Patent Application: US-24835794-A

Abstract:
the human immunodeficiency virus type 1 gag gene product is capable of directing the assembly of virion particles independent of other viral elements . the gag protein also plays an important role during the early stages of viral replication . employing the yeast two - hybrid system , a cdna expression library was screened and two host proteins identified . these proteins , designated cyclophilins a and b , interacted specifically with the hiv - 1 gag polyprotein pr55 gag . glutathione s - transferase - cyp fusion proteins bind tightly to pr55 gag in vitro . cyclosporin a efficiently disrupts the gag - cypa binding interaction . the identification of novel compounds capable of abrogating this protein - protein interaction employing the disclosed screening assay will facilitate the development of hiv - 1 antiviral agents .

Description:
this invention is directed to a method for determining whether a compound is capable of interfering with the formation of a complex between a retrovirus gag protein and a cyclophilin , which comprise the following steps : a ) incubating the compound with an appropriate cylophilin affinity fusion protein and the gag protein ; b ) contacting the incubate of step ( a ) with an appropriate affinity medium under conditions so as to bind the cyclophilin affinity protein complex , if such a complex forms ; and c ) measuring the amount of the cyclophilin affinity protein complex formed in step ( b ) so as to determine whether the compound is capable of interfering with the formation of the complex between the retrovirus gag protein and the cyclophilin . in one preferred embodiment the cyclophilin is selected from the group comprising cyclophilin a , b , c or d or combinations thereof . the affinity fusion protein may be gst - cyp and the gag protein may be pr55 gag or p24 . the affinity medium may be glutathione - agarose beads . the bound affinity protein may be analyzed using monoclonal or polyclonal antibodies . the above method may also be performed using an appropriate retrovirus gag affinity fusion protein . in one embodiment the gag protein or cylophilin protein may be labelled with a detectable moiety selected from a group consisting of a fluorescent label , a radioactive atom , and a chemiluminescent label . the cyclophilin affinity protein complex or the retrovirus gag affinity protein complex may be bound to the affinity medium . the cyclophilin affinity protein complex or the retrovirus gag affinity protein complex may be purified and removed from the affinity medium and the amount of the gag protein or cyclophilin may be determined . the above assays may be performed in vivo or in vitro . the above assay can also be extended to assays using protein expressed in baculovirus , tissue culture cells or gag purified from virus . a further embodiment of the invention is the use of an elisa assay , in which cyclophilin protein is bound to the bottom of 96 - well plates ; gag protein is added , and binding is detected using anti - gag antibodies . in addition gag protein may be labelled with a radioisotope , or a chemical marker such as biotin or β - galactosidase , thus precluding the need for an antibody for detection of binding . the invention also provides a method of disrupting a retrovirus life cycle in a cell which comprises contacting the cell with a compound which is capable of disrupting a retrovirus gag protein - cyclophilin interaction so as to thereby disrupt the retrovirus life cycle . the compound contacting the cell may be chemical molecule , cyclosporin , gag protein or fragments thereof . other compounds contacting the cell may be cylophilin or fragments thereof . the invention further provides for a method of disrupting a retrovirus life cycle in a mammal which comprises administering to the mammal a compound which is capable of disrupting a retrovirus gag protein - cyclophilin interaction so as to thereby disrupt the retrovirus life cycle . the compound administered to the mammal may be , a chemical molecule , cyclosporin a , gag protein or fragments thereof . other compounds administered to the mammal may be cylophilin or fragments thereof . for the above - identified compounds and methods the retrovirus may be selected from the following groups , avian leukosisarcoma , mammalian c - type , b - type viruses , d - type viruses , htlv - blv group , lentiviruses and &# 34 ; foamy viruses . the retroviruses may also be selected from the following examples , rous sarcoma virus ( rsv ), avian myeloblastosis virus ( amv ), avian erythroblastosis virus ( aev ), rous - associated virus ( rav )- 1 to 50 , rav - 0 , moloney murine leukemia virus ( mo - mlv ), harvey murine sarcoma virus ( ha - msv ), abelson murine leukemia virus ( a - mulv ), akr - mulv , feline leukemia virus ( felv ), simian sarcoma virus , endogenous and exogenous viruses in mammals , reticuloendotheliosis virus ( rev ), spleen necrosis virus ( snv ), mouse mammary tumor virus ( mmtv ), mason - pfizer monkey virus ( mpmv ), &# 34 ; saids &# 34 ; viruses , human t - cell leukemia ( or lymphotropic ) virus ( htlv ), bovine leukemia virus ( blv ), human immunodeficiency virus ( hiv - 1 and - 2 ), simian immunodeficiency virus ( siv ), feline immunodeficiency virus ( fiv ), ssv , rem , visna / maedi virus , equine infectious anemia virus ( eiav ), caprine arthritis - encephalitis virus ( caev ), progressive pneumonia virus , many human and primate isolates e . g ., simian foamy virus ( sfv ). this invention is also directed to pharmaceutical compositions comprising therapeutically effective amounts of compounds of the invention together with suitable diluents , preservatives , solubilizers , emulsifiers and adjuvants . administering a therapeutically effective amount refers to that amount which provides therapeutic effect for a given condition and administration regime . such compositions are liquids or lyophilized or otherwise dried formulations and include diluents of various buffer content ( e . g ., tris - hcl , acetate , phosphate ), ph and ionic strength , additives such as albumin or gelatin to prevent adsorption to surfaces , detergents ( e . g ., tween 20 , tween 80 , pluronic f68 , bile acid salts ), solubilizing agents ( e . g ., glycerol , polyethylene glycol ), anti - oxidants ( e . g ., ascorbic acid , sodium metabisulfite ), preservatives ( e . g ., thimerosal , benzyl alcohol , parabens ), bulking substances or tonicity modifiers ( e . g ., lactose , mannitol ), complexation with metal ions , or incorporation of the material into or onto particulate preparations of polymeric compounds such as polylactic acid , polyglycolic acid , hydrogels , etc . or into liposomes , microemulsions , micelles , unilamellar or multilamellar vesicles , erythrocyte ghosts , or spheroplasts . such compositions will influence the physical state , solubility , stability , rate of in vivo release . controlled or sustained release compositions include formulation in lipophilic deposits ( e . g ., fatty acids , waxes , oils ). also included in this invention are particulate compositions coated with polymers ( e . g ., poloxamers or poloxamines ). other embodiments of the compositions of the invention incorporate particulate forms protective coatings and permeation enhancers for various routes of administration , including parenteral , pulmonary , nasal and oral . the following examples are offered to more fully illustrate the invention , but are not to be construed to limit the scope thereof . identification of cdnas encoding proteins that interact with pr55 gag using the two hybrid system to identify host proteins that interact specifically with pr55 gag , a library of plasmids that express gal4 activation domain - cdna expression library fusion proteins was first created . inserts from an undifferent human leukemia cell line ( hl - 60 ) cdna library were subcloned into a gal4 activation domain expression plasmid , pgadnot , and five pools were collected , each consisting of more than 150 , 000 bacterial colonies . saccharomyces cerevisiae strain ggy1 :: 171 containing a gal4 - responsive lacz gene ( gill and ptashne , 1987 ) was transformed with pgal4db - hg ( luban et al ., 1992 ), encoding a gal4 dna - binding domain - pr55 gag fusion protein , and transformants were selected for histidine prototrophy . these lines were then transformed with the pgadnot - cdna library dna , selecting for leucine prototrophy . cotransformants were plated at a density of approximately 3000 colonies per 100 mm plate . nitrocellulose replicas of the colonies were assayed for β - gal activity by freeze fracturing the cells and incubating in buffer containing 5 - bromo - 4 - chloro - 3 - indolyl - β - d - galactoside ( x - gal )( breedon and nasmyth , 1985 ). colonies were considered to express β - gal activity if they turned blue within 8 hours . of 500 , 000 colonies screened for β - gal activity , 20 were scored as positive . eleven pgadnot cdna plasmids were successfully isolated , and all produced β - gal activity when retested against pgal4db - hg in ggy1 :: 171 ( table 1 ). table 1__________________________________________________________________________hl - 60 cdna library pgadnot clones promoting β - gal activity in yeastcotransformedwith pgal4db - hginsert size β - gal activity in yeast . sup . a ( number of genebank match versus versusclone . sup . b nucleotides ) ( locus ; accession #) pgal4db - hg pgal4db clone alone__________________________________________________________________________2 . 1 1 , 300 human mrna for t cell + -- -- cypa ( gb : humcycr ; y00052 ) 4 . 1 900 human cypb mrna ( gb : + -- -- humcypba ; m60857 ) 3 . 1 620 rat mrna for ribosomal + + -- protein l8 ( gb : ratrpl8 ; x62145 ) 3 . 2 560 rat mrna for ribosomal + + -- protein l23a ( gb : ratrpl23a ; x65228 ) 2 . 2 650 chicken mrna for ribosomal + + -- protein l27 ( gb : chkrpl27 ; x56852 ) 1 . 4 , 1 . 5 , 400 yeast yl41a gene for + + -- 2 . 4 ribosomal protein yl41 ( gb : yscyl41a ; x16065 ) 3 . 3 250 human 28s ribosomal rna + + -- gene ( gb : humrgm ; m11167 ) 2 . 3 650 human autoantigen small + + -- nuclear ribonucleoprotein sm - d mrna ( gb : humsnrnpd ; j03798 ) 1 . 3 1 , 300 no match + + -- __________________________________________________________________________ . sup . a the first number refers to the library pool , the second to the individual clone . . sup . b following plasmid isolated in bacteria , pgadnotcdna clones were retransformed into yeast strain ggy1 :: 171 using standard methods ( becker and guarente , 1991 ) with the indicated plasmids . colonies were lifted and stained for gal activity as described ( breedon and nasmyth , 1985 ). entrie indicate the presence or absence of blue color with transformants . two of the clones ( 2 . 1 and 4 . 1 ) were more active than the others ; while some of the clones required as much as 8 hours before activity was detectable , these two clones were clearly positive within 10 minutes . though none of the plasmids produced β - gal activity when singly transformed into yeast , nine of the clones were active when cotransformed with pma424 , the parent plasmid encoding the gal4 dna - binding domain without pr55 gag . this result suggested that these nine clones did not depend on the presence of the pr55 gag protein for activity . the two true positive clones ( 2 . 1 and 4 . 1 ) were the clones that produced the most activity in combination with pgal4db - hg . to test whether the activity of these clones was somehow peculiar to transcriptional regulation by gal4 , all 11 pgadnot clones were tested for the ability to produce β - gal activity in a different yeast strain , cty 10 - 5d , which possesses an operator with lexa - binding sites upstream of the transcriptional start site of the gal1 - lacz gene . each of the 11 pgadnot clones produced β - gal activity when cotransformed with a plasmid encoding a lexa - pr55 gag fusion protein . curiously , unlike the false positive activity detected with 9 of the 11 clones using the gal - 4 system , none of the clones produced β - gal activity when co - transformed with the parent lexa plasmid that contained no pr55 gag sequences . thus , all 11 clones seemed to exhibit pr55 gag - dependent activation in this system . cdna clones identified in the genetic screen encode rna - binding protein and cyps dna sequences were obtained for the inserts of the 11 clones identified in the genetic screen , and all but one clone ( 1 . 3 ) gave a highly significant match with sequences from genbank ( table 1 ). of the nine false positive clones , eight were found to encode proteins with rna binding activity . this finding suggests that some property of these clones ( either the rna binding activity itself or , perhaps , merely the presence of basic amino acids ) contributes to the false positivity . the two true positive clones , 2 . 1 and 4 . 1 , encoded two proteins of the same family , cypa and cypb . the sequences at the 5 &# 39 ; end of the inserts of clones 2 . 1 and 4 . 1 are shown in fig1 b and 1c , respectively . the insert in clone 2 . 1 begins in the 5 &# 39 ; untranslated portion of the cypa rna , 9 nt before the initiator methionine , and continues through the entire open reading frame past the non - coding sequences at the 3 &# 39 ; end of the gene . the insert in clone 4 . 1 begins at the tenth codon of cypb and continues through the open reading frame past the 3 &# 39 ; noncoding sequences of the gene . in subsequent screening of the same pools , recovered three additional plasmids containing cypb cndas were recovered ; one of these was identical to clone 4 . 1 , and two have distinct junction positions at the 5 &# 39 ; end . fragments of pr55 gag fused to the gal4 dna - binding domain retain the ability to activate transcription in yeast expressing gal4 - cyp fusion proteins to localize the portion of gag that mediates binding to the cyps , the effect on binding of mutations in the pr55 gag coding sequence was examined . a panel of mutants , including deletions of 5 &# 39 ; and internal coding sequences and insertions of linkers with stop codons ( fig2 ), was transferred into the expression vector encoding the gal4 dna - binding domain . each of these plasmids encodes a stable fusion protein of the expected size detected on western blot ( luban et al ., 1993 ). none of these fusion proteins was capable of activating lacz activity independently . these plasmids were tested for the ability to activate transcription from the lacz gene in yeast cotransformed with either of the two gal4 activation domain - cyp fusion protein expression plasmids ( fig2 ). in all cases , the results were the same for the cypa and the cypb fusion proteins , gag sequences 5 &# 39 ; of nucleotide 906 and 3 &# 39 ; of nucleotide 1787 could be deleted with no effect on activity ; these regions clearly were not essential for the interaction of pr55 gag with cyp proteins . nine linker insertion mutations in the pr55 gag coding sequence , each with a 12 nt insertion , were tested for their effects on binding to the cyps . of the nine linker mutations , three had effects on pr55 gag - cyp interactions ( fig2 ). mutant r1509 disrupted binding to either cypa or cypb . mutants dr1337 and a1411 were unable to binding to cypa ; dr1337 was partially disruptive of binding to cypb , but a1411 had no effect on binding to cypb . the three disruptive mutants cluster within the 5 &# 39 ; half of the ca coding sequences . taken together , the results of the analysis with the pr55 gag deletion and linker insertion mutants demonstrate that the part of pr55 gag necessary for binding to the cyps lies within the amino - terminal two - thirds of ca and the carboxy - terminal half of the matrix protein . cyps do not bind gag polyproteins of retroviruses distantly related to hiv - 1 the gag polyproteins of simian immunodeficiency virus type 1 ( siv - 1 ), mason - pfizer monkey virus ( mpmv ), and moloney murine leukemia virus ( momlv ), as well as the integrase protein ( in ) of hiv - 1 were tested to determine whether they were capable of interacting with the cyp proteins in the two hybrid system . each retroviral gag polyprotein , as well as in , is capable of forming homomultimers ( j . l and s . p . g ., unpublished data ; g . v . k . and s . p . g ., submitted ). as shown previously , hiv - 1 pr55 gag showed activity against both cypa and cypb ( table 2 ). table 2______________________________________β - gal activity in yeast expressing gal4 hybrid proteins . sup . a β - gal activity versus versus gene fused to gal4 clone clone cloneplasmid dna - binding domain 2 . 1 4 . 1 alone______________________________________pgal4db - hg hiv - 1 pr55 . sup . gag + + -- pgal4db - sg siv . sub . mac230 pr57 . sup . gag -- + -- pgal4db - mpg mpmv pr76 . sup . gag -- -- -- pgal4db - mg momlv pr65 . sup . gag -- -- -- pgal4db - in hiv - 1 p32 ( in ) -- -- -- ______________________________________ . sup . a yeast strain ggy1 :: 171 was transformed with the indicated plasmids using standard procedures ( becker and guarente , 1991 ). yeast colonies wer lifted and stained for gal activity as described ( breedon and nasmyth , 1985 ). entries indicate the presence or absence of blue color with transformants . the gag polyprotein of siv also had activity against cypb but not against cypa . the gag polyproteins of mpmv or momlv and of hiv - 1 in had no detectable activity against either of the cyps tested . the gag polyproteins of hiv - 1 and closely related retroviruses interact with the cyp proteins , but that the gag polyproteins of more distantly related retroviruses are not capable of carrying out this interaction . to demonstrate in vitro binding of gag polyproteins to the cyps , inserts from clones 2 . 1 and 4 . 1 were first subcloned into a bacterial expression plasmid , to express the cyp proteins as glutathione s - transferase ( gst ) fusion proteins . gst fusion proteins may be purified in a single step using glutathione - agarose beads ( g beads ) ( smith and johnson , 1988 ), and this system has been used to demonstrate protein - protein interactions in vitro ( kaelin et al ., 1991 ). in addition , other groups have shown that gst - cyp fusion proteins retain both peptidylprolyl cis - trans isomerase and drug binding activities ( friedman and weissman , 1991 ; liu et al ., 1991 ). the resulting plasmids , pgcypa and pgcypb , encoding gst - cypa and gst - cypb fusion proteins , were transformed into bacteria . following induction with isopropyl - β - d - thiogalactopyranoside , the fusion proteins gst - cypa ( fig3 lane 4 ) and gst - cypb ( fig3 lane 2 ) constituted a significant fraction of the total bacterial protein in crude lysates . the fusion proteins were readily recovered by incubating the soluble fraction of the total bacterial lysate with g beads and washing the beads three times . the purity of the proteins could be assessed by electrophoresis after elution with sodium dodecyl sulfate ( sds ) ( fig3 ). roughly 70 % of the protein had the expected mobility for the cyp fusion proteins . additional proteins corresponding to the mobility of gst alone , as well as several unidentified bands of slower mobility , were detected . as a source of pr55 gag protein , a preparation of total soluble protein from bacteria transformed with pt7hg ( pro - ) ( luban and goff , 1991 ) was first used . in addition to intact pr55 gag , two smaller degradation products are reproducibly seen on western blot with anti - p24 monoclonal antibody ( fig4 a , lane 1 ). when the gag protein was incubated with lysates containing either gst - cypa or gst - cypb prior to or concurrent with the addition of g beads , pr55 gag was quantitatively recovered and easily detected on western blot ( fig4 a , lanes 4 and 5 ) or on coomassie blue - stained gels . in control experiments , no detectable gag protein bound to g beads alone ( fig4 a , lane 2 ) or to gst bound to g beads ( fig4 a , lane 3 ). the ability of bacterially expressed hiv - 1 in to bind to the gst - cyp proteins was tested . in showed very faint binding to the gst - cyp proteins ( fig4 b , lane 4 ), but this binding was below the background level of in binding to g beads alone ( fig4 b , lane 2 ). also , this binding was insignificant when compared with the binding of in to gibp ( fig4 b , lane 5 ), a gst fusion protein with a new host protein identified in the gal4 two hybrid system that binds to hiv - 1 in ( g . v . k . and s . p . g ., unpublished data ). using the same in vitro binding assay , the ability of fragments of pr55 gag to bind to the gst - cyp proteins was tested . two gag proteins encoded by plasmids with terminators at positions 1906 and 1787 ( with respect to the 5 &# 39 ; end of the dna provirus ) bound specifically to the gst - cyp proteins . the bacterially expressed hiv - 1 ca ( p24 ) was also capable of binding specifically ( fig4 c ). thus , using the in vitro binding assay to map the gag sequences necessary for binding to cyp , results consistent with those obtained in the yeast two hybrid system were obtained . two gag protein , pr55 gag and p24 , are capable of binding to the cyp proteins . pr55 gag - cyp binding persists under conditions of high salt and detergent the effect of salt and detergent on the recovery of gag by the gst - cyp proteins was examined . the substitution of edta for mg 2 + and ca 2 + in the incubation buffer caused a 2 - fold decrease in binding ( compare lanes 2 and 3 in fig5 a ). the pr55 gag - gst - cypa interaction was inhibited by increases of salt in the binding buffer , but was still easily detected in the presence of 200 mm kci ( fig5 a , lane 4 ). binding was still apparent after the addition of 0 . 03 % sds ( fig5 a , lane 8 ). with gst - cypb there was detectable pr55 gag bound with as much as 1000 mm kci ( fig5 b , lane 3 ) or 0 . 1 % sds ( fig5 b , lane 5 ). the interaction of pr55 gag with the gst - cyp proteins is of a respectable strength , but that the binding to gst - cypb is more resistant to disruption by both salt and ionic detergents than that of gst - cypa . the cyps are the intracellular targets of the immunosuppressive drug csa and are known to bind with a dissociation constant of roughly 6 × 10 - 9 mol / l ( liu et al ., 1992 ), though values in the range of 200 to 2 × 10 - 9 have been reported ( sigal and dumont , 1992 ). to determine whether csa would affect the pr55 gag - cyp interaction , the gst - cyp proteins with csa prior to the addition of pr55 gag protein were incubated . pr55 gag binding to either gst - cypa or gst - cypb protein was inhibited by csa ( fig6 a ). titration of csa showed that the concentrations of csa required for inhibition of pr55 gag - cyp binding were different for the two gst - cyp proteins . in these experiments it was estimate that the concentration of the pr55 gag was roughly 0 . 2 μm and that of gst - cyp was roughly 0 . 8 μm . for gst - cypa , the slope of the pr55 gag binding inhibition curve was very steep ( fig6 a and 6b ), such that pr55 gag binding was not affected at 0 . 4 μm csa but was completely disrupted by 0 . 8 μm , close to the concentration of the gst - cypa . surprisingly , the same curve was not seen with gst - cypb ; there was a gradual inhibition of binding seen from 0 . 08 - 8 μm csa , but even at 80 μm there was still detectable pr55 gag bound . control experiments showed that csa had no effect on the p32 ( in ) interaction with gibp . csa specifically disrupts the interaction of pr55 gag with gst - cyp proteins . either the binding sites overlap or binding of csa induces conformational changes that prevent binding of pr55 gag . csa was less effective at disruption of the cypb interaction than the cypa interaction . the ca 2 + - calmodulin - dependent protein phosphatase calcineurin ( cn ) is an important enzyme in the signaling pathways that lead to interleukin - 2 release following t lymphocyte activation ( clipstone and crabtree , 1992 ). a complex consisting of cyp protein and csa has been shown to bind to and inhibit the activity of cn ( liu et al ., 1991 , 1992 ) and thus to disrupt the process of t cell activation . neither cyp protein nor csa is capable of binding to cn independently . since infection with hiv - 1 disrupts t cell function and number ( fauci , 1988 ), the complex of gst - cyp proteins with pr55 gag could bind to cn was examined . detection of the binding of cn by the complex of gst - cypa plus csa was first demonstrated ( fig7 a , lane 2 ; fig7 b , lanes 2 and 3 ; fig7 c , lane 1 ). cn was detected with as little as 0 . 08 μm csa added to the reactions . as expected , gst - cypa alone does not bind cn ( fig7 a , lane 1 ; fig7 b , lane 5 ; fig7 c , lane 2 ). the complex of gst - cypa ( fig7 a , lane 3 ) or gst - cypb ( fig7 b , lane 7 ) plus pr55 gag was not capable of binding detectable quantities of cn . the same result was obtained in multiple experiments , including some in which the gst - cyp proteins were incubated with milligram quantities of pr55 gag ( fig7 b , lane 7 ); the pr55 gag concentrations in these experiments were at least 10 - fold greater than the csa concentrations necessary to detect binding of cn . there was no factor present in the bacterial lysates containing pr55 gag that inhibited csa - gst - cyp from binding cn . the binding of cn to a complex of gst - cyp and p24 was not seen ( fig7 c ). thus , the complex of pr55 gag or p24 with either of the cyp proteins was capable of binding to cn was not observed . the two hybrid system was used to screen for cdnas encoding proteins that interact with pr55 gag has revealed a significant interaction with the class of proteins known as cyps . colonies ( 5 × 10 5 ) were initially screened , and two clones were identified , both of which express gal4 - cyp fusion proteins . subsequent screening resulted in the recovery of three additional cyp clones . this binding is readily demonstrated in vitro , persists under conditions of high salt and detergent ( fig5 ), and is inhibited by csa at concentrations that suggest that the binding of csa titrates the binding sites on the cyps for the pr55 gag ( fig6 ). csa is more effective at disruption of the gag - cypa interaction than the gag - cypb interaction . these results extend the proteins identified with the two hybrid system from those that interact with transcriptional regulators ( chevray and nathans , 1992 ; chien et al ., 1991 ; hardy et al ., 1992 ) and protein kinases ( yang et al ., 1992 ) to include proteins that interact with a viral structural protein . the nine false positive clones identified in the assay all encode proteins with rna binding activity ( table 1 ). why such clones score positive , a similar array of genes encoding rna - binding proteins in screens with other retroviral gags have been recovered . these clones were identified as false positive because they had activity against the parent gal4 dna - binding domain expression plasmid without gag sequences . though they were active against a lexa - pr55 gag expression plasmid , they did not interact with the parent lexa expression plasmid and would have been falsely identified as true positives if the library had only been screened with the lexa two hybrid system . since at least two different cyps bind to gag protein , the conserved core that is common between the different cyps ( stamnes et al ., 1992 ) most likely confers the ability to bind to the gag protein . from the data it is not possible to conclude whether one cyp is more important than another in terms of binding to gag . a member ( s ) of the cyp family other than the two that were cloned could also be a relevant partner ( s ) for interaction with gag . knowledge of the cellular compartment in which the gag - cyp interaction takes place would provide an important clue as to which cyp is the relevant partner for gag protein . the central portion of pr55 gag ( fig2 ) and the separate p24 ( ca ) ( fig4 c ) are capable of binding to cyps . therefore , either pr55 gag or p24 may be the biologically relevant partner in the gag - cyp interaction . since pr55 gag is present in the cell at the time of virion particle assembly and p24 is probably only present in the cell acutely following infection , it is possible that the gag - cyp takes place at either stage of the retroviral life cycle . there is no obvious structural similarity between pr55 gag and csa that would suggest a binding motif . the csa - cyp is probably monomeric in solution ( theriault et al ., 1993 ), but may form a complex decameric structure consisting of two pentamers at high concentrations ( pflugl et al . 1993 ). competition data between pr55 gag and csa for binding to cypa have a very steep curve . pr55 gag is capable of forming homomultimers ( luban et al ., 1992 ), the curve may reflect the need for the complete titration of all available csa - binding sites on the cypa before displacement of a large oligomeric gag complex occurs . alternatively , it may reflect a cooperativity of gag binding within the gag - cyp complex that is disrupted by csa . although there is a tremendous amount of information about the cyps , a class of proteins found throughout nature ( heitman et al ., 1992 ; stamnes et al ., 1992 ), all the functions of the cyps are not known with any certainty . the cyps possess a conserved core sequence with variable amino and carboxyl termini that direct them to different cellular compartments . these proteins possess peptidyl - prolyl cis - trans isomerase activity and may have a role in directing the proper folding of cellular proteins . csa , a drug that disrupts the cyp isomerase activity , blocks collagen triple helix assembly in fibroblasts ( steinmann et al ., 1991 ) and prevents formation of the correct disulfide - bonded form of transferrin in hepg2 cells ( lodish and kong , 1991 ). cyps may also play a role in directing proteins to the proper locations within cells . transit from the endoplasmic reticulum of specific isoforms of rhodopsin is blocked in drosophila by mutations in the ninaa gene , a member of the cyp family ( colley et al ., 1991 ; stamnes et al ., 1991 ). thus , the cyp proteins may be important for the proper folding of gag proteins or for targeting them to the cell membrane . preliminary experiments examining the effect of csa on hiv - 1 replication have revealed that the drug may block infection if present at the time of infection ( wainberg et al ., 1988 ) or decrease the yield of infectious particles released by the cells ( karpas et al ., 1992 ). these effects are confounded by the effects of the drug on the activation state of the t cell and on transcription from the viral promoter . some of these issues might by clarified by studying the effect on viral replication of compounds such as meala - csa ( sigal et al ., 1991 ) that bind to cyps but do not suppress t cell activation . the gag - cyp interaction may not be important for other retroviruses , since the gag polyproteins of mpmv and momlv did not bind to the cyps ( table 2 ). interestingly , the gag polyprotein of siv - 1 , an immunosuppressive retrovirus closely related to hiv - 1 , had activity against cypb . as part of a complex with cyp , csa inactivates the phosphatase activity of cn and disrupts pathways that lead to transcriptional activation in t cells ( mckeon , 1991 ; schreiber and crabtree , 1992 ). it may be postulated that gag might inhibit t cell responses via a similar mechanism . hiv - 1 gag protein exhibits csa - inhibitable binding to cyp proteins was not demonstrated and the gag - cyp complex was capable of binding to cn was not demonstrated ( fig7 ). thus , gag protein does not seem directly to mimic csa in its effect on the t cell activation pathway . the relationship between gag protein and csa may be analogous to that of rapamycin and fk506 . rapamycin and fk506 are immunosuppressive compounds that inhibit t cell responses via an interaction with the same immunophilin , fkbp . as with the csa - cyp complex , the fk506 - fkbp complex is capable of binding to and inhibiting the phosphatase activity of cn ( liu et al ., 1991 , 1992 ), thereby blocking pathways of t cell activation . rapamycin competes with fk506 for binding to fkbp ( bierer et al ., 1990 ), but the complex of rapamycin - fsbp is not capable of binding cn . perhaps the rapamycin - fkbp complex binds to a phosphatase as yet unidentified ( schreiber , 1992 ) that is also a target of the gag - cyp complex . it has been suggested that there is a native ligand for cyp that regulates the activation state of the t cell ( schreiber and crabtree , 1992 ). a 77 kd cyp - binding protein has been identified that might serve this function ( friedman and weissman , 1991 ). rather than promoting binding to a regulatory enzyme like cn , gag protein might affect the host cell by disrupting the binding of cyps with a native ligand . several hiv - 1 genes have been associated with the cytotoxic or immunosuppressive effects of the virus . hiv - 1 protease has been shown to be active in the cytoplasm of infected cells ( kaplan and swanstrom , 1991 ) and to be toxic in cell culture ( krausslich et al ., 1993 ). this might be because intermediate filaments serve as protease substrates in cells ( shoeman et al ., 1990 ). purified tat protein , as well as synthetic tat peptide , inhibits antigen - stimulated lymphocyte proliferation ( viscidi et al ., 1989 ). there are conflicting reports about the ability of the nef gene product to block the induction of interleukin - 2 transcription ( luria et al ., 1991 ; schwartz et al ., 1992 ). the env gene product gp120 has been implicated in the immunopathogenesis of hiv - 1 by several mechanisms . env protein is cytotoxic via syncytia formation and may serve as a cell surface signal for the immune system to eliminate hiv - infected cells ( pantaleo et al ., 1993 ). there are also conflicting reports about the role of env gene products in immunosuppression ; purified gp120 may ( kornfeld et al ., 1988 ; weinhold et al . 1989 ) or may not ( horak et al ., 1990 ; kaufmann et al ., 1992 ) affect t cell activation , and gp120 - cd4 interactions may or may not be necessary or the activation - induced cell death ( apoptosis ) that is hypothesized to play a role in the cd4 + t cell destruction seen in aids patients ( groux et al ., 1992 ; laurent - crawford et al ., 1991 ; meynaard et al ., 1992 ; terai et al ., 1991 ). the apoptosis observed with hiv - 1 - infected t cells can be blocked by csa ( groux et al ., 1992 ) and might in fact be related to the gag - cyp interaction . murine monoclonal antibody against hiv - 1 p24 was obtained from biotech research labs , incorporated , billerica , mass . murine monoclonal antibody against hiv - 1 p32 ( in ) was a gift from dr . dag helland ( university of bergen , bergen , norway ). horseradish peroxidase - linked sheep anti - mouse immunoglobulin antibody was obtained from amersham international ( england ). bovine brain cn ( phosphatase 2b ) and calmodulin and murine monoclonal antibody against the cn β subunit were obtained from upstate biotechnology , incorporated , lake placid , n . y . csa ( sandimmune i . v .) was obtained from sandoz pharmaceuticals corporation , east hanover , n . j . the construction of plasmids pgal4acx - hg , pgal4db - hg , and pgal4db - mg was previously described ( luban et al ., 1992 ), as was the construction of plasmid pt7hg ( pro - ) ( luban and goff , 1991 ). pgemex - 1 was obtained from promega corporation , madison , wis . psh2 - 1 is a yeast shuttle vector that expresses fusion proteins with lexa amino acids 1 - 87 under control of the adh1 promoter ( hanes and brent , 1989 ). plag was constructed by inserting the hiv - 1 pr55 gag containing bamhi - sal1 fragment from pgal4acx - hg into psh2 - 1 . all recombinant dna methods were performed according to standard protocols ( sambrook et al ., 1989 ). pt7p24 was constructed from the product of a polymerase chain reaction using pt7hg ( pro - ) as template , with the mutagenic oligos 5 &# 39 ;- cgcgcatatgcctatagtgcagaacatccaggg - 3 &# 39 ; ( seq . id no . 7 ) and 5 &# 39 ;- gcgcgtcgacttaaactcttgccttatggcc - 3 &# 39 ; ( seq . id no . 8 ). this product was digested with ndel and sal1 and ligated to a modified version of pgemex - 1 ( luban and goff , 1991 ) digested with the same enzymes . the constructions of the panel of linker insertion mutations in the hiv - 1 gag coding sequence has been described ( luban et al ., 1993 ). these mutant gag sequences were used to replace wild - type coding sequences in pgal4db - hg , using standard procedures ( sambrook et al ., 1989 ). the construction of plasmids pgal4db - mpg , pgal4db - sg , and pgal4db - in and of the various pr55 gag deletion mutations is described elsewhere ( g . v . k . and s . p . g ., submitted ; j . l . and s . p . g ., unpublished data ). pgex - 2t ( smith and johnson , 1988 ) was obtained from pharmacia lkb biotechnology , piscataway , n . j . bamhi and bgl fragments containing the 4cdna library inserts from clones 2 . 1 and 4 . 1 were subcloned into pgex - 2t cleaved with bamh , and the resulting gst - cyp expression plasmids were called pgcypa and pgcypb , respectively . pgadnot was constructed from pgal4acx - hg ( luban et al ., 1992 ) to facilitate subcloning of cdna library inserts . the parental pgal4acx - hg dna was digested with bamh plus sal , and the resulting 8 . 4 kb fragment was ligated to two annealed oligonucleotide adaptors ( 5 &# 39 ;- gatccgcggccgccatatgg - 3 &# 39 ; ( seq . id no . 9 ) and 5 &# 39 ;- tcgaccatatggcggccgcg - 3 &# 39 ; ( seq . id no . 10 ) using standard methods ( sambrook et al ., 1989 ), yielding pgadnot . this dna was digested with not plus sal and ligated to not - xhol fragments excised from a cdna library constructed from hl - 60 rna ( stratagene ®, la jolla , calif .). pools of more than 150 , 000 bacterial colonies were collected and used to prepare plasmid dna . yeast were transformed using the lithium - acetate method ( becker and guarente , 1991 ). to screen the hl - 60 cdna library , s . cerevisiae ggy1 :: 171 ( gal4 , gal80 , ura3 , his3 , leu2 ) ( gill and ptashne , 1987 ), carrying a gal1 - lacz fusion gene integrated into the chromosome , was sequentially transformed with pgal4db - hg followed by transformation with dna from an individual pgadnot - hl - 60 cdna pool , and double transformants were selected for histidine and leucine prototrophy . β - gal activity was assayed on nitrocellulose filter replicas of yeast transformants ( breedon and nasmyth , 1985 ). filters were placed at - 70 ° c . for 20 minutes and incubated for 8 hours in buffer containing x - gal . if transformants expressed β - gal activity , the x - gal was cleaved and only replicas turned blue . individual colonies were isolated , replanted , and retested sequentially for β - gal activity three times . plasmid dna was isolated from the blue colonies ( strathern and higgins , 1991 ) and used to transform escherichia coli dh5α to ampicillin resistance by electroporation . bacteria transformed with pgadnot - cdna plasmids were identified by restriction digest patterns , and the isolated plasmids were then retested in yeast for β - gal activity . for testing pgadnot - cdna library clones against plag , s . cerevisiae was utilized cyt 10 - 5d ( gal4 , gal80 , ade2 , his3 , leu2 , trp1 , ura3 ) that has lexa dimer - binding sites upstream of the transcription start site of an integrated copy of gal1 - lacz ( a gift from stanley fields and rolf sternglanz , state university of new york at stony brook , stony brook , n . y .). sequences at the 5 &# 39 ; and 3 &# 39 ; ends of the cdna inserts were obtained by dideoxy sequencing using oligonucleotide primers from gal4 sequences 5 &# 39 ;- gatgatgaagatacc - 3 &# 39 ; ( seq . id no . 11 ) and 5 &# 39 ;- ggtgcacgatgcacag - 3 &# 39 ; ( seq . id no . 12 ) annealed to gal4 sequences . gst - cyp fusion protein expression plasmids were grown in e . coli strain dh5α . plasmids expressing native pr55 gag , p24 , and p32 ( in ) proteins from the t7 promoter were grown in jb - de3 , a long mutant stain containing the t7 polymerase under the control of the lac4 mutant uv5 promoter ( luban and goff , 1991 ). protein was induced from bacterial expression plasmids with isopropyl - β - d - thiogalactopyranoside according to standard methods ( sambrook et al ., 1989 ). bacteria were pelleted 3 hours after induction , washed in tek buffer ( 20 mm tris - hcl ph 7 . 5 !, 1 mm edta , and 100 mm kcl ), and resuspended in lysis buffer ( 10 mm tris - hcl ph 7 . 5 !, kcl 100 mm , 1 mm edta , 5 mm dithiothreitol , 1 . 0 mm phenylmethylsulfonyl fluoride , and 0 . 5 % nonidet p - 40 ). the suspended bacteria were frozen and thawed six times and sonicated on ice for 30 seconds with a branson sonifier 250 ( branson sonic power company , danbury , conn . ), at an output setting of 1 with a 30 % duty cycle . insoluble material was pelleted at 90 ° k . for 10 minutes in a beckman tl - 100 ultracentrifuge . total protein concentration in the supernatant was determined by the bradford dye - binding procedure ( bio - rad laboratories , hercules , calif .). supernatants were adjusted to 20 % glycerol and stored at - 70 ° c . g beads ( sigma ® chemical corporation , st . louis , mo .) were swollen overnight at 4 ° c . in tek buffer , washed three times in tek buffer with 0 . 5 % powdered milk , and stored at 4 ° c . in binding buffer ( 20 mm tris - hcl ph 7 . 5 !, 100 mm ck1 , 2 mm cacl 2 , 2 mm mgcl 2 , 5 mm dithiothreitol , 0 . 5 % nonidet p - 40 , 0 . 5 mm phenylmethylsolfonyl fluoride , and 5 % glycerol ). typical binding reactions used crude bacterial lysates in a total volume of 200 μl of binding buffer containing approximately 2 μg of pr55 gag ( approximately 0 . 2 μm ) and 2 μg of gst - cyp ( approximately 0 . 2 μm ). after incubation at 4 ° c . on a nutator ( becton - dickinson , parsippany , n . j . ), 25 μl of 50 % ( v / v ) g beads in binding buffer was added , and incubation was continued for another 30 minutes . the g beads were collected with a 5 s pulse in a microfuge and washed three times with 400 μl of binding buffer . washed g beads were resuspended in 25 μl of 2 × sds sample buffer ( sambrook et al ., 1989 ), heated in boiling water for 5 minutes , and pelleted in a microfuge . the supernatant ( 5 μl ) was subjected to sds - polyacrylamide gel electrophoresis ( sds - page ). gels were either stained with coomassie blue or processed for western blot analysis . for csa competition experiments , the gst - cyp protein was incubated for 5 minutes with csa in binding buffer , prior to the addition of the bacterial lysate containing pr55 gag . cn adsorption experiments were performed two ways . in some experiments , gst - cyp protein was incubated as described above with either pr55 gag or csa but with the addition of 2 μg of cn ( 0 . 1 μm ) and 2 μg of calmodulin ( 0 . 5 μm ). g beads were added , incubated , and processed normally . in other experiments , gst - cyp protein was first adsorbed to g beads in binding buffer for 1 hour at 4 ° c . the g beads were then washed two times and incubated with csa or bacterial lysates containing pr55 gag . in some of these experiments , bacterial cultures were scaled up so that gst - cyp - g bead complexes were incubated with 1 - 2 mg of pr55 gag . beads were incubated another hour at 4 ° c . and washed twice . binding buffer with cn and calmodulin was added , and the mixture was incubated for 1 hour . the g beads were washed and subjected to sds - page and western blot analysis as before . western blot analysis of pr55 gag , p32 ( in ), and cn proteins were electrotransferred to nitrocellulose membranes with the bio - rad ® mini - blotting apparatus ( bio - rad laboratories , hercules , calif .). blots were incubated with either the mouse monoclonal anti - pr55 gag , anti - p32 ( in ), or anti - cn a subunit antibodies , followed by horseradish peroxidase - linked sheep anti - mouse immunoglobulin . antibody binding was detected with ecl western blotting detection reagents ( amersham , england ). 1 . becker , d ., and guarente , l . 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( 1993 ) mxi1 , a protein that specifically interacts with max to bind myc - max recognition sites . cell , 72 : 223 - 232 . __________________________________________________________________________sequence listing ( 1 ) general information :( iii ) number of sequences : 12 ( 2 ) information for seq id no : 1 :( i ) sequence characteristics :( a ) length : 75 base pairs ( b ) type : nucleic acid ( c ) strandedness : single ( d ) topology : linear ( ii ) molecule type : dna ( genomic )( xi ) sequence description : seq id no : 1 : cccccaaaaaaagagatcccggatcggatccgcggccgctctagaactagtggatccccc60gggctgcaggaattc75 ( 2 ) information for seq id no : 2 :( i ) sequence characteristics :( a ) length : 25 amino acids ( b ) type : amino acid ( c ) strandedness : single ( d ) topology : linear ( ii ) molecule type : amino acid ( xi ) sequence description : seq id no : 2 : proprolyslysgluileproaspargileargglyargserargthr151015serglyserproglyleuglngluphe2025 ( 2 ) information for seq id no : 3 :( i ) sequence characteristics :( a ) length : 33 base pairs ( b ) type : nucleic acid ( c ) strandedness : single ( d ) topology : linear ( ii ) molecule type : dna ( genomic )( xi ) sequence description : seq id no : 3 : gaattcctattagccatggtcaaccccaccgtg33 ( 2 ) information for seq id no : 4 :( i ) sequence characteristics :( a ) length : 11 amino acids ( b ) type : amino acid ( c ) strandedness : single ( d ) topology : linear ( ii ) molecule type : amino acid ( xi ) sequence description : seq id no : 4 : glupheleuleualametvalasnprothrval1510 ( 2 ) information for seq id no : 5 :( i ) sequence characteristics :( a ) length : 33 base pairs ( b ) type : nucleic acid ( c ) strandedness : single ( d ) topology : linear ( ii ) molecule type : dna ( genomic )( xi ) sequence description : seq id no : 5 : gaattccggaattccatcgcggggtccgtcttc33 ( 2 ) information for seq id no : 6 :( i ) sequence characteristics :( a ) length : 11 amino acids ( b ) type : amino acid ( c ) strandedness : single ( d ) topology : linear ( ii ) molecule type : amino acid ( xi ) sequence description : seq id no : 6 : glupheargasnserilealaglyservalphe1510 ( 2 ) information for seq id no : 7 :( i ) sequence characteristics :( a ) length : 33 base pairs ( b ) type : nucleic acid ( c ) strandedness : single ( d ) topology : linear ( ii ) molecule type : dna ( genomic )( iii ) hypothetical : n ( iv ) anti - sense : n ( v ) fragment type : n - terminal ( xi ) sequence description : seq id no : 7 : cgcgcatatgcctatagtgcagaacatccaggg33 ( 2 ) information for seq id no : 8 :( i ) sequence characteristics :( a ) length : 31 base pairs ( b ) type : nucleic acid ( c ) strandedness : single ( d ) topology : linear ( ii ) molecule type : dna ( genomic )( iii ) hypothetical : n ( iv ) anti - sense : n ( v ) fragment type : n - terminal ( xi ) sequence description : seq id no : 8 : gcgcgtcgacttaaactcttgccttatggcc31 ( 2 ) information for seq id no : 9 :( i ) sequence characteristics :( a ) length : 20 base pairs ( b ) type : nucleic acid ( c ) strandedness : single ( d ) topology : linear ( ii ) molecule type : dna ( genomic )( iii ) hypothetical : n ( iv ) anti - sense : n ( v ) fragment type : n - terminal ( xi ) sequence description : seq id no : 9 : gatccgcggccgccatatgg20 ( 2 ) information for seq id no : 10 :( i ) sequence characteristics :( a ) length : 20 base pairs ( b ) type : nucleic acid ( c ) strandedness : single ( d ) topology : linear ( ii ) molecule type : dna ( genomic )( iii ) hypothetical : n ( iv ) anti - sense : n ( v ) fragment type : n - terminal ( xi ) sequence description : seq id no : 10 : tcgaccatatggcggccgcg20 ( 2 ) information for seq id no : 11 :( i ) sequence characteristics :( a ) length : 16 base pairs ( b ) type : nucleic acid ( c ) strandedness : single ( d ) topology : linear ( ii ) molecule type : dna ( genomic )( iii ) hypothetical : n ( iv ) anti - sense : n ( v ) fragment type : n - terminal ( xi ) sequence description : seq id no : 11 : cgatgatgaagatacc16 ( 2 ) information for seq id no : 12 :( i ) sequence characteristics :( a ) length : 16 base pairs ( b ) type : nucleic acid ( c ) strandedness : single ( d ) topology : linear ( ii ) molecule type : dna ( genomic )( iii ) hypothetical : n ( iv ) anti - sense : n ( v ) fragment type : n - terminal ( xi ) sequence description : seq id no : 12 : ggtgcacgatgcacag16__________________________________________________________________________