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P GAL. ATT site. ORF. ATT site. His6. HA. 3C. ZZ. Fermentor culture (autoinduction galactose). P GAL. PGK1 5’. LIC site. ORF. LIC site. 3C. His10. KCl-stripping of membranes. Un-stripped membranes. 0.7 M KCl-stripped membranes. YNL275w-40. Harvest, lyse (Avestin). P GAL.

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ATT site


ATT site





Fermentor culture

(autoinduction galactose)



LIC site


LIC site



KCl-stripping of membranes

Un-stripped membranes

0.7 M KCl-stripped membranes


Harvest, lyse (Avestin)



LIC site


LIC site




Amount of YNL275W-40 1/6 liter

Loading: 1/200th ofpurification

3,000 x g spin

Talon-binding proteases of yeast










Each purification:

300 OD mls

PMSF + - + - + - + - + - + -

Marker, 15 uL

Wash 1

Wash 2

100,000 x g spin


50 mM imidazole



15 mM imidazole

5 mM imidazole

5 mM imidazole

15 mM imidazole

50 mM imidazole

500 mM imidazole

500 mM imidazole

150 mM imidazole

300 mM imidazole

150 mM imidazole

300 mM imidazole

275W-40 from IgG

275W-40, from IgG






Strain 1: BJ5460pep4-prb1

Strain 2: EJG1117pep4-prb1-

Strain 3: EJG1364pep4-PRB1+

Endogenous yeast proteases that degrade the Ste24p target as well as 3C protease include protease B (Prb1p) and can be inhibited by PMSF (but not all serine protease inhibitors.)


Ste24p cleaved from Talon

with GST-tagged 3C protease

Ste24p stripped from Talon

using EDTA

Ynl275w (un-cleaved)

Multi-step purification of the

anion transporter YNL275w

1-Step Purification of Ste24p (CAAX protease) on Talon



Detergent: dodecyl maltoside

Culture: 96,000 ODmls

Fraction #

49 kDa



3C-His6 elution

3C-His6 elution

500 mM imidazole


20 ul

10 ul

5 ul

3C-6HIS protease

( 7 ug)

3C-GST protease

( 5 ug)

Gel Filtration

Superdex 200



Talon Elution 1

Talon Elution 2

Talon Elution 3

Urea/SDS stripped Talon

IgG super rebound to IgG

IgG Elution 1

IgG Elution 2

IgG Elution 3

IgG stripped urea/SDS

Elutions after GST resin

Ste24p expressed from vector pSGP40 was solubilized from KCl-washed membranes, bound to Talon, then eluted by cleavage with His6-tagged 3C protease. After elution, the Talon column was treated ith 500 mM imidazole to visualize


Yln275w 10 l

Ynl275w 5 l

3C-GST 5 g

Bind to IMAC or IgG

affinity matrices



Purification from

96,000 OD mls

tag (Z-domain)

3C-cleavage site

Concentration of purified protein in the presence of detergent

Comparison of 50 kD-cutoff (expected to retain DDM micelles) and 100 kD-cutoff (expected to pass DDM micelles1) membranes in purification of Ste24p (CAAX protease.)

Anion transporter YNL275w (pSGP40, cleaved)

Gel filtration

0.2 M KSCN pH 7

20% PEG 3350

0.1 M NH4Br 0.1M Tris pH 8

20% PEG 8000

0.1 M NH4Br 0.1M Acetate pH 5

20% PEG 8000


50 kDa concentrate

50 kDa filtrate

100 kDa concentrate

100 kDa filtrate


Expression and Purification of Integral Membrane Proteins from Yeast for the

Center for High-Throughput Structural Biology

Kathy Clark*, Nadia Fedoriw*, Katrina Robinson*, Mark Sullivan†,

Michael G. Malkowski‡, George T. DeTitta‡, and Mark E. Dumont†*

*Department of Pediatrics and †Department of Biochemistry and Biophysics University of Rochester Medical Center

Rochester, NY 14642 and ‡The Hauptman-Woodward Institute, 700 Ellicott Street, Buffalo, New York 14203

Target selection

Vectors for yeast membrane protein expression


To address the severe lack of three dimensional structural information for eukaryotic transmembrane proteins (TMPs), the Center for High-Throughput Structural Biology is developing protocols for expression and purification of TMPs in the yeast Saccharomyces cerevisiae. We have focused initially on a set of endogenous yeast TMPs that are the highest expressing reading frames in a previously-constructed genomic collection of S. cerevisiae expression clones and for which there are established biochemical assays for determining whether the protein is maintained in a native state. Genes encoding the target TMPs are transferred via ligation-independent cloning procedures to a series of vectors that allow galactose-controlled expression of reading frames fused to C-terminal His6, His10, and ZZ (IgG-binding) domains that are separated from the reading frame by a cleavage site for rhinovirus 3C protease. Several TMP targets expressed from these vectors have been purified via affinity chromatography and gel filtration chromatography at levels and purities sufficient for ongoing crystallization trials. Single chain antibodies (scFvs) recognizing several targets have been developed as aids to crystallization and purification. Current efforts are focused on overcoming bottlenecks in protein production and crystallization by introducing the following improvements at different levels of the production pipeline: 1) improving overall levels of cellular expression of TMPs by altering protocols for cell growth and induction of expression; 2) increasing efficiency of cell lysis; 3) increasing the efficiency of detergent solubilization; 4) increasing the yield of 3C protease cleavage; 5) reducing the number of steps required for effective purification; 6) optimizing the amount of residual lipid purifying with the TMP; 7) developing protocols that allow production of highly concentrated protein solutions that do not also contain high detergent concentrations; 8) the use of additives such as lipids and enzyme inhibitors to stabilize purified proteins.

Targeting Strategies

30 Target ORFs are currently selected based on the following criteria:

1. Prediction of two or more transmembrane segments based on TMHMM and HMMTop

2. Absence of evidence that ORF is part of a hetero-multimeric complex, based on genomic/proteomic databases.

3. High level expression in C-terminal-tagged genomic Saccharomyces cerevisiae MORF library of Gelperin et al. (2005). (263 predicted integral membrane proteins in MORF library are expressed at levels of ~1mg/l. Of these, 90 have human orthologs)

4. Existence of a published procedure for assaying native state of produced protein.

MORF library vector (Gateway cloning)1

pSGP36 (Ligation independent cloning)

ORF cloning

pSGP40 (Ligation independent cloning)

Culture conditions: Issues

S. cerevisiae achieves >100 g/liter (dry cell weight) in fermentation on rich media

BUT: Plasmid losses of ~50% are observed for some of our strains on rich medium

ALSO: We find that growth at low temperatures (26oC) stabilizes some membrane proteins against subsequent precipitation.

Yeast Membrane Proteins Expressed in Yeast

1. To date, only three structures of heterologously expressed eukaryotic transmembrane proteins have been solved by x-ray crystallography. Both of these proteins were expressed in yeast.

2. Advantages of homologous expression system for post-translational modifications, membrane targeting, protein folding, lipid requirements

3. Extensive annotation of yeast genome as far as protein-protein interactions, subcellular localization, expression levels, protein function

4. Availability of yeast strains with altered protein degradation, unfolded protein response, post-translational modifications, intracellular trafficking

5. Rapid and inexpensive conditions for culturing yeast cells


Membrane Pellet

1.2M KCl;

120,000 x g spin

Salt-washed membranes

Detergent solubilization

26,000 x g spin


The C-terminal tags of many yeast membrane

proteins may be obscured by detergents

1. Many tagged yeast membrane proteins

are not efficiently cleaved by 3C protease

2. The activity of 3C protease is not

intrinsically sensitive to detergents.

3. Inefficient cleavage can sometimes be

overcome by adding large amounts of protease.

4. Affinity tags on yeast membrane proteins

do not appear to be as accessible as the

same tags on soluble proteins (His10 is

useful but His6 generally is not.)

5. Also: Use of Nickel-NTA resin inhibits

subsequent 3C protease cleavage whereas use of cobalt (Talon) does not.


(solubilized protein)

Detergent exchange

and dilution

Current bottlenecks/solutions

1. High-purity yeast transmembrane proteins are now being produced for crystallization and have successfully served as antigens for generating recombinant single chain antibodies for co-crystallization. The best yields of purified protein are 0.3 mg/l of culture.

2. The goal of “E. coli-fying” yeast as an expression system for membrane proteins will benefit from ongoing development of improvements in the following areas:

- Development of culture and induction conditions leading to increased overall expression of folded proteins.

- Use of repeated cycles of cell lysis for more complete recovery of targets.

- Selection of optimum detergent for efficient solubilization based on recent genome-scale surveys of detergent effectiveness such as that of White et al. (2007).

- Development of purification protocols that do not rely on cleavage of tags or engineering of specific proteases with enhanced activity toward detergent-solubilized proteins.

- Development of rapid purification protocols that maintain a population of protein-bound lipids.

- Maintenance of high protein concentration throughout purification to avoid extensive concentration of detergent in final steps.

3C protease




Static Light Scattering

Crystallization trials