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  • 1
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 1999-02-05
    Description: The sterile alpha motif (SAM) domain is a protein interaction module that is present in diverse signal-transducing proteins. SAM domains are known to form homo- and hetero-oligomers. The crystal structure of the SAM domain from an Eph receptor tyrosine kinase, EphB2, reveals two large interfaces. In one interface, adjacent monomers exchange amino-terminal peptides that insert into a hydrophobic groove on each neighbor. A second interface is composed of the carboxyl-terminal helix and a nearby loop. A possible oligomer, constructed from a combination of these binding modes, may provide a platform for the formation of larger protein complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thanos, C D -- Goodwill, K E -- Bowie, J U -- New York, N.Y. -- Science. 1999 Feb 5;283(5403):833-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UCLA-DOE Laboratory of Structural Biology and Molecular Medicine and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9933164" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; Dimerization ; GRB10 Adaptor Protein ; Humans ; Hydrogen Bonding ; Kinesin/metabolism ; Models, Molecular ; Myosins/metabolism ; Phosphorylation ; *Protein Conformation ; Protein Structure, Secondary ; Protein Tyrosine Phosphatases/metabolism ; Proteins/metabolism ; Receptor Aggregation ; Receptor Protein-Tyrosine Kinases/*chemistry/metabolism ; Receptor, EphB2 ; Recombinant Proteins/chemistry/metabolism ; Surface Properties
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 1990-03-16
    Description: An amino acid sequence encodes a message that determines the shape and function of a protein. This message is highly degenerate in that many different sequences can code for proteins with essentially the same structure and activity. Comparison of different sequences with similar messages can reveal key features of the code and improve understanding of how a protein folds and how it performs its function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bowie, J U -- Reidhaar-Olson, J F -- Lim, W A -- Sauer, R T -- AI-15706/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1990 Mar 16;247(4948):1306-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2315699" target="_blank"〉PubMed〈/a〉
    Keywords: *Amino Acid Sequence ; Computer Graphics ; *DNA-Binding Proteins ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Proteins/*physiology/ultrastructure ; Repressor Proteins ; Structure-Activity Relationship ; Surface Properties ; Viral Proteins ; Viral Regulatory and Accessory Proteins
    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
    Publication Date: 1991-07-12
    Description: The inverse protein folding problem, the problem of finding which amino acid sequences fold into a known three-dimensional (3D) structure, can be effectively attacked by finding sequences that are most compatible with the environments of the residues in the 3D structure. The environments are described by: (i) the area of the residue buried in the protein and inaccessible to solvent; (ii) the fraction of side-chain area that is covered by polar atoms (O and N); and (iii) the local secondary structure. Examples of this 3D profile method are presented for four families of proteins: the globins, cyclic AMP (adenosine 3',5'-monophosphate) receptor-like proteins, the periplasmic binding proteins, and the actins. This method is able to detect the structural similarity of the actins and 70- kilodalton heat shock proteins, even though these protein families share no detectable sequence similarity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bowie, J U -- Luthy, R -- Eisenberg, D -- New York, N.Y. -- Science. 1991 Jul 12;253(5016):164-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biology Institute, University of California, Los Angeles 90024-1570.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1853201" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/chemistry/ultrastructure ; Algorithms ; Amino Acid Sequence ; Animals ; Carrier Proteins/chemistry ; *Escherichia coli Proteins ; Molecular Structure ; Myoglobin/chemistry/ultrastructure ; *Periplasmic Binding Proteins ; *Protein Conformation ; Proteins/*chemistry ; Receptors, Cyclic AMP/chemistry/ultrastructure ; Structure-Activity Relationship
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2006-01-28
    Description: The postsynaptic density (PSD) is a complex assembly of proteins associated with the postsynaptic membrane that organizes neurotransmitter receptors, signaling pathways, and regulatory elements within a cytoskeletal matrix. Here we show that the sterile alpha motif domain of rat Shank3/ProSAP2, a master scaffolding protein located deep within the PSD, can form large sheets composed of helical fibers stacked side by side. Zn2+, which is found in high concentrations in the PSD, binds tightly to Shank3 and may regulate assembly. Sheets of the Shank protein could form a platform for the construction of the PSD complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baron, Marisa K -- Boeckers, Tobias M -- Vaida, Bianca -- Faham, Salem -- Gingery, Mari -- Sawaya, Michael R -- Salyer, Danielle -- Gundelfinger, Eckart D -- Bowie, James U -- R01 CA081000/CA/NCI NIH HHS/ -- R01 GM063919/GM/NIGMS NIH HHS/ -- R01 GM063919-07/GM/NIGMS NIH HHS/ -- R01 GM063919-08/GM/NIGMS NIH HHS/ -- R01 GM075922/GM/NIGMS NIH HHS/ -- R01 GM075922-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Jan 27;311(5760):531-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095-1570, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16439662" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/analysis/*chemistry/genetics/metabolism ; Animals ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Hippocampus/chemistry ; Microscopy, Electron ; Models, Molecular ; Mutation ; Nerve Tissue Proteins ; Neurons/chemistry ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Rats ; Recombinant Fusion Proteins/analysis ; Solubility ; Synapses/*chemistry ; Zinc/metabolism
    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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  • 5
    Publication Date: 2008-06-28
    Description: Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined approximately 32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hackett, Shannon J -- Kimball, Rebecca T -- Reddy, Sushma -- Bowie, Rauri C K -- Braun, Edward L -- Braun, Michael J -- Chojnowski, Jena L -- Cox, W Andrew -- Han, Kin-Lan -- Harshman, John -- Huddleston, Christopher J -- Marks, Ben D -- Miglia, Kathleen J -- Moore, William S -- Sheldon, Frederick H -- Steadman, David W -- Witt, Christopher C -- Yuri, Tamaki -- New York, N.Y. -- Science. 2008 Jun 27;320(5884):1763-8. doi: 10.1126/science.1157704.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18583609" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; Biological Evolution ; Birds/*classification/*genetics ; Ecosystem ; Flight, Animal ; *Genome ; *Genomics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2014-05-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rocha, L A -- Aleixo, A -- Allen, G -- Almeda, F -- Baldwin, C C -- Barclay, M V L -- Bates, J M -- Bauer, A M -- Benzoni, F -- Berns, C M -- Berumen, M L -- Blackburn, D C -- Blum, S -- Bolanos, F -- Bowie, R C K -- Britz, R -- Brown, R M -- Cadena, C D -- Carpenter, K -- Ceriaco, L M -- Chakrabarty, P -- Chaves, G -- Choat, J H -- Clements, K D -- Collette, B B -- Collins, A -- Coyne, J -- Cracraft, J -- Daniel, T -- de Carvalho, M R -- de Queiroz, K -- Di Dario, F -- Drewes, R -- Dumbacher, J P -- Engilis, A Jr -- Erdmann, M V -- Eschmeyer, W -- Feldman, C R -- Fisher, B L -- Fjeldsa, J -- Fritsch, P W -- Fuchs, J -- Getahun, A -- Gill, A -- Gomon, M -- Gosliner, T -- Graves, G R -- Griswold, C E -- Guralnick, R -- Hartel, K -- Helgen, K M -- Ho, H -- Iskandar, D T -- Iwamoto, T -- Jaafar, Z -- James, H F -- Johnson, D -- Kavanaugh, D -- Knowlton, N -- Lacey, E -- Larson, H K -- Last, P -- Leis, J M -- Lessios, H -- Liebherr, J -- Lowman, M -- Mahler, D L -- Mamonekene, V -- Matsuura, K -- Mayer, G C -- Mays, H Jr -- McCosker, J -- McDiarmid, R W -- McGuire, J -- Miller, M J -- Mooi, R -- Mooi, R D -- Moritz, C -- Myers, P -- Nachman, M W -- Nussbaum, R A -- Foighil, D O -- Parenti, L R -- Parham, J F -- Paul, E -- Paulay, G -- Perez-Eman, J -- Perez-Matus, A -- Poe, S -- Pogonoski, J -- Rabosky, D L -- Randall, J E -- Reimer, J D -- Robertson, D R -- Rodel, M-O -- Rodrigues, M T -- Roopnarine, P -- Ruber, L -- Ryan, M J -- Sheldon, F -- Shinohara, G -- Short, A -- Simison, W B -- Smith-Vaniz, W F -- Springer, V G -- Stiassny, M -- Tello, J G -- Thompson, C W -- Trnski, T -- Tucker, P -- Valqui, T -- Vecchione, M -- Verheyen, E -- Wainwright, P C -- Wheeler, T A -- White, W T -- Will, K -- Williams, J T -- Williams, G -- Wilson, E O -- Winker, K -- Winterbottom, R -- Witt, C C -- New York, N.Y. -- Science. 2014 May 23;344(6186):814-5. doi: 10.1126/science.344.6186.814.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉California Academy of Sciences, San Francisco, CA 94118, USA. LRocha@calacademy.org. ; Museu Paraense Emilio Goeldi, Belem, PA, 66040-170, Brazil. ; Western Australian Museum, Perth, WA, 6986, Australia. ; California Academy of Sciences, San Francisco, CA 94118, USA. ; Smithsonian Institution, Washington, DC 20560, USA. ; Natural History Museum, London, SW7 5BD, UK. ; Field Museum of Natural History, Chicago, IL 60605, USA. ; Villanova University, Villanova, PA 19085, USA. ; University of Milano-Bicocca, Milan, 20126, Italy. ; Utica College, Utica, NY 13502, USA. ; King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia. ; Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica. ; University of California, Berkeley, CA 94720-3161, USA. ; University of Kansas, Lawrence, KS 66045, USA. ; Universidad de los Andes, Bogota, 4976, Colombia. ; Old Dominion University, Norfolk, VA 23529, USA. ; Museu Nacional de Historia Natural e da Ciencia, Lisbon, 7005-638, Portugal. ; Louisiana State University, Baton Rouge, LA 70803, USA. ; James Cook University, Townsville, 4811, Australia. ; University of Auckland, Auckland, 1142, New Zealand. ; NOAA Systematics Laboratory, Washington, DC 20013, USA. ; University of Chicago, Chicago, IL 60637, USA. ; American Museum of Natural History, New York, NY 10024, USA. ; Universidade de Sao Paulo, Sao Paulo, SP, 05508-090, Brazil. ; Universidade Federal do Rio de Janeiro, Macae, RJ, 27965-045, Brazil. ; University of California, Davis, CA 95616, USA. ; Conservation International, Denpasar, Bali, 80235, Indonesia. ; University of Nevada, Reno, NV 89557-0314, USA. ; Natural History Museum of Denmark, Copenhagen, DK-2100, Denmark. ; Museum National d'Histoire Naturelle, Paris, 75005, France. ; Addis Ababa University, Addis Ababa, 1176, Ethiopia. ; University of Sydney, Sydney, NSW, 2006, Australia. ; Museum Victoria, Melbourne, 3001, VIC, Australia. ; University of Colorado, Boulder, CO 80309-0334, USA. ; Harvard University, Cambridge, MA 02138, USA. ; Smithsonian Institution, Washington, DC 20560, USA. National University of Singapore, 117543, Singapore. ; Museum and Art Gallery of the Northern Territory, Darwin, 0820, NT, Australia. ; CSIRO Marine & Atmospheric Research, Hobart, TAS, 7000, Australia. ; Australian Museum, Sydney, NSW, 2010, Australia. ; Smithsonian Tropical Research Institute, Balboa, 0843-03092, Panama. ; Cornell University, Ithaca, NY 14853, USA. ; Universite Marien Ngouabi, Brazzaville, B.P. 69, Republic of Congo. ; National Museum of Nature and Science, Tsukuba, 305-0005, Japan. ; University of Wisconsin-Parkside, Kenosha, WI 53141-2000, USA. ; Cincinnati Museum Center, Cincinnati, OH 45203, USA. ; The Manitoba Museum, Winnipeg, MB, R3B 0N2, Canada. ; Australian National University, Canberra, ACT, 0200, Australia. ; University of Michigan, Ann Arbor, MI 48109-1079, USA. ; California State University, Fullerton, CA 92831, USA. ; The Ornithological Council, Chevy Chase, MD 20815, USA. ; University of Florida, Gainesville, fl32611, USA. ; Universidad Central de Venezuela, Caracas, 1041, Venezuela. ; Pontif cia Universidad Catolica de Chile, Santiago 6513677, Chile. ; University of New Mexico, Albuquerque, NM 87131-0001, USA. ; Bernice P. Bishop Museum, Honolulu, HI 96817, USA. ; University of the Ryukyus, Nishihara, 903-0213, Japan. ; Museum fur Naturkunde, Berlin, 10115, Germany. ; Naturhistorisches Museum der Burgergemeinde Bern, Bern, CH-3005, Switzerland. ; American Museum of Natural History, New York, NY 10024, USA. Long Island University, Brooklyn, NY 11201-8423, USA. ; Auckland Museum, Auckland, 1142, New Zealand. ; Centro de Ornitologia y Biodiversidad, Lima, 33, Peru. ; Royal Belgian Institute of Natural Sciences, Brussels, 1000, Belgium. ; McGill University, Montreal, QC, H9X 3V9, Canada. ; University of Alaska Museum, Fairbanks, AK 99775, USA. ; Royal Ontario Museum, Toronto, ON, M5S 2C6, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24855245" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biology/*methods ; Classification/*methods ; *Endangered Species ; *Extinction, Biological
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-01-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bowie, James U -- R01GM063919/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Jan 25;339(6118):398-9. doi: 10.1126/science.1228655.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA. bowie@mbi.ucla.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23349275" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/*chemistry ; Hydrogen Bonding ; Lipid Bilayers/chemistry ; Membrane Proteins/*chemistry ; Models, Molecular ; Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; Protein Subunits/chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 1987-03-27
    Description: Many RNAs are complex, globular molecules formed from elements of secondary and tertiary structure analogous to those found in proteins. Little is known about recognition of RNAs by proteins. In the case of transfer RNAs (tRNAs), considerable evidence suggests that elements dispersed in both the one- and three-dimensional structure are important for recognition by aminoacyl tRNA synthetases. Fragments of alanine tRNA synthetase were created by in vitro manipulations of the cloned alaS gene and examined for their interaction with alanine-specific tRNA. Sequences essential for recognition were located near the middle of the polypeptide, juxtaposed to the carboxyl-terminal side of the domain for aminoacyl adenylate synthesis. The most essential part of the tRNA interaction strength and specificity was dependent on a sequence of fewer than 100 amino acids. Within this sequence, and in the context of the proper conformation, a segment of no more than 17 amino acids was responsible for 25% or more of the total synthetase-tRNA free energy of association. The results raise the possibility that an important part of specific RNA recognition by an aminoacyl tRNA synthetase involves a polypeptide segment that is short relative to the total size of the protein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Regan, L -- Bowie, J -- Schimmel, P -- GM23562/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1987 Mar 27;235(4796):1651-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2435005" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Alanine-tRNA Ligase/metabolism ; Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/*metabolism ; Base Sequence ; Cloning, Molecular ; Escherichia coli/enzymology ; RNA/*metabolism ; RNA, Transfer, Amino Acyl/metabolism ; Structure-Activity Relationship ; Substrate Specificity ; Thermodynamics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2019
    Description: 〈p〉Atmospheric deposition is a source of potentially bioavailable iron (Fe) and thus can partially control biological productivity in large parts of the ocean. However, the explanation of observed high aerosol Fe solubility compared to that in soil particles is still controversial, as several hypotheses have been proposed to explain this observation. Here, a statistical analysis of aerosol Fe solubility estimated from four models and observations compiled from multiple field campaigns suggests that pyrogenic aerosols are the main sources of aerosols with high Fe solubility at low concentration. Additionally, we find that field data over the Southern Ocean display a much wider range in aerosol Fe solubility compared to the models, which indicate an underestimation of labile Fe concentrations by a factor of 15. These findings suggest that pyrogenic Fe-containing aerosols are important sources of atmospheric bioavailable Fe to the open ocean and crucial for predicting anthropogenic perturbations to marine productivity.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 10
    Publication Date: 2018-03-06
    Description: The computational design of transmembrane proteins with more than one membrane-spanning region remains a major challenge. We report the design of transmembrane monomers, homodimers, trimers, and tetramers with 76 to 215 residue subunits containing two to four membrane-spanning regions and up to 860 total residues that adopt the target oligomerization state in detergent solution. The designed proteins localize to the plasma membrane in bacteria and in mammalian cells, and magnetic tweezer unfolding experiments in the membrane indicate that they are very stable. Crystal structures of the designed dimer and tetramer—a rocket-shaped structure with a wide cytoplasmic base that funnels into eight transmembrane helices—are very close to the design models. Our results pave the way for the design of multispan membrane proteins with new functions.
    Keywords: Biochemistry
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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