, Watza D, Findley A, Alazizi A, Wen X, Pai A, et al. Environmental perturbations lead to extensive directional shifts in RNA processing. PLoS Genet. 2017;13:e1006995 pubmed publisher
    ..Together, these results demonstrate that RNA processing is dramatically changed in response to environmental perturbations through specific mechanisms regulated by trans factors...
  24. Gong T, Shin J, Burmeister M, Lomax M. Complete cDNAs for CDC42 from chicken cochlea and mouse liver. Biochim Biophys Acta. 1997;1352:282-92 pubmed
    ..Cdc42l1 was mapped to distal mouse Chromosome 4, near Cappb1. Cdc42l2 mapped more proximal on Chromosome 4, whereas Cdc42l3 mapped to the X Chromosome. ..
  25. Russell M, Baker P, Izumo S. Cloning, chromosomal mapping, and expression of the human eHAND gene. Mamm Genome. 1997;8:863-5 pubmed
  26. Law D, Tarle S, Merchant J. The human ZBP-89 homolog, located at chromosome 3q21, represses gastrin gene expression. Mamm Genome. 1998;9:165-7 pubmed
  27. Chamberlain J, Lee Y, Lane W, Engelke D. Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes Dev. 1998;12:1678-90 pubmed
    ..The degree of structural similarity between nuclear RNase P and RNase MRP suggests that some aspects of their functions in pre-tRNA and pre-rRNA processing pathways might overlap or be coordinated. ..
  28. Wu D, Chen P, Chen S, Hu Y, Nunez G, Ellis R. C. elegans MAC-1, an essential member of the AAA family of ATPases, can bind CED-4 and prevent cell death. Development. 1999;126:2021-31 pubmed
    ..These results suggest that MAC-1 identifies a new class of proteins that are essential for development, and which might regulate cell death in specific circumstances. ..
  29. Li L, Ernsting B, Wishart M, Lohse D, Dixon J. A family of putative tumor suppressors is structurally and functionally conserved in humans and yeast. J Biol Chem. 1997;272:29403-6 pubmed
    ..Our results suggest that CDC14 and YNL128W/PTEN/MMAC1 represent two related, but distinct, families of human and yeast phosphatases. ..
  30. Jang W, Hua A, Spilson S, Miller W, Roe B, Meisler M. Comparative sequence of human and mouse BAC clones from the mnd2 region of chromosome 2p13. Genome Res. 1999;9:53-61 pubmed
  31. Cho S, Jin S, Cohen A, Ellis R. A phylogeny of caenorhabditis reveals frequent loss of introns during nematode evolution. Genome Res. 2004;14:1207-20 pubmed publisher
    ..The small size of C. elegans introns should increase the rate at which each of these types of loss can occur, and might account for the dramatic difference in loss rate between nematodes and mammals...
  32. Sulavik M, Gambino L, Miller P. The MarR repressor of the multiple antibiotic resistance (mar) operon in Escherichia coli: prototypic member of a family of bacterial regulatory proteins involved in sensing phenolic compounds. Mol Med. 1995;1:436-46 pubmed
    ..Some of the MarR homologs appear more likely to control systems expressed in animal hosts, suggesting that phenolic sensing by bacteria is important in a variety of environments and in the regulation of numerous processes. ..
  33. Gong T, Winnicki R, Kohrman D, Lomax M. A novel mouse kinesin of the UNC-104/KIF1 subfamily encoded by the Kif1b gene. Gene. 1999;239:117-27 pubmed
    ..In addition, alternative splicing of two exons in the conserved region adjacent to the motor domain generates four different isoforms of each kinesin, leading to eight kinesin isoforms derived from the Kif1b gene. ..
  34. Gee P, Kent C. Multiple isoforms of choline kinase from Caenorhabditis elegans: cloning, expression, purification, and characterization. Biochim Biophys Acta. 2003;1648:33-42 pubmed
    ..These results provide a foundation for future studies on the structure and function of choline kinases, as well as studies on the genetic analysis of the function of the multiple isoforms in this organism. ..
  35. McCrea K, Xie J, Marrs C, Gilsdorf J. Prevalence of genetic differences in phosphorylcholine expression between nontypeable Haemophilus influenzae and Haemophilus haemolyticus. BMC Microbiol. 2010;10:286 pubmed publisher
  36. Mady A, Zolova O, Millán M, Villamizar G, de la Calle F, Lombo F, et al. Characterization of TioQ, a type II thioesterase from the thiocoraline biosynthetic cluster. Mol Biosyst. 2011;7:1999-2011 pubmed publisher
  37. Koseki T, Inohara N, Chen S, Nunez G. ARC, an inhibitor of apoptosis expressed in skeletal muscle and heart that interacts selectively with caspases. Proc Natl Acad Sci U S A. 1998;95:5156-60 pubmed
    ..Delivery of ARC by gene transfer or enhancement of its endogenous activity may provide a strategy for the treatment of diseases that are characterized by inappropriately increased cell death in muscle tissue. ..
  38. Patel P, Pontrello C, Burke S. Robust and tissue-specific expression of TPH2 versus TPH1 in rat raphe and pineal gland. Biol Psychiatry. 2004;55:428-33 pubmed
    ..The robust expression of TPH2 in brainstem should facilitate studies on the transcriptional regulation of raphe serotonin biosynthesis. ..
  39. He C, Bartholomew C, Zhou W, Klionsky D. Assaying autophagic activity in transgenic GFP-Lc3 and GFP-Gabarap zebrafish embryos. Autophagy. 2009;5:520-6 pubmed
    ..In addition, zebrafish Gabarap accumulates within lysosomes upon autophagy induction. Thus, we established a convenient zebrafish tool to assay autophagic activity during embryogenesis in vivo. ..
  40. Drennan C, Pattridge K, Weber C, Metzger A, Hoover D, Ludwig M. Refined structures of oxidized flavodoxin from Anacystis nidulans. J Mol Biol. 1999;294:711-24 pubmed
    ..The structures reported here provide the starting point for structure-function studies of the reduced states and of mutants, described in the accompanying paper. ..
  41. Escayg A, Heils A, MacDonald B, Haug K, Sander T, Meisler M. A novel SCN1A mutation associated with generalized epilepsy with febrile seizures plus--and prevalence of variants in patients with epilepsy. Am J Hum Genet. 2001;68:866-73 pubmed
    ..The SCN1A haplotypes and SNPs identified here will be useful in future association and linkage studies. ..
  42. Kim Y, Patel J. A framework for protein structure classification and identification of novel protein structures. BMC Bioinformatics. 2006;7:456 pubmed
    ..The method is effective in classifying new domains and suggesting new domain families, and it is also very efficient. A web site offering access to proCC is freely available at http://www.eecs.umich.edu/periscope/procc. ..
  43. Moore B, Robinson H, Xu Z. The crystal structure of mouse Exo70 reveals unique features of the mammalian exocyst. J Mol Biol. 2007;371:410-21 pubmed
    ..cerevisiae Exo70 structures. Given the low level of sequence conservation within Exo70, this structure provides new insights into our understanding of many species-specific functions of the exocyst. ..
  44. Richard A, Withey J, Beyhan S, Yildiz F, DiRita V. The Vibrio cholerae virulence regulatory cascade controls glucose uptake through activation of TarA, a small regulatory RNA. Mol Microbiol. 2010;78:1171-81 pubmed publisher
    ..cholerae. Although somewhat functionally analogous to SgrS of Escherichia coli, TarA does not encode a regulatory peptide, and its expression is activated by the virulence gene pathway in V. cholerae and not by glycolytic intermediates. ..
  45. Michele D, Albayya F, Metzger J. A nemaline myopathy mutation in alpha-tropomyosin causes defective regulation of striated muscle force production. J Clin Invest. 1999;104:1575-81 pubmed
  46. Zhao X, Alvarado D, Rainier S, Lemons R, Hedera P, Weber C, et al. Mutations in a newly identified GTPase gene cause autosomal dominant hereditary spastic paraplegia. Nat Genet. 2001;29:326-31 pubmed
    ..Its protein (spastin) is predicted to participate in the assembly or function of nuclear protein complexes. Here we report the identification of mutations in a newly identified GTPase gene, SPG3A, in ADHSP affected individuals. ..
  47. Raeker M, Su F, Geisler S, Borisov A, Kontrogianni Konstantopoulos A, Lyons S, et al. Obscurin is required for the lateral alignment of striated myofibrils in zebrafish. Dev Dyn. 2006;235:2018-29 pubmed
    ..The diminished capacity to generate and organize new myofibrils in response to obscurin depletion suggests that it may have a vital role in the causation of or adaptation to cardiac and skeletal myopathies. ..
  48. Peng Y, Tang F, Weisman L. Palmitoylation plays a role in targeting Vac8p to specific membrane subdomains. Traffic. 2006;7:1378-87 pubmed
    ..In addition, our studies provide evidence that palmitoylation targets Vac8p to specific membrane subdomains. ..
  49. Ozkan E, Lee F, Ueda T. A protein factor that inhibits ATP-dependent glutamate and gamma-aminobutyric acid accumulation into synaptic vesicles: purification and initial characterization. Proc Natl Acad Sci U S A. 1997;94:4137-42 pubmed
    ..We propose that IPF could be a novel component of a presynaptic regulatory system. Such a system might modulate neurotransmitter accumulation into synaptic vesicles and thus regulate the overall efficacy of neurotransmission. ..
  50. Kazen Gillespie K, Ragsdale D, D Andrea M, Mattei L, Rogers K, Isom L. Cloning, localization, and functional expression of sodium channel beta1A subunits. J Biol Chem. 2000;275:1079-88 pubmed
    ..These effects of beta1A subunits on sodium channel function may be physiologically important events in the development of excitable cells. ..
  51. Makarova O, Roh M, Liu C, Laurinec S, Margolis B. Mammalian Crumbs3 is a small transmembrane protein linked to protein associated with Lin-7 (Pals1). Gene. 2003;302:21-9 pubmed
    ..CRB3 is a specialized isoform of the Crumbs protein family that is expressed in epithelia and can tie the apical membrane to the tight junction. ..
  52. Begley M, Taylor G, Kim S, Veine D, Dixon J, Stuckey J. Crystal structure of a phosphoinositide phosphatase, MTMR2: insights into myotubular myopathy and Charcot-Marie-Tooth syndrome. Mol Cell. 2003;12:1391-402 pubmed
    ..Finally, the MTMR2 structure will serve as a model for other members of the myotubularin family and provide a framework for understanding the mechanism whereby mutations in these proteins lead to disease. ..
  53. Duda T, Bolin M, Meyer C, Kohn A. Hidden diversity in a hyperdiverse gastropod genus: discovery of previously unidentified members of a Conus species complex. Mol Phylogenet Evol. 2008;49:867-76 pubmed publisher
    ..Two of these fit the original description of C. sponsalis; three forms appear to represent C. nanus but differ in adult shell size or possess a unique shell color pattern. ..
  54. Cheng A, Zhang M, Okubo M, Omichi K, Saltiel A. Distinct mutations in the glycogen debranching enzyme found in glycogen storage disease type III lead to impairment in diverse cellular functions. Hum Mol Genet. 2009;18:2045-52 pubmed publisher
  55. Gonzalez Garcia M, PEREZ BALLESTERO R, Ding L, Duan L, Boise L, Thompson C, et al. bcl-XL is the major bcl-x mRNA form expressed during murine development and its product localizes to mitochondria. Development. 1994;120:3033-42 pubmed
    ..Based on its tissue and developmental patterns of expression, it appears that bcl-x may play an important role in the regulation of cell death during development and tissue homeostasis. ..
  56. Knight S, Tamai K, Kosman D, Thiele D. Identification and analysis of a Saccharomyces cerevisiae copper homeostasis gene encoding a homeodomain protein. Mol Cell Biol. 1994;14:7792-804 pubmed
  57. Blandizzi C, Song I, Yamada T. Molecular cloning and structural analysis of the rabbit gastrin/CCKB receptor gene. Biochem Biophys Res Commun. 1994;202:947-53 pubmed
    ..The putative protein-coding region of the gene exhibits 93 to 97% amino acid similarity with corresponding cDNAs previously identified in human, canine and rodent brain or gastric tissues. ..
  58. Guo R, Ward P, Hu S, McDuffie J, Huber Lang M, Shi M. Molecular cloning and characterization of a novel human CC chemokine, SCYA26. Genomics. 1999;58:313-7 pubmed
    ..This gene symbol has been approved by the HUGO Gene Nomenclature Committee. ..
  59. Inohara N, Nunez G. ML -- a conserved domain involved in innate immunity and lipid metabolism. Trends Biochem Sci. 2002;27:219-21 pubmed
    ..These single-domain proteins were predicted to form a beta-rich fold containing multiple strands, and to mediate diverse biological functions through interacting with specific lipids. ..
  60. Sutter S, Raeker M, Borisov A, Russell M. Orthologous relationship of obscurin and Unc-89: phylogeny of a novel family of tandem myosin light chain kinases. Dev Genes Evol. 2004;214:352-9 pubmed
  61. Vijayalakshmi J, Akerley B, Saper M. Structure of YraM, a protein essential for growth of Haemophilus influenzae. Proteins. 2008;73:204-17 pubmed publisher
    ..We discuss possible biological functions of YraM considering its predicted location in the outer membrane, a novel place for such a binding protein...
  62. Zhong Y, Lu L, Zhou J, Li Y, Liu Y, Clemmons D, et al. IGF binding protein 3 exerts its ligand-independent action by antagonizing BMP in zebrafish embryos. J Cell Sci. 2011;124:1925-35 pubmed publisher
    ..Knockdown of Igfbp3 enhanced the ventralized phenotype caused by chordin knockdown. These results suggest that Igfbp3 exerts its IGF-independent actions by antagonizing Bmp signaling and that this mechanism is conserved. ..
  63. Lillie S, Brown S. Suppression of a myosin defect by a kinesin-related gene. Nature. 1992;356:358-61 pubmed
    ..Here we report the identification of such a suppressor (SMY1) that (surprisingly) encodes a predicted polypeptide sharing sequence similarity with the motor portion of proteins in the kinesin superfamily. ..
  64. Chen F, Ro D, Petri J, Gershenzon J, Bohlmann J, Pichersky E, et al. Characterization of a root-specific Arabidopsis terpene synthase responsible for the formation of the volatile monoterpene 1,8-cineole. Plant Physiol. 2004;135:1956-66 pubmed
    ..These data demonstrate that divergence of organ expression pattern and product specificity are ongoing processes within the Arabidopsis TPS family. ..
  65. Hirata H, Saint Amant L, Waterbury J, Cui W, Zhou W, Li Q, et al. accordion, a zebrafish behavioral mutant, has a muscle relaxation defect due to a mutation in the ATPase Ca2+ pump SERCA1. Development. 2004;131:5457-68 pubmed
    ..As SERCA1 mutations in humans lead to Brody disease, an exercise-induced muscle relaxation disorder, zebrafish accordion mutants could be a useful animal model for this condition. ..
  66. Cheng S, Brooks C. Viral capsid proteins are segregated in structural fold space. PLoS Comput Biol. 2013;9:e1002905 pubmed publisher
    ..Also importantly, our work highlights a guiding principle for virus-based nanoplatform design in a wide range of biomedical applications and materials science. ..
  67. Xie G, Meng F, Mansour A, Thompson R, Hoversten M, Goldstein A, et al. Primary structure and functional expression of a guinea pig kappa opioid (dynorphin) receptor. Proc Natl Acad Sci U S A. 1994;91:3779-83 pubmed
    ..Species differences in the pharmacology and mRNA distribution between the cloned guinea pig and rat kappa receptors may be worthy of further examination...
  68. Kim I, Crippen G, Amidon G. Structure and specificity of a human valacyclovir activating enzyme: a homology model of BPHL. Mol Pharm. 2004;1:434-46 pubmed
    ..The homology model of BPHL provides a basis for further investigation of the catalytic and active site residues, can account for the observed structure activity profile of BPHL, and will be useful in the design of nucleoside prodrugs. ..
  69. Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc. 2010;5:725-38 pubmed publisher
    ..This protocol provides new insights and guidelines for designing of online server systems for the state-of-the-art protein structure and function predictions. The server is available at http://zhanglab.ccmb.med.umich.edu/I-TASSER. ..
  70. Vornhagen J, Stevens M, McCormick D, Dowd S, Eisenberg J, Boles B, et al. Coaggregation occurs amongst bacteria within and between biofilms in domestic showerheads. Biofouling. 2013;29:53-68 pubmed publisher
    ..Characterization of the mechanisms mediating coaggregation, and the inter-species interactions they facilitate, may allow for novel strategies to inhibit biofilm development. ..
  71. Zhang Y, Skolnick J. Segment assembly, structure alignment and iterative simulation in protein structure prediction. BMC Biol. 2013;11:44 pubmed publisher
  72. Yang J, Roy A, Zhang Y. Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics. 2013;29:2588-95 pubmed publisher
    ..These data demonstrate a new robust approach to protein-ligand binding site recognition, which is ready for genome-wide structure-based function annotations. http://zhanglab.ccmb.med.umich.edu/COACH/ ..
  73. Astrom A, Tavakkol A, Pettersson U, Cromie M, Elder J, Voorhees J. Molecular cloning of two human cellular retinoic acid-binding proteins (CRABP). Retinoic acid-induced expression of CRABP-II but not CRABP-I in adult human skin in vivo and in skin fibroblasts in vitro. J Biol Chem. 1991;266:17662-6 pubmed
    ..The marked inducibility of the CRABP-II gene is compatible with the idea that this isoform is important in retinoic acid-mediated regulation of human skin growth and differentiation. ..
  74. Clarke T, Bain P, Greco T, Payne A. A novel mouse kidney 3 beta-hydroxysteroid dehydrogenase complementary DNA encodes a 3-ketosteroid reductase instead of a 3 beta-hydroxysteroid dehydrogenase/delta 5-delta 4-isomerase. Mol Endocrinol. 1993;7:1569-78 pubmed
    ..Mouse 3 beta HSD IV is functionally and structurally most closely related to rat 3 beta HSD III, an isoform expressed predominantly in male rat liver. ..
  75. Pogozheva I, Lomize A, Mosberg H. The transmembrane 7-alpha-bundle of rhodopsin: distance geometry calculations with hydrogen bonding constraints. Biophys J. 1997;72:1963-85 pubmed
    ..The rhodopsin model and the published structure of bacteriorhodopsin have very similar retinal-binding pockets. ..
  76. Hoover D, Ludwig M. A flavodoxin that is required for enzyme activation: the structure of oxidized flavodoxin from Escherichia coli at 1.8 A resolution. Protein Sci. 1997;6:2525-37 pubmed
    ..Structural comparisons with flavodoxins from Synechococcus PCC 7942 and Anaebaena PCC 7120 suggest other residues that may also be critical for recognition by methionine synthase. ..
  77. Jones S, Luo M, Healy A, Peters Golden M, Brock T. Structural and functional criteria reveal a new nuclear import sequence on the 5-lipoxygenase protein. J Biol Chem. 2002;277:38550-6 pubmed
    ..Moreover, we suggest that another sequence that can mediate nuclear import of 5-lipoxygenase remains to be identified. ..
  78. Chen F, D Auria J, Tholl D, Ross J, Gershenzon J, Noel J, et al. An Arabidopsis thaliana gene for methylsalicylate biosynthesis, identified by a biochemical genomics approach, has a role in defense. Plant J. 2003;36:577-88 pubmed
    ..Upon thrip damage to leaves, AtBSMT1 promoter activity was induced specifically around the lesions. ..
  79. Kim I, Song X, Vig B, Mittal S, Shin H, Lorenzi P, et al. A novel nucleoside prodrug-activating enzyme: substrate specificity of biphenyl hydrolase-like protein. Mol Pharm. 2004;1:117-27 pubmed
  80. Zhou W, Horstick E, Hirata H, Kuwada J. Identification and expression of voltage-gated calcium channel beta subunits in Zebrafish. Dev Dyn. 2008;237:3842-52 pubmed publisher
    ..Sequence homology, genomic synteny and expression patterns suggest that there are three pairs of duplicate genes for beta2, beta3, and beta4 in zebrafish with distinct expression patterns during embryonic development. ..
  81. Kondrashov A, Assis R. Bridges: a tool for identifying local similarities in long sequences. Bioinformatics. 2010;26:2055-6 pubmed publisher
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