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Faculty of Science |
Entries Since September 2006
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Table of Content Equipment Selected Protocols |
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The Protein Purification Facility is a learning station and a
resource of information and assistance available to researches and
students as well as biotech and pharmaceutical companies interested in
protein purification. Mainly we provide consultation and active support
for researchers, students and people from the biotechnology industry in
resolving protein purification projects.
The Facility offers complete and fully automated liquid chromatography
systems (AKTA Explorer and AKTA Avant) designed for method development
and research applications that simplifies the transition from
laboratory to full-scale production. We have columns and resins for
purification according to size, charge, hydrophobicity and substrate
affinity. In addition, the Facility is equipped with many other
essential instruments in protein production and characterization: gel
electrophoresis and blotting apparatus. Different cell disruption and
ultrafiltration systems. Multi-Angle Light Scattering (MALS) and
Refraction Index (RI) on line with an analytical AKTA Pure 25 system to
allow measurement of absolute molar mass, size, and shape of
protein or other types of macromolecules during size exclusion
chromatography (SEC-MALS) or ion exchange chromatography (IEX-MALS)
Main expertise and areas of scientific interest:
Purification strategy design according to each protein
Develop, optimize and upscale protocols for protein purification from
samples of different sources (natural or recombinant sources).
Overcome the major bottleneck in structure determination by X-Ray
crystallography or NMR that is the preparation of suitable crystalline
and homogeneous samples.
Hundreds of different projects with different Academic and Industry groups
Isolation and identification of unknown factors
Many courses in the field in the Hebrew University, International Meetings and for Pharma Companies
For protein characterization, in addition to SDS-PAGE, Native gels,
we offer Analytical Size Exclusion Chromatography (SEC) or Ion Exchange
Chromatography (IEX) alone or coupled on-line to Multi-Angle Light
Scattering (MALS) and Refraction Index (RI): SEC-MALS and IEX-MALS (new
method for protein or macromolecules characterization)
Actively involved with a team of experts of the Association of Resources for Biophysical Research in Europe (ARBRE-MOBIEU) and from the Production and Purification Partnership in Europe (P4EU) in establishing Guidelines for Minimal Protein Quality Standard. Rules that intended to lay the groundwork for the standardization and reproducibility of data (https://p4eu.org/P4EU-Inhalt/uploads/2018/04/Extended-guideline-7.pdf) (https://p4eu.org/protein-quality-standard-pqs)
Tools to increase solubility, and/or stability of proteins as well as avoid or reduce aggregation
Tools to refold proteins and refolding on-column
A few publications in the field of production of prone to aggregate proteins
Many courses in the field in International Meetings (PEGS, PepTalk, EMBO) for Pharma and Academic staff
Protein Information Submission Form (pdf)
Protein Quality Guidelines for Biophysical and Biochemical Studies
ÄKTA Explorer 100 from GE-Healthcare: Two refrigerated systems and one system
on line with miniDAWN™ TREOSR and OPTILAB T-rEX-Refractive Index detector
ÄKTA avant 25 from GE-Healthcare
WYATT miniDAWN™ TREOSR: Triple-angle
MALS light scattering detector for the measurement of absolute molecular
weight, size, and conformation of macromolecules in solution
WYATT OPTILAB T-rEX-Refractive Index detector
ÄKTA Pure M25 from GE-Healthcare on line with Triple-angle MALS light scattering detector and Refractive Index detector
Microfluidics micro-fluidizer (model M-110 EHIS) for cell rupture (pdf)
(Interdepartmental
Instrumentation Unit of the LSI)
AVESTIN EmulsiFlex™ - C3 High-Pressure
Homogenizer for cell rupture (pdf)
(Interdepartmental
Instrumentation Unit of the LSI)
Selected Protocols of The Protein
Purification Unit and Others
Preparation
of Cell Lysates / Different Disruption Methods
Bacterial
Protein Extraction (mini-scale) Sonication
Bacterial
Protein Screen (DDM lysis) - Small affinity binding
PROTEIN EXPRESSION
FACILITY of THE HEBREW UNIVERSITY Sonication
of bacterial samples
Choice
of Buffers
AMERSHAM
BIOSCIENCES Recommended buffers for Anion Exchange Chromatography
AMERSHAM BIOSCIENCES
Recommended buffers for Cation Exchange Chromatography
AMERSHAM
BIOSCIENCES Recommended Volatile buffers systems for Ion Exchange
Chromatography
PROTEIN
EXPRESSION AND PURIFICATION FACILITY OF THE EUROPEAN MOLECULAR
BIOLOGY LABORATORY
Choice
of lysis buffer and additives
PROTEIN
EXPRESSION AND PURIFICATION FACILITY OF THE EUROPEAN MOLECULAR
BIOLOGY LABORATORY
Solubility
Studies Preparation
of soluble/insoluble protein from cells
DNA removal - Endotoxin removal
Removal of Nucleic Acids - Different Protocols
Endotoxin Clearance
with Triton X-114 – Selected protocols from the literature
Purification Strategy - Others
Test Tube for Ion Exchange Resins
Test tube for Mixed Mode Resins
Test Tube for Hydrophobic Exchange Resins
Buffer solubility screen to avoid protein aggregation during concentration
Limited proteolysis - Partial Proteolytic Digestion
Purification of Recombinant Proteins
Small scale GST-fusion
protein purification under nature conditions
Small
and large scale His-Tag fusion protein purification under nature conditions
Small scale His-Tag
fusion protein purification under denaturative conditions
Protein Refolding
Protein Refolding on IMAC resin - Batch Screening Procedure
- On-Column Scale-up
Additives Used to Increase Folding
and Prevent Aggregation
Contaminant
Removal from Inclusion Bodies Before Solubilization
Protein
Quantitation
Comparision
of Different Protein Determination Methods
Absorbance 280nmAccording
to Protein Protocols in CD Rom
Bradford
Lowry According
to Protein Protocols in CD Rom
Lowry-Peterson
For membrane proteins, diluted solutions or solutions with
s interferant
Protein
Precipitation Methods to concentrate or eliminate interferences
before electrophoresis or protein determination
Publications Related to The Protein Purification
Unit
Schwaiger, M., Lebendiker, M., Yerushalmi,H.,
Coles, M., Groger, A., Schwartz, C., Schuldiner,S.,and Kessler,
H. (1998).
NMR-Investigation of the Multidrug Transporter Emr-E
an Integral Membrane Protein.
Eur. J. of Biochemistry
254: 610-619. (pdf)
Muth T.R. and Schuldiner S. (2000)
A membrane-embedded
glutamate is required for ligand binding to the multidrug transporter
EmrE.
EMBO J. 19: 234-240 (pdf)
Tate C., Kunji E., Lebendiker M., and Schuldiner
S. (2001).
The projection structure of EmrE, a proton linked multidrug
transporter from Escherichia coli, at 7Å resolution.
The
EMBO Journal 20: 77-81 (pdf)
Orzech E., Okhrimenko H., Reich V., Cohen S., Weiss
A., Melamed-Book N., Lebendiker M., Altschuler Y.and Aroeti
B.(2001).
The AP-1 adaptor of the clathrin coat associates with
microtubules via microtubule associated proteins.
J.of Biol.
Chemistry 276 (33): 31340-31348 (pdf)
Ben-Zimra M, Koler M, and Orly J. (2002)
Transcription
of Cholesterol Side-Chain Cleavage Cytochrome P450 in the Placenta:
Activating Protein-2 Assumes the Role of Steroidogenic
Factor-1
by Binding to an Overlapping Promoter Element.
Mol. Endocrinol.16:
1864-1880 (pdf)
Fish A, Lebendiker M, Nechushtai R & Livnah
O (2003).
Purification, crystallization and preliminary X-ray analysis
of ferredoxin isolated from thermophilic cyanobacterium Mastigocladus
laminosus.
Acta Crys. D-59: 734-736 (pdf)
Zhang M, Fishman Y, Sher D and Zlotkin E (2003).
Hydralisin,
a Novel Animal Group-Selective Paralytic and Cytolytic Protein
from Noncnidocystic Origin in Hydra.
Biochemistry 42:
8939-8944 (pdf)
Rosen G, Nisimov I, Helcer M, and Sela M (2003)
Actinobacillus
actinomycetemcomitans Serotype b Lipopolysaccharide Mediates Coaggregation
with Fusobacterium nucleatum.
Infection and Immunity 71 (6):
3652–3656 (pdf)
Listovsky T, Oren Y, Yudkovsky Y, Mahbubani H, Weiss
A, Lebendiker M and Brandeis M (2004)
Cdh1/Fzr mediates
its own degradation
The EMBO Journal 00: 1–8 (pdf)
Soskine M, Adam Y, and Schuldiner S (2004)
Direct Evidence for Substrate-induced
Proton Release in Detergent-solubilized EmrE, a Multidrug
Transporter
J.of Biol. Chemistry 279 (11): 9951-9955 (pdf)
Neubig R, and Roman D, (2004)
Sites of interest on the World Wide Web
Mol.
Interv.4: 298 (pdf)
Klein S, Geiger T, Linchevski I, Lebendiker M, Itkin A, Assayag
K and Levitzki A (2005)
Expression and purification of active
PKB kinase from Escherichia coli.
Protein Expression and Purification
41: 162–169 (pdf)
Sher D., Fishman Y., Zhang M., Lebendiker M., Gaathon A.,
Manchenio J. and Zlotkin E. (2005)
Hydralisins: a new category
of diverse Beta-Poreforming toxins in Cnidaria. Characterization
and preliminary structure-function analysis.
J. of Biol. Chemistry
280: 22847 - 22855 (pdf)
Fish A., Danieli T., Ohad I., Nechushtai R. and Livnah O. (2005)
Structural
Basis for the Thermostability of Ferredoxin from the Cyanobacterium
Mastigocladus laminosus.
J. Mol. Biol. 350: 599–608 (pdf)
Copty A., Sakran F., Popov O., Ziblat R., Danieli T., Golosovsky M.and
Davidov D. (2005)
Probing of the microwave radiation effect
on the green fluorescent protein luminescence in solution
Synthetic
Metals 155: 422–425 (pdf)
Elia N., Frechter S., Gedi Y., Minke B., and Selinger Z. (2005)
Excess
of Gße over Gqαe in vivo prevents dark, spontaneous activity of
Drosophila photoreceptors.
The Journal of Cell Biology 171(3):
517-526 (pdf)
Soskine M., Mark S., Tayer N., Mizrachi R. and Schuldiner S. (2006)
On
Parallel and Antiparallel Topology of a Homodimeric Multidrug Transporter
J. of Biol. Chemistry 281: 36205–36212 (pdf)
Taylor A. , Haze-Filderman A, Blumenfeld A., Shay B., Dafni L., Rosenfeld
E., Leiser Y., Fermon E., Gruenbaum-Cohen Y.
and Deutsch D. (2006)
High yield of biologically active recombinant human amelogenin
using the baculovirus expression system.
Protein Expression
and Purification 45: 43–53 (pdf)
Diskin R., Lebendiker M., Engelberg L. And Livnah O. (2007)
Structures
of p38α Active Mutants Reveal Conformational Changes in L16 Loop
that Induce Autophosphorylation and Activation.
J. Mol. Biol.
365, 66–76 (pdf)
Funkenstein B. and Rebhan Y. (2007)
Expression, purification, renaturation
and activation of fish myostatin expressed in Escherichia coli: Facilitation
of refolding and activity
inhibition by myostatin prodomain.
Protein
Expression and Purification 54: 54–65 (pdf)
Hayouka Z., Rosenbluh J., Levin A., Loya S., Lebendiker M., Veprintsev
D., Kotler M., Hizi A., Loyter A. & Friedler A. (2007)
Inhibiting
HIV-1 Integrase by Shifting its Oligomerization Equilibrium
PNAS
104 (20): 8316-8321 (pdf)
Weiss Y., Bromberg Z., Raj N., Raphael J., Goloubinoff P., Ben-Neriah
Y.and Deutschman D. (2007)
Enhanced heat shock protein 70 expression alters
proteasomal degradation of I[kappa]B kinase in experimental acute respiratory
distress syndrome.
Critical Care Medicine. 35(9):2128-2138 (pdf)
Coster G, Hayouka Z, Argaman L, Strauss C, Friedler A, Brandeis M and
Goldberg M (2007)
The DNA Damage Response Mediator MDC1 Directly Interacts with the Anaphase-promoting Complex/Cyclosome
J. of Biol.
Chemistry 282 (44): 32053–32064 (pdf)
Shalev-Malul G., Viner-Mozzini Y., Sukenik A., Gaathon A., Lebendiker
M. and Kaplan A. (2008)
An AbrB-like protein might be involved
in the regulation of cylindrospermopsin production by Aphanizomenon ovalisporum.
Environmental Microbiology 10(4), 988–999 (pdf)
Rotem S, Katz C, Benyamini H, Lebendiker M, Veprintsev D, Rudiger
S, Danieli T and Friedler A. (2008)
The structure and interactions of the
proline-rich domain of ASPP2 (2008)
J. of Biol. Chemistry 283 (27),
18990–18999 (pdf)
Mayshar Y, Rom E, Chumakov I, Kronman A, Yayon A and Benvenisty N (2008)
FGF4 And its Novel Splice Isoform Have Opposing Effects on the
Maintenance of Human Embryonic Stem Cell Self Renewal
Stem Cells
Express, published online January 10, 2008; doi:10.1634/stemcells.2007-1037
(pdf)
Katz C., Benyamini H.,Rotem S., Lebendiker M., Danieli T., Iosub
A., Refaely H., Dines M., Bronner V., Bravman T., Shalev D.,
Rüdiger S.,
and Friedler A. (2008)
Molecular basis of the interaction between the antiapoptotic
Bcl-2 family proteins and the proapoptotic protein ASPP2
PNAS 105
(34): 12277–12282 (pdf)
Amsili S, Zer H, Hinderlich S, Krause S, Becker-Cohen M, MacArthur D, North K and Mitrani-Rosenbaum S (2008)
UDP-N-Acetylglucosamine 2-Epimerase/N-Acetylmannosamine Kinase (GNE)
Binds to Alpha-Actinin 1: Novel Pathways in
Skeletal Muscle?
PLoS ONE 3(6): e2477 1-9. (pdf)
Steiner-Mordoch S, Soskine M, Solomon D, Rotem D,
Gold A, Yechieli M, Adam Y and Schuldiner S (2008)
Parallel topology of genetically fused EmrE
Homodimers
The EMBO Journal 27,
17–26 (pdf)
Reingewertz T.; Benyamini H.; Lebendiker M.; Shalev D.and Friedler
A.(2009)
The C-Terminal Domain of the HIV-1 Vif Protein is Natively Unfolded
in its Unbound State.
PEDS (Protein Engineering, Design, and Selection)
1–7, doi: 10.1093/protein/gzp004 (pdf)
Lieman-Hurwitz J, Haimovich M, Shalev-Malul G, Ishii A, HiharaY, Gaathon
A, Lebendiker M and Kaplan A. (2009)
A cyanobacterial AbrB-like protein
affects the apparent photosynthetic affinity for CO2 by modulating low-CO2-induced
gene expression.
Environmental Microbiology 11(4), 927–936
(pdf)
Lederman L. (2009)
Protein Isolation and Purification – Tech News
BioTechniques
46:87-89 (pdf)
Sela M., Babitski E., Steinberg D., Kohavi D. and Rosen G. (2009)
Degradation of collagen-guided tissue regeneration membranes by
proteolytic enzymes of Porphyromonas gingivalis and its
inhibition by antibacterial agents
Clin. Oral Impl. Res. 20, 496–502 (pdf)
Tabib A., Krispin A., Trahtemberg U., Verbovetsk I., Lebendiker M., Danieli T., and Mevorach D.
(2009)
Thrombospondin-1-N-terminal
domain (heparin binding N-terminal domain) induces a phagocytic state,
and Thrombospondin-1-C-terminal
domain induces a tolerizing phenotype in dendritic cells.
PLoS ONE 4(8) e6840 1-7 (pdf)
Shay B,
Gruenbaum-Cohen Y, Tucker AS, Taylor AL, Rosenfeld E, Haze A, Dafni L, Leiser Y, Fermon E,
Danieli T,
Blumenfeld A,
Deutsch D. (2009)
High yield expression of biologically active recombinant full length human tuftelin protein
in baculovirus-infected
insect cells.
Protein Expr Purif. 2009 Nov; 68(1):90-98 (pdf)
Kasherman Y,Sturup S,and Gibson D (2009)
Is Glutathione the Major Cellular Target of Cisplatin? A Study of the Interactions of Cisplatin with Cancer Cell Extracts
J. Med. Chem., 52, 4319–4328 (pdf)
Elbaz Y, Danieli T, Kanner B and Schuldiner S (2010)
Expression of neurotransmitter
transporters for structural and biochemical studies.
Protein Expr Purif. 73:152-160. (pdf)
Lebendiker M., and Danieli T. (2011)
Purification
of Proteins fused to Maltose-binding Protein.
Protein Chromatography: Methods and Protocols. Editor(s): Dermot Walls, Sinéad T. T. Loughran
Series:
Methods in Molecular Biology Vol.681: 281-293 (pdf)
Tzarum N., Diskin R.,
Engelberg D. and Livnah O.(2011)
Active Mutants of the TCR-Mediated p38α Alternative Activation Site Show Changes in the Phosphorylation Lip and DEF
Site Formation
J. Mol. Biol. 405, 1154–1169 (pdf)
Reingewertz T.,
Shalev D., Sukenik S., Blatt O., Rotem S., Lebendiker M., Larisch S. &
Friedler A. (2011)
Mechanism of the
Interaction between the Intrinsically Disordered C-terminus of the Proapoptotic ARTS
Protein
and the Bir3 Domain of
XIAP
PLoS ONE vol 6, issue 9, e24655 (pdf)
Siman P.,
Blatt O., Moyal T.,
Danieli T.,Lebendiker M., Lashuel H.,
Friedler A. and Brik A.
(2011)
Chemical
Synthesis and Expression of the HIV-1 Rev Protein
ChemBioChem 12 (7): 1097-1104 -
DOI: 10.1002/cbic.201100033 (pdf)
Weiss S.,
Kohn E., Dadon D., Katz
B., Lebendiker M.,
Kosloff M., Colley N. and Minke B.
(2012)
Ca2+segregation mediated by calphotin prevents
light induced retinal degeneration.
The Journal of Neuroscience 32(42):14696 –14708 (pdf)
Amartely
H , David
A, Lebendiker M, Benyamini H, Izraeli S and
Friedler A (2013)
The STIL protein contains intrinsically disordered regions that mediate its
protein-protein interactions
Chemical Communication DOI: 10.1039/c3cc45096a (pdf)
Lebendiker M., and Danieli T.
(2014)
Production
of prone-to-aggregate proteins (Review)
FEBS Letters 588: 236–246 - DOI information: 10.1016/j.febslet.2013.10.044 (pdf)
Buch M., Wine
Y., Dror Y., Rosenheck S., Lebendiker M., Giordano R., Leal R., Popov A.,
Freeman A and Frolow F. (2014)
Protein Products Obtained by Site-Preferred Partial Crosslinking in
Protein Crystals and ‘‘Liberated’’ by Redissolution.
Biotechnology and Bioengineering DOI 10.1002/bit.25186 (pdf)
Joubran
S., Zigler M, Pessah N., Klein S., Shir A.,
Edinger N.Sagalov A., Razvag Y., Reches M., and
Levitzki A. (2014)
Optimization of Liganded PolyethyleniminPolyethylene Glycol
Vector for Nucleic Acid Delivery
dx.doi.org/10.1021/bc500252a Bioconjugate Chem. (pdf)
Sharabi
O., Shirian J., Grossman M., Lebendiker M., Sagi I,
and Shifman J. (2014)
Affinity- and specificity-enhancing mutations are frequent in multispecific
interactions between TIMP2 and MMPs
PLoS ONE 9(4): e93712.
doi:10.1371/journal.pone.0093712 (pdf)
Lebendiker M.,
Danieli T. and de Marco A. (2014)
The Trip Adviser guide to the protein science world: a proposal to improve the
awareness concerning the quality of
recombinant proteins.
BMC Research Notes (2014) 7:585 doi:10.1186/1756-0500-7-58 (pdf) (pdf-figure)
Maes M.;
Amit E.; Danieli T.; Lebendiker M.; Loyter A.and Friedler
A. (2014)
The disordered region of Arabidopsis VIP1 binds the Agrobacterium
VirE2
protein outside its DNA binding
site
Protein Engineering, Design, and Selection" (PEDS)1-8
doi:10.1093/protein/gzu036 (pdf)
Lebendiker M., Maes M. and
Friedler A. (2015)
A screening methodology for purifying proteins with
aggregation problems.
Methods in Molecular Biology: "Insoluble
Proteins" book (Springer)1258: 261-281 (pdf)
Iosub Amir A., van Rosmalen M.,
Mayer G., Lebendiker M., Danieli
T. and Friedler A. (2015)
Highly homologous proteins exert opposite biological activities by using
different interaction interfaces.
Scientific Reports (Nature) 5, 11629; doi: 10.1038/srep 11629 (pdf)
Reingewertz T., Iosub-Amir A., Bonsor D., Mayer G., Amartely H., Friedler and Sundberg E. (2015)
An Intrinsically Disordered Region in the Proapoptotic ASPP2 Protein Binds to the Helicobacter pylori Oncoprotein CagA
Biochemistry 2015, 54, 3337−3347 DOI: 10.1021/acs.biochem.5b00084 (pdf)
Shavit R., Lebendiker M., Pasternak Z., Burdman S. and Helman Y. (2016)
The vapB-vapC Operon of Acidovorax citrulli Functions as a bona-fide Toxin-Antitoxin Module
Front. Microbiol., 06 January 2016 | http://dx.doi.org/10.3389/fmicb.2015.01499 (pdf)
Shoshan M., Dekel N., Goch W., Shalev D., Danieli T., Lebendiker M., Bal W. and Tshuva E. (2016)
Unbound Position II in MXCXXC Metallochaperone Model Peptides Impacts Metal Binding Mode and Reactivity:
Distinct Similarities to Whole Proteins.
Journal of Inorganic Biochemistry doi: 10.1016/j.jinorgbio.2016.02.016 (pdf)
Amartely H., David A., Shamir M., Lebendiker M., Izraeli S. and Friedler A. (2016)
Differential effects of Zinc binding on structured and disordered regions in the multidomain STIL protein.
Chemical Science DOI: 10.1039/x0xx00000x (pdf)
Edinger N., Lebendiker M., Klein S., Zigler M., Langut Y and Levitzki A. (2016)
Targeting polyIC to EGFR over-expressing cells using a dsRNA binding protein domain tethered to EGF
PLoS ONE 11(9): e0162321. doi:10.1371/journal.pone.0162321 (pdf)
Nasser L., Weissman Z., Pinsky M., Amartely H., Dvir H. and Kornitzer D.
Structural basis of haem-iron acquisition by fungal pathogens (2016)
NATURE MICROBIOLOGY | VOL 1 | NOVEMBER 2016 DOI: 10.1038/NMICROBIOL.2016.1 (pdf) (pdf supplement)
Rimon O., Suss O.,1, Goldenberg M., Fassler R.,Yogev O., Amartely H., Propper G., Friedler A. & Reichmann D. (2017)
A Role of Metastable Regions and Their Connectivity in the Inactivation of a Redox-Regulated Chaperone and Its Inter-Chaperone Crosstalk
Antioxid Redox Signal. 2017 Apr 10. doi: 10.1089/ars.2016.6900 (pdf)
Lebendiker M., and Danieli T. (2017)
Purification of Proteins fused to Maltose-binding Protein.
Methods Mol Biol 1485 257-273: Protein Chromatography: Methods and Protocols. Editor(s): Dermot Walls, Sinéad T. T. Loughran
Letnik Y., Avrahami R., Port R., Greiner A., Zussman E.,Rokem J. and Greenblatt C. (2017)
Biosorption of copper from aqueous environments by Micrococcusluteus in cell suspension and when encapsulated
International Biodeterioration & Biodegradation 116 (2017) 64e72 http://dx.doi.org/10.1016/j.ibiod.2016.09.029 (pdf)
Zauberman A., Vagima Y., Tidhar A., Aftalion M., Gur D., Rotem S., Chitlaru T., Levy Y.and Mamroud E. (2017)
Host Iron Nutritional Immunity Induced by a Live Yersinia pestis
Vaccine Strain Is Associated with Immediate Protection against Plague
Front. Cell. Infect. Microbiol. 7:277. doi: 10.3389/fcimb.2017.00277 (pdf)
Sporny, M., Guez-Haddad, J., Kreusch, A., Shakartzi,
S., Neznansky, A., Cross, A., Isupov, M., Qualmann, B.,
Kessels, M. and Opatowsky, Y. (2017)
Structural History of Human SRGAP2 Proteins
Mol. Biol. Evol. 34(6):1463–1478 doi:10.1093/molbev/msx094 (pdf)
Gura Sadovsky, R., Brielle, S., Kaganovich, D. & England, J. (2017)
Measurement of Rapid Protein Diffusion in the Cytoplasm by Photo-Converted Intensity Profile Expansion
Cell Reports 18, 2795–2806 (pdf)
Dynamics of venom composition across a complex life
cycle (2017)
Columbus-Shenkar Y., Sachkova M., Fridrich A., Modepalli V.,
Sunagar K. and Moran Y.
bioRxiv doi: https://doi.org/10.1101/159889 (pdf)
Langut Y., Talhami A., Mamidib S., Shir A., Zigler
M., Joubran S., Sagalov A., Flashner-Abramson E., Edinger N., Klein S.,
and Levitzki A. (2017)
PSMA-targeted polyinosine/polycytosine vector induces prostate tumor
regression and invokes an antitumor immune response in mice
PNAS 114: 13655-136 (2017) (pdf)
Langut Y., Edinger N., Flashner-Abramson E., Melamed-Book N., Lebendiker M., Klein S., and Levitzki A. (2017)
PSMA-homing dsRNA chimeric protein vector kills prostate cancer cells and evokes anti-tumor immunity
Oncotarget (2017) 8: 24046-24062 (pdf)
Amartely H.,Avraham O.,Friedler A.,Livnah O. and Lebendiker M. (2018)
Coupling Multi Angle Light Scattering to Ion Exchange chromatography (IEX-MALS) for protein characterization
Scientific Reports (2018) 8:6907 DOI:10.1038/s41598-018-25246-6 (pdf)
Amartely H., Some D., Tzadok A. and Lebendiker M. (2019)
Ion Exchange chromatography (IEX) coupled to Multi Angle Light
Scattering (MALS) – for protein separation and characterization
J. Vis. Exp. (146), e59408, doi:10.3791/59408 (2019). (pdf)
Ion Exchange Chromatography (IEX) Coupled to Multi-angle Light
Scattering (MALS) for Protein Separation and Characterization
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Sporny M., Guez-Haddad J., Lebendiker M. ‚ Ulisse V., Volf A., Mim C., Isupov M., and Opatowsky Y. (2019)
Structural Evidence for an Octameric Ring Arrangement of SARM1
Journal Molecular Biology 431, 3591–3605 (pdf)
Shamir M., Amartely H., and Lebendiker M. and Friedler A (2019)
Characterization of protein oligomers by multi-angle light scattering (MALS)
Encyclopedia of Analytical Chemistry DOI: 10.1002/9780470027318.a9545 (pdf)
Onn L., et al. and Toiber D. (2020)
SIRT6 is a DNA double-strand break sensor
eLife 2020;9:e51636. DOI: https://doi.org/10.7554/eLife.51636 (pdf)
Dekel N., Einsenberg-Domovich Y., Karlas A., von Kries J., Lebendiker M., Danieli T, and Livnah O.(2020)
Expression, Purification and Crystallization of Clk1 Kinase – a possible target for anti-influenza therapy
Protein Expression and Purification 176, 105742 (2020) https://doi.org/10.1016/j.pep.2020.105742 (pdf)
Berrow N., deMarco A., Lebendiker M., Remans K., Garcia-Alai M., Knauer S., Lopez‑Mendez B., Matagne A., Parret A., Remans K.,
Uebel S., Raynal B. (2021)
Quality control of purified proteins to improve data quality
and reproducibility: results from a large‑scale survey
Eur Biophys J (2021). https://doi.org/10.1007/s00249-021-01528-2 (pdf)
deMarco A., Berrow N., Lebendiker M., Remans K., Garcia-Alai M., Knauer S., Lopez‑Mendez B., Matagne A., Parret A., Remans K.,
Uebel S., Raynal B. (2021)
Quality control of protein reagents for the improvement of research data reproducibility.
Nat Commun 12, 2795 (2021). https://doi.org/10.1038/s41467-021-23167-z (pdf) (pdf Suppl)
Protein Expression Facility - Dr Tsafi Danieli - Wolfson Centre for
Applied Structural Biology - Hebrew University of Jerusalem.
A detailed collection of information on expression system and cloning strategies
Initial Bioinformatic
Investigation - Dr Nurit Kleinberger Doron - Hebrew University of Jerusalem
A detailed collection of information on initial bioinformatic investigation, and the use of bioinformatic tools to strategically design expression/purification
projects
ExPASy - ProtParam:
A tool which allows the computation of various physical and chemical
parameters for a given protein. The computed
parameters include
the molecular weight, theoretical pI, amino acid composition,
atomic composition, extinction coefficient, estimated half-life,
instability index, aliphatic index and grand average of
hydropathicity (GRAVY)
PROTEIN CALCULATOR v3.3 - Scripps :
A tool which allows the computation of various physical and chemical
parameters for a given
protein. The computed parameters include the
molecular weight, theoretical pI, amino acid composition, atomic
composition, extinction
coefficient, charge, protease cleavage.
Recombinant Protein Solubility Prediction - University of Oklahoma:
The statistical
model predicts protein solubility assuming the protein is being overexpressed
in Escherichia coli. Reference: Predicting the solubility
of
recombinant proteins in Escherichia coli. Wilkinson et al. Biotechnology (N
Y). 1991 May;9(5):443-8.
ESPRESSO (EStimation of PRotein Expression and SOlubility):
A sequence-based predictor for estimating protein expression and solubility
ExPASy - Peptide Cutter:
Predicts potential protease and cleavage sites and sites cleaved
by chemicals in a given protein sequence.
FoldIndex© - Weizmann Institute of Science:
FoldIndex©: a simple tool to predict whether a given protein
sequence is intrinsically unfolded. Prilusky et al. BIOINFORMATICS
APPLICATIONS
NOTE Vol. 21 no. 16 2005, pages 3435–3438
doi:10.1093/bioinformatics/bti537
CYSPRED - Predictor of the bonding state of cysteines in
proteins
The role of evolutionary information in predicting the disulfide
bonding state of cysteines in proteins- Fariselli et al. Proteins 36:
340-346 (1999)
DISULFIND
- Cysteines Disulfide Bonding State and Connectivity Predictor - Univ. Of Firenze
A server for the prediction of the bonding state and connectivity
pattern of the cysteines in a given amino acid sequence
DiANNA 1.1 - Cysteine state and Disulfide Bond partner prediction - Boston College
Determines the cysteine species: free cysteine, half-cystine or
ligand-bound; and if a cysteine is predicted to be ligand-bound,
then the most likely of
the four most common ligands (iron, zinc,
cadmium, carbon)
CUSABIO Buffer calculating, molecular weight calculating and solution reconstitution calculating.
GlobPlot - Intrinsic Protein Disorder, Domain & Globularity
Prediction - EMBL GlobPlot: exploring protein sequences for globularity and
disorder. Linding et. al. Nucleic Acids Research, 2003, Vol. 31, No. 13 3701–3708
Stormoff: Weight to Molar Quantity (for proteins)
This program helps you to convert the weight (weight concentration) in the molar
quantity (molar concentration)
and vice versa.
SIGMA (MERCK) Mass Molarity Calculator:
The mass molarity calculator tool calculates the mass of compound required to achieve a specific molar concentration and volume
SIGMA (MERCK) Mass Molarity CalculatorNormality & Molarity Calculator:
The molarity calculator tool provides lab-ready directions describing
how to prepare an acid or base solution of specified Molarity (M) or
Normality (N)
from a concentrated acid or base solution.
SIGMA (MERCK) Buffer Calculator
The Sigma-Aldrich Buffer Calculator is a useful tool for
calculating buffer solutions, including concentration calculations by
Molarity or by Percentage,
with relevant links to Sigma-Aldrich products.
SIGMA (MERCK) Buffer Reference Center
Useful pH Ranges of Selected Biological Buffers (25 °C, 0.1M)
Trizma Buffer Table – pH vs. Temperature
Phosphate Buffer Table – 0.2M solution
Citric Acid – Na2HPO4 Buffer Solutions, pH approx. 2.6–7.6
Citric Acid – Sodium Citrate Buffer Solutions, pH 3.0–6.2
Sodium Acetate – Acetic Acid Buffer Solutions, pH 3.7–5.6
Na2HPO4 – NaH2PO4 Buffer Solutions, pH 5.8–8.0 at 25 °C
Sodium Carbonate – Sodium Bicarbonate Buffer Solutions, pH 9.2–10.8
SIGMA (MERCK) Unit Converters
Temperature
Volume
Mass/Weight
Length
Pressure
Flow rate
Absorbance/Transmittance
Unit Converters
Temperature
Volume
Mass/Weight
Length
Pressure
Others....
Ammonium Sulfate Calculator - EnCor Biotechnology Inc.
The program calculates how much solid Ammonium Sulfate you need to add to
a specific volume of a solution to get a specific percentage
saturation at a
specific temperature.
CRAPome: a contaminant repository for affinity purification–mass spectrometry data (pdf)
A web-accessible resource that stores and annotates negative
controls generated by the proteomics research community and enables
their use for
scoring AP-MS data.
Crystallography and Recombinant Proteins
Production and Purification of Recombinant Proteins
Protein Refolding
Altamirano M., Refolding
Chromatography with Immobilized Mini-Chaperones.
PNAS 1997,94:
3576-3578 (pdf)
Armstrong N.,A New Protein Folding Screen...etc.
Protein
Science 1999, 8: 1475-1483 (pdf)
Chen G., Overexpression of a Glutamate Receptor
(GluR2) ligand binding domain in E.Coli: Application of a novel
protein folding screen (pdf)
De Bernardez Clark E., Refolding of Recombinant
Proteins .
Current Opinion in Biotechnology 1998, 9:
157–163 (pdf)
De Bernardez Clark E., Protein refolding for
industrial processes.
Current Opinion in Biotechnology
2001, 12: 202–207 (pdf).
Eiler S., Overexpression, Purification, and
Crystal Structure of Native ER alphaLBD
Protein Expression
and Purification (2001) 22, 165–173 (pdf)
Machida S., Cycloamylose as an efficient
artificial chaperone for protein refolding.
FEBS Letters486
(2000) 131-135 (pdf)
Middelberg A.,Preparative Protein Folding.
TRENDS in Biotechnology 2002,20 (10):
437-443
(pdf)
Ming Li et al.,In vitro protein refolding
by chromatographic procedures.
Protein Expr.
and Purif. 2004,33: 1-10 (pdf)
Tsumoto K.,Practical Considerations in Refolding
Proteins from Inclusion Bodies.
Protein Expr. and Purif.
2003,28: 1-8 (pdf)
Dr. Mario Lebendiker
The Protein Purification Facility
mario.l@mail.huji.ac.il
Tel: 972-2-6586920
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