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:S2059798324006594|Crystal structure of glycerol kinase from ''Trypanosoma cruzi'', a potential molecular target in Chagas disease]], Lipinski, Sonani & Dubin

# [[Journal:Acta Cryst D:S2059798324007733|Structural analysis of a ligand-triggered intermolecular disulfide switch in a major latex protein from opium poppy]], Samuel C. Carr, Peter J. Facchini, Kenneth K.S. Ng

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# [[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:S2053230X24003911|Structural and biochemical characterization of the M405S variant of ''Desulfovibrio vulgaris'' formate dehydrogenase]], Guilherme Vilela-Alves, Rita Rebelo Manuel, Neide Pedrosa, Ines A. Cardoso Pereira, Maria Joao Romao and Cristiano Mota

# [[Journal:Acta Cryst F:S2053230X24004655|Cryo-EM structure and functional analysis of chromatin remodeler RSF]],  Jiale Zhang, Heyu Zhao, Binqian Zou, Huadong Li, Shuqi Dong, Jiali Guan, Chi Wang, Weijie Li, Yutong Liu, Yingying Chen, Nadia Rasheed and Jun He

# [[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''===

# [[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

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# [[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

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# [[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

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# [[Journal:FEBS Open Bio:1| Crystal structure of the essential biotin-dependent carboxylase AccA3 from ''Mycobacterium tuberculosis'' ]], Matthew Bennett, Martin Högbom

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# [[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

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# [[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

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# [[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:S2052252524001969|The ABC Toxin Complex from ''Yersinia entomophaga'' Can Package a Cytotoxin Expressed from an “Orphan” Genetic Locus: the Structures of Both the RHS Shell and its Cargo.]], Jason N. Busby, Sarah Trevelyan, Cassandra L. Pegg, Edward D. Kerr, Benjamin L. Schulz, Irene Chassagnon, Michael J. Landsberg, Mitchell K. Weston, Mark R. H. Hurst, and J. Shaun Lott

# [[Journal:IUCrJ:S2052252524004627|From X-ray crystallographic structure to intrinsic thermodynamics of protein–ligand binding using carbonic anhydrase isozymes as a model system]], Vaida Paketuryte-Latve, Alexey Smirnov, Elena Manakova, Lina Baranauskiene, Vytautas Petrauskas, Asta Zubriene, Jurgita Matuliene, Virginija Dudutiene, Edita Capkauskaite, Audrius Zaksauskas, Janis Leitans, Saulius Grazulis, Kaspars Tars and Daumantas Matulis

===JBIC ''Journal of Biological Inorganic Chemistry''===

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===JSB ''Journal of Structural Biology''===

# [[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

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# [[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:000867|''Gossypium hirsutum'' gene of unknown function Gohir.A03G0737001 encodes a potential Chaperone-like Protein of protochlorophyllide oxidoreductase (CPP1)]], Alana N. Osborne, Andrew Osagiede, Amanda R. Storm, Amanda M. Hulse-Kemp, Angela K. Stoeckman

# [[Journal:MicroPubl Biol:000868|''Gossypium hirsutum'' gene of unknown function Gohir.A02G131900 encodes a potential plant-specific, dual-domain exo-1,3-β-glucosidase]], Gillian Hernandez, Amanda M Hulse-Kemp, and Amanda R Storm

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# [[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

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# [[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

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# [[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

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# [[Journal:Protein Science:1| Structural and functional characterization of the interaction of the photosensitizing probe methylene blue with ''Torpedo californica'' acetylcholinesterase ]], Aviv Paz, Esther Roth, Yacov Ashani, Yechun Xu, Valery L. Shnyrov, Joel L. Sussman, Israel Silman, and Lev Weiner

# [[Journal:Protein Science:2|The Impact of Crystallization Conditions on Structure-Based Drug Design: a Case Study on the Methylene Blue/Acetylcholinesterase Complex]], Orly Dym, Wanling Song, Clifford Felder, Esther Roth, Valery Shnyrov, Yacov, Ashani, Yechun Xu, Robbie P. Joosten, Lev Weiner, Joel L. Sussman, and Israel Silman

# [[Journal:Protein Science:3|''Torpedo californica'' acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif]], Israel Silman, Valery L. Shnyrov, Yacov Ashani, Esther Roth, Anne Nicolas, Joel L Sussman, and Lev Weiner

===Proteins ''''===

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

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

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