Proteopedia:I3DC: Difference between revisions
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===Acta Cryst D ''Acta Crystallographica Section D''=== | ===Acta Cryst D ''Acta Crystallographica Section D''=== | ||
# [[Journal:Acta Cryst D:S0907444911047251|Flexibility of the flap in the active site of BACE1 as revealed by crystal structures and molecular dynamics simulations]], Yechun Xu, Minjun Li, Harry Greenblatt, Wuyan Chen, Aviv Paz, Orly Dym, Yoav Peleg, Tiantian Chen, Xu Shen, Jianhua He, Hualiang Jiang, Israel Silman & Joel L Sussman | # [[Journal:Acta Cryst D:S0907444911047251|Flexibility of the flap in the active site of BACE1 as revealed by crystal structures and molecular dynamics simulations]], Yechun Xu, Minjun Li, Harry Greenblatt, Wuyan Chen, Aviv Paz, Orly Dym, Yoav Peleg, Tiantian Chen, Xu Shen, Jianhua He, Hualiang Jiang, Israel Silman & Joel L Sussman | ||
# [[Journal:Acta Cryst D:S2059798318000050|A DNA structural alphabet provides new insight into DNA flexibility]], Bohdan Schneider, Paulina Bozikova, Iva Necasova, Petr Cech, Daniel Svozil and Jiri Cerny | # [[Journal:Acta Cryst D:S2059798318000050|A DNA structural alphabet provides new insight into DNA flexibility]], Bohdan Schneider, Paulina Bozikova, Iva Necasova, Petr Cech, Daniel Svozil and Jiri Cerny | ||
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# [[Journal:Acta Cryst D:S2059798326000422|Crystal structure of Schistosoma mansoni Cathepsin D1 in complex with a nanobody reveals the conformation of the propeptide bound state]], Professor Raymond J Owens | # [[Journal:Acta Cryst D:S2059798326000422|Crystal structure of Schistosoma mansoni Cathepsin D1 in complex with a nanobody reveals the conformation of the propeptide bound state]], Professor Raymond J Owens | ||
===Acta Cryst F ''Acta Crystallographica Section F''=== | ===Acta Cryst F ''Acta Crystallographica Section F''=== | ||
# [[Journal:Acta Cryst F:S1744309112003326|Structure of recombinant human carboxylesterase 1 isolated from whole cabbage looper larvae]], Harry M. Greenblatt, Tamara C. Otto, Melanie G. Kirkpatrick, Elena Kovaleva, Susan Brown, George Buchman, Douglas M. Cerasoli and Joel L. Sussman | # [[Journal:Acta Cryst F:S1744309112003326|Structure of recombinant human carboxylesterase 1 isolated from whole cabbage looper larvae]], Harry M. Greenblatt, Tamara C. Otto, Melanie G. Kirkpatrick, Elena Kovaleva, Susan Brown, George Buchman, Douglas M. Cerasoli and Joel L. Sussman | ||
# [[Journal:Acta Cryst F:S1744309112050270|Crystal structure of ADL1, a plant-specific homologue of the universal diaminopimelate amino transferase enzyme of lysine biosynthesis]], Vladimir Sobolev, Marvin Edelman, Orly Dym, Tamar Unger, Shira Albeck, Menny Kirma and Gad Galili | # [[Journal:Acta Cryst F:S1744309112050270|Crystal structure of ADL1, a plant-specific homologue of the universal diaminopimelate amino transferase enzyme of lysine biosynthesis]], Vladimir Sobolev, Marvin Edelman, Orly Dym, Tamar Unger, Shira Albeck, Menny Kirma and Gad Galili | ||
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# [[Journal:Acta Cryst F:S2053230X25006181|The structures of Listeria monocytogenes MenD in ThDP-bound and in-crystallo captured intermediate I-bound forms]], Michelle Bailey, Fiona M. Given, Ngoc Anh Thu Ho, F. Grant Pearce, Timothy M. Allison and Jodie M. Johnston | # [[Journal:Acta Cryst F:S2053230X25006181|The structures of Listeria monocytogenes MenD in ThDP-bound and in-crystallo captured intermediate I-bound forms]], Michelle Bailey, Fiona M. Given, Ngoc Anh Thu Ho, F. Grant Pearce, Timothy M. Allison and Jodie M. Johnston | ||
===Angew Chem Int Ed ''''=== | ===Angew Chem Int Ed ''''=== | ||
# [[Journal:Angew Chem Int Ed:1|Fine tuning of chlorophyll spectra by protein-induced ring deformation]], Dominika Bednarczyk, Orly Dym, Yoav Peleg, Vadivel Prabahar, and Dror Noy | # [[Journal:Angew Chem Int Ed:1|Fine tuning of chlorophyll spectra by protein-induced ring deformation]], Dominika Bednarczyk, Orly Dym, Yoav Peleg, Vadivel Prabahar, and Dror Noy | ||
===BAMBEd ''Biochemistry and Molecular Biology Education''=== | ===BAMBEd ''Biochemistry and Molecular Biology Education''=== | ||
# [[Journal:BAMBEd:Acetylcholinesterase: Substrate Traffic and Inhibition|Acetylcholinesterase: Substrate traffic and inhibition]], Mary G. Acheampong, Daviana E. Dueño, Bobby K. Glover, Alafia A. Henry, Randol Mata, Marisa L. VanBrakle, Lars F. Westblade, Joel L. Sussman, Allison L. Granberry | # [[Journal:BAMBEd:Acetylcholinesterase: Substrate Traffic and Inhibition|Acetylcholinesterase: Substrate traffic and inhibition]], Mary G. Acheampong, Daviana E. Dueño, Bobby K. Glover, Alafia A. Henry, Randol Mata, Marisa L. VanBrakle, Lars F. Westblade, Joel L. Sussman, Allison L. Granberry | ||
# [[Journal:BAMBEd:Citrate Synthase|Citrate Synthase]], Wayne A. Decatur, Daniel B. Eddelman | # [[Journal:BAMBEd:Citrate Synthase|Citrate Synthase]], Wayne A. Decatur, Daniel B. Eddelman | ||
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# [[Journal:CHEMBIOINT:2|Molecular Dynamics Simulations of the Interaction of Mouse and ''Torpedo'' Acetylcholinesterase with Covalent Inhibitors Explain Their Differential Reactivity: Implications for Drug Design]], Nellore Bhanu Chandar, Irena Efremenko, Israel Silman, Jan M. L. Martin, and Joel L. Sussman | # [[Journal:CHEMBIOINT:2|Molecular Dynamics Simulations of the Interaction of Mouse and ''Torpedo'' Acetylcholinesterase with Covalent Inhibitors Explain Their Differential Reactivity: Implications for Drug Design]], Nellore Bhanu Chandar, Irena Efremenko, Israel Silman, Jan M. L. Martin, and Joel L. Sussman | ||
===Cell === | ===Cell === | ||
# [[Journal:Cell:1|Structural linkage between ligand discrimination and receptor activation by type I interferons]], Christoph Thomas, Ignacio Moraga, Doron Levin, Peter O. Krutzik, Yulia Podoplelova, Angelica Trejo, Choongho Lee, Ganit Yarden, Susan E. Vleck, Jeffrey S. Glenn, Garry P. Nolan, Jacob Piehler, Gideon Schreiber, K. Christopher Garcia | # [[Journal:Cell:1|Structural linkage between ligand discrimination and receptor activation by type I interferons]], Christoph Thomas, Ignacio Moraga, Doron Levin, Peter O. Krutzik, Yulia Podoplelova, Angelica Trejo, Choongho Lee, Ganit Yarden, Susan E. Vleck, Jeffrey S. Glenn, Garry P. Nolan, Jacob Piehler, Gideon Schreiber, K. Christopher Garcia | ||
===FEBS Journal === | ===FEBS Journal === | ||
# [[Journal:FEBS Journal:1|Flexible regions govern promiscuous binding of IL-24 to receptors IL-20R1 and IL-22R1]], Jiří Zahradník, Lucie Kolářová, Yoav Peleg, Petr Kolenko, Silvie Svidenská, Tatsiana Charnavets, Tamar Unger, Joel L. Sussman, and Bohdan Schneider | # [[Journal:FEBS Journal:1|Flexible regions govern promiscuous binding of IL-24 to receptors IL-20R1 and IL-22R1]], Jiří Zahradník, Lucie Kolářová, Yoav Peleg, Petr Kolenko, Silvie Svidenská, Tatsiana Charnavets, Tamar Unger, Joel L. Sussman, and Bohdan Schneider | ||
===FEBS Open Bio === | ===FEBS Open Bio === | ||
# [[Journal:FEBS Open Bio:1|Crystal structure of the essential biotin-dependent carboxylase AccA3 from ''Mycobacterium tuberculosis'']], Matthew Bennett, Martin Högbom | # [[Journal:FEBS Open Bio:1|Crystal structure of the essential biotin-dependent carboxylase AccA3 from ''Mycobacterium tuberculosis'']], Matthew Bennett, Martin Högbom | ||
# [[Journal:FEBS Open Bio:2|Structural evidence for Arabidopsis glutathione transferase AtGSTF2 functioning as a transporter of small organic ligands]], Laziana Ahmad, Elizabeth L. Rylott, Neil C. Bruce, Robert Edwards and Gideon Grogan | # [[Journal:FEBS Open Bio:2|Structural evidence for Arabidopsis glutathione transferase AtGSTF2 functioning as a transporter of small organic ligands]], Laziana Ahmad, Elizabeth L. Rylott, Neil C. Bruce, Robert Edwards and Gideon Grogan | ||
===FLS ''Frontiers in Life Science''=== | ===FLS ''Frontiers in Life Science''=== | ||
# [[Journal:FLS:1|Crystal structure of porcine pancreatic phospholipase A<sub>2</sub> in complex with 2-methoxycyclohexa-2-5-diene-1,4-dione]], K. V. Dileep, I. Tintu, P. K. Mandal, P. Karthe, M. Haridas and C. Sadasivan | # [[Journal:FLS:1|Crystal structure of porcine pancreatic phospholipase A<sub>2</sub> in complex with 2-methoxycyclohexa-2-5-diene-1,4-dione]], K. V. Dileep, I. Tintu, P. K. Mandal, P. Karthe, M. Haridas and C. Sadasivan | ||
===Genes === | ===Genes === | ||
# [[Journal:Genes:1|A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle]], Bohdan Schneider, Paulina Bozikova, Petr Cech, Daniel Svozil and Jiri Cerny | # [[Journal:Genes:1|A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle]], Bohdan Schneider, Paulina Bozikova, Petr Cech, Daniel Svozil and Jiri Cerny | ||
===IUCrJ === | ===IUCrJ === | ||
# [[Journal:IUCrJ:S2052252518018274|A cytosine modification mechanism revealed by the ternary complex structure of deoxycytidylate hydroxymethylase from bacteriophage T4 with its cofactor and substrate]], Si Hoon Park, Se Won Suh and Hyun Hyu Song | # [[Journal:IUCrJ:S2052252518018274|A cytosine modification mechanism revealed by the ternary complex structure of deoxycytidylate hydroxymethylase from bacteriophage T4 with its cofactor and substrate]], Si Hoon Park, Se Won Suh and Hyun Hyu Song | ||
# [[Journal:IUCrJ:S2052252519001568|Structure of mammalian plasma fetuin-B and its mechanism of selective metallopeptidase inhibition]], Anna Cuppari, Hagen Körschgen, Dirk Fahrenkamp, Carlo Schmitz, Tibisay Guevara, Konstantin Karmilin, Michael Kuske, Mario Olf, Eileen Dietzel, Irene Yiallouros, Daniele de Sanctis, Theodoros Goulas, Ralf Weiskirchen, Willi Jahnen-Dechent, Julia Floehr, Walter Stöcker, Luca Jovine and F. Xavier Gomis-Rüth | # [[Journal:IUCrJ:S2052252519001568|Structure of mammalian plasma fetuin-B and its mechanism of selective metallopeptidase inhibition]], Anna Cuppari, Hagen Körschgen, Dirk Fahrenkamp, Carlo Schmitz, Tibisay Guevara, Konstantin Karmilin, Michael Kuske, Mario Olf, Eileen Dietzel, Irene Yiallouros, Daniele de Sanctis, Theodoros Goulas, Ralf Weiskirchen, Willi Jahnen-Dechent, Julia Floehr, Walter Stöcker, Luca Jovine and F. Xavier Gomis-Rüth | ||
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# [[Journal:IUCrJ:S2052252525006645|Time-resolved serial synchrotron and serial femtosecond crystallography of heme proteins using photocaged nitric oxide]], Peter Smyth, Sofia Jaho, Lewis J. Williams, Gabriel Karras, Ann Fitzpatrick, Amy J. Thompson,a Sinan Battah, Danny Axford, Sam Horrell, Marina Lučić, Kotone Ishihara, Machika Kataoka, Hiroaki Matsuura, Kanji Shimba, Kensuke Tono, Takehiko Tosha, Hiroshi Sugimoto, Shigeki Owada, Michael A. Hough, Jonathan A.R. Worrall, Robin L. Owen | # [[Journal:IUCrJ:S2052252525006645|Time-resolved serial synchrotron and serial femtosecond crystallography of heme proteins using photocaged nitric oxide]], Peter Smyth, Sofia Jaho, Lewis J. Williams, Gabriel Karras, Ann Fitzpatrick, Amy J. Thompson,a Sinan Battah, Danny Axford, Sam Horrell, Marina Lučić, Kotone Ishihara, Machika Kataoka, Hiroaki Matsuura, Kanji Shimba, Kensuke Tono, Takehiko Tosha, Hiroshi Sugimoto, Shigeki Owada, Michael A. Hough, Jonathan A.R. Worrall, Robin L. Owen | ||
===JBIC ''Journal of Biological Inorganic Chemistry''=== | ===JBIC ''Journal of Biological Inorganic Chemistry''=== | ||
# [[Journal:JBIC:1|Crystal structure of the zinc, cobalt and iron containing adenylate kinase from ''Desulfovibrio gigas'': a novel metal containing adenylate kinase from Gram-negative bacteria]], A. Mukhopadhyay, A.V. Kladova, S.A. Bursakov, O. Yu. Gavel, J.J. Calvete, V.L. Shnyrov, I. Moura, J.J.G. Moura, M.J. Romão, J. Trincão | # [[Journal:JBIC:1|Crystal structure of the zinc, cobalt and iron containing adenylate kinase from ''Desulfovibrio gigas'': a novel metal containing adenylate kinase from Gram-negative bacteria]], A. Mukhopadhyay, A.V. Kladova, S.A. Bursakov, O. Yu. Gavel, J.J. Calvete, V.L. Shnyrov, I. Moura, J.J.G. Moura, M.J. Romão, J. Trincão | ||
# [[Journal:JBIC:2|Structure of Anticancer Ruthenium Half-Sandwich Complex Bound to Glycogen Synthase Kinase 3ß]], G. Atilla-Gocumen, L. Di Costanzo, E. Meggers | # [[Journal:JBIC:2|Structure of Anticancer Ruthenium Half-Sandwich Complex Bound to Glycogen Synthase Kinase 3ß]], G. Atilla-Gocumen, L. Di Costanzo, E. Meggers | ||
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# [[Journal:JBIC:33|Structural characterization of zinc-bound Zmp1, a zinc-dependent metalloprotease secreted by Clostridium difficile]], Jeffrey T. Rubino, Manuele Martinelli, Francesca Cantini, Andrea Castagnetti, Rosanna Leuzzi, Lucia Banci and Maria Scarselli | # [[Journal:JBIC:33|Structural characterization of zinc-bound Zmp1, a zinc-dependent metalloprotease secreted by Clostridium difficile]], Jeffrey T. Rubino, Manuele Martinelli, Francesca Cantini, Andrea Castagnetti, Rosanna Leuzzi, Lucia Banci and Maria Scarselli | ||
===JBSD ''Journal of Biomolecular Structure and Dynamics''=== | ===JBSD ''Journal of Biomolecular Structure and Dynamics''=== | ||
# [[Journal:JBSD:1|An Insight to the Dynamics of Conserved Water Mediated Salt Bridge Interaction and Inter-Domain Recognition in hIMPDH Isoforms]], Hridoy R Bairagya and Bishnu P Mukhopadhyay | # [[Journal:JBSD:1|An Insight to the Dynamics of Conserved Water Mediated Salt Bridge Interaction and Inter-Domain Recognition in hIMPDH Isoforms]], Hridoy R Bairagya and Bishnu P Mukhopadhyay | ||
# [[Journal:JBSD:2|Elucidation by NMR solution of neurotensin in Small Unilamellar Vesicle environment: molecular surveys for neurotensin receptor recognition]], Grégory Da Costa, Arnaud Bondon, Olivier Delalande, Liza Mouret, Jean-Pierre Monti | # [[Journal:JBSD:2|Elucidation by NMR solution of neurotensin in Small Unilamellar Vesicle environment: molecular surveys for neurotensin receptor recognition]], Grégory Da Costa, Arnaud Bondon, Olivier Delalande, Liza Mouret, Jean-Pierre Monti | ||
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# [[Journal:JSB:1|Structural and functional insights into a dodecameric molecular machine – The RuvBL1/RuvBL2 complex]], Sabine Gorynia, Tiago M. Bandeiras, Filipa G. Pinho, Colin E. McVey, Clemens Vonrhein, Adam Round, Dmitri I. Svergun, Peter Donner, Pedro M. Matias and Maria Arménia Carrondo | # [[Journal:JSB:1|Structural and functional insights into a dodecameric molecular machine – The RuvBL1/RuvBL2 complex]], Sabine Gorynia, Tiago M. Bandeiras, Filipa G. Pinho, Colin E. McVey, Clemens Vonrhein, Adam Round, Dmitri I. Svergun, Peter Donner, Pedro M. Matias and Maria Arménia Carrondo | ||
===MicroPubl Biol ''MicroPublication Biology''=== | ===MicroPubl Biol ''MicroPublication Biology''=== | ||
# [[Journal:MicroPubl Biol:000570|Biochemical and structural characterization of the flavodoxin-like domain of the ''Schizosaccharomyces japonicus'' putative tRNAPhe 4-demethylwyosine synthase TYW1 in complex with FMN]], Ljiljana Sjekloća, Adrian R. Ferré-D’Amaré | # [[Journal:MicroPubl Biol:000570|Biochemical and structural characterization of the flavodoxin-like domain of the ''Schizosaccharomyces japonicus'' putative tRNAPhe 4-demethylwyosine synthase TYW1 in complex with FMN]], Ljiljana Sjekloća, Adrian R. Ferré-D’Amaré | ||
# [[Journal:MicroPubl Biol:000574|''Gossypium hirsutum'' gene of unknown function, Gohir.A02G044702.1, encodes a potential B3 Transcription Factor of the REM subfamily]], Michael Allen, Amanda M. Hulse-Kemp, Amanda R. Storm | # [[Journal:MicroPubl Biol:000574|''Gossypium hirsutum'' gene of unknown function, Gohir.A02G044702.1, encodes a potential B3 Transcription Factor of the REM subfamily]], Michael Allen, Amanda M. Hulse-Kemp, Amanda R. Storm | ||
