User:Alexander Berchansky

From Proteopedia

Revision as of 12:48, 17 July 2018

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

My interesting pages:

• Acetylcholinesterase
• AChE inhibitors and substrates
• Mutations in BRCA1/BARD1 RING-domain heterodimer
• Mutations in Brca1 BRCT Domains
• Lactate Dehydrogenase
• Missense Mutations in Phenylalanine Hydroxylase
• Phosphofructokinase (PFK)
• Alcohol dehydrogenase
• Beta-glucosidase

CRISPR-Cas (under development):

• CRISPR-Cas9
• CRISPR-Cas Part I
• CRISPR-Cas Part II

CRISPR Class 1

CRISPR subtype I-A (Cascade) - SEE CRISPR subtype I-A

CRISPR subtype I-B (Cascade) - SEE CRISPR subtype I-B

CRISPR subtype I-C (Cascade) - SEE CRISPR subtype I-C

CRISPR subtype I-E (Cascade) - SEE CRISPR subtype I-E

CRISPR subtype I-F (Cascade) - SEE CRISPR subtype I-F

CRISPR subtype III-A (Csm complex) - SEE CRISPR subtype III-A (Csm complex)

CRISPR subtype III-B (Cmr complex)

CRISPR subtype Orphan

CRISPR type IV (Csf1)

CRISPR Class 2

CRISPR type II - SEE CRISPR-Cas9

CRISPR type V (Cpf1) - SEE CRISPR type V

CRISPR type VI (C2c2)

• Flexibility of the flap in the active site of BACE1 as revealed by crystal structures and molecular dynamics simulations
• A DNA structural alphabet provides new insight into DNA flexibility
• Crystal structure of ADL1, a plant-specific homologue of the universal diaminopimelate amino transferase enzyme of lysine biosynthesis
• Structure of recombinant human carboxylesterase 1 isolated from whole cabbage looper larvae
• Fine tuning of chlorophyll spectra by protein-induced ring deformation
• 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
• N-Butylisocyanide Oxidation at the [NiFe₄S₄OH_x]-cluster of CO Dehydrogenase
• Multifaceted SlyD from Helicobacter pylori: implication in [NiFe] hydrogenase maturation
• 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
• Laue Crystal Structure of Shewanella oneidensis Cytochrome c Nitrite Reductase from a High-yield Expression System
• Peptidylglycine α-Hydroxylating Monooxygenase (PHM)-coordination of peroxide to Cu_M center. Structural and computational study
• Solution structure and dynamics of human S100A14
• The crystal structure of Sporosarcina pasteurii urease in a complex with citrate provides new hints for inhibitor design
• The mechanism of copper uptake by tyrosinase from Bacillus megaterium
• The crystal structure of an extracellular catechol oxidase from the ascomycete fungus Aspergillus oryzae
• Selectivity of Ni(II) and Zn(II) binding to Sporosarcina pasteurii UreE, a metallo-chaperone in the urease assembly: a calorimetric and crystallographic study
• Solution structure and metal ion binding sites of the human CPEB3 ribozyme's P4 domain
• Synthesis, characterization and binding properties towards CT-DNA and Lipoxygenase, of mixed ligand silver(I) complexes with 2-mercapto-thiazole and its derivatives and triphenylphosphine.
• Fluoride inhibition of Sporosarcina pasteurii urease: structure and thermodynamics
• Aromatic aldehydes at the active site of Aldehyde Oxidoreductase from Desulfovibrio gigas: Reactivity and Molecular Details of the Enzyme-Substrate and Enzyme-Product Interactions
• Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states
• High-resolution crystal structure of Z-DNA in complex with Cr3+ cations
• Structural Characterization of Metal Binding to a Cold-adapted Frataxin
• Conformational control of the binding of diatomic gases to cytochrome c’
• Analyzing the Catalytic Role of Active Site Residues in the Fe-Type Nitrile Hydratase from Comamonas testosteroni Ni1
• Structural characterization of zinc-bound Zmp1, a zinc-dependent metalloprotease secreted by Clostridium difficile
• Structural evidence for Arabidopsis glutathione transferase AtGSTF2 functioning as a transporter of small organic ligands
• Crystal structure of porcine pancreatic phospholipase A₂ in complex with 2-methoxycyclohexa-2-5-diene-1,4-dione
• A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle
• Structural and kinetic studies of imidazole binding to two members of the cytochrome c6 family reveal an important role for a conserved heme pocket residue
• Protein and metal cluster structure of the wheat metallothionein domain γ-Ec-1. The second part of the puzzle.
• Ferredoxin
• A Cryo-Crystallographic Time Course for Peroxide Reduction by Rubrerythrin from Pyrococcus furiosus
• Cyt1Aa Toxin: High Resolution Structure Reveals Implications for its Membrane-Perforating Function
• Catalytic metal ion rearrangements underline promiscuity and evolvability of a metalloenzyme
• Structure of estradiol metal chelate and estrogen receptor complex: The basis for designing a new class of SERMs
• Structural and functional insights into a dodecameric molecular machine – The RuvBL1/RuvBL2 complex
• Automated computational design of human enzymes for high bacterial expression and stability
• Antiviral Activity of 3(2H)- and 6-Chloro-3(2H)-Isoflavenes against Highly Diverged, Neurovirulent Vaccine-Derived, Type2 Poliovirus Sewage Isolates
• Structural Basis of Enzymatic Activity for the Ferulic Acid Decarboxylase (FADase) from Enterobacter sp. Px6-4
• Structural and functional characterization of the interaction of the photosensitizing probe methylene blue with Torpedo californica acetylcholinesterase
• The Impact of Crystallization Conditions on Structure-Based Drug Design: a Case Study on the Methylene Blue/Acetylcholinesterase Complex
• Structural basis of transcription activation
• Promiscuous Protein Binding as a Function of Protein Stability
• An Insight to the Dynamics of Conserved Water Mediated Salt Bridge Interaction and Inter-Domain Recognition in hIMPDH Isoforms
• Elucidation by NMR solution of neurotensin in Small Unilamellar Vesicle environment: molecular surveys for neurotensin receptor recognition
• Dominant-negative Effects in Prion Diseases: Insights from Molecular Dynamics Simulations on Mouse Prion Protein Chimeras
• Influence of divalent magnesium ion on DNA: molecular dynamics simulation studies
• Evidence-based docking of the urease activation complex
• Carbon monoxide binding to the heme group at the dimeric interface modulates structure and copper accessibility in the Cu,Zn superoxide dismutase from Haemophilus ducreyi: in silico and in vitro evidences
• Para-(benzoyl)-phenylalanine as a potential inhibitor against LpxC of Leptospira spp.: Homology modeling, docking and molecular dynamics study
• Drug resistance mechanism of PncA in Mycobacterium Tuberculosis
• Mechanism of BAG1 repair on Parkinson’s disease-linked DJ1 mutation
• Traditional Chinese medicine as dual guardians against hypertension and cancer?
• The molecular origin of the MMR-dependent apoptosis pathway from dynamics analysis of MutSα-DNA complexes
• The extracellular subunit interface of the 5-HT3 receptors: a computational alanine scanning mutagenesis study
• DNA Conformation and Energy in Nucleosome Core: A Theoretical Approach
• Molecular modeling study for conformational changes of Sirtuin 2 due to substrate and inhibitor binding
• Crystal structure of the CN-hydrolase SA0302 from the pathogenic bacterium Staphylococcus aureus belonging to the Nit and NitFhit Branch of the nitrilase superfamily
• Insight into TPMT*23 Mutation Mis-folding Using Molecular Dynamics Simulation and Protein Structure Analysis
• Identification of structural motifs in the E2 glycoprotein of Chikungunya involved in virus - host interaction
• Molecular dynamics simulations of the thermal stability of tteRBP and ecRBP
• Investigation on the Site-Selective Binding of Bovine Serum Albumin by Erlotinib Hydrochloride
• Interhelical loops within the bHLH domain are determinant in maintaining TWIST1-DNA complexes
• Investigation of Silent Information Regulator 1 (Sirt1) Agonists from Traditional Chinese Medicine
• Han ethnicity-specific type 2 diabetic treatment from traditional Chinese medicine?
• Conformational dynamics of full-length inducible human Hsp70 derived from microsecond molecular dynamics simulations in explicit solvent
• Non-specificity and synergy at the binding site of the carboplatin-induced DNA adduct via molecular dynamics simulations of the MutSα-DNA recognition complex
• A Possible Strategy against Head and Neck Cancer: In Silico. Investigation of Three-in-One inhibitors
• Structural Insights into the South African HIV-1 Subtype C Protease: Impact of hinge region dynamics and flap flexibility in drug resistance
• Memory-Enhancement by Traditional Chinese Medicine?
• The remarkable efficiency of a Pin-II proteinase inhibitor sans two conserved disulfide bonds is due to enhanced flexibility and hydrogen-bond density in the reactive loop
• Traditional Chinese medicine application in HIV: An in silico study
• Molecular Mechanism of HIV-1 gp120 Mutations That Reduce CD4 Binding Affinity
• SUMO
• AMP-activated protein kinase
• Xanthine dehydrogenase
• Nicotinic Acetylcholine Receptor
• Cytochrome c
• Methotrexate
• Kemp elimination catalyst
• Urease
• Phosphoglycerate Kinase
• Plant-derived glucocerebrosidase
• NADH quinone oxidoreductase (NQO1) with inhibitor dicoumarol
• Matrix metalloproteinase
• Amino acid oxidase
• Mutant immunity protein 9 (variant R12-13)
• Acetylcholine binding protein
• Hydroxylase
• Actin
• Torpedo Californica Acetylcholinesterase in complex with an (R)-Tacrine-(10)-Hupyridone inhibitor
• Dronpa
• Major histocompatibility complex
• Mutant immunity protein 9 (variant R12-2)
• Butyrylcholinesterase
• Human acid-beta-glucosidase covalently bound to conduritol B epoxide
• Avidin
• Proteasome
• Human Acetylcholinesterase
• FK506 binding protein
• Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis
• Ubiquitin protein ligase
• Catalase
• Albumin
• Aminopeptidase
• Staphylococcal nuclease
• Virus protease
• Asparaginase
• NAC transcription factor
• Kemp eliminase
• Antizyme Inhibitor
• NADPH-Cytochrome P450 Reductase
• Prolyl hydroxylase domain
• Neuraminidase
• Carbonic anhydrase
• Carboxypeptidase
• ABC transporter
• Ubiquitin
• Cytochrome P450
• TEM1-beta-Lactamase/beta-lactamase Inhibitor Protein (BLIP)
• Acid beta-glucosidase with N-butyl-deoxynojirimycin
• Treatment of Gaucher disease
• Acyl carrier protein synthase
• Chimeras of alcohol dehydrogenases
• Dihydrodipicolinate synthase
• Directed evolution
• Colicin Immunity Protein
• Human FKBP52
• Opioid receptor
• Acetylcholine
• Heat Shock Proteins
• Dioxygenase
• Flavodoxin
• Phospholipase A2
• Tyrosine kinase
• Cellobiohydrolase
• Acid phosphatase
• Neuroglobin
• Hirudin
• GTP-binding protein
• Aldehyde dehydrogenase
• Delta-endotoxin
• Beta-lactamase
• Estrogen receptor
• DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1
• Alkaline phosphatase
• Cathepsin
• Prolyl Endopeptidase
• Subtilisin
• Hyaluronidase
• Lysine-specific histone demethylase
• Glycolate oxidase
• Chaperonin
• Nucleoprotein
• Transcriptional activator
• Chitinase
• Cluster of Differentiation CD38
• Aricept Complexed with Acetylcholinesterase (Russian)
• Tubulin
• SAM-dependent methyltransferase
• Lignin peroxidase
• Gyrase
• Methylesterase
• CAMP-dependent protein kinase
• Plasminogen
• Choline Oxidase
• Thioesterase
• Kinesin
• Gelsolin
• DNA glycosylase
• Mitogen-activated protein kinase
• BtuB
• BLUF domain protein
• Botulinum neurotoxin
• Blue copper oxidase CueO
• Beta-phosphoglucomutase
• Beta-ketoacyl-ACP reductase
• Beta-adrenergic receptor kinase
• Barnase
• Bacteriorhodopsin
• BA42
• Azurin
• Avirulence protein
• Autophagy-related protein
• ATP-citrate synthase
• Atlastin
• Aspartoacylase
• Aspartate carbamoyltransferase
• Proliferating Cell Nuclear Antigen
• Aspartate-semialdehyde dehydrogenase
• Ascorbate peroxidase
• Aromatic amine dehydrogenase
• Arginine kinase
• Antigen 85
• Anti-sigma factor antagonist
• Anthrax protective antigen
• Anthrax edema factor
• Annexin
• Aminotransferase
• Alpha-tubulin N-acetyltransferase
• Alpha-lytic protease
• Aldose Reductase
• Alanine racemase
• Agglutinin
• ADP-ribose pyrophosphatase
• Poly (ADP-ribose) polymerase
• Adenylosuccinate lyase
• Adenosine kinase
• Adenosine deaminase
• Adenosine A2A receptor
• Adaptin
• Acylaminoacyl peptidase
• Acyl carrier protein
• Acyl-CoA dehydrogenase
• Acetylxylan esterase
• Acetyl-CoA carboxylase
• Acetyl-CoA synthetase
• Acetyl-CoA synthase
• Purine repressor
• Protein phosphatase
• 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
• 6-aminohexanoate-dimer hydrolase
• 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
• 7,8-dihydro-8-oxoguanine triphosphatase
• Cell division protein
• 12-oxophytodienoate reductase
• Alpha-glucosidase
• Apoptotic protease-activating factor
• Arginase
• Adhesin
• Arabinanase
• Biotin Protein Ligase
• Androgen receptor
• 14-3-3 protein
• 3C protease
• GTPase KRas
• 6-phosphogluconate dehydrogenase
• Mineralocorticoid receptor
• Thyroid hormone receptor
• Progesterone receptor
• Serpin
• Leucine transporter
• Microtubule-associated protein
• Ectonucleotide pyrophosphatase/phosphodiesterase
• Ribosome biogenesis protein
• Liver X receptor
• Nitrophorin
• VprBP
• Signal recognition particle receptor
• Liver receptor homolog-1
• Orexin and Orexin receptor
• Spindlin
• Prostaglandin E synthase
• Terminase
• Mandelate racemase/muconate lactonizing enzyme
• GABA(A) receptor-associated protein
• IspG
• Cytochrome P450 hydroxylase
• Period circadian protein
• Proteinase
• Sialyltransferase
• Thiolase
• Tripeptidyl peptidase
• Tryptophan synthase
• Rho GTPase activating protein
• Prostaglandin D synthase
• Prestin
• Polyamine oxidase
• Phosphotransferase
• Phosphodiesterase
• Plexin
• Plasminogen activator
• Plasmid segregation protein ParM
• Phospholipase C
• Phosphoenolpyruvate carboxylase
• Peptide N-glycanase
• Penicillopepsin
• Penicillin acylase
• PCSK9
• Paired box protein
• Oligopeptide-binding protein
• Nuclear receptor coactivator
• Neuropilin
• NADH peroxidase
• P63
• Leukotriene B4 hydroxydehydrogenase
• Leukocyte immunoglobulin-like receptor
• Alpha-lactalbumin
• 3-phosphoinositide-dependent protein kinase 1
• 2-isopropylmalate synthase
• Mur ligase
• Monooxygenase
• Vanillyl-alcohol oxidase
• Tumor necrosis factor
• Tumor necrosis factor receptor
• Mannosidase
• Transthyretin
• Transport inhibitor response 1
• Transducin
• L-rhamnose isomerase
• TRAIL
• Inosine monophosphate dehydrogenase
• Survivin
• UDP-N-acetylglucosamine acyltransferase
• Haptoglobin receptor
• Glutaminyl cyclase
• Severin
• Isoaspartyl dipeptidase
• Thiaminase
• Acetylcholinesterase with OTMA
• D275P mutant of alcohol dehydrogenase from protozoa Entamoeba histolytica
• Ferripyoverdine receptor
• Fatty acid-binding protein
• Rho-associated protein kinase
• Endonuclease
• Epoxidase
• Elastase
• N-acetylornithine carbamoyltransferase
• Ornithine carbamoyltransferase
• Pantothenate kinase
• Pantothenate synthetase
• Parvalbumin
• Dipeptidyl peptidase
• Transferrin
• Transketolase
• Dihydropteroate synthase
• Trichodiene synthase
• DAHP synthase
• Trehalulose synthase
• TRNA-guanine transglycosylase
• Cyclophilin
• Cutinase
• Trypanothione reductase
• Trypsin inhibitor
• Tryptase
• Tubulin tyrosine ligase
• Transaldolase
• Urokinase
• Undecaprenyl pyrophosphate synthase
• UDP-galactose 4-epimerase
• Uridine 5'-monophosphate synthase
• Arsenate reductase
• Rac
• Rho GTPase
• Dedicator of cytokinesis protein
• Phosphoribosylaminoimidazole carboxylase
• Retinoid isomerohydrolase
• Calcium uptake protein 1
• Abscisic acid receptor
• Apoptosis-inducing factor
• Nucleolin
• Aldo-keto reductase
• SAICAR synthetase
• Prolactin receptor
• Siderocalin
• Latrophilin
• Folypolyglutamate synthase
• WD repeat-containing protein
• Xylosidase
• Uridylate kinase
• Penicillin-binding protein
• Pentaerythritol tetranitrate reductase
• Thymidine kinase
• Thymidylate kinase
• Tissue factor pathway inhibitor
• Thioredoxin Reductase
• Peptidyl-tRNA hydrolase
• Peroxiredoxin
• Phenylethanolamine N-methyltransferase
• Tetracycline repressor protein
• Phenylpyruvate decarboxylase
• Succinate-semialdehyde dehydrogenase
• Spermidine/spermine N-acetyltransferase
• Sulfotransferase
• Phosphomannomutase
• Strictosidine Synthase
• Phosphoenolpyruvate carboxykinase
• Phosphoribosyltransferase
• Phosphoserine aminotransferase
• Phosphoserine phosphatase
• Shikimate kinase
• Shikimate dehydrogenase
• Selectin
• Selenocysteine synthase
• Semaphorin
• Serine palmitoyltransferase
• SAM decarboxylase
• SAM synthetase
• S-adenosylhomocysteine hydrolase
• Plasmepsin
• RNA uridylyltransferase
• Ribosomal protein S6 kinase
• Poly(A) RNA polymerase protein Cid1
• Ribonucleotide reductase
• Phycocyanobilin:ferredoxin oxidoreductase
• Poly (ADP-ribose) glycohydrolase
• Rhomboid protease
• Rhodopsin kinase
• Retinol-binding protein
• Polyneuridine Aldehyde Esterase
• Retinoid X receptor
• Porphobilinogen synthase
• Retinoblastoma-binding protein
• Pyruvate dehydrogenase kinase
• Pyruvate-ferredoxin oxidoreductase
• Pyrroline-5-carboxylate dehydrogenase
• Purine nucleoside phosphorylase
• Proline utilization A
• Protein kinase C
• Nucleoside diphosphate kinase