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  • Binding Sites  (57)
  • *Biological Evolution  (50)
  • American Association for the Advancement of Science (AAAS)  (107)
  • 2005-2009  (107)
  • 1950-1954
  • 2008  (28)
  • 2007  (40)
  • 2006  (39)
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  • 2005-2009  (107)
  • 1950-1954
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  • 2008  (28)
  • 2007  (40)
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  • 2009  (32)
  • 2005  (32)
  • 1
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    The Chlamydomonas genome reveals the evolution of key animal and plant functions (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-13
    Description: Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875087/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875087/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Merchant, Sabeeha S -- Prochnik, Simon E -- Vallon, Olivier -- Harris, Elizabeth H -- Karpowicz, Steven J -- Witman, George B -- Terry, Astrid -- Salamov, Asaf -- Fritz-Laylin, Lillian K -- Marechal-Drouard, Laurence -- Marshall, Wallace F -- Qu, Liang-Hu -- Nelson, David R -- Sanderfoot, Anton A -- Spalding, Martin H -- Kapitonov, Vladimir V -- Ren, Qinghu -- Ferris, Patrick -- Lindquist, Erika -- Shapiro, Harris -- Lucas, Susan M -- Grimwood, Jane -- Schmutz, Jeremy -- Cardol, Pierre -- Cerutti, Heriberto -- Chanfreau, Guillaume -- Chen, Chun-Long -- Cognat, Valerie -- Croft, Martin T -- Dent, Rachel -- Dutcher, Susan -- Fernandez, Emilio -- Fukuzawa, Hideya -- Gonzalez-Ballester, David -- Gonzalez-Halphen, Diego -- Hallmann, Armin -- Hanikenne, Marc -- Hippler, Michael -- Inwood, William -- Jabbari, Kamel -- Kalanon, Ming -- Kuras, Richard -- Lefebvre, Paul A -- Lemaire, Stephane D -- Lobanov, Alexey V -- Lohr, Martin -- Manuell, Andrea -- Meier, Iris -- Mets, Laurens -- Mittag, Maria -- Mittelmeier, Telsa -- Moroney, James V -- Moseley, Jeffrey -- Napoli, Carolyn -- Nedelcu, Aurora M -- Niyogi, Krishna -- Novoselov, Sergey V -- Paulsen, Ian T -- Pazour, Greg -- Purton, Saul -- Ral, Jean-Philippe -- Riano-Pachon, Diego Mauricio -- Riekhof, Wayne -- Rymarquis, Linda -- Schroda, Michael -- Stern, David -- Umen, James -- Willows, Robert -- Wilson, Nedra -- Zimmer, Sara Lana -- Allmer, Jens -- Balk, Janneke -- Bisova, Katerina -- Chen, Chong-Jian -- Elias, Marek -- Gendler, Karla -- Hauser, Charles -- Lamb, Mary Rose -- Ledford, Heidi -- Long, Joanne C -- Minagawa, Jun -- Page, M Dudley -- Pan, Junmin -- Pootakham, Wirulda -- Roje, Sanja -- Rose, Annkatrin -- Stahlberg, Eric -- Terauchi, Aimee M -- Yang, Pinfen -- Ball, Steven -- Bowler, Chris -- Dieckmann, Carol L -- Gladyshev, Vadim N -- Green, Pamela -- Jorgensen, Richard -- Mayfield, Stephen -- Mueller-Roeber, Bernd -- Rajamani, Sathish -- Sayre, Richard T -- Brokstein, Peter -- Dubchak, Inna -- Goodstein, David -- Hornick, Leila -- Huang, Y Wayne -- Jhaveri, Jinal -- Luo, Yigong -- Martinez, Diego -- Ngau, Wing Chi Abby -- Otillar, Bobby -- Poliakov, Alexander -- Porter, Aaron -- Szajkowski, Lukasz -- Werner, Gregory -- Zhou, Kemin -- Grigoriev, Igor V -- Rokhsar, Daniel S -- Grossman, Arthur R -- GM07185/GM/NIGMS NIH HHS/ -- GM42143/GM/NIGMS NIH HHS/ -- R01 GM032843/GM/NIGMS NIH HHS/ -- R01 GM042143/GM/NIGMS NIH HHS/ -- R01 GM042143-09/GM/NIGMS NIH HHS/ -- R01 GM060992/GM/NIGMS NIH HHS/ -- R01 GM062915-06/GM/NIGMS NIH HHS/ -- R37 GM030626/GM/NIGMS NIH HHS/ -- R37 GM042143/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Oct 12;318(5848):245-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17932292" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/*genetics/*physiology ; Animals ; *Biological Evolution ; Chlamydomonas reinhardtii/*genetics/physiology ; Chloroplasts/metabolism ; Computational Biology ; DNA, Algal/genetics ; Flagella/metabolism ; Genes ; *Genome ; Genomics ; Membrane Transport Proteins/genetics/physiology ; Molecular Sequence Data ; Multigene Family ; Photosynthesis/genetics ; Phylogeny ; Plants/genetics ; Proteome ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-02
    Description: Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oomycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oomycete avirulence genes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tyler, Brett M -- Tripathy, Sucheta -- Zhang, Xuemin -- Dehal, Paramvir -- Jiang, Rays H Y -- Aerts, Andrea -- Arredondo, Felipe D -- Baxter, Laura -- Bensasson, Douda -- Beynon, Jim L -- Chapman, Jarrod -- Damasceno, Cynthia M B -- Dorrance, Anne E -- Dou, Daolong -- Dickerman, Allan W -- Dubchak, Inna L -- Garbelotto, Matteo -- Gijzen, Mark -- Gordon, Stuart G -- Govers, Francine -- Grunwald, Niklaus J -- Huang, Wayne -- Ivors, Kelly L -- Jones, Richard W -- Kamoun, Sophien -- Krampis, Konstantinos -- Lamour, Kurt H -- Lee, Mi-Kyung -- McDonald, W Hayes -- Medina, Monica -- Meijer, Harold J G -- Nordberg, Eric K -- Maclean, Donald J -- Ospina-Giraldo, Manuel D -- Morris, Paul F -- Phuntumart, Vipaporn -- Putnam, Nicholas H -- Rash, Sam -- Rose, Jocelyn K C -- Sakihama, Yasuko -- Salamov, Asaf A -- Savidor, Alon -- Scheuring, Chantel F -- Smith, Brian M -- Sobral, Bruno W S -- Terry, Astrid -- Torto-Alalibo, Trudy A -- Win, Joe -- Xu, Zhanyou -- Zhang, Hongbin -- Grigoriev, Igor V -- Rokhsar, Daniel S -- Boore, Jeffrey L -- BB/C509123/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2006 Sep 1;313(5791):1261-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. bmtyler@vt.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16946064" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/genetics/physiology ; *Biological Evolution ; DNA, Algal/*genetics ; Genes ; *Genome ; Hydrolases/genetics/metabolism ; Photosynthesis/genetics ; Phylogeny ; Physical Chromosome Mapping ; Phytophthora/classification/*genetics/*pathogenicity/physiology ; Plant Diseases/microbiology ; Polymorphism, Single Nucleotide ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Symbiosis ; Toxins, Biological/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007
    Description: We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rensing, Stefan A -- Lang, Daniel -- Zimmer, Andreas D -- Terry, Astrid -- Salamov, Asaf -- Shapiro, Harris -- Nishiyama, Tomoaki -- Perroud, Pierre-Francois -- Lindquist, Erika A -- Kamisugi, Yasuko -- Tanahashi, Takako -- Sakakibara, Keiko -- Fujita, Tomomichi -- Oishi, Kazuko -- Shin-I, Tadasu -- Kuroki, Yoko -- Toyoda, Atsushi -- Suzuki, Yutaka -- Hashimoto, Shin-Ichi -- Yamaguchi, Kazuo -- Sugano, Sumio -- Kohara, Yuji -- Fujiyama, Asao -- Anterola, Aldwin -- Aoki, Setsuyuki -- Ashton, Neil -- Barbazuk, W Brad -- Barker, Elizabeth -- Bennetzen, Jeffrey L -- Blankenship, Robert -- Cho, Sung Hyun -- Dutcher, Susan K -- Estelle, Mark -- Fawcett, Jeffrey A -- Gundlach, Heidrun -- Hanada, Kousuke -- Heyl, Alexander -- Hicks, Karen A -- Hughes, Jon -- Lohr, Martin -- Mayer, Klaus -- Melkozernov, Alexander -- Murata, Takashi -- Nelson, David R -- Pils, Birgit -- Prigge, Michael -- Reiss, Bernd -- Renner, Tanya -- Rombauts, Stephane -- Rushton, Paul J -- Sanderfoot, Anton -- Schween, Gabriele -- Shiu, Shin-Han -- Stueber, Kurt -- Theodoulou, Frederica L -- Tu, Hank -- Van de Peer, Yves -- Verrier, Paul J -- Waters, Elizabeth -- Wood, Andrew -- Yang, Lixing -- Cove, David -- Cuming, Andrew C -- Hasebe, Mitsuyasu -- Lucas, Susan -- Mishler, Brent D -- Reski, Ralf -- Grigoriev, Igor V -- Quatrano, Ralph S -- Boore, Jeffrey L -- BBS/E/C/00004948/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Jan 4;319(5859):64-9. Epub 2007 Dec 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079367" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Angiosperms/genetics/physiology ; Animals ; Arabidopsis/genetics/physiology ; *Biological Evolution ; Bryopsida/*genetics/physiology ; Chlamydomonas reinhardtii/genetics/physiology ; Computational Biology ; DNA Repair ; Dehydration ; Gene Duplication ; Genes, Plant ; *Genome, Plant ; Metabolic Networks and Pathways/genetics ; Multigene Family ; Oryza/genetics/physiology ; Phylogeny ; Plant Proteins/genetics/physiology ; Repetitive Sequences, Nucleic Acid ; Retroelements ; Sequence Analysis, DNA ; Signal Transduction/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Genomic minimalism in the early diverging intestinal parasite Giardia lamblia (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-29
    Description: The genome of the eukaryotic protist Giardia lamblia, an important human intestinal parasite, is compact in structure and content, contains few introns or mitochondrial relics, and has simplified machinery for DNA replication, transcription, RNA processing, and most metabolic pathways. Protein kinases comprise the single largest protein class and reflect Giardia's requirement for a complex signal transduction network for coordinating differentiation. Lateral gene transfer from bacterial and archaeal donors has shaped Giardia's genome, and previously unknown gene families, for example, cysteine-rich structural proteins, have been discovered. Unexpectedly, the genome shows little evidence of heterozygosity, supporting recent speculations that this organism is sexual. This genome sequence will not only be valuable for investigating the evolution of eukaryotes, but will also be applied to the search for new therapeutics for this parasite.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morrison, Hilary G -- McArthur, Andrew G -- Gillin, Frances D -- Aley, Stephen B -- Adam, Rodney D -- Olsen, Gary J -- Best, Aaron A -- Cande, W Zacheus -- Chen, Feng -- Cipriano, Michael J -- Davids, Barbara J -- Dawson, Scott C -- Elmendorf, Heidi G -- Hehl, Adrian B -- Holder, Michael E -- Huse, Susan M -- Kim, Ulandt U -- Lasek-Nesselquist, Erica -- Manning, Gerard -- Nigam, Anuranjini -- Nixon, Julie E J -- Palm, Daniel -- Passamaneck, Nora E -- Prabhu, Anjali -- Reich, Claudia I -- Reiner, David S -- Samuelson, John -- Svard, Staffan G -- Sogin, Mitchell L -- AI42488/AI/NIAID NIH HHS/ -- AI43273/AI/NIAID NIH HHS/ -- AI51687/AI/NIAID NIH HHS/ -- R01 AI043273/AI/NIAID NIH HHS/ -- R01 AI048082/AI/NIAID NIH HHS/ -- R01 HG004164/HG/NHGRI NIH HHS/ -- R01 HG004164-01/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 28;317(5846):1921-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Marine Biological Laboratory, Woods Hole, MA 02543-1015, USA. morrison@mbl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17901334" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Biological Evolution ; DNA Replication/genetics ; *Eukaryotic Cells ; Gene Transfer, Horizontal ; Genes, Protozoan ; *Genome, Protozoan ; Genomics ; Giardia lamblia/classification/*genetics/physiology ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Kinases/genetics/metabolism ; Protozoan Proteins/chemistry/genetics/metabolism ; RNA Processing, Post-Transcriptional ; Signal Transduction ; Transcription, Genetic
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-05-27
    Description: We describe a pathogenetic mechanism underlying a variant form of the inherited blood disorder alpha thalassemia. Association studies of affected individuals from Melanesia localized the disease trait to the telomeric region of human chromosome 16, which includes the alpha-globin gene cluster, but no molecular defects were detected by conventional approaches. After resequencing and using a combination of chromatin immunoprecipitation and expression analysis on a tiled oligonucleotide array, we identified a gain-of-function regulatory single-nucleotide polymorphism (rSNP) in a nongenic region between the alpha-globin genes and their upstream regulatory elements. The rSNP creates a new promoterlike element that interferes with normal activation of all downstream alpha-like globin genes. Thus, our work illustrates a strategy for distinguishing between neutral and functionally important rSNPs, and it also identifies a pathogenetic mechanism that could potentially underlie other genetic diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉De Gobbi, Marco -- Viprakasit, Vip -- Hughes, Jim R -- Fisher, Chris -- Buckle, Veronica J -- Ayyub, Helena -- Gibbons, Richard J -- Vernimmen, Douglas -- Yoshinaga, Yuko -- de Jong, Pieter -- Cheng, Jan-Fang -- Rubin, Edward M -- Wood, William G -- Bowden, Don -- Higgs, Douglas R -- MC_U137961143/Medical Research Council/United Kingdom -- MC_U137961145/Medical Research Council/United Kingdom -- MC_U137961147/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2006 May 26;312(5777):1215-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, OX3 9DS, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16728641" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cells, Cultured ; Chromatin Immunoprecipitation ; Chromosomes, Human, Pair 16/*genetics ; Erythroblasts ; GATA1 Transcription Factor/metabolism ; Gene Expression ; Gene Expression Profiling ; Globins/*genetics ; Haplotypes ; Humans ; Melanesia ; Minisatellite Repeats ; Multigene Family ; Oligonucleotide Array Sequence Analysis ; *Polymorphism, Single Nucleotide ; *Promoter Regions, Genetic ; Regulatory Elements, Transcriptional ; Transcription, Genetic ; alpha-Thalassemia/*genetics
    Print ISSN: 0036-8075
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  • 6
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    Leiomodin is an actin filament nucleator in muscle cells (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-04-12
    Description: Initiation of actin polymerization in cells requires nucleation factors. Here we describe an actin-binding protein, leiomodin, that acted as a strong filament nucleator in muscle cells. Leiomodin shared two actin-binding sites with the filament pointed end-capping protein tropomodulin: a flexible N-terminal region and a leucine-rich repeat domain. Leiomodin also contained a C-terminal extension of 150 residues. The smallest fragment with strong nucleation activity included the leucine-rich repeat and C-terminal extension. The N-terminal region enhanced the nucleation activity threefold and recruited tropomyosin, which weakly stimulated nucleation and mediated localization of leiomodin to the middle of muscle sarcomeres. Knocking down leiomodin severely compromised sarcomere assembly in cultured muscle cells, which suggests a role for leiomodin in the nucleation of tropomyosin-decorated filaments in muscles.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845909/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845909/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chereau, David -- Boczkowska, Malgorzata -- Skwarek-Maruszewska, Aneta -- Fujiwara, Ikuko -- Hayes, David B -- Rebowski, Grzegorz -- Lappalainen, Pekka -- Pollard, Thomas D -- Dominguez, Roberto -- GM026338/GM/NIGMS NIH HHS/ -- GM073791/GM/NIGMS NIH HHS/ -- HL086655/HL/NHLBI NIH HHS/ -- P01 HL086655/HL/NHLBI NIH HHS/ -- P01 HL086655-01A10004/HL/NHLBI NIH HHS/ -- R01 GM073791/GM/NIGMS NIH HHS/ -- R01 GM073791-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Apr 11;320(5873):239-43. doi: 10.1126/science.1155313.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Boston Biomedical Research Institute, Watertown, MA 02472, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18403713" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*metabolism ; Actins/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Cells, Cultured ; Cytoskeletal Proteins/chemistry/*metabolism ; Humans ; Microfilament Proteins/chemistry/*metabolism ; Molecular Sequence Data ; Muscle Proteins/chemistry/*metabolism ; Myocytes, Cardiac/*metabolism ; Protein Structure, Tertiary ; RNA Interference ; Rabbits ; Rats ; Sarcomeres/*metabolism ; Tropomodulin/chemistry ; Tropomyosin/chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 7
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    De novo computational design of retro-aldol enzymes (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-03-08
    Description: The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431203/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431203/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiang, Lin -- Althoff, Eric A -- Clemente, Fernando R -- Doyle, Lindsey -- Rothlisberger, Daniela -- Zanghellini, Alexandre -- Gallaher, Jasmine L -- Betker, Jamie L -- Tanaka, Fujie -- Barbas, Carlos F 3rd -- Hilvert, Donald -- Houk, Kendall N -- Stoddard, Barry L -- Baker, David -- R01 CA097328/CA/NCI NIH HHS/ -- R01 GM049857/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Mar 7;319(5868):1387-91. doi: 10.1126/science.1152692.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18323453" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde-Lyases/*chemistry/metabolism ; *Algorithms ; Binding Sites ; Catalysis ; Catalytic Domain ; Computer Simulation ; Crystallography, X-Ray ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Molecular ; Protein Conformation ; Protein Engineering
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    The dynamic energy landscape of dihydrofolate reductase catalysis (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-16
    Description: We used nuclear magnetic resonance relaxation dispersion to characterize higher energy conformational substates of Escherichia coli dihydrofolate reductase. Each intermediate in the catalytic cycle samples low-lying excited states whose conformations resemble the ground-state structures of preceding and following intermediates. Substrate and cofactor exchange occurs through these excited substates. The maximum hydride transfer and steady-state turnover rates are governed by the dynamics of transitions between ground and excited states of the intermediates. Thus, the modulation of the energy landscape by the bound ligands funnels the enzyme through its reaction cycle along a preferred kinetic path.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boehr, David D -- McElheny, Dan -- Dyson, H Jane -- Wright, Peter E -- GM56879/GM/NIGMS NIH HHS/ -- GM75995/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Sep 15;313(5793):1638-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute for Chemical Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16973882" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Escherichia coli/*enzymology ; Kinetics ; Ligands ; Models, Molecular ; NADP/metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; *Protein Conformation ; Tetrahydrofolate Dehydrogenase/*chemistry/*metabolism ; Tetrahydrofolates/metabolism ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Crystal structure of inhibitor-bound human 5-lipoxygenase-activating protein (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-30
    Description: Leukotrienes are proinflammatory products of arachidonic acid oxidation by 5-lipoxygenase that have been shown to be involved in respiratory and cardiovascular diseases. The integral membrane protein FLAP is essential for leukotriene biosynthesis. We describe the x-ray crystal structures of human FLAP in complex with two leukotriene biosynthesis inhibitors at 4.0 and 4.2 angstrom resolution, respectively. The structures show that inhibitors bind in membrane-embedded pockets of FLAP, which suggests how these inhibitors prevent arachidonic acid from binding to FLAP and subsequently being transferred to 5-lipoxygenase, thereby preventing leukotriene biosynthesis. This structural information provides a platform for the development of therapeutics for respiratory and cardiovascular diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ferguson, Andrew D -- McKeever, Brian M -- Xu, Shihua -- Wisniewski, Douglas -- Miller, Douglas K -- Yamin, Ting-Ting -- Spencer, Robert H -- Chu, Lin -- Ujjainwalla, Feroze -- Cunningham, Barry R -- Evans, Jilly F -- Becker, Joseph W -- New York, N.Y. -- Science. 2007 Jul 27;317(5837):510-2. Epub 2007 Jun 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicinal Chemistry, Merck Research Laboratories, Rahway, NJ 07065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17600184" target="_blank"〉PubMed〈/a〉
    Keywords: 5-Lipoxygenase-Activating Proteins ; Arachidonate 5-Lipoxygenase/metabolism ; Arachidonic Acid/metabolism ; Binding Sites ; Carrier Proteins/antagonists & inhibitors/*chemistry/genetics/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Cytosol/chemistry ; Humans ; Hydrophobic and Hydrophilic Interactions ; Indoles/*chemistry/metabolism/pharmacology ; Membrane Proteins/antagonists & inhibitors/*chemistry/genetics/metabolism ; Models, Molecular ; Mutagenesis ; Nuclear Envelope/chemistry ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Quinolines/*chemistry/metabolism/pharmacology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    An inhibitor of FtsZ with potent and selective anti-staphylococcal activity (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-09-20
    Description: FtsZ is an essential bacterial guanosine triphosphatase and homolog of mammalian beta-tubulin that polymerizes and assembles into a ring to initiate cell division. We have created a class of small synthetic antibacterials, exemplified by PC190723, which inhibits FtsZ and prevents cell division. PC190723 has potent and selective in vitro bactericidal activity against staphylococci, including methicillin- and multi-drug-resistant Staphylococcus aureus. The putative inhibitor-binding site of PC190723 was mapped to a region of FtsZ that is analogous to the Taxol-binding site of tubulin. PC190723 was efficacious in an in vivo model of infection, curing mice infected with a lethal dose of S. aureus. The data validate FtsZ as a target for antibacterial intervention and identify PC190723 as suitable for optimization into a new anti-staphylococcal therapy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haydon, David J -- Stokes, Neil R -- Ure, Rebecca -- Galbraith, Greta -- Bennett, James M -- Brown, David R -- Baker, Patrick J -- Barynin, Vladimir V -- Rice, David W -- Sedelnikova, Sveta E -- Heal, Jonathan R -- Sheridan, Joseph M -- Aiwale, Sachin T -- Chauhan, Pramod K -- Srivastava, Anil -- Taneja, Amit -- Collins, Ian -- Errington, Jeff -- Czaplewski, Lloyd G -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2008 Sep 19;321(5896):1673-5. doi: 10.1126/science.1159961.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Prolysis, Begbroke Science Park, Oxfordshire OX5 1PF, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18801997" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacillus subtilis/chemistry/*drug effects/genetics ; Bacterial Proteins/*antagonists & inhibitors/chemistry/genetics/metabolism ; Binding Sites ; Cell Division/drug effects ; Crystallography, X-Ray ; Cytoskeletal Proteins/*antagonists & inhibitors/chemistry/genetics/metabolism ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial ; Ligands ; Methicillin Resistance ; Mice ; Microbial Sensitivity Tests ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Pyridines/chemistry/metabolism/*pharmacology/therapeutic use ; Staphylococcal Infections/*drug therapy ; Staphylococcus aureus/chemistry/*drug effects ; Thiazoles/chemistry/metabolism/*pharmacology/therapeutic use ; Tubulin/chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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