Proteopedia:I3DC: Difference between revisions

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# [[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:S2059798325007089|Off-Target Structural Insights: ArnA and AcrB in Bacterial Membrane Protein Cryo-EM Analysis]], Mehmet Caliseki, Ufuk Borucu, Sathish K. N. Yadav, Christiane Schaffitzel and Burak Veli Kabasakal

# [[Journal:Acta Cryst D:S2059798325007673|Complex formation of Streptomyces griseolus CYP105A1 with statins by room-temperature crystal data collection]], Teisuke Takita, Sachiyo Yoneda, Kaori Yasuda, Kimihiko Mizutani, Kiyoshi Yasukawa, Toshiyuki Sakaki and Bunzo Mikami

# [[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: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 ''''===

# [[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: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:Ricin|Ricin]], Ann Taylor

# [[Journal:BAMBEd:Rossmann fold: A beta-alpha-beta fold at dinucleotide binding sites|Rossmann fold: A beta-alpha-beta fold at dinucleotide binding sites]], Israel Hanukoglu

# [[Journal:BMC:3|Identification of novel isocytosine derivatives as xanthine oxidase inhibitors from a set of virtual screening hits]], Chandrika B-Rao, Asha Kulkarni-Almeida, Kamlesh V. Katkar, Smriti Khanna, Usha Ghosh, Ashish Keche, Pranay Shah, Ankita Srivastava, Vaidehi Korde, Kumar V. S. Nemmani, Nitin J. Deshmukh, Amol Dixit, Manoja K. Brahma, Umakant Bahirat, Lalit Doshi, Rajiv Sharma, H. Sivaramakrishnan

# [[Journal:CHEMBIOINT:1|The four-helix bundle in cholinesterase dimers: structural and energetic determinants of stability]], Dana A. Novichkova, Sofya V. Lushchekina, Orly Dym, Patrick Masson, Israel Silman 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

# [[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: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 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:FLS:1|Crystal structure of porcine pancreatic phospholipase A₂ 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: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: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:S2052252524010170|Crystal structure of a bacterial photoactivated adenylate cyclase determined at room temperature by serial femtosecond crystallography]], Kapetanaki SM, Coquelle N, von Stetten D, Byrdin M, Rios-Santacruz R, Bean R, Bielecki J, Boudjelida M, Fekete Z, Grime GW, Han H, Hatton C, Kantamneni S, Kharitonov K, Kim C, Kloos M, Koua FHM, de Diego Martinez I, Melo D, Rane L, Round A, Round E, Sarma A, Schubert R, Schulz J, Sikorski M, Vakili M, Valerio J, Vitas J, de Wijn R, Wrona A, Zala N, Pearson A, Dörner K, Schirò G, Garman EF, Lukács A, Weik M.

# [[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: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:32|Analyzing the Catalytic Role of Active Site Residues in the Fe-Type Nitrile Hydratase from ''Comamonas testosteroni'' Ni1]], Salette Martinez, Rui Wu, Karoline Krzywda, Veronika Opalka, Hei Chan, Dali Liu, and Richard C. Holz

# [[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: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:40|Traditional Chinese medicine application in HIV: An ''in silico'' study]], Hung-Jin Huanga, Yi-Ru Jianb, Calvin Yu-Chian Chen

# [[Journal:JBSD:41|Molecular Mechanism of HIV-1 gp120 Mutations That Reduce CD4 Binding Affinity]], Kristin Kassler and Heinrich Sticht

# [[Journal:JMB:1|Cyt1Aa Toxin: High Resolution Structure Reveals Implications for its Membrane-Perforating Function]], Cohen S, Albeck S, Ben-Dov E, Cahan R, Firer M, Zaritsky A, Dym O.

# [[Journal:JMB:2|Catalytic versatility and backups in enzyme active sites: The case of serum paraoxanase 1]], Moshe Ben-David, Mikael Elias, Jean-Jacques Filippi, Elisabet Dunach, Israel Silman, Joel Sussman and Dan Tawfik, PhD

# [[Journal:JMB:3|Catalytic metal ion rearrangements underline promiscuity and evolvability of a metalloenzyme]], Moshe Ben-­David, Grzegorz Wieczorek, Mikael Elias, Israel Silman, Joel L. Sussman and Dan S. Tawfik

# [[Journal:JMedChem:1|Structure of estradiol metal chelate and estrogen receptor complex: The basis for designing a new class of SERMs]], Min-Jun Li, Harry M. Greenblatt, Orly Dym, Shira Albeck, Adi Pais, Chidambaram Gunanathan, David Milstein, Hadassa Degani, and Joel L. Sussman

# [[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: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:Molecular Cell:1|Automated computational design of human enzymes for high bacterial expression and stability]], Adi Goldenzweig, Moshe Goldsmith, Shannon E Hill, Or Gertman, Paola Laurino, Yacov Ashani, Orly Dym, Tamar Unger, Shira Albeck, Jaime Prilusky, Raquel L Lieberman, Amir Aharoni, Israel Silman, Joel L Sussman, Dan S Tawfik and Sarel J Fleishman

# [[Journal:Molecular Cell:2|Automated design of efficient and functionally diverse enzyme repertoires]], Olga Khersonsky, Rosalie Lipsh, Ziv Avizemer, Yacov Ashani, Moshe Goldsmith, Haim Leader, Orly Dym, Shelly Rogotner, Devin L. Trudeau, Jaime Prilusky, Pep Amengual-Rigo, Victor Guallar, Dan S. Tawfik, and Sarel J. Fleishman

# [[Journal:Neuropharmacology:1|Slow-binding inhibitors of acetylcholinesterase of medical interest]], Sofya V. Lushchekina and Patrick Masson

# [[Journal:Neuropharmacology:2|Computational Studies on Cholinesterases: Strengthening our Understanding of the Integration of Structure, Dynamics and Function]], Joel L. Sussman and Israel Silman

# [[Journal:PLoS ONE:1|Antiviral Activity of 3(2H)- and 6-Chloro-3(2H)-Isoflavenes against Highly Diverged, Neurovirulent Vaccine-Derived, Type2 Poliovirus Sewage Isolates]], Lester M. Shulman, Danit Sofer, Yossi Manor, Ella Mendelson, Jean Balanant, Anna Laura Salvati, Francis Delpeyroux, Lucia Fiore

# [[Journal:PLoS ONE:2|Structural Basis of Enzymatic Activity for the Ferulic Acid Decarboxylase (FADase) from Enterobacter sp. Px6-4]], Wen Gu, Jinkui Yang, Zhiyong Lou, Lianming Liang, Yuna Sun, Jingwen Huang, Xuemei Li, Yi Cao, Zhaohui Meng, Ke-Qin Zhang

# [[Journal:PMC:1|Stereochemical Basis for a Unified Structure Activity Theory of Aromatic and Heterocyclic Rings in Selected Opioids and Opioid Peptides]], Joel S. Goldberg

===Protein Science ''''===

# [[Journal:Proteins:2|Protein Stability and ''in Vivo'' Concentration of Missense Mutations in Phenylalanine Hydroxylase]], Zhen Shi, Jenn Sellers, and John Moult

# [[Journal:Proteins:3|Do ‘''Newly Born''’ Orphan Proteins Resemble ‘''Never Born''’ Proteins? A Study Using Three Deep Learning Algorithms]], Jing Liu, Rongqing Yuan, Wei Shao, Jitong Wang, Israel Silman and Joel Sussman

# [[Journal:Science:1|Structural basis of transcription activation]], Yu Feng, Yu Zhang, Richard H. Ebright

# [[Journal:Structure:1|Promiscuous Protein Binding as a Function of Protein Stability]], Ruth Cohen-Khait, Orly Dym, Shelly Hamer-Rogotner and Gideon Schreiber