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  • 1
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    Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-11-30
    Description: A combinatorial disulfide cross-linking strategy was used to prepare a stalled complex of human immunodeficiency virus-type 1 (HIV-1) reverse transcriptase with a DNA template:primer and a deoxynucleoside triphosphate (dNTP), and the crystal structure of the complex was determined at a resolution of 3.2 angstroms. The presence of a dideoxynucleotide at the 3'-primer terminus allows capture of a state in which the substrates are poised for attack on the dNTP. Conformational changes that accompany formation of the catalytic complex produce distinct clusters of the residues that are altered in viruses resistant to nucleoside analog drugs. The positioning of these residues in the neighborhood of the dNTP helps to resolve some long-standing puzzles about the molecular basis of resistance. The resistance mutations are likely to influence binding or reactivity of the inhibitors, relative to normal dNTPs, and the clustering of the mutations correlates with the chemical structure of the drug.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, H -- Chopra, R -- Verdine, G L -- Harrison, S C -- GM-18621/GM/NIGMS NIH HHS/ -- GM-39589/GM/NIGMS NIH HHS/ -- GM-44853/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Nov 27;282(5394):1669-75.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9831551" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-HIV Agents/metabolism/*pharmacology ; Binding Sites ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; DNA Primers/chemistry/metabolism ; DNA, Viral/chemistry/metabolism ; Deoxyribonucleotides/chemistry/metabolism ; Dimerization ; Drug Resistance, Microbial ; HIV Reverse Transcriptase/*chemistry/genetics/metabolism ; HIV-1/*drug effects/enzymology ; Humans ; Hydrogen Bonding ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; Protein Conformation ; Reverse Transcriptase Inhibitors/metabolism/*pharmacology ; Templates, Genetic
    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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  • 2
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    The linear ubiquitin-specific deubiquitinase gumby regulates angiogenesis (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-05-28
    Description: A complex interaction of signalling events, including the Wnt pathway, regulates sprouting of blood vessels from pre-existing vasculature during angiogenesis. Here we show that two distinct mutations in the (uro)chordate-specific gumby (also called Fam105b) gene cause an embryonic angiogenic phenotype in gumby mice. Gumby interacts with disheveled 2 (DVL2), is expressed in canonical Wnt-responsive endothelial cells and encodes an ovarian tumour domain class of deubiquitinase that specifically cleaves linear ubiquitin linkages. A crystal structure of gumby in complex with linear diubiquitin reveals how the identified mutations adversely affect substrate binding and catalytic function in line with the severity of their angiogenic phenotypes. Gumby interacts with HOIP (also called RNF31), a key component of the linear ubiquitin assembly complex, and decreases linear ubiquitination and activation of NF-kappaB-dependent transcription. This work provides support for the biological importance of linear (de)ubiquitination in angiogenesis, craniofacial and neural development and in modulating Wnt signalling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rivkin, Elena -- Almeida, Stephanie M -- Ceccarelli, Derek F -- Juang, Yu-Chi -- MacLean, Teresa A -- Srikumar, Tharan -- Huang, Hao -- Dunham, Wade H -- Fukumura, Ryutaro -- Xie, Gang -- Gondo, Yoichi -- Raught, Brian -- Gingras, Anne-Claude -- Sicheri, Frank -- Cordes, Sabine P -- IHO 94384/Canadian Institutes of Health Research/Canada -- MOP 111199/Canadian Institutes of Health Research/Canada -- MOP 97966/Canadian Institutes of Health Research/Canada -- MOP119289/Canadian Institutes of Health Research/Canada -- England -- Nature. 2013 Jun 20;498(7454):318-24. doi: 10.1038/nature12296. Epub 2013 May 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Samuel Lunenfeld Research Institute, Mt Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23708998" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/metabolism ; Alleles ; Amino Acid Sequence ; Animals ; Base Sequence ; Crystallography, X-Ray ; Embryo, Mammalian/blood supply/embryology/metabolism ; Endopeptidases/*chemistry/deficiency/genetics/*metabolism ; Female ; Gene Expression Profiling ; HEK293 Cells ; Humans ; Mice ; Models, Molecular ; Molecular Sequence Data ; *Neovascularization, Physiologic/genetics ; Phenotype ; Phosphoproteins/metabolism ; Protein Conformation ; Ubiquitin/*chemistry/*metabolism ; Ubiquitin-Protein Ligases/metabolism ; *Ubiquitination ; Wnt Signaling Pathway
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Crystal structure of a potassium ion transporter, TrkH (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-02-15
    Description: The TrkH/TrkG/KtrB proteins mediate K(+) uptake in bacteria and probably evolved from simple K(+) channels by multiple gene duplications or fusions. Here we present the crystal structure of a TrkH from Vibrio parahaemolyticus. TrkH is a homodimer, and each protomer contains an ion permeation pathway. A selectivity filter, similar in architecture to those of K(+) channels but significantly shorter, is lined by backbone and side-chain oxygen atoms. Functional studies showed that TrkH is selective for permeation of K(+) and Rb(+) over smaller ions such as Na(+) or Li(+). Immediately intracellular to the selectivity filter are an intramembrane loop and an arginine residue, both highly conserved, which constrict the permeation pathway. Substituting the arginine with an alanine significantly increases the rate of K(+) flux. These results reveal the molecular basis of K(+) selectivity and suggest a novel gating mechanism for this large and important family of membrane transport proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077569/" 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/PMC3077569/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cao, Yu -- Jin, Xiangshu -- Huang, Hua -- Derebe, Mehabaw Getahun -- Levin, Elena J -- Kabaleeswaran, Venkataraman -- Pan, Yaping -- Punta, Marco -- Love, James -- Weng, Jun -- Quick, Matthias -- Ye, Sheng -- Kloss, Brian -- Bruni, Renato -- Martinez-Hackert, Erik -- Hendrickson, Wayne A -- Rost, Burkhard -- Javitch, Jonathan A -- Rajashankar, Kanagalaghatta R -- Jiang, Youxing -- Zhou, Ming -- DK088057/DK/NIDDK NIH HHS/ -- GM05026/GM/NIGMS NIH HHS/ -- GM05026-SUB0007/GM/NIGMS NIH HHS/ -- HL086392/HL/NHLBI NIH HHS/ -- K05 DA022413/DA/NIDA NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 DK088057/DK/NIDDK NIH HHS/ -- R01 DK088057-01/DK/NIDDK NIH HHS/ -- R01 HL086392/HL/NHLBI NIH HHS/ -- R01 HL086392-05/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Mar 17;471(7338):336-40. doi: 10.1038/nature09731. Epub 2011 Feb 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology & Cellular Biophysics, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21317882" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/chemistry ; Amino Acid Sequence ; Crystallography, X-Ray ; Escherichia coli Proteins/chemistry ; Ion Channel Gating ; Ion Transport ; Models, Molecular ; Molecular Sequence Data ; Potassium/metabolism ; Potassium Channels/*chemistry/*metabolism ; Structure-Activity Relationship ; Substrate Specificity ; Vibrio parahaemolyticus/*chemistry
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    DAXX envelops a histone H3.3-H4 dimer for H3.3-specific recognition (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-10-19
    Description: Histone chaperones represent a structurally and functionally diverse family of histone-binding proteins that prevent promiscuous interactions of histones before their assembly into chromatin. DAXX is a metazoan histone chaperone specific to the evolutionarily conserved histone variant H3.3. Here we report the crystal structures of the DAXX histone-binding domain with a histone H3.3-H4 dimer, including mutants within DAXX and H3.3, together with in vitro and in vivo functional studies that elucidate the principles underlying H3.3 recognition specificity. Occupying 40% of the histone surface-accessible area, DAXX wraps around the H3.3-H4 dimer, with complex formation accompanied by structural transitions in the H3.3-H4 histone fold. DAXX uses an extended alpha-helical conformation to compete with major inter-histone, DNA and ASF1 interaction sites. Our structural studies identify recognition elements that read out H3.3-specific residues, and functional studies address the contributions of Gly 90 in H3.3 and Glu 225 in DAXX to chaperone-mediated H3.3 variant recognition specificity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4056191/" 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/PMC4056191/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Elsasser, Simon J -- Huang, Hongda -- Lewis, Peter W -- Chin, Jason W -- Allis, C David -- Patel, Dinshaw J -- 1S10RR022321-01/RR/NCRR NIH HHS/ -- 1S10RR027037-01/RR/NCRR NIH HHS/ -- MC_U105181009/Medical Research Council/United Kingdom -- P30 EB009998/EB/NIBIB NIH HHS/ -- P30-EB-009998/EB/NIBIB NIH HHS/ -- S10 RR022321/RR/NCRR NIH HHS/ -- S10 RR027037/RR/NCRR NIH HHS/ -- U105181009/PHS HHS/ -- UD99999908/PHS HHS/ -- Medical Research Council/United Kingdom -- England -- Nature. 2012 Nov 22;491(7425):560-5. doi: 10.1038/nature11608. Epub 2012 Oct 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23075851" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/chemistry/metabolism ; Amino Acid Sequence ; Binding, Competitive ; Cell Cycle Proteins/genetics/metabolism ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; Histone Chaperones/chemistry/metabolism ; Histones/*chemistry/*metabolism ; Humans ; Models, Molecular ; Molecular Sequence Data ; Nuclear Proteins/chemistry/metabolism ; Nucleosomes/chemistry/metabolism ; Protein Conformation ; Protein Multimerization ; Substrate Specificity ; Water/chemistry/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    Gating of the TrkH ion channel by its associated RCK protein TrkA (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-04-20
    Description: TrkH belongs to a superfamily of K(+) transport proteins required for growth of bacteria in low external K(+) concentrations. The crystal structure of TrkH from Vibrio parahaemolyticus showed that TrkH resembles a K(+) channel and may have a gating mechanism substantially different from K(+) channels. TrkH assembles with TrkA, a cytosolic protein comprising two RCK (regulate the conductance of K(+)) domains, which are found in certain K(+) channels and control their gating. However, fundamental questions on whether TrkH is an ion channel and how it is regulated by TrkA remain unresolved. Here we show single-channel activity of TrkH that is upregulated by ATP via TrkA. We report two structures of the tetrameric TrkA ring, one in complex with TrkH and one in isolation, in which the ring assumes two markedly different conformations. These results suggest a mechanism for how ATP increases TrkH activity by inducing conformational changes in TrkA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726529/" 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/PMC3726529/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cao, Yu -- Pan, Yaping -- Huang, Hua -- Jin, Xiangshu -- Levin, Elena J -- Kloss, Brian -- Zhou, Ming -- DK088057/DK/NIDDK NIH HHS/ -- GM098878/GM/NIGMS NIH HHS/ -- HL086392/HL/NHLBI NIH HHS/ -- R01 DK088057/DK/NIDDK NIH HHS/ -- R01 GM098878/GM/NIGMS NIH HHS/ -- R01 HL086392/HL/NHLBI NIH HHS/ -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54 GM095315/GM/NIGMS NIH HHS/ -- U54GM095315/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Apr 18;496(7445):317-22. doi: 10.1038/nature12056.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology & Cellular Biophysics, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23598339" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Bacterial Proteins/*chemistry/*metabolism ; Crystallography, X-Ray ; Electric Conductivity ; *Ion Channel Gating ; Ion Transport ; Models, Molecular ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Vibrio parahaemolyticus
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    The structure of a human p110alpha/p85alpha complex elucidates the effects of oncogenic PI3Kalpha mutations (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-15
    Description: PIK3CA, one of the two most frequently mutated oncogenes in human tumors, codes for p110alpha, the catalytic subunit of a phosphatidylinositol 3-kinase, isoform alpha (PI3Kalpha, p110alpha/p85). Here, we report a 3.0 angstrom resolution structure of a complex between p110alpha and a polypeptide containing the p110alpha-binding domains of p85alpha, a protein required for its enzymatic activity. The structure shows that many of the mutations occur at residues lying at the interfaces between p110alpha and p85alpha or between the kinase domain of p110alpha and other domains within the catalytic subunit. Disruptions of these interactions are likely to affect the regulation of kinase activity by p85 or the catalytic activity of the enzyme, respectively. In addition to providing new insights about the structure of PI3Kalpha, these results suggest specific mechanisms for the effect of oncogenic mutations in p110alpha and p85alpha.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Chuan-Hsiang -- Mandelker, Diana -- Schmidt-Kittler, Oleg -- Samuels, Yardena -- Velculescu, Victor E -- Kinzler, Kenneth W -- Vogelstein, Bert -- Gabelli, Sandra B -- Amzel, L Mario -- CA 43460/CA/NCI NIH HHS/ -- GM 07184/GM/NIGMS NIH HHS/ -- GM066895/GM/NIGMS NIH HHS/ -- GM07309/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Dec 14;318(5857):1744-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079394" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate ; Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Molecular Sequence Data ; *Mutation ; Neoplasms/*genetics ; Phosphatidylinositol 3-Kinases/*chemistry/genetics/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/genetics/metabolism ; src Homology Domains
    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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  • 7
    Electronic Resource
    Electronic Resource
    Elastic plates: Theory and application, Herbert Reismann, Wiley (New York), 1988. 400 pp, £54.20, ISBN 0 471856010 (1989)
    Chichester [u.a.] : Wiley-Blackwell
    International Journal for Numerical Methods in Engineering 28 (1989), S. 2710-2710 
    Details
    ISSN: 0029-5981
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/nme.1620281115
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  • 8
    Electronic Resource
    Electronic Resource
    Some novel techniques for the finite element analysis of heat and mass transfer problems (1988)
    Chichester [u.a.] : Wiley-Blackwell
    International Journal for Numerical Methods in Engineering 25 (1988), S. 611-624 
    Details
    ISSN: 0029-5981
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: The coupled heat and mass transfer partial differential equations as derived by Luikov are used to analyse freezing problems in porous media. A numerical model is subsequently developed to depict the frost heave mechanism in a freezing soil system. An example is given of the application of the model and the results are compared with those achieved from field experiments.Also, a novel application of the coincident node technique is presented for the coupled heat and mass transfer problem. This circumvents the numerical problems usually associated with flow through thin layers, in this case a vapour barrier, sandwiched between materials of greater thickness.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/nme.1620250221
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  • 9
    Electronic Resource
    Electronic Resource
    Multigrid methods: Theory, applications and supercomputing, ed. S. F. McCormick, Marcel Dekker, New York, 1988. Price: $99.75 (U.S.A. and Canada), $119.50 (All other countries). No. of pages: 641 pp (1989)
    Chichester [u.a.] : Wiley-Blackwell
    International Journal for Numerical Methods in Engineering 28 (1989), S. 2711-2711 
    Details
    ISSN: 0029-5981
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/nme.1620281118
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  • 10
    Electronic Resource
    Electronic Resource
    A new nine node degenerated shell element with enhanced membrane and shear interpolation (1986)
    Chichester [u.a.] : Wiley-Blackwell
    International Journal for Numerical Methods in Engineering 22 (1986), S. 73-92 
    Details
    ISSN: 0029-5981
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: A new nine node degenerated shell element is presented in this paper. In the formulation of the new element, an enhanced interpolation of the transverse shear strains in the natural co-ordinate system is used to overcome the shear locking problem, and an enhanced interpolation of the membrane strains in the local Cartesian co-ordinate system is applied to avoid membrane locking behaviour. It is shown that the resulting element has the requisite number of zero eigenvalues and associated rigid body modes. The element does not exhibit membrane or shear locking for large span/thickness ratios. To illustrate the good performance of the new element some examples are presented including comparisons with the behaviour of the selectively integrated Lagrangian degenerated shell elements.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/nme.1620220107
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