Protein Phosphatase 2A Holoenzyme Assembly

Protein Phosphatase 2A Holoenzyme Assembly
Protein Phosphatase 2A Holoenzyme Assembly

Protein Phosphatase 2A Holoenzyme Assembly

IDENTIFICATION OF CONTACTS BETWEEN B-FAMILY REGULATORY AND SCAFFOLDING A SUBUNITS*

Received for publication,March 27,2002,and in revised form,March 29,2002Published,JBC Papers in Press,April 2,2002,DOI 10.1074/jbc.M202992200

Stefan Strack?§,Ralf Ruediger ?,Gernot Walter ?,Ruben K.Dagda?,Chris A.Barwacz?,and J.Thomas Cribbs?

From the ?Department of Pharmacology,University of Iowa,Iowa City,Iowa 52242and ?Department of Pathology,University of California at San Diego,La Jolla,California 92093

Protein serine/threonine phosphatase (PP)2A is a ubiquitous enzyme with pleiotropic functions.Trimeric PP2A consists of a structural A subunit,a catalytic C subunit,and a variable regulatory subunit.Variable subunits (B,B ?,and B ?families)dictate PP2A substrate specificity and subcellular localization.B-family sub-units contain seven WD repeats predicted to fold into a ?-propeller structure.We carried out mutagenesis of B ?to identify domains important for association with A and C subunits in vivo .Several internal deletions in B ?abolished coimmunoprecipitation of A and C subunits expressed in COS-M6cells.In contrast,small N-and C-terminal B ?deletions had no effect on incorporation into the PP2A heterotrimer.Thus,holoenzyme associa-tion of B-family subunits requires multiple,precisely aligned contacts within a core ?-propeller domain.Charge-reversal mutagenesis of B ?identified a cluster of conserved critical residues in B ?WD repeats 3and 4.Acidic substitution of paired basic residues in B ?(RR165EE)abolished association with wild-type A and C subunits,while fostering incorporation of B ?into a PP2A heterotrimer containing an A subunit with an op-posite charge-reversal mutation (EE100RR).Thus,bind-ing of A and B subunits requires electrostatic interac-tions between conserved pairs of glutamates and arginines.By expressing complementary charge-rever-sal mutants in neuronal PC6-3cells,we further show that holoenzyme incorporation protects B ?from rapid degradation by the ubiquitin/proteasome pathway.

The balance of protein kinase and phosphatase activities toward key proteins is central to many aspects of cellular https://www.360docs.net/doc/2b7543283.html,pared with kinases,protein phosphatases have received little attention,and appreciation that they may be just as precisely regulated as the enzymes whose action they oppose is relatively recent.

PP2A 1is one of the four major classes of serine/threonine phosphatases that also include PP1,PP2B (calcineurin),and PP2C.PP2A is highly conserved in eukaryotes (for recent re-views,see Refs.1and 2).It constitutes between 0.3%and 1%of

total protein in mammalian cells (3,4)and supplies the major-ity of soluble phosphatase activity toward phospho-serine and -threonine.PP2A is a holoenzyme of two or three subunits.A 36-kDa catalytic or C subunit complexes with a 65-kDa scaf-folding A subunit to form the AC core enzyme;the core enzyme can bind a third,variable subunit to form the PP2A heterotri-mer.In mammals,A and C subunits are each encoded by two highly similar genes (A ?/?and C ?/?),with A ?and C ?isoforms being more abundant.Regulatory subunits are encoded by three multigene families referred to as B,B ?,and B ?.The B family (also known as PR55)consists of four genes,B ?,B ?,B ?,and B ?,that give rise to proteins with molecular masses of 54–57kDa (5–9).The B ?family (also referred to as B56or PR61)consists of at least seven isoforms encoded by five genes (B ??,B ??,B ??,B ??,and B ??)(10–15),with molecular masses between 54and 74kDa.The four known members of the B ?family are designated according to their masses as PR48(16),PR59(17),and PR72/130(18).Several PP2A regulatory sub-units show restricted tissue expression;for instance,B ?and B ?can only be detected in brain (6,19).Proteins encoded by DNA tumor viruses,SV40small t and polyoma virus small and middle T antigen,are a fourth group of proteins that bind to the PP2A core enzyme and subvert its activity as a suppressor of cellular transformation (20–22).The AC dimer has also been shown to interact with other proteins,including the WD re-peat-containing proteins striatin and SG2NA (23).

Evidence is accumulating that regulatory subunits impart specific functions to PP2A holoenzymes (24,25).For example,B-family regulatory subunits have been implicated in the reg-ulation of cytoskeletal protein assembly (26–28),B ?subunits participate in the developmental Wnt/?-catenin signal trans-duction cascade (29,30),and B ?subunits may control the G 1-S cell cycle transition (16,17).Adenovirus type 5appears to induce apoptosis by interaction of its E4orf4protein with the B ?subunit of PP2A (31,32).How regulatory subunits function to mediate the diverse physiological functions of PP2A is poorly understood.There is in vitro evidence that regulatory subunits affect enzymatic activity and substrate specificity of PP2A (33).Localization studies have suggested that regulatory subunits target PP2A holoenzymes to distinct subcellular compartments (11,14,19).

The crystal structure of the scaffolding A ?subunit of PP2A has been solved (34),confirming a previous model based on secondary structure prediction and mutagenesis studies (35).The A subunit is a hook-shaped protein made up almost en-tirely of 15imperfect repeats,each about 40amino acids long.Each of these HEAT repeats (named after proteins that contain them:h untingtin,e longation factor,A subunit,and T OR ki-nase)consists of two antiparallel,amphipathic ?-helices.Loops between the two helices (intrarepeat loops)form a continuous

*This work was supported by funds from the Department of Phar-macology and the Biosciences Initiative of the University of Iowa and by seed grants from the Diabetes and Endocrinology Research Center (DK25295)and the College of Medicine.The costs of publication of this article were defrayed in part by the payment of page charges.This article must therefore be hereby marked “advertisement ”in accordance with 18U.S.C.Section 1734solely to indicate this fact.

§To whom correspondence should be addressed:Dept.of Pharmacol-ogy,University of Iowa College of Medicine,2-432BSB,51Newton Rd.,Iowa City,IA 52242.Tel.:319-384-4439;Fax:319-335-8930;E-mail:stefan-strack@https://www.360docs.net/doc/2b7543283.html,.1

The abbreviation used is:PP,protein serine/threonine phosphatase.

T HE J OURNAL OF B IOLOGICAL C HEMISTRY

Vol.277,No.23,Issue of June 7,pp.20750–20755,2002

?2002by The American Society for Biochemistry and Molecular Biology,Inc.Printed in U.S.A.

This paper is available on line at https://www.360docs.net/doc/2b7543283.html,

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ridge along the inside of the hook,providing interaction sur-faces for catalytic and regulatory subunits.Regulatory sub-units and viral antigens bind to the 10N-terminal repeats,whereas the catalytic subunit binds via repeats 11–15(35,36).The PP2A C subunit is thought to have a roughly globular structure similar to that of the related PP1C subunit (37,38).Knowing how regulatory subunits fold and interact with the core PP2A dimer is crucial for our understanding of the diverse roles of PP2A in cells.Here,we carry out deletion and site-directed mutagenesis in combination with structure modeling to identify domains and amino acids important for holoenzyme association of B-family regulatory subunits.By complementary charge-reversal mutagenesis,we show that adjacent arginines in B ?critically interact with adjacent glutamates in the A ?subunit.

EXPERIMENTAL PROCEDURES

Structure Modeling—An amino acid alignment of B-family regula-tory subunits from different phyla was submitted to the 3D-PSSM protein fold recognition web server (39),which generated a first-round model based on the structure of the G ?1subunit of heterotrimeric G proteins (40).This model was globally and locally optimized for bond lengths,angles,and torsions of side chains using the steepest decent algorithm of the Swiss PDB Viewer software (41).In addition,breaks in the C ?trace were ligated with a cutoff value of 3.0?,and missing hydrogen atoms were added to the model.Ribbon diagrams and surface representations of the optimized B subunit model were rendered,an-notated,and analyzed using Rasmol and Swiss PDB Viewer software.Mutagenesis—The rat cDNA for B ?was isolated by reverse tran-scription-PCR from rat brain total RNA (Access reverse transcription-PCR kit;Promega,Madison,WI),subcloned into a pcDNA3.1mamma-lian expression vector under control of the cytomegalovirus promoter,and FLAG epitope tagged at the N terminus by PCR.

The B ??26–38and ?379–447mutants were generated by restric-tion digestion of the wild-type plasmid with uniquely cutting restriction enzymes,followed by fill-in and recircularization reactions.The B ??1–20N-terminal truncation mutant was generated by PCR amplifica-tion of the coding sequence with nested primers encoding the FLAG tag and amino acids 21–25of B ?.

Generation of internal deletion mutants involved PCR amplification of two halves of the B ?cDNA-containing plasmid,one extending from the 5?end of the deletion to approximately halfway around the plasmid,and the other extending from the 3?deletion boundary to the same site in the vector backbone in the opposite direction.Reverse primers an-nealing to sequences 5?of the deletion and forward primers annealing to 3?deletion boundaries also included a unique Sac II site encoding a neutral “stuffer ”sequence (Ala,Ala-Ala,or Ala-Ala-Gly),and comple-mentary forward and reverse primers annealing to the plasmid back-bone introduced a unique Asc I site.PCR-generated plasmid halves were digested with Sac II and Asc I and ligated to produce the complete plasmid carrying the deletion.

The B ??434–447and ?440–447C-terminal truncation mutants were generated by site-directed mutagenesis of residues 434and 440,respectively,to termination codons.Site-directed mutagenesis was car-ried out by whole-plasmid synthesis with complementary primers har-boring mutations utilizing Pfu Turbo polymerase (Stratagene),followed by destruction of the template plasmid by digestion with Dpn I.All mutations were verified by automated sequencing.All A ?subunit plas-mids have been described previously (42).

Transfection and Immunoprecipitation—COS-M6cells (43)were cul-tured in Dulbecco ’s modified Eagle ’s medium containing 10%fetal bo-vine serum and 4.5g/liter glucose and seeded into 6-well plates for transfection on the next day at ?80%confluence.Cells were transfected with 4?l of LipofectAMINE 2000(Invitrogen)and 2?g of plasmid DNA.A ?and B ?subunits plasmids were cotransfected at 1:1mass ratios.After 36–48h,cells were rinsed once with phosphate-buffered saline,lysed in 250?l/well immunoprecipitation buffer (1%Triton X-100,150m M NaCl,20m M Tris,pH 7.5,1m M EDTA,1m M EGTA,1m M ?-glycerolphosphate,1m M Na 3VO 4,1m M Na 4P 2O 7,1?M microcystin-LR,1m M phenylmethylsufonyl fluoride,1?g/ml leupeptin,and 1m M benzamidine),and sonicated for 2s at low intensity with a probe tip sonicator.Debris was pelleted (20,000?g ,15min),and FLAG-tagged B ?subunits were immunoprecipitated from the cleared lysate with 6?l of anti-FLAG tag antibody (M2)conjugated to agarose (Sigma)by end-over-end rotation at 4°C for 3–16h.In some experiments,200?g/ml

FLAG epitope peptide was added to the cleared lysate as a specificity control.Immunoprecipitates were washed with 6–8ml of immunopre-cipitation buffer and solubilized in SDS sample buffer for immunoblot analysis using the following antibodies:rabbit anti-FLAG tag (Affinity Bioreagents,Golden,CO),mouse anti-EE tag (Babco,Richmond,CA),mouse anti-PP2A catalytic subunit (BD PharMingen),and rabbit anti-ubiquitin (Novocastra,Newcastle,UK).Blots were processed for chemi-luminescence detection (Pierce SuperSignal,Pierce,New York,NY),and digital images were captured on a Kodak Imaging Station 440.Signal intensities were quantified by digital densitometry using Na-tional Institutes of Health Image software (https://www.360docs.net/doc/2b7543283.html,/nih-image/).

RESULTS AND DISCUSSION

Structure Prediction of PP2A B-family Regulatory Sub-units—Mammalian B-family regulatory PP2A subunits (B ?-?)display high degrees of sequence conservation (?80%amino acid identity).Secondary structure prediction suggests that B-family regulatory subunits are almost entirely composed of ?-sheets and turns,whereas the B ?and B ?subunits are mostly ?-helical.Thus,PP2A regulatory subunit families have distinct primary and secondary structures.As has been noted previ-ously (44),B-family regulatory subunits contain several degen-erate WD repeats (four to seven,depending on the isoform and motif search threshold).WD (also called WD40or G ?)repeats are loosely defined,?40-amino acid sequence motifs that often end with the tryptophan-aspartate (WD)dipeptide (45).The amino acid sequence of B ?,a representative member of the B subunit family,aligned by WD repeat motifs is shown in Fig.1A .Seven degenerate WD repeats are separated by regions of 13–46residues in length (c-d loops).

The two WD repeat-containing proteins whose three-dimen-sional structure has been solved to date are the G ?1subunit of heterotrimeric G proteins (40)and the p40subunit of the arp2/3actin filament branching complex (p40-ARC;Ref.46).Both proteins fold into a seven-bladed ?-propeller,a toroid structure in which seven twisted,antiparallel ?-sheets are radially arranged around a common center.Each WD repeat contributes the outer (d)?-strand of one propeller blade and the inner three ?-strands (a ?c)of the next propeller blade (Fig.1B ).This phase-shift of sequence and structural motifs allows for closure of the torus by a “velcro ”mechanism (45).Sequences preceding the first WD repeat and trailing the last repeat may protrude from the core toroid (Fig.1B ).

Three web-based threading protein fold prediction algo-rithms (3D-PSSM (39),FUGUE (47),and 123D (https://www.360docs.net/doc/2b7543283.html,/123D/123D.html))identified G ?1as the closest structural homolog of PP2A B-family regulatory subunits,de-spite low sequence similarity (?15%identity).The structure of B-family regulatory subunits was modeled based on the G ?1crystal structure (see “Experimental Procedures ”).A ribbon diagram of this model shows the seven-bladed ?-propeller fold characteristic of WD repeat-containing proteins (Fig.1C ).Be-cause PP2A B-family regulatory subunits are larger than G ?1,portions of the larger loops connecting WD repeats are missing from the model.

Deletion Mutagenesis—To define regions and residues in B-family regulatory subunits critical for association with the AC core dimer,we carried out deletion and site-directed mutagen-esis of the B ?coding sequence.Mutant B ?cDNAs carrying an N-terminal FLAG epitope tag were transiently expressed in COS-M6cells in combination with the scaffolding A ?subunit tagged with a C-terminal EE epitope (42).FLAG-B ?was im-munoprecipitated and washed extensively,and in vivo incor-poration into the PP2A heterotrimer was assayed by blotting B ?immunoprecipitates for transfected A ?and endogenous C subunits.The ability of B ?mutants to associate with the core enzyme was quantified by densitometry as the ratio of C to B ?subunit bands in the same lane.In general,mutating B ?af-

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fected A ?and C subunit binding to similar degrees,supporting the notion that regulatory subunits interact with a structural unit of A and C subunits.A schematic diagram of the B ?deletion and truncation mutants is shown in Fig.2A .

B subunit family members differ considerably in their first 20–30residues.Deletion of the variable 20N-terminal amino acids of B ?(?1–20)had little effect on binding to the A and

C subunit (Fig.2B ),consistent with a role of these residues in mediating isoform-specific functions.This deletion extends into the predicted first (d)?-strand of W

D repeat 1,which,accord-ing to the crystal structures of G ?1and p40-ARC,is critical for closure of the ?-propeller core by interacting with the c-strand of WD repeat 7(see Fig.1B ).It is conceivable that the FLAG epitope tag can substitute for the 5residues deleted from WD repeat 1;alternatively,the boundaries of this structural motif in B ?may require revision.

At the C terminus,truncating the 8amino acids that follow the last WD repeat in B ?(?440–447)had no effect on holoen-zyme association.Extending the truncation by just 6amino acids (?434–447)to include the predicted c-strand of WD re-peat 7caused an almost complete loss of A and C subunit binding.Thus,residues 434–439are required for holoenzyme association,presumably because they interact with N-terminal residues to maintain the toroid structure of B ?.

Four internal deletions throughout the B ?protein ranging from 12to 32residues in length completely abrogated coimmu-noprecipitation of A and C subunits (3–7%of wild-type);only the ?381–401deletion displayed close to wild-type binding activity (Fig.2B ).Three of these critical deletions (?128–156,?259–270,and ?370–401)are predicted to affect surface-ex-posed loops connecting WD repeats,whereas ?26–38deletes a portion of WD repeat 1predicted to be buried in the protein.The apparent intolerance of the B ?core (residues 21–439)to small deletions suggests that the interaction of B-family sub-units with the AC dimer requires precise alignment of multiple interacting residues.

Charge-reversal Mutagenesis —Site-directed mutagenesis was carried out to delineate specific sites of holoenzyme inter-action.All B ?residues that were mutated are perfectly con-served in other mammalian B-family isoforms and their or-

thologs in worms,fruit flies,and yeast.Carrying out similar mutagenesis experiments with the A ?subunit,we had previ-ously identified charged residues in HEAT repeats 3(Glu

100

F I

G .2.Mapping the holoenzyme association domains of B ?by deletion mutagenesis.Wild-type (w.t.)FLAG-tagged B ?,the dia-grammed deletion mutants (A ),or vector alone was transiently expressed in COS-M6cells,immunoprecipitated (IP ),and tested for association with cotransfected A ?subunit (EE epitope-tagged)and endogenous C subunit by immunoblotting.A representative immunoblot is shown in B ;the broad band below the A ?subunit band is immunoglobulin heavy chain.Coimmunoprecipitated C subunit (C coIP )was quantified as the ratio of C to B ?subunit in each lane and is listed relative to wild-type B ?below the blot (average of two to four independent

experiments).

F I

G .1.Structure prediction of B-family regulatory subunits.A ,the amino acid sequence of B ?was aligned according to boundaries of the seven WD repeats and component ?-strands (d and a ?c )provided by the Pfam web application (https://www.360docs.net/doc/2b7543283.html,;Ref.54).Sequence conservation of WD repeats is indicated by gray and black shading .B ,schematic of ?-strand arrangement of the ?-propeller fold,highlighting the phase-shift of WD repeats (identified by shading )and propeller blades.C ,ribbon view of the B subunit model based on the G ?1crystal structure;note that the large loops connecting WD repeats (c –d loops)were not completely modeled.

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and Glu 101)and 5(Arg 183)important for binding to regulatory subunits and viral tumor antigens (42).Hence,we focused the B ?mutagenesis on charge-reversal of basic and acidic residues with the goal of identifying electrostatic interactions with the A ?subunit.

Three acidic-to-basic mutations of conserved residues in the N-terminal third of B ?(E66R,EE89RR,and D112K)had no effect on holoenzyme association (Fig.3).In contrast,four B ?mutants in WD repeat 3(RR165EE,D184K,E186R,and DD192RR)and two mutants in the loop connecting WD repeat 3and WD repeat 4(D212K and IK213EE)displayed severely reduced binding to A and C subunits (between 2%and 12%of wild-type).Mapping to WD repeat 4,B ?mutant ED219RR incorporated into the PP2A holoenzyme normally,whereas E223R was defective.Because B ??259–270was binding-in-competent (Fig.2B ),we tested the effect of mutating all acidic residues in this region.B ?D259R did not bind to the AC dimer,whereas B ?EE266RR,E269R,and D270R had little or no effect on the ability of B ?to associate with A and C https://www.360docs.net/doc/2b7543283.html,stly,the E343R mutation in WD repeat 6had an interme-diate effect on the ability of B ?to incorporate into the PP2A heterotrimer (40%residual binding of the C subunit;Fig.3).The results of the deletion and site-directed mutagenesis experiments are summarized in Fig.3B .B ?mutants were classified as critical or noncritical depending on the amount of coimmunoprecipitated C subunit (?15%and ?40%of wild-type,respectively).Most critical amino acid substitutions clus-ter in the middle of the molecule (165–259)encompassing WD repeats 3and 4.

Li and Virshup (48)have recently reported that two frag-ments of B ??can bind to the A ?subunit in glutathione S -transferase pull-down assays.Intriguingly,the corresponding regions in B ?and B ?/PR72also interacted with A ?,even though PP2A regulatory subunit families display little primary amino acid similarity and are classified into different struc-tural families according to protein fold prediction algorithms

(39,47).The N-terminal “A subunit binding domain ”defined by Li and Virshup corresponds to B ?residues 172–270,a region that we show here contains many residues necessary for ho-loenzyme association in vivo .The C-terminal A subunit binding domain encompasses B ?residues 302–360.We mutated E343in this region,which,according to Li and Virshup ’s domain alignment (48),is invariant in B,B ?,B ?subunits,and we observed an intermediate effect on PP2A holoenzyme formation.

Identification of Interacting Residues —We speculated that evolutionarily conserved and surface-exposed,charged resi-dues of B ?interact with residues of opposite charge in A ?

that

F I

G .4.Identification of interacting residues in B ?and A ?.Wild-type (w.t.)or mutant FLAG-tagged B ?and EE-tagged A ?subunits were coexpressed in the indicated combinations in COS-M6cells and tested for association by FLAG immunoprecipitation,followed by im-munoblotting for PP2A

subunits.

F I

G .5.Ubiquitination and proteasome-mediated degradation of monomeric B ?subunits in PC6-3cells.A ,the indicated combi-nations of wild-type (w.t.)and mutant B ?and A ?subunits (ER,EE100RR)were transiently expressed in PC6-3cells,and total lysates were immunoblotted for B ?(FLAG tag)and the endogenous C subunit.B ,indicated B ?mutants or the ?isoform of calcium/calmodulin-depend-ent protein kinase II (CaMKII ?)were expressed in PC6-3cells and treated for 2h before lysis without (?)or with (?)the proteasome inhibitor MG-132(50?M ).Total lysates were immunoblotted for the indicated proteins.C ,FLAG-B ?D212K was transfected and immuno-precipitated from PC6-3cells treated for 6h in the absence or presence of 50?M MG-132.Aliquots of immunoprecipitates were blotted for the FLAG tag (left )and ubiquitin (right ).To account for increased levels of B ?after MG-132treatment,twice the volume of the control immuno-precipitate was analyzed.The distributions of high molecular weight FLAG tag and ubiquitin immunoreactivities do not correspond well because of the disproportion of ubiquitin and FLAG epitopes in larger B ?

species.

F I

G .3.Identification of B ?residues important for holoenzyme association.A ,wild-type (w.t.)FLAG-tagged B ?,the indicated site-directed mutants,or empty vector was expressed in COS-M6cells and tested for association with transfected A ?(EE-tagged)and endogenous C subunits by coimmunoprecipitation (coIP ).The percentage binding of the C subunit was quantified as described in the Fig.2legend and is shown as the average of two to five experiments.B ,summary of B ?deletion and site-directed mutagenesis results.Critical mutations dis-playing ?15%wild-type C subunit binding activity are indicated on the top of the domain diagram;noncritical mutations (?40%wild-type binding)are indicated on the bottom of the domain diagram.

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we previously identified as critical for regulatory subunit asso-ciation (Glu 100,Glu 101,and Arg 183;Ref.42).Consequently,we coexpressed charge-reversal mutants of the A ?subunit (EE100RR and R183E)with all opposite charge-reversal mu-tants of the B ?subunit and tested for complementation,i.e.restoration of holoenzyme assembly by coimmunoprecipitation.We were unable to show association of any of the acidic-to-basic mutants of B ?with the basic-to-acidic mutant A ?R183E (data not shown).There are three potential reasons for this:1)we may have not mutated the interacting residue in B ?,2)A ?or B ?mutations,while potentially affecting interacting residues,may introduce structural changes that misalign other impor-tant amino acids,and 3)A ?R183may not interact directly with regulatory subunits.

However,when we paired A ?EE100RR with B ?RR165EE,we observed binding that was comparable to wild-type subunits (Fig.4).B ?RR165EE was unable to coimmunoprecipitate an-other binding-defective,acidic-to-basic A ?mutant,DW139RR (data not shown),demonstrating that the observed complemen-tation is not a consequence of altering the overall charge of the proteins.Thus,PP2A holoenzyme association is critically de-pendent on electrostatic interactions between adjacent gluta-mates in the A subunit (Glu 100and Glu 101in A ?)and adjacent arginines in B-family regulatory subunits (Arg 165and Arg 166in B ?).Because the EE100RR mutation in A ?interferes with binding of all regulatory subunit families (42),it is likely that B ?and B ?subunits also interact via basic residues.We reversed the charge of a pair of conserved lysine residues in B ??that is in a position similar to B ?Arg 165and Arg 166(B ??KK173DD),but this mutation did not disrupt PP2A holoenzyme assembly (data not shown).Additional studies are necessary to identify points of contact between A ?and B ?/B ?subunits.

Monomeric B ?Is Degraded by the Ubiquitin /proteasome Pathway —All B ?mutants could be expressed to similar,high levels in COS-M6cells,a cell line that supports plasmid repli-cation due to expression of the SV40large T antigen.Studying the effects of B ?mutants in the neuronal PC6-3subline of PC12cells (49),in which much lower levels of expression can be achieved,we noticed that holoenzyme formation-defective mu-tants could be expressed to at most 10%of wild-type B ?levels.This is shown for two mutants in Fig.5A .Importantly,expres-sion levels of B ?RR165EE,but not D212K,could be rescued by coexpression of the complementary A ?EE100RR mutant,in-dicating that low expression is a consequence of failure to incorporate into the PP2A holoenzyme.To investigate the mechanism of this effect,PC6-3cells were treated with the proteasome inhibitor MG-132for 2h before immunoblotting.Proteasome inhibition resulted in a massive increase of B ?protein levels but had no effect on levels of another transfected protein (calcium/calmodulin-dependent protein kinase II ?)or the endogenous PP2A C subunit (Fig.5B ).MG-132treatment led to the accumulation of higher molecular weight species of B ?D212K that were immunoreactive for ubiquitin (Fig.5C ).Similar results were obtained with the RR165EE mutant and wild-type B ?.

It was previously shown that transfected B ?subunits quan-titatively incorporate into the PP2A holoenzyme (11)and that ablation of PP2A A or C subunits by RNA interference de-creases the stability of regulatory subunits in Drosophila Schneider cells (25).The present results provide further evi-dence that PP2A subunit expression levels are stringently con-trolled in cells and suggest ubiquitination and proteasome-mediated degradation as a mechanism for rapid removal of monomeric regulatory subunits.

Structure modeling and site-directed mutagenesis support the model of PP2A holoenzyme structure shown in Fig. 6.B-family regulatory subunits adopt a ?-propeller fold that is found in other proteins engaged in multiple

protein-protein

F I

G .6.Model of the PP2A holoenzyme.A space-filling representation of the structure of the A ?subunit (34)is arranged with model structures of the C and B ?subunits (based on the PP1catalytic subunit (38)and G ?1(40),respectively;see the text).Residues whose mutation disrupts subunit association (critical)are indicated in black ;interacting residues are colored green .Arg 183(R183)and Trp 257(W257)are highlighted as representative of several critical residues in HEAT repeats 5and 7of the A ?subunit (42).Some critical B ?residues are not shown because they are either absent from the model (Lys 214and Asp 259)or are buried (Asp 192).

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interactions (40,46).By mutational complementation,we iden-tified electrostatic interactions between two conserved argin-ines in the outer (d)strand of WD repeat 3of B ?and two glutamates in the intrarepeat loop of HEAT repeat 3of A ?.Previous domain mapping and site-directed mutagenesis of the A subunit (35,36,42)and the present data argue for multiple additional contacts between regulatory and scaffolding sub-units.Also,regulatory subunit binding to the AC dimer is likely stabilized by direct interactions between B and C sub-units,possibly involving the carboxyl-methylated C terminus of the C subunit (50–53).Critical amino acids in B ?are located C-terminal of the A subunit-contacting residues Arg 165and Arg 166and cluster in WD repeats 3and 4and the intervening loop.We propose that this region forms extensive contacts with the intrarepeat loops of HEAT repeats 4–7of the A ?subunit,where many residues important for regulatory subunit binding are localized (42).Consistent with possible isoform-specific functions,we find that the divergent N-terminal tail of B ?is expendable for intersubunit interactions.Instead,N-terminal residues of B-family regulatory subunits may determine the subcellular localization of PP2A holoenzymes by interacting with specific anchoring proteins (19).Compatible with this view,the B ?N terminus faces away from the A subunit in our PP2A holoenzyme model.This report addresses the structural basis of PP2A holoenzyme function but requires ultimate verification and refinement by other methods such as crystallography.

Acknowledgments —We thank Nancy Lill for advice on the protea-some experiments and gifts of MG-132and ubiquitin antibody,Henry Paulson for PC6-3cells,Raul Dagda for technical assistance,and John Koland for comments on the manuscript.

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PP2A Holoenzyme Assembly

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二、产品应用 1,抗体纯化 纯化抗体一般用Protein A作为纯化的配体,也可以用Protein G或Protein L或异源性抗体作为配体。 2,小分子物质提取(以提取黄曲霉毒素M1为例) 试样通过免疫亲和柱时,黄曲霉毒素M1被提取。亲和柱内含有的黄曲霉毒素M1特异性单克隆抗体交联在固体支持物上,当样品通过亲和柱时,抗体选择性的与黄曲霉毒素M1(抗原)键合,形成抗体一抗原复合体。用水洗柱除去柱内杂质,然后用洗脱剂洗脱吸附在柱上的黄曲霉毒素M1,收集洗脱液。用带有荧光检测器的高效液相色谱仪测定洗脱液中黄曲霉毒素M1含量。 3,重组蛋白纯化 近年来,随着生物技术,特别是基因工程技术的迅猛发展,重组蛋白表达和纯化越来越容易。常用的重组蛋白表达策略是把蛋白与亲和标签融合表达,利用亲和标签一步纯化出目标蛋白。此方法无需了解蛋白质的生化特性或生理活性,就可通过带标签的重组融合蛋白选择性地与层析基质上的配体结合,从而得以纯化任何蛋白质。此方法与常规的层析方法不同之处在于,无需针对不同的蛋白质开发特定的配体和方法。采用保护蛋白质结构和功能完整性的温和条件,可一步亲和层析从粗提物中纯化出重组蛋白,纯度可达90%以上。 亲和标签已成为后基因组学时代纯化重组蛋白常用手段。亲和标签系统一般具有以下特征:(a)一步的吸附纯化;(b)对三级结构和生物活性影响小;(c)可方便且专一的去除以产生天然蛋白质;(d)在纯化过程中重组蛋白的分析简便准确;(e)适用于大量的不同蛋白质。但是没有哪个标签是完美的,只能根据实际需要去自己筛选,下表是分的标签以及纯化的方案。

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蛋白质结构预测方法综述

蛋白质结构预测方法综述 卜东波陈翔王志勇 《计算机不能做什么?》是一本好书,其中文版序言也堪称佳构。在这篇十余页的短文中,马希文教授总结了使用计算机解决实际问题的三步曲,即首先进行形式化,将领域相关的实际问题抽象转化成一个数学问题;然后分析问题的可计算性;最后进行算法设计,分析算法的时间和空间复杂度,寻找最优算法。 蛋白质空间结构预测是很有生物学意义的问题,迄今亦有很多的工作。有意思的是,其中一些典型工作恰恰是上述三步曲的绝好示例,本文即沿着这一路线作一总结,介绍于后。 1 背景知识 生物细胞种有许多蛋白质(由20余种氨基酸所形成的长链),这些大分子对于完成生物功能是至关重要的。蛋白质的空间结构往往决定了其功能,因此,如何揭示蛋白质的结构是非常重要的工作。 生物学界常常将蛋白质的结构分为4个层次:一级结构,也就是组成蛋白质的氨基酸序列;二级结构,即骨架原子间的相互作用形成的局部结构,比如alpha螺旋,beta片层和loop区等;三级结构,即二级结构在更大范围内的堆积形成的空间结构;四级结构主要描述不同亚基之间的相互作用。 经过多年努力,结构测定的实验方法得到了很好的发展,比较常用的有核磁共振和X光晶体衍射两种。然而由于实验测定比较耗时和昂贵,对于某些不易结晶的蛋白质来说不适用。相比之下,测定蛋白质氨基酸序列则比较容易。因此如果能够从一级序列推断出空间结构则是非常有意义的工作。这也就是下面的蛋白质折叠问题: 1蛋白质折叠问题(Protein Folding Problem) 输入: 蛋白质的氨基酸序列

输出: 蛋白质的空间结构 蛋白质结构预测的可行性是有坚实依据的。因为一般而言,蛋白质的空间结构是由其一级结构确定的。生化实验表明:如果在体外无任何其他物质存在的条件下,使得蛋白质去折叠,然后复性,蛋白质将立刻重新折叠回原来的空间结构,整个过程在不到1秒种内即可完成。因此有理由认为对于大部分蛋白质而言,其空间结构信息已经完全蕴涵于氨基酸序列中。从物理学的角度讲,系统的稳定状态通常是能量最小的状态,这也是蛋白质预测工作的理论基础。 2 蛋白质结构预测方法 蛋白质结构预测的方法可以分为三种: 同源性(Homology )方法:这类方法的理论依据是如果两个蛋白质的序列比较相似,则其结构也有很大可能比较相似。有工作表明,如果序列相似性高于75%,则可以使用这种方法进行粗略的预测。这类方法的优点是准确度高,缺点是只能处理和模板库中蛋白质序列相似性较高的情况。 从头计算(Ab initio ) 方法:这类方法的依据是热力学理论,即求蛋白质能量最小的状态。生物学家和物理学家等认为从原理上讲这是影响蛋白质结构的本质因素。然而由于巨大的计算量,这种方法并不实用,目前只能计算几个氨基酸形成的结构。IBM 开发的Blue Gene 超级计算机,就是要解决这个问题。 穿线法(Threading )方法:由于Ab Initio 方法目前只有理论上的意义,Homology 方法受限于待求蛋白质必需和已知模板库中某个蛋白质有较高的序列相似性,对于其他大部分蛋白质来说,有必要寻求新的方法。Threading 就此应运而生。 以上三种方法中,Ab Initio 方法不依赖于已知结构,其余两种则需要已知结构的协助。通常将蛋白质序列和其真实三级结构组织成模板库,待预测三级结构的蛋白质序列,则称之为查询序列(query sequence)。 3 蛋白质结构预测的Threading 方法 Threading 方法有三个代表性的工作:Eisenburg 基于环境串的工作、Xu Ying 的Prospetor 和Xu Jinbo 、Li Ming 的RAPTOR 。 Threading 的方法:首先取出一条模版和查询序列作序列比对(Alignment),并将模版蛋白质与查询序列匹配上的残基的空间坐标赋给查询序列上相应的残基。比对的过程是在我们设计的一个能量函数指导下进行的。根据比对结果和得到的查询序列的空间坐标,通过我们设计的能量函数,得到一个能量值。将这个操作应用到所有的模版上,取能量值最低的那条模版产生的查询序列的空间坐标为我们的预测结果。 需要指出的是,此处的能量函数却不再是热力学意义上的能量函数。它实质上是概率的负对数,即 ,我们用统计意义上的能量来代替真实的分子能量,这两者有大致相同的形式。 p E log ?=如果沿着马希文教授的观点看上述工作 ,则更有意思:Eisenburg 指出如果仅仅停留在简单地使用每个原子的空间坐标(x,y,z)来形式化表示蛋白质空间结构,则难以进一步深入研究。Eisenburg 创造性地使用环境串表示结构,从而将结构预测问题转化成序列串和环境串之间的比对问题;其后,Xu Ying 作了进一步发展,将蛋白质序列表示成一系列核(core )组成的序列,Core 和Core 之间存在相互作用。因此结构就表示成Core 的空间坐标,以及Core 之间的相互作用。在这种表示方法的基础上,Xu Ying 开发了一种求最优匹配的动态规划算法,得到了很好的结果。但是由于其较高的复杂度,在Prospetor2上不得不作了一些简化;Xu Jinbo 和Li Ming 很漂亮地解决了这个问题,将求最优匹配的过程表示成一个整数规划问题,并且证明了一些常用

蛋白质结构预测

实习 5 :蛋白质结构预测 学号20090***** 姓名****** 专业年级生命生技**** 实验时间2012.6.21 提交报告时间2012.6.21 实验目的: 1.学会使用GOR和HNN方法预测蛋白质二级结构 2.学会使用SWISS-MODEL进行蛋白质高级结构预测 实验内容: 1.分别用GOR和HNN方法预测蛋白质序列的二级结构,并对比异同性。 2.利用SWISS-MODEL进行蛋白质的三级结构预测,并对预测结果进行解释。 作业: 1. 搜索一条你感兴趣的蛋白质序列,分别用GOR和HNN进行二级结构预测,解释预测结果,分析两个方法结果有何异同。 答:所选用蛋白质序列为>>gi|390408302|gb|AFL70986.1| gag protein, partial [Human immunodeficiency virus] (1)GOR预测结果: 图1 图1是每个氨基酸在序列中所处的状态,可以看出序列的二级结构预测结果为: 1到9位个氨基酸为无规卷曲,10到33位氨基酸为α螺旋,34到37位为β折叠,38到45位为无规卷曲,46到49位为α螺旋,50到53位为无规卷曲,54到65为α螺旋,66到72位为无规卷曲,73到95位为α螺旋,96到101位为无规卷曲,102到108为β折叠,109到115位为无规卷曲,117位为β折叠。 图2 图2为各种结构在序列中所占的比例,其中Alpha helix占53.85%,Extended strand占11.11%,Random coil占35.04%,无他二级结构。

图3 图3为各个氨基酸在序列中的状态以及二级结构在全序列中二级结构分布情况。 (2)HNN预测: 图4 图4是每个氨基酸在序列中所处的状态,可以看出序列的二级结构预测结果为: 1到6位个氨基酸为无规卷曲,7到34位氨基酸为α螺旋,35到37位为β折叠,38位为α螺旋,39到44位为无规卷曲,45到49位为α螺旋,50到55位为无规卷曲,56到65为α螺旋,66到71位为无规卷曲,72到83位为α螺旋,84到86位为无规卷曲,87到95位为α螺旋,96到102为无规卷曲,103到108位为β折叠,108到117位为无规卷曲。 图5 图5为各种结构在序列中所占的比例,其中Alpha helix占55.56%,Extended strand占7.69%,Random coil占36.75%,无他二级结构。

蛋白质功能-结构-相互作用预测网站工具合集

蛋白质组学 蛋白质是生物体的重要组成部分,参与几乎所有生理和细胞代谢过程。此外,与基因组学和转录组学比较,对一个细胞或组织中表达的所有蛋白质,及其修饰和相互作用的大规模研究称为蛋白质组学。 蛋白质组学通常被认为是在基因组学和转录组学之后,生物系统研究的下一步。然而,蛋白质组的研究远比基因组学复杂,这是由于蛋白质内在的复杂特点,如蛋白质各种各样的翻译后修饰所决定的。并且,研究基因组学的技术要比研究蛋白质组学的技术强得多,虽然在蛋白质组学研究中,质谱技术的研究已取得了一些进展。 尽管存在方法上的挑战,蛋白质组学正在迅速发展,并且对癌症的临床诊断和疾病治疗做出了重要贡献。几项研究鉴定出了一些蛋白质在乳腺癌、卵巢癌、前列腺癌和食道癌中表达变化。例如,通过蛋白质组学技术,人们可以在患者血液中明确鉴定出肿瘤标志物。表1列出了更多的蛋白质组学技术用于研究癌症的例子。 另外,高尔基体功能复杂。最新研究表明,它除了参与蛋白加工外,还能参与细胞分化及细胞间信号传导的过程,并在凋亡中扮演重要角色,其功能障碍也许和肿瘤的发生、发展有某种联系。根据人类基因组研究,约1000多种人类高尔基体蛋白质中仅有500~600种得到了鉴定,建立一条关于高尔基体蛋白质组成的技术路线将有助于其功能的深入研究。 蛋白质组学是一种有效的研究方法,特别是随着亚细胞器蛋白质组学技术的迅猛发展,使高尔基体的全面研究变为可能。因此研究人员希望能以胃癌细胞中的高尔基体为研究对象,通过亚细胞器蛋白质组学方法,建立胃癌细胞中高尔基体的蛋白质组方法学。 研究人员采用蔗糖密度梯度的超速离心方法分离纯化高尔基体,双向凝胶电泳(2-DE)分离高尔基体蛋白质,用ImageMaster 2D软件分析所得图谱,基质辅助激光解吸离子化飞行时间质谱(MALDI-TOF MS)鉴定蛋白质点等一系列亚细胞器蛋白质组学方法建立了胃癌细胞内高尔基体的蛋白图谱。 最后,人们根据分离出的纯度较高的高尔基体建立了分辨率和重复性均较好的双向电泳图谱,运用质谱技术鉴定出12个蛋白质,包括蛋白合成相关蛋白、膜融合蛋白、调节蛋白、凋亡相关蛋白、运输蛋白和细胞增殖分化相关蛋白。通过亚细胞器分离纯化、双向电泳的蛋白分离及MALDI-TOF MS蛋白鉴定分析,研究人员首次成功建立了胃癌细胞SGC7901中高尔基体的蛋白质组学技术路线。 3.1 蛋白质功能预测工具 也许生物信息学方法在癌症研究中最常用的就是基因功能预测方法,但是这些数据库只存储了基因组的大约一半基因的功能。为了在微阵列资料基础上完成功能性的富集分析,基因簇的功能注解是非常重要的。近几年生物学家研发了一些基因功能预测的方法,这些方法旨在超越传统的BLAST搜索来预测基因的功能。基因功能预测可以以氨基酸序列、三级结构、与之相互作用的配体、相互作用过程或基因的表达方式为基础。其中最重要的是基于氨基酸序列的分析,因为这种方法适合于微阵列分析的全部基因。 在表3中,前三项列举了三种同源搜索方法。FASTA方法虽然应用还不太广泛,但它要优于BLAST,或者至少相当。FASTA程序是第一个使用的数据库相似性搜索程序。为了达到较高的敏感程度,程序引用取代矩阵实行局部比对以获得最佳搜索。美国弗吉尼亚大学可以提供这项程序的地方版本,当然数据库搜索结果依赖于要搜索的数据库序列。如果最近的序列数据库版本在弗吉尼亚大学不能获得,那么就最好试一下京都大学(Kyoto University)的KEGG站点。PSI-BLAST(位点特异性反复BLAST)是BLAST的转化版本,PSI-BLAST的特色是每次用profile 搜索数据库后再利用搜索的结果重新构建profile,然后用新的profile再次搜索数据库,如此反复直至没有新的结果产生为止。PSI-BLAST先用带空位的BLAST搜索数据库,将获得的序列通过多序列比对来构建第一个profile。PSI-BLAST自然地拓展了BLAST方法,能寻找蛋白质序列中的隐含模式,有研究表明这种方法可以有效地找到很多序列差异较大而结构功能相似的相关蛋白,所以它比BLAST和FASTA有更好的敏感性。PSI-BLAST服务可以

亲和层析预装柱和填料选择指南

18-1121-86Edition AG Affinity CHROMATOGRAPHY columns AND media Product profile

Ordering Information

Affinity Chromatography (AC) Affinity Chromatography separates proteins on the basis of a reversible interaction between a protein (or group of proteins)and a specific ligand attached to a chromatographic matrix. Affinity Chromatography can be used whenever a suitable ligand is available. The target protein(s) is specifically and reversibly bound by a complementary binding substance (ligand). The sample is applied under conditions that favour specific binding to the ligand. Unbound material is washed away, and the bound target protein is recovered by changing conditions to those favouring desorption.Desorption is performed specifically, using a competitive ligand,or non specifically, by changing the pH, ionic strength or polarity.Proteins are concentrated during binding and collected in a purified, concentrated form. The key stages in a separation are shown in Figure 1. Affinity Chromatography may also be used to remove specific contaminants, for example Benzamidine Sepharose FF (high sub)removes serine proteases such as trypsin, thrombin and factor Xa,and Blue Sepharose HP removes albumin. Media selection Parameters such as scale of purification and commercial availability of affinity matrices should be considered when selecting affinity media. HiTrap affinity columns are ideal for method optimization or small scale purification of target proteins using well established protocols. Affinity media can be prepared by coupling a ligand to a selected gel matrix. HiTrap NHS-activated HP is designed specifically to facilitate this process and is supplied with a recommended coupling procedure for coupling primary amines. For separations of glycoproteins and polysaccharides, media screening may be required to select the correct specificity. Figure 1. Typical affinity separation. Immunoglobulins While protein A and protein G affinity media are similar in many respects, their specificities for IgG differ. Protein G affinity media are the better choice for general purpose capture of antibodies since they bind IgG from a broader range of eukaryotic species and bind more subclasses of IgG. Species-specific examples include stronger binding of polyclonal IgG from cow, sheep and horse to protein G. Polyclonal rat IgG, human IgG 3 and mouse IgG 1 are bound by protein G but not by protein A. Generally,protein G has greater affinity for IgG and minimal binding of albumin resulting in cleaner preparations and greater yield.Conversely, protein A may be the better choice for isolating certain subclasses of IgG or for removing cross-species IgG contaminants from horse or foetal calf serum, for example.Purification of human and mouse IgM is possible by the use of HiTrap IgM Purification HP 1 ml column. The thiophilic adsorption media with 2-mercaptopyridine coupled to Sepharose HP is designed for one-step purification protocol resulting in 80–95%pure IgM. Purification of IgY from egg yolk is easily performed using HiTrap IgY Purification HP 5 ml column. The purity is over 70% in one-step using this special designed medium. Fusion proteins Expression of fusion proteins is needed when larger quantities of target protein are required for further characterization. We offer products to facilitate every step in this process, from choosing the correct expression system through to selecting the most suitable purification solution for GST and His-tagged proteins. Purification of a glutathione S-transferase fusion protein is simple, using mild elution conditions that minimize the risk of damage to the functionality of the target protein. The GST-tag is easily detected and can be removed in one-step if required.For routine purification of larger quantities of GST-tagged proteins, GSTrap FF, prepacked HiTrap 1 ml and 5 ml columns with Glutathione Sepharose 4 FF and HisTrap or HiTrap Chelating HP , for His-tagged proteins, provide the ideal solution.The columns are compatible with ?KTAdesign chromatography systems to ensure reproducible results under optimized conditions. Optimization parameters 1.Select correct specificity for target protein. 2.Follow manufacturer’s recommendations for binding and elution conditions. 3.Select optimum flow rate for sample application to achieve efficient binding. 4.Select optimum flow rate for elution to maximize recovery. 5.Select maximum flow rate for column regeneration to minimize run times. adsorption of sample and flow through of wash away unbound elute bound

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