Faculty of Science


Wolfson Home NMR Labrotary X-Ray Labrotary Protein Purification Protein Expression Academic Committee Wolfson  Foundation Wolfson Centre Personnel Wolfson Centre Search

The Protein Purification Facility

Entries Since September 2006

Table of Content
Selected Protocols



Dr. Hadar Amartely

Dr. Mario Lebendiker

Tel: 972-2-6586920


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 ( (

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)

CV from Mario Lebendiker

Protein Quality Guidelines for Biophysical and Biochemical Studies

Table of Content

Bacterial Exression Systems

poly His 
Two Step: poly His and Strep-Tag
Solubility enhancement tags (SETs)
Cold Expression vector and Trigger Factor
Single Protein Production
Profinity eXact™
Pseudomonas fluorescens
ESETEC Secretion System
Brevibacillus Expression System
Preparation of Cell Lysates /
Different Disruption Methods 

Mitochondria, Nuclear & Membrane Isolation
Purification Strategy -
and more

Test Tube
Removal of Nucleic Acids 
Buffer for Tag purification

Cleaning and Regeneration of Resins
High-throughput process development    (HTPD)
Purification of large biomolecules

Protein Quantitation 
Absorbance 280nm
Biotinylated proteins
Comparision of Methods>
Glycoprotein Carbohydr.
Interfering Substances
Nano Orange
Preparation Reagent
Protein Precipitation

Publications Related to The Protein Purification Unit

Recommended Links

Recommended Publications
Drosophila Expression System

Mammalian Expression

Insect Expression System

Leishmania Expression Systems

Expression Systems

Bryophytes (Mosses)

Choice of Buffers
Purification of Recombinant Proteins

poly His 
Nus A
Halo tag Fusion
Solubility enhancement tags (SETs)
Fluorescent Protein
Cold Expression
LYTAG Two PhaseSystem
Profinity eXact™
Bispecific Affinity
CaptureSelect C‐tag
CL7/Im7 tag

Gel Electrophoresis

PAGE-SDS (Laemmli)
Phosphate affinity SDS-PAGE

Protein extraction from Polyacrylamide Gel

Proteomics Sample Preparation
Protein Precipitation

Protein extraction from Polyacrylamide Gel 


Gel Stain

Coomasie Blue

Silver Stain
Zinc Stain
In-Vitro Translation

Apoptosis Inhibitors
Cell Division / Cell Cycle / Cell Adhesion
Lipid Signal
Neurodegeneration Inhibitors
Nitric Oxid/Oxidative Stress
Phosphorilation / Dephosphorilation
Protease Inhibitors


Cleavage of Recombinant Proteins

Cleavage Sites Table for Fusion Proteins



DNA removal

Endotoxin removal and endotoxin test

Cell Penetration
Affinity Chromatography
Activated resins
Antibody Purification and Antibody fragmentation
Lectins and Glycoprotein
Mimetics Ligands, Antibody fragments and Similar Technology

A detailed collection of information on initial bioinformatic investigation
using bioinformatic tools to strategically design expression/purification projects, can be found on the website page of  Dr. Nurit Kleinberger-Doron inside the website of the  Protein Expression Facility directed by Dr Tsafi Danieli (Wolfson Centre for Applied Structural Biology - Hebrew University of Jerusalem).


Expanded Bed Adsorption

Gel Filtration

Hydrophobic Interaction


Ion Exchange

Multimodal and Hydrophobic Charge-Induction Chromatography 

Reverse Phase


Protein-Protein Interaction


Light Scattering

Circular Dichroism

High Abundant Serum Proteins Removal

Crystallography and Recombinant Methods

Phospho-Protein Purification

Polyubiquitin-modified proteins

Protein Aggregation

Protein Labeling with Biotin

Protein Refolding / Inclusion Bodies

Simulated Moving Bed Chromatography

Storage of Purified Proteins

Viral Purification


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™ TREOSRTriple-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

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
Choice of lysis buffer and additives

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

Small and large scale MBP-fusion protein purification 
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

Cleavage of Recombinant Proteins

Cleavage Sites Table for Fusion Proteins
Factor Xa Cleavage of a MBP fusion protein
Thrombin Cleavage of a GST fusion protein

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

Storage of Purified Proteins

Protein Quantitation
Comparision of Different Protein Determination Methods
Absorbance 280nmAccording to Protein Protocols in CD Rom
Lowry According to Protein Protocols in CD Rom
Lowry-Peterson For membrane proteins, diluted solutions or solutions with s
Protein Precipitation Methods to concentrate or eliminate interferences before electrophoresis or protein determination

Gel Electrophoresis
PAGE-SDS (Laemmli)
Basic-Native: For Acidic and Neutral proteins (pI < 7.0)
Acidic-Native: For Basic proteins (pI > 7.0)
Tricine: SDS gel for low MW proteins (<25 kDa)
Protein Precipitation Methods to concentrate or eliminate interferences before electrophoresis or protein determination
Silver Stain

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

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

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

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

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

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

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

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

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

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

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

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

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

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  

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

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

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

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

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  

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  

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  
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

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

Lederman L. (2009) 
Protein Isolation and Purification – Tech News
BioTechniques 46:87-89

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  

Yannay-Cohen N.,Carmi-Levy I.,Kay G.,Yang C.,Min HanJ. ,Kemeny M., Kim S.,Nechushtan H.,and Razin E.  (2009)
LysRS Serves as a Key Signaling Molecule in the Immune Response by Regulating Gene Expression

Molecular Cell 34, 603–611  

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

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

Gabizon R, Brandt T, Sukenik S, Lahav N, Lebendiker M, Shalev D, Veprintsev D and Friedler A. (2012)  
Modulating the oligomerization equilibrium of p53 by peptides that bind its C terminal domain.

7 (5) e38060 - doi:10.1371/journal.pone.0038060   (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

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  Bioconjugate Chem.

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

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

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  

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 | (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

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:   (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)

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

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).

Ion Exchange Chromatography (IEX) Coupled to Multi-angle Light Scattering (MALS) for Protein Separation and Characterization ">(video)

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

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: (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)

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).  (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).  (pdf) (pdf Suppl)

Recommended Links 

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

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.
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
   Flow rate

Unit Converters

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.

Recommended Publications

Crystallography and Recombinant Proteins

Derewenda Z., The use of recombinant methods and molecular engineering in protein crystallization.
    Methods (2004), 34:354–363 (pdf)
Smyth D., REVIEW Crystal structures of fusion proteins with large-affinity tags.
    Protein Science (2003),12:1313–1322 (pdf)
Geerlof A.  The impact of protein characterization in structural proteomics.
    Acta Cryst. (2006) D62: 1125-1136   (pdf) 
Newby Z.  A general protocol for the crystallization of membrane proteins for X-ray structural investigation.
    Nature Protocols (2009) 4: 619-637  (pdf)  
Lee J.  An efficient platform for screening expression and crystallization of glycoproteins produced in human cells.  
    Nature Protocols (2009) 4: 592-604  (pdf)

Production and Purification of Recombinant Proteins

Structural Genomics Consortium  Protein production and purification.
    Nature Methods 2008, 5: 135-146
 (pdf-I)  (pdf-II)
Jonasson P.,Genetic Design for Facilitated Production and Recovery of Recombinant Proteins in E.Coli.
    Biotechnol.Appl.Biochem 2002,35: 91-105 (pdf)

Nilsson J.,Affinity Fusion Strategies for Detection, Purification and Immobilization of Recombinant Proteins.
    Protein Expr. and Purif. 1997, 11: 1-16

Stevens R., Design of Hgh-Throughput Methods of Protein Production for Structural Biology.
    Structure 2000,8: R177-R185

Swartz J. Advances in E.Coli Production of Therapeutic Proteins.
    Current Opinion in Biotechnology 2001,12: 195-210 (pdf)

Protein Refolding

Altamirano M., Refolding Chromatography with Immobilized Mini-Chaperones.
    PNAS 1997,94: 3576-3578
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
Eiler S.,
Overexpression, Purification, and Crystal Structure of Native ER alphaLBD
    Protein Expression and Purification (2001) 22, 165–173
Machida S., Cycloamylose as an efficient artificial chaperone for protein refolding.
    FEBS Letters486 (2000) 131-135
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
Tsumoto K.,Practical Considerations in Refolding Proteins from Inclusion Bodies.
    Protein Expr. and Purif. 2003,28: 1-8


Dr. Mario Lebendiker The Protein Purification Facility Tel: 972-2-6586920

Copyright ©, 1997, The Hebrew University of Jerusalem. All Rights Reserved