User:Alexander Berchansky

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*[[Aricept Complexed with Acetylcholinesterase (Russian)]]
*[[Aricept Complexed with Acetylcholinesterase (Russian)]]
*[[Prion]]
*[[Prion]]
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*[[Canine parvovirus]]
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*[[Viral capsids]]
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*[[Opioids]]
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*[[Journal:Acta Cryst D:S2059798320011869|Lattice-translocation defects in some specific crystals of the catalytic head domain of influenza neuraminidase]], Linghui Li, Shuliu Dai, George F. Gao and Jiawei Wang [http://dx.doi.org/10.1107/S2059798320011869 http://dx.doi.org/10.1107/S2059798320011869]
 +
*[[Proteins from Mycobacterium tuberculosis]]
 +
*[[Treatment of Tuberculosis]]
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*[[Iron–sulfur proteins]]
 +
*[[Hemeproteins]]
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*[[Neurotransmitters]]
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*[[Growth factors]]
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*[[Receptor]]
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*[[Hormones and their receptors]]
'''CRISPR-Cas (under development):'''
'''CRISPR-Cas (under development):'''
Line 77: Line 85:
CRISPR type VI (Cas13a (previously known as C2c2), Cas13b, Cas13c, Cas13d) - see [[CRISPR type VI]]
CRISPR type VI (Cas13a (previously known as C2c2), Cas13b, Cas13c, Cas13d) - see [[CRISPR type VI]]
-
*[[Journal:Acta Cryst D:S0907444911047251|Flexibility of the flap in the active site of BACE1 as revealed by crystal structures and molecular dynamics simulations]]
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*[[Journal:Protein Science:3|''Torpedo californica'' acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif]]
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*[[Journal:Acta Cryst D:S2059798318000050|A DNA structural alphabet provides new insight into DNA flexibility]]
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*[[Journal:IUCrJ:S2052252521005340|X-ray crystallography studies of RoAb13 bound to PIYDIN, a part of the CCR5 N-terminal domain]]
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*[[Journal:Acta Cryst D:S2059798319000676|Crystal structures of pyrrolidone-carboxylate peptidase I from ''Deinococcus radiodurans'' reveal the mechanism of L-pyroglutamate recognition]]
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*[[Journal:Acta Cryst F:S2053230X20016015|Using Yeast Surface Display to Engineer a Soluble and Crystallizable Construct of HPK1]]
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*[[Journal:Acta Cryst F:S1744309112050270|Crystal structure of ADL1, a plant-specific homologue of the universal diaminopimelate amino transferase enzyme of lysine biosynthesis]]
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*[[Journal:Acta Cryst D:S2059798320015004|The substrate binding in the bile acid transporter ASBT<sub>Yf</sub> of ''Yersinia frederiksenii'']]
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*[[Journal:Acta Cryst F:S1744309112003326|Structure of recombinant human carboxylesterase 1 isolated from whole cabbage looper larvae]]
+
*[[Journal:Acta Cryst D:S205979832001517X|An engineered disulfide bridge traps and validates an outward-facing conformation in a bile acid transporter]]
 +
*[[Journal:Acta Cryst D:S2059798321003922|Structure of the human factor VIIa/soluble tissue factor with calcium, magnesium and rubidium]]
*[[Journal:Angew Chem Int Ed:1|Fine tuning of chlorophyll spectra by protein-induced ring deformation]]
*[[Journal:Angew Chem Int Ed:1|Fine tuning of chlorophyll spectra by protein-induced ring deformation]]
*[[Journal:JBIC:8|A hydrogen-bonding network formed by the B10-E7-E11 residues of a truncated hemoglobin from Tetrahymena pyriformis is critical for stability of bound oxygen and nitric oxide detoxification]]
*[[Journal:JBIC:8|A hydrogen-bonding network formed by the B10-E7-E11 residues of a truncated hemoglobin from Tetrahymena pyriformis is critical for stability of bound oxygen and nitric oxide detoxification]]
Line 87: Line 96:
*[[Journal:JBIC:13|{{nowrap|N-Butylisocyanide Oxidation}} at the {{nowrap|&#91;NiFe<sub>4</sub>S<sub>4</sub>OH<sub>x</sub>&#93;-cluster}} of CO Dehydrogenase]]
*[[Journal:JBIC:13|{{nowrap|N-Butylisocyanide Oxidation}} at the {{nowrap|&#91;NiFe<sub>4</sub>S<sub>4</sub>OH<sub>x</sub>&#93;-cluster}} of CO Dehydrogenase]]
*[[Journal:JBIC:14|Multifaceted SlyD from ''Helicobacter pylori'': implication in [NiFe] hydrogenase maturation]]
*[[Journal:JBIC:14|Multifaceted SlyD from ''Helicobacter pylori'': implication in [NiFe] hydrogenase maturation]]
 +
*[[Journal:Acta Cryst D:S2059798320014540|Statistically correcting dynamical electron scattering improves refinement of protein nanocrystals, including charge refinement of coordinated metals]]
*[[Journal:JBIC:15|Potent Inhibition of Dinuclear Zinc(II) Peptidase, an Aminopeptidase from Aeromonas proteolytica, by 8-Quinolinol Derivatives: Inhibitor Design Based on Zn2+ Fluorophores, Kinetic, and X-ray Crystallographic Study]]
*[[Journal:JBIC:15|Potent Inhibition of Dinuclear Zinc(II) Peptidase, an Aminopeptidase from Aeromonas proteolytica, by 8-Quinolinol Derivatives: Inhibitor Design Based on Zn2+ Fluorophores, Kinetic, and X-ray Crystallographic Study]]
*[[Journal:JBIC:16|Laue Crystal Structure of ''Shewanella oneidensis'' Cytochrome c Nitrite Reductase from a High-yield Expression System]]
*[[Journal:JBIC:16|Laue Crystal Structure of ''Shewanella oneidensis'' Cytochrome c Nitrite Reductase from a High-yield Expression System]]
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*[[Journal:JBSD:41|Molecular Mechanism of HIV-1 gp120 Mutations That Reduce CD4 Binding Affinity]]
*[[Journal:JBSD:41|Molecular Mechanism of HIV-1 gp120 Mutations That Reduce CD4 Binding Affinity]]
*[[Book:Structural Proteomics and its Impact on the Life Sciences:6]]‎
*[[Book:Structural Proteomics and its Impact on the Life Sciences:6]]‎
-
*[[Journal:IUCrJ:S2052252518018274|A cytosine modification mechanism revealed by the ternary complex structure of deoxycytidylate hydroxymethylase from bacteriophage T4 with its cofactor and substrate]]
+
*[[Journal:Acta Cryst D:S0907444911047251|Flexibility of the flap in the active site of BACE1 as revealed by crystal structures and molecular dynamics simulations]]
 +
*[[Journal:Acta Cryst D:S2059798318000050|A DNA structural alphabet provides new insight into DNA flexibility]]
 +
*[[Journal:Acta Cryst D:S2059798319000676|Crystal structures of pyrrolidone-carboxylate peptidase I from ''Deinococcus radiodurans'' reveal the mechanism of L-pyroglutamate recognition]]
*[[Journal:Acta Cryst D:S2059798318014900|Structure of the AmyC GH13 alpha-amylase from Alicyclobacillus sp, reveals accommodation of starch branching points in the alpha-amylase family]]
*[[Journal:Acta Cryst D:S2059798318014900|Structure of the AmyC GH13 alpha-amylase from Alicyclobacillus sp, reveals accommodation of starch branching points in the alpha-amylase family]]
*[[Journal:Acta Cryst D:S2059798318017047|The crystal structure of the N-acetylglucosamine 2-epimerase from Nostoc sp. KVJ10 reveals the true dimer]]
*[[Journal:Acta Cryst D:S2059798318017047|The crystal structure of the N-acetylglucosamine 2-epimerase from Nostoc sp. KVJ10 reveals the true dimer]]
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*[[Journal:Acta Cryst D:S2059798319000214|In-house high energy remote SAD-phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations on the same human IBA57 crystal to increase multiplicity]]
*[[Journal:Acta Cryst D:S2059798319000214|In-house high energy remote SAD-phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations on the same human IBA57 crystal to increase multiplicity]]
*[[Journal:Acta Cryst D:S2059798319002912|Crystal structure of the pseudoenzyme PDX1.2 in complex with its cognate enzyme PDX1.3]]
*[[Journal:Acta Cryst D:S2059798319002912|Crystal structure of the pseudoenzyme PDX1.2 in complex with its cognate enzyme PDX1.3]]
-
*[[Journal:Acta Cryst F:S2053230X18016217|The structure of ''Mycobacterium tuberculosis'' HtrA reveals an auto-regulatory mechanism]], Arvind Kumar Gupta, Debashree Behera and Balasubramanian Gopal [http://dx.doi.org/10.1107/S2053230X18016217 http://dx.doi.org/10.1107/S2053230X18016217]
+
*[[Journal:Acta Cryst D:S2059798319007113|Crystal Structure Determination of ''Pseudomonas stutzeri'' A1501 endoglucanase Cel5A]]
-
*[[Journal:Acta Cryst F:S2053230X18014814|Crystal structure and kinetic analyses of a hexameric form of (S)-3-hydroxybutyryl-CoA dehydrogenase from Clostridium acetobutylicum]], Mihoko Takenoya, Seiichi Taguchi and Shunsuke Yajima [http://dx.doi.org/10.1107/S2053230X18014814 http://dx.doi.org/10.1107/S2053230X18014814]
+
*[[Journal:Acta Cryst D:S2059798319006995|Structural insight into a matured humanized monoclonal antibody HuA21 against HER2-overexpressing cancer cells]]
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*[[Journal:Acta Cryst F:S2053230X19000815|Crystal structure of Type VI immunity protein Tdi1 (Atu4351) from Agrobacterium tumefaciens]], Lingling Shi, Zengqiang Gao, Tianyi Zhang, Heng Zhang and Yuhui Dong [http://dx.doi.org/10.1107/S2053230X19000815 http://dx.doi.org/10.1107/S2053230X19000815]
+
*[[Journal:Acta Cryst D:S2059798319002304|The third structural switch in the molecule of archaeal translation initiation factor 2 and its possible role in initiation of GTP hydrolysis and removal of aIF2 from the ribosome]]
-
*[[Journal:Acta Cryst F:S2053230X19004151|Phasing with calcium at home]], Shuaiqi Guo, Robert Campbell, Peter L. Davies and John S. Allingham [http://dx.doi.org/10.1107/S2053230X19004151 http://dx.doi.org/10.1107/S2053230X19004151]
+
*[[Journal:Acta Cryst D:S2059798319004169|Structural and functional insights into phosphomannose isomerase]]
-
*[[Journal:Acta Cryst F:S2053230X19001213|Substrate analogue complex structure of ''Mycobacterium tuberculosis'' decaprenyl diphosphate synthase]], Tzu-Ping Ko, Xiansha Xiao, Rey-Ting Guo, Jian-Wen Huang, Weidong Liu, Chun-Chi Chen [http://dx.doi.org/10.1107/S2053230X19001213 http://dx.doi.org/10.1107/S2053230X19001213]
+
*[[Journal:Acta Cryst F:S2053230X18016217|The structure of ''Mycobacterium tuberculosis'' HtrA reveals an auto-regulatory mechanism]]
-
*[[Journal:Acta Cryst F:S2053230X19004618|Novel T9 loop interaction of Filamenting Temperature-sensitive mutant Z from ''Mycobacterium tuberculosis'']], E. O. Lazo, J. Jakoncic, S. RoyChowdhury, D. Awasthi, I. Ojima [http://dx.doi.org/10.1107/S2053230X19004618 http://dx.doi.org/10.1107/S2053230X19004618]
+
*[[Journal:Acta Cryst F:S2053230X18014814|Crystal structure and kinetic analyses of a hexameric form of (S)-3-hydroxybutyryl-CoA dehydrogenase from Clostridium acetobutylicum]]
-
*[[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 [http://www.ncbi.nlm.nih.gov/pubmed/23385743 http://www.ncbi.nlm.nih.gov/pubmed/23385743]
+
*[[Journal:Acta Cryst F:S2053230X19000815|Crystal structure of Type VI immunity protein Tdi1 (Atu4351) from Agrobacterium tumefaciens]]
-
*[[Journal:Acta Cryst F:S2053230X19002863|Functional and structural characterization of IdnL7, an adenylation enzyme involved in incednine biosynthesis]], Jolanta Cieślak, Akimasa Miyanaga, Makoto Takaishi, Fumitaka Kudo, Tadashi Eguchi [http://dx.doi.org/10.1107/S2053230X19002863 http://dx.doi.org/10.1107/S2053230X19002863]
+
*[[Journal:Acta Cryst F:S2053230X19004151|Phasing with calcium at home]]
-
*[[Journal:Acta Cryst F:S2053230X19004424|Structure of the Ebola virus nucleoprotein - RNA complex]], Robert N. Kirchdoerfer, Erica Ollmann Saphire, Andrew B. Ward [http://dx.doi.org/10.1107/S2053230X19004424 http://dx.doi.org/10.1107/S2053230X19004424]
+
*[[Journal:Acta Cryst F:S2053230X19001213|Substrate analogue complex structure of ''Mycobacterium tuberculosis'' decaprenyl diphosphate synthase]]
-
*[[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 [http://dx.doi.org/10.1107/S1744309112003326 http://dx.doi.org/10.1107/S1744309112003326]
+
*[[Journal:Acta Cryst F:S2053230X19004618|Novel T9 loop interaction of Filamenting Temperature-sensitive mutant Z from ''Mycobacterium tuberculosis'']]
-
*[[Journal:Acta Cryst F:S2053230X18018083|An assessment of three human methylenetetrahydrofolate dehydrogenase/cyclohydrolase ligand complexes following further refinement]], Renata V. Bueno, Alice Dawson and William N. Hunter [http://dx.doi.org/10.1107/S2053230X18018083 http://dx.doi.org/10.1107/S2053230X18018083]
+
*[[Journal:Acta Cryst F:S1744309112050270|Crystal structure of ADL1, a plant-specific homologue of the universal diaminopimelate amino transferase enzyme of lysine biosynthesis]]
-
*[[Journal:Acta Cryst F:S2053230X19002693|Crystal structure of phosphoribulokinase from ''Synechococcus sp.'' strain PCC 6301]], Robert Wilson, Manajit Hayer-Hartl and Andreas Bracher [http://dx.doi.org/10.1107/S2053230X19002693 http://dx.doi.org/10.1107/S2053230X19002693]
+
*[[Journal:Acta Cryst F:S2053230X19002863|Functional and structural characterization of IdnL7, an adenylation enzyme involved in incednine biosynthesis]]
 +
*[[Journal:Acta Cryst F:S2053230X19004424|Structure of the Ebola virus nucleoprotein - RNA complex]]
 +
*[[Journal:Acta Cryst F:S1744309112003326|Structure of recombinant human carboxylesterase 1 isolated from whole cabbage looper larvae]]
 +
*[[Journal:Acta Cryst F:S2053230X18018083|An assessment of three human methylenetetrahydrofolate dehydrogenase/cyclohydrolase ligand complexes following further refinement]]
 +
*[[Journal:Acta Cryst F:S2053230X19002693|Crystal structure of phosphoribulokinase from ''Synechococcus sp.'' strain PCC 6301]]
 +
*[[Journal:Acta Cryst F:S1744309112003326|Structure of recombinant human carboxylesterase 1 isolated from whole cabbage looper larvae]]
 +
*[[Journal:Acta Cryst F:S2053230X19007192|Crystal Structure of Flavin Dependent Thymidylate Synthase, Thy1, from ''Thermus thermophilus'' having an Extra C Terminal Domain]]
 +
*[[Journal:BMC:3|Identification of novel isocytosine derivatives as xanthine oxidase inhibitors from a set of virtual screening hits]]
 +
*[[Journal:FEBS Open Bio:2|Structural evidence for Arabidopsis glutathione transferase AtGSTF2 functioning as a transporter of small organic ligands]]
 +
*[[Journal:IUCrJ:S2052252519002926|Determination of the Molecular Basis for Coprogen Import by Gram Negative Bacteria]]
 +
*[[Journal:IUCrJ:S2052252519001568|Structure of mammalian plasma fetuin-B and its mechanism of selective metallopeptidase inhibition]]
 +
*[[Journal:IUCrJ:S2052252518018274|A cytosine modification mechanism revealed by the ternary complex structure of deoxycytidylate hydroxymethylase from bacteriophage T4 with its cofactor and substrate]]
 +
*[[Journal:IUCrJ:S2052252519005372|The structural characterisation of a glucosylglycerate hydrolase provides insights into the molecular mechanism of mycobacterial recovery from nitrogen starvation]]
 +
*[[Journal:IUCrJ:S2052252519005761|Room-temperature photo-induced martensitic transformation in a protein crystal]]
*[[SUMO]]
*[[SUMO]]
*[[EPSP synthase]]
*[[EPSP synthase]]
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*[[Torpedo californica acetylcholinesterase with alkylene-linked tacrine dimer (5 carbon linker)]]
*[[Torpedo californica acetylcholinesterase with alkylene-linked tacrine dimer (5 carbon linker)]]
*[[Thioredoxin Glutathione Reductase]]
*[[Thioredoxin Glutathione Reductase]]
 +
*[[Journal:PMC:1]]

Current revision

Dr. Alexander Berchansky, Ph.D., Israel Structural Proteomics Center, Weizmann Institute of Science

My interesting pages:

CRISPR-Cas (under development):

Classification according to the Wikipedia page CRISPR [1] with additions

CRISPR Class 1 uses a complex of multiple Cas proteins

CRISPR type I (Cas3)

CRISPR type I-A (Cascade) - see CRISPR subtype I-A

CRISPR type I-B (Cascade) - see CRISPR subtype I-B

CRISPR type I-C (Cascade) - see CRISPR subtype I-C

CRISPR type I-D (Cas10d)

CRISPR type I-E (Cascade) - see CRISPR subtype I-E

CRISPR type I-F (Csy1, Csy2, Csy3) - see CRISPR subtype I-F

CRISPR type I-U (GSU0054)

CRISPR type III (Cas10)

CRISPR type III-A (Csm complex) - see CRISPR subtype III-A (Csm complex)

CRISPR type III-B (Cmr complex)

CRISPR type III-C (Cas10 or Csx11)

CRISPR type III-D (Csx10)

CRISPR type Orphan

CRISPR type IV (Csf1)

CRISPR type IV-A

CRISPR type IV-B

CRISPR Class 2 uses a single large Cas protein

CRISPR type II-A - see CRISPR-Cas9

CRISPR type II-B (Cas4)

CRISPR type II-C

CRISPR type V (Cpf1, C2c1, C2c3) - see CRISPR type V

CRISPR type VI (Cas13a (previously known as C2c2), Cas13b, Cas13c, Cas13d) - see CRISPR type VI

Proteopedia Page Contributors and Editors (what is this?)

Alexander Berchansky, Eran Hodis

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