Membrane protein structure prediction Hydrophobicity analysis and the positive-inside rule

8/6/2019 Membrane protein structure prediction Hydrophobicity analysis and the positive-inside rule

http://slidepdf.com/reader/full/membrane-protein-structure-prediction-hydrophobicity-analysis-and-the-positive-inside 1/8

.I . Mol. Bid. (1992) 225, 487494

Membrane Protein Structure Prediction

Hydrophobicity Analysis and the Positive-inside Rule

Gunnar von Heijne

Department of Molecular Biology

Karolinska Institute Center for 8tructural BiochemistryNOVT’Af. S-141 57 Huddinge. Suleden

(Received 14 October 1991; accepted 20 Jan,uary 1992)

A new strategy for predicting the topology of bacterial inner membrane proteins is proposed

on the basis of hydrophobicity analysis , automatic generation of a set of possible topologies

and ranking of these according to the positive-inside rule. A straightforward

implementation with no attempts at optimization predict’s the correct topology for 23 out of

24 inner membrane proteins with experimentally determined topologies, and cborrectly

identifies 135 transmembrane segments with only one overprediction.

Keywords: membrane protein: protein struct’urr; prediction

1. IntroductionThe prediction of protein structure from sequence

is a central problem in molecular biology. For

globular proteins, even secondary structure predic-

tion is fraught with di fficul ties and not very reliable

(Kabsch & Sander. 1983); however, recent progress

in the field of membrane protein assembly and

folding has fuelled hopes that a solution to the

folding problem may be within reach for t,his impor-

tant class of proteins (von Heijne & Manoil, 1990).

The basic structura l building-block in plasma

membrane proteins of both prokaryotic and eukary-

otic cells is the apolar, often slightly amphipathic,

transmembrane a-helix (Jennings, 1989; Pattus,

1990), and the arguably most important event

during the biogenesis of an integral membrane pro-

tein is the insertion of its transmembrane

segment(s) into the lipid bilayer. Once this has been

accomplished, the basic topology of the molecule is

defined. What t’hen remains is for the trans-

membrane helices to assemble into a membrane-

embedded helix bundle and for the polar segments

exposed outside t#he bilayer to fold into their proper

tertiary structure. It should be noted that the situa-

tion may be very different for outer membrane

proteins m Gram negative bacteria, where the cano-

nical structural principle is that o f a large, antipar-

allel P-barrel rather than a helical bundle (Jeanteur

et al., 1991; Weiss et al., 1991); this latter type of

protein will not’ be considered further here.

Thus. at least for multi-spanning (polytopic)

membrane prot.eins with most of their mass buried

within the bilayer in the form of transmembrane

helices, the insertion event is decisive. For structure

prediction, this means that a good part of the

problem is solved if the transmembrane organiza-

tion of the chain can be eff ect ive ly calculated from

the amino acid sequence. At the present state of the

art. this is best attempted using some method of

hydrophobicity analysis , where t,he amino acid

sequence is scanned to locate segments rich in

apolar residues. Typical ly, such an analysis will

identrfy some segments of such high average hydro-

phoblalty that they can be considered “certain”

transmembrane segments, but will also produce one

or more candidate segments of intermediate average

hydrophobicity that cannot be confidently

predicted as transmembrane.

Clearly, the ultimate hydrophobicity analysis

method would be able to discriminate perfectly

between transmembrane and non-membrane

segrnents in any protein chain; this might be accom-

plished by bett’er algorithms and better hydrophobi-

cit y scales. Here, however, I suggest a

complementary approach: to “bootstrap” the

output from a standard hydrophobicity analysis by

a subsequent step of charge-bias analysts t’hat ranks

all possible structures on the basis of their confor-

mit y with the positive-inside rule; i.e. on the

observation that positi vely charged amino acids are

manifold more abundant in cytoplasmic, as

compared to periplasmic, segments of integral

membrane proteins (von Heijne, 1986; von Heijne &

Gavel, 1988; Gavel et aE., 1991) and that) positive ly

charged residues can be used to manipulate the

0022-“836/92/100487-08 $03.00/O187

c 1992 Academic Press Limited



Figure 1. Sliding window used in the hydrophobicity

analysis. For a given window-position, the hydrophobi-ci ty value hi for each residue in the window is multiplied

by the corresponding window-weight, wi, and the sumover the window is taken. wi is given by u+ = {i/S for

I<i<n-q+l; (n-q+l)/S for (n-q+l)<i<(n+q+l):(%+2--Q/S for (n+q+l)<i<2n+l}. where S =

(1 + n)’ -q2 is a normalization factor to make.

2ntl-C~wi=li=l

In the calculations reported here, n = 10 and q = 5

topology of such proteins (Boyd & Beckwith, 1990:

Dalbey, 1990; von Heijne & Manoil, 1990). As

shown below, this strategy leads to a considerable

improvement in prediction accuracy. at least for

bacterial inner membrane proteins.

2. Methods

(a) Collection of sequence data

Twenty-four bacterial inner membrane proteins of

known sequence and with experimentally well-character-ized topologies were collected f rom the literature (Table

1). In most cases, the topology has been determined byfusion protein analysis (Manoil & Beckwith, 1986).

Although this method seems to be a very reliable way ofobtaining topological information, it, should be kept in

mind that the 3-dimensional structure has been deter-mined for only 3 of the proteins listed in Table 1, namely

bacteriorhodopsin, and the recation center L and Msubunits.

(b) Hydrophobic ity analysis

Hydrophobic ity analysis was carried out using theGES-scale (Engelman et al., 1986) and a trapezoid slidingwindow composed o f a central, ll-residue rectangular

section and 2 flanking wedge-like sections, each 5 residueslong (Fig.1). This window-shape was chosen to combine

the favorable noise-reduction of a triangular window

(Claverie & Daulmiere, 1991) with a physically morerealistic rectangular window representing the centralapolar part of a lipid bilayer. In this way, one obtains a

physically reasonable, sof t transition from the apolarinterior to the polar surface of the membrane.

From the hydrophobicity profile, candidate trans-membrane segments were extracted automatically by a

procedure that 1st identifies the highest peak, records its

average hydrophobicity (H), and removes the part of theprofile that corresponds to the 21 residues in this segment.This is repeated until either no stretch longer than 20residues remains, or until no peak higher than the lowercutof f ((H) = 0.5) remains. All peaks with (H) 2 1.0 areconsidered “certain” transmembrane segments, and allwith 95 I(H) < 1.0 are considered putative candidates.

-4 -3 -2 -I 0 I 2

<l-f4

Figure 2. Peak-height distributions derived fromhydrophobicity analysis of 92 bacterial inner membrane

proteins ( q ), 25 periplasmic Escherichia coli proteins (+).and the 135 transmembrane segments identified in the 24bacterial inner membrane proteins discussed in t,he t,ext

(ml.

These cutoff values were chosen on t,he basis of an initialanalysis of the bimodal peak-height distribution for the

whole sequence sample obtained with no cutoff s (Fig. 2:

see von Heijne, 1986).Finally, all possible topologies that include the certain

transmembrane segments and either include or exclude

each of the candidate segments were automatically gener-

ated. a,nd the difference in the number of posnivelycharged amino acid residues (Arg and Lys ) between the 2sides of each structure was calculated. If the penultimate

N-terminal amino acid was neither Arg, Lys, Leu. Phe norHe (i.e. residues that block f-Met removal in prokaryotes

(Flinta et al., 1986)) an additional posi tive charge repre-

senting the free N-terminal amino group was added to the1st polar segment. Polar segments longer than 70 residueswere not included in the charge-bias calculation, since

t,heir content of charged residues does not seem to be

dependent on their cytoplasmic or periplasmic location(von Heijne & Gavel, 1988). The possible topologies were

then ranked in decreasing order o f charge bias, and theirorientation wa s predicted as the one with the more highlycharged side facing the cytoplasm. A program called

TOP-PRED (TOPology PREDiction program. writt!en in

THINK Pascal for Macintosh computers) implementingthese steps is available upon request.

3. Results

(a) The positive-inside rule holds for all exposed

loops in bacterial inner membrane proteins

The positive-inside rule was originally suggested

by the observation that positi vely charged amino

acid residues (Arg and Lys ) are much more ahun-

dant in cytoplasmic as compared to periplasmic

regions of bacterial inner membrane proteins (von

Heijne, 1986), and has since been confirmed by a

number of experimental as well as further stat’istlcal

studies (von Heijne, 1989; Boyd & Beckwith, 1990;

Dalbey, 1990; Nilsson & von Heijne, 1990; von

Heijne & Manoil, 1990). However, to be able t’o

make use of this rule for prediction purposes. it was



Membrane Protein Structure Prediction

Table 1

489

Membrane segments identi$ed by hydrophobicity and charge-bias analysis

I’rotrin

Membrane Segment Charge

segments categoryt biasf Reference

lkc~trriorhodopsin 22-42

57-77

96116

119-139

151-171

189-209

217-237

C’olA immun it\ 17-37

protein 72-92

104-124

143-163

(‘olE1 immunity G-26

protein 37-57

90-110

(‘yoA 9-29

4C-8688-108

(‘,td< 16-36

57-77

105-125

143-163

194-214

235-255

265-285

286-306

313-333

342-362

380-400

G-441

456-476

494-514

539-559

590-6 10

611-631

( ‘yd ’ 35-55

71-91

97-l 17

1455165

184-204

19-39

40-60

78-98

11-31

36-56

85-105

107-127

133-153

160-180

208-228

231-2.51

264-284

CyW558 12-32

6G80

93-l 13

137-1,57

178-198

‘i-27

45-65

78-98

102~12%

145p I65

167YlRi

219-239263- 283

291L311

315.-335

34%369

382-402

Phage Ml3 prowat 5-25

protein 44-64

C+

C+

t, +

C+

C+

C+

t+

C+

c+

c+

c+

c+

t+

c+

c+

c+C+

c+

c+

c+

c+

c+

c+

t,-

c+

c+

Cf

c+

c+

C+

c+

t-

C+

C+

C+

C+

c+

C+

C+

C+

C+

C+

c+

c+

C+

C+

C+

(‘+

C+

C+

C-t

C+

c+

Cf

C+

c +

C+

c+

C+

C’ +

C+

(‘+

c+C+

C+

tt

C+

Cf

Cf

Cf

-5, +7* Song & (Iramer ( 1991)

-IS* +6.

-6,‘-4

Chepuri & Gennis (1990)

-2. 0. +3

-5*

+4*

+7*

+6*

+ :3*

+ lo*

+4*

+6*

Henderson et al. (1990)

Geli ct al. (1989)



(‘hepuri & Gennis (1990)

C’hepuri & Gennis (1990)

Fridkn (1989)

Kuhn et al. (1986)

+9, +17* (klamia & Manoil (1990)



Light-harvesting

complex LH 1

Light-harvesting

complex LH:!

Keac%ion crntrr

complex

L-subunit

I’hpT

PI* Rohrw & Kuhn (1990)

OX. -2 Moore $2 Miura (1987)

-I. +9* Munoa rf (11. ( I ! , ! , ] )

+4* Ihws (19%)

+1* Ihws ( I9X:i)

+x*. t-" Michel rt /I/. (1986)

+9*. +:I

+fi* Schatz rt al. ( 19X9)

+?A*. +x .Ikiyarna & Ito (1987)

+ 1:3*

+27* Lloyd & Kadnrr (1990)



Membrane Protein Structure Prediction 491

Table 1

C’ontd.

Membrane Segment Charge

Protein segme nts categoryt bias: Reference

299-319 (‘+

38tk34ti c-+

351-371 C+

405-425 C’+

427447 (‘+

t’trr~F: 11-31 Cf -2* Drckers-Hebestreit, C

59-79 c + Altendorf (1986)

tr. certain; t, tentative; +, a membrane segmen t present in the known structure; -, a membrane

segmen t not present in the known structure.

$The t,otai difference in the number of Arg+I,ys residues between thr 2 sides of the structure for all

po&hlr topologies generated as described in Methods are given, with the value corresponding to the

kuown topology marked with an asterisk. Positive values correspond to topologies where the S

terminus is predicted to be cytoplasm ic. negative values to topologies predicted to have the X t~rrminu~

import,ant to establish that it, holds for all segmentsof a transmembrane protein, and not just for theN-terminal or (‘-t,erminal ends, say.

To this end. 24 bacterial inner membrane proteinsof known sequence and with experimentallymapped topologies were analyzed (seeTable 1). Foreach protein, the number of Arg and Lys residues neach cytoplasmic and periplasmic segment wasrecorded, and t,hr counts were pooled according tothe position of the segment (counting from the r\;terminus) and its cytoplasmic or periplasmic loca-tion. As shown in Figure 3: the bias in the distribu-tion of’ Arg+ Lys is equally strong throughout, thesequences; .e. all cytoplasmic loops have a similarlyhigh content (- IS”/,) whereas all periplasmic loopshave a low content (-SOL). It is thus clear that allparts of a multi-spanning inner membrane protein[*onform to the positive-inside rule.

(b) Thr positiwinxide rule can be used to improrr

thw prediction of transmembrane sepents

Since the positive-inside rule apparently appliesto any part of a bacterial inner membrane protein.it should provide a strong crit,erion for testingwhether a putative transmembrane topology islikely to be correct or not. One is thus led t’oconsider the following procedure. First, make a listof all possible transmembrane segments in the pro-t)ein based on some standard method of hydrophobi-city analysis and a liberal cutoff criterion; second.decide which of these candidat’es are certain and

which must be regarded as tentative based on a

more stringent cutoff criterion; third, construct’ allpossible transmembrane st’ructures always includingthr cert,ain candidates but either including or

excluding each of the tentative segment#s: andfourth, rank these structures according to theirdegree of bias in the dist’ribution of positivelycshargrd residues. The rationale behind the last st,ep.is that any structure with an incorrect number oftransmembrane segments would have one or morepolar domains placed on the wrong side of the

membrane, and hence would be likely to have asmaller charge bias than the corre& structure.

As an example. consider the 1,acY protein. whichis known to have a cytoplasmic N terminus followedby 12 transmembrane segments (Calamia B Manoil,1990). The hgdrophobicity plot shown in Figure4(a). predicts 11 certain segments and one putativecandidate. Thus, two topologies can be generated,one excluding and one including the putative candi-date (Fig. 4(b)). The former has a bias in the distri-bution of positively charged residues of nine, thelatt’er of 17, and it is clear from the Figure that theC-terminal part of the second. correct model has amuch better correspondence with the positive-insiderule.

To test this strategy more thoroughly, hydropho-bicity analysis was carried out on the 24 proteinslisted in Table 1 as described in -Methods, with alower cutoff set to (H) = 0.5 and a higher cutoff set

Segment positlon

Figure 3. Mean number of Lys+ hrg in v)-toplasmic

(stippled bars) and periplasm ic (open bars) polar segme nts

as a function of the position of the segment (1st cyto-

plasm ic segment. 2nd cytoplasm ic segmen t. rt,c., counting

from the N terminus) in a samp le of 24 bac*twial inner

membra,ne prot,eins with known topology.



2

I

A 0

$v

-I u v

1 li

U I

-2

-3

-41 I I 1

0 100 200

Posltion

(a)

300 400

A+ = 9

A+=17

2 3 5 4 2 2 2

(b)

Figure 4. (a) Hydrophobicity plot for the SecY protein.The upper and lower cutoffs are marked. A tentative

transmembrane segment with a mean hydrophobicitfalling between the 2 cutof fs is marked by an arrow.

(b) Two possible topologies for the SecY protein based on

the hydrophobicity plot. The putative transmembranesegment is shown in black. The number of Arg+Lysresidues is shown next to each polar segment. IVote that

t)hr correct, alternative (bottom, including the putativetransmembrane segment) has a much higher charge-bias

than the incorrect. one.

to (H) = 1.0 (i.e. t’he criterion for tentative trans-membrane segments was 0.5 _< H) < 1.0). Fourteenprot’eins were predicted to contain only certaintransmembrane segments with no additional tenta-tive candidat,es; all of these turned out to be correctand their orientation in the membrane was correctlypredicted by the positive-inside rule in all cases.Forthe remaining ten proteins, the correct structurehad the highest charge bias (highest differencehetween the number of periplasmic and cytoplasmicArg+ Lys) in eight cases Table 1). An extra. incor-rect certain transmembrane segment ((H) = 1.06)

was predicted for the SecY protein; closer inspectionrevealed that this resulted from a “shoulder” on ahigher, somewhat broad peak. Inclusion of thissegment gave a topology with a charge bias of eight.and its exclusion gave a charge bias of 26. Thus.

Thus. using the positive-inside rule as :I J(‘r(‘en.

t)he transmcmhranr topologies of 22 (or. wit)h somegootl-will. 23) out of 21 proteins were (*orrec+lJ

predicted. atld all of the 135 transrnrm t)ranc>segments wTt‘re dentif ied with onl?- oru’ ovtq)rerl icn-

tion (I,tlf)).

(c) Possibilities for improvements in thv

hydrophobicity scnlrCs

In the a,bove analysis. the standard (JES hydra-phobicity scale (Engelman rt nl.. 1986) based rriti-matrly on physico-chemical caonsiderationswas usedand no at,tempt at, optimization was made. Withthis scale and through application of t,he positivr-

inside rule. 135 t’ransmembrnne segments werecorrectI\- identified in t.hr 24 proteins analvzrd.From t,hese data, we derived a new. statistically

based scale by comparing the amino acid frequen-cies fi M in the cent,ral I 1 -residue stretch of t,ht>transmembrane segments with the amino acidfrequencies f;” m the non-meml)raneous srgrnent#s(taking the membrane-embedded segments to hf. 17residues long): Ai = In(fiM/fiA), Table 2. \Vith a11upper cutoff of O$.i and a lower of - 0. I and t hts

Table 2Hydrophobicity scak bused on 735 transmemhrane

segments from 24 bacterial inner ,membrane proteins



Memhranr Protein Strwtuw Prediction 493

same sliding window as above, this scale seems ’operform slightfly better than the original GES-scale,with 18 out of the 24 proteins (including SecY) nowbeing predicted to contain only certain trans-membrane segments (a.11correct). Again. ranking

based on the positive-inside rule produced thecorrecst topolop~ for iLlI but one (I,ep) of theremaining prot,elns.

4. Discussion

Two important conclusions can be drawn fromt.he data present,ed here: first., the posit’ive-insiderule applies with equal strength to all parts ofpolytopic bacxterial transmembrane proteins, and.second. the positive-inside rule can very efficientlybe used to rank possible predicted transmembranc

topologies and thus in a sense t’o bootstrap thest.andard hydrophobicit? analysis.

The first, c*onclusionhas certain mechanistic impli-rations, and suggests a mode of assembly ofbacterial membrane proteins where locally formed“helical hairpins” composed of two neighboringhydrophobic- helices and a connecting loopcontaining few positively charged residues insertinto the membrane more or less independently oft*he remaining parts of the polypeptide chain(Engelman & Steitz, 1981; von Heijne, 1986).A similar model is also suggested by recent experi-mental data on the t,opological consequences of

deleting one or more transmembrane segment.(Yatnane et al., 1990; Kibi et al.. 1991: Ehrmann 8:Krckwit’h. 1991: McGovern et al.. 1991). This is incontrast t.0 it “linear” insertion model, where themost S-terminal transmembrane segment(s) insertfirst. and the rest of the chain simply follows thetopological dictate of this first insertion (Vessels &

Spiess. 1988: Hartmann et al., 1989). It may be.though. t’hat the latter model more accuratelydescribes membrane protein assembly into the endo-plasmic reticulum membrane, which is t’hought tobe obligatlorily co-translational and hence likely toproceed in an K to C-terminal direction (High et al..

1991). It should be noted in this regard that the biasin i he dist,ribnt.ion of positively charged residues.although clearly t,here, is nevertheless less marked in

eukary-otic plasma membrane proteins (von Heijne& Gavel. 198X).

For predi&m purposes, a combination of hydro-phobicity analysis and charge-bias analysis clearl>improves the reault,s. almost to the point where veqlittle experiment.al work would have t.o be done tocoonfirm a predicted t,opologg. In this study. thetopology of 9.5(& of the prot.eins was correctlypredi&ed I)!- a fully automatic method. even whenthe initial hydrophobicity analysis method had notbeen consc~iou+,- optimized. Thus, the topology ofbacterial inner membrane proteins seems to berather straightforward to predict direc+ from theirsequence. setting the stage for attempts t,o developmethods for modeling their fIlli three-dimensionalstructure.

This work was supported hv grants from the Swedish

Natural Sciences Research &unc:il and thr BwrdishBoard fo r Technical Development.

References

Akiyama. Y. & Ito. K. (1987). Topology analysis of’ theSrcY protein. an integral membrane protrin involved

in protein rlxport in Eschrrichitr roli. h’.MBO ,I. 6.

3465 -3470.Bibi. IX.. Verner. (i.. (‘hang. (‘. 1.. & Kabwk. H. R.

(1991). Organization and stabil ity of a polytopicmembrane protein-deletion analysis of’ the Iac+osepermease of EarhfwZchiu coli. Pror Sat. ;Icrrd. S ri..

l’.S.A 88. i2’il-727s.

Rilgin. X.. Lee. .I. 1.. Zhu. H.. J)alt)r!-. Ii. & van Heijnr,(;. (1990). Mapping of c.atal~ticalI~ importantdomains in Eschrrichin roli leadel. prl~t~tiase, EURO

,J. 9. %il’i m”iP?.Hoyt i. I). d l+ckwith. ,I. (1990). The role of c,harped

amino acids in the localieatiorl of ~rc*rt~trd andmemhraneproteins. Cell. 62. 1031 IOXX.

(‘alamia. .J. k Manoil. (‘. (lR!)O). ],a(. lwrmcas(z of

Esrhvrichicz co/i&topology and srquen~e elementspromoting membrane insertion I’rvc .V///. .-Iwcl. Sci..

l‘.S.d. 87. -4937-4941.(‘hrpuri. \‘. & (irnnis, R. 13. (1990). Tbr use of gene

fusions to d&ermine the topology of all of the sub-

units of t,hr cytochrome o terminal oxidase wmplexof Ewherichin coli. J. Biol. C’h~m. 265. 12978P1ZM6.

(‘la.verir. .1.-M. & Daulmiere, (‘. (1991). Smoot.hing profiles

with sliding windows: better to wear A hat! /‘.-1 f?I f)S

7. 113-115.I)albe>-. R,. E. ( 1990). Positively c*hargtad wsidues are

important determinants of tncmbranr proWin topo-logy. Twnda Biochem. Sci. 15. %54-?.5i.

T)rc~kers-H~bestreit. (:. & r\Itendorf. K. (1986).r\ccrssibilit> of F, suhunit)s from KsrhPrirhirr coli

ATI- synthase. Ew. ./. HiochPv. 161. ~~T,-~Sl.Drrna. ( :. (l!P&). Structure and func+ionnl organization

of light-harvesting complexes and phot.oc~hrnricaIreaction c,enters in membranes of l~hototrophic~

bacteria. N icrobiol. Hev. 49. Z-70.

Eckert. R. & Reck, C. F. (1989). Topology of the trans-poson TnlO-encoded tetracycline resistance protein

within the inner membrane of Escherichia col i .

J Bid Chum. 264. 11633-11670.

Ehrmann. 1cl. & Reckwith. *J. (1991). I’ropw insertion of acomplex mt\mhranr prot.rin in the absrnw 01‘ itsamino-terminal export. signal. .I. /1;0/ (‘him. 266.

165‘3W 1651’i.. I.<Engelman. I). 11 8: St,ritz. T. A. (1981 i. The spontaneous

insertion of proteins int,o and across membranes: The

helical hairpin hypothesis. (‘~11. 23. -411-4ZE:ngcelman. I) . 11.. Steitz. T. A. Xr C:oldtnan. ,1. (19X6).

Identify ing nonpolar transbilayrr hrlicbrh in amino

wid srquenc~es of mrmhrane proteins. .~lnrclc. Rw.Biophys. Bicyhys. C’h.Pm. 15. 4”l -8X1.

Flinta. t‘.. Pwsson, R.. ,Jiirnvall . H. & \-on Hrijne. (G.(1986). Sequence determinants of cytosolicX-terminal protein processing!. L:crr. .J. Hiockrm. 154.

193 196.Fridin. H. (1989). Studies on the c~ytoc~hrornr B-558 sub-

unit of HacilZ?Ls su6ti l is succ~inate:yuino~~r oxidorr-duct,ase. Phi) t’hesis. und IrniversitJ-. C;wedrn.

Froshauer. S.. Green. G. X.. Boyd. I).. Mc(:overn, K. &

Rrckw-ith. .I. (1988). (>metic ana.lysis of t.hrmembrane insertion and t.opolog?- of MaIF. a cyto-



plasmic membrane protein of Exherichicl co/i. J, .Ilo/

Riol. 200. WI 511.(:avc~l. E’.. Steppuhn. J . Herrmann, R. & van Heijntx. ( :.

(1991). The posit,&-inside rule applies to thvlakoi t]membrane proeeins. FEBA’ L&w. 282, 11 46.

(ieli. \‘ .. Katy. I).. l’attus. F. & Lazdunski. (‘. (1989).Topology and fun&ion of the integral membrane

protein conferring immunity to colicin A. Tklol.

Microbid. 3. 679. 687.

Hartmann, E., Rapoport, T. A. 8r Lodish, H. F. (1989).

I’rrdic*ting t)hr orient’ation of eukaryotic membraneproteins. Pror. ,Vat. A cad. sc i., 1’JS.d. 86.r,786X790.

Henderson. R.. Baldwin, J. M.. (‘eska, T. A.. Zemlin. F..

Beckmann. E. & Downing, K. H. (1990). 4 model forthe structure of bacteriorhodopsin based on highrrsolut,ion electron cqo-mivroscsopy. -1. No/. Hiol.

213. 899-929.

High. S.. Flint. X. & Dobberstein, K. (1991).Rtyuirrments for the membrane insertion of signal-

anchor type proteins. J. Call. Riol. 113. 2.5 34.Jeant,rur. I).. Lakey. J. H. & Pattus, F. (1991). The

ba&erial porin superfamily-sequence alignment andstructure prediction. Mol. Microhiol. 5, %]53%2164.

.lennings, M. I,. (1989). Topography of membrane pro-teins. A~anu. Krv. Biochem. 58, 999.-1oP7.

Ka1~sc.h. M’. & Sander. C. (1983). How good are predic-tions of’ protein secondary structure? FERS Ltittux.

155. 179-182.Kuhn. A.. Kreil. (:. & Wickner. W. (1986). Both hydro-

phobic~ domains of Ml3 provoat are required toinitiate membrane insertion. ENRO. .I. 5.

3681~ 3685.

T~loytl. A. I>. & Kadnrr. R. ,J. (1990). Topology of the

h’sch~richia roli &pT sugar-phosphate transporteranalyzed by using TnphoA fusions. ./. Bactrriol. 172.

I6H8~1693.Manoil. (‘. & Beckwith, J. (1986). A genetic approach to

analyzing membrane protein topology. Science. 233.

1403-140x.Mv(:ovrrn. K.. Ehrmann. M. $ Heekwith. .J. (1991).

I)ec*oding signals for membrane protein assemhll

using alkaline phosphatase fusions. EA’RO ./. 10.

2773 %7X”.Michrl. H ., IVryer. K. A.. Gruenberg, H., Dunger, I..

Orsterhelt, D. B Lottspeich, F. (1986). The ‘light’

and .medium’ subunits of the photosynthetic reaca-

tion ventre from tlhodopseudomonacs kdis: isolation

of the genes. nucleotide and amino avid seyuenc.r.F;MKO .I. 5. 1149~1158.

l\loorv. K. E:. R Miura. S. (19X71. .\ small hytlrc~l~hohit~

domain anc*hors Ieadt?r pr])t,ittascl t,o the (.yto])lastllic .tnrmbranr of Escl~~rirhirr ~oli. J Iiiol C’he,~/ 262.

8XO6~~881:1.

Mrmoa. I’. .I Miller. K. 1V.. ISeers. It.. (:raharrl. Xl. & \$‘I].H ( ‘. ( 199 I ). Membrane topology of /fschrrichirr co/;

prolipoprot,ein signal peptidase (signal pt’])tidasr II ).

.I. Hid. C’hPm. 266. 17667 1767”.Nilssolt. 1. &I. 8r van Heijne. (;. (1990). Fine-tuning thr

topology of a polytopic, mrmbrane ])rotrin. l<ol~~ of

positix-taly and nrgativrly c.hargetl residuc~s. c r/l. 62.1135 1111.

I’attus. F. (1990). Mrmbranr prot,eitr struc%urv t ‘err.

Opi,/ion (‘41. Biol. 2, 68lm 68.Y

Rohrer. *I. 8: Kuhn. A. (1990). The furtvtion of’ a leaderprptidr in transloczat)ing caharged amino acsy l resitluvsacross a mrmbranr. Srirwr. 250, 141 8 1121

Schatz. 1’. .] liiggs. 1’. I).. .Jaq. L\.. Fath. hl. .I. &

Brvkwith. ,I. (1989). Thr sr~E gene t~nc~odvs anintegral membrane protein required for protein

export in Eschrrichicr r~ol;. (:etrP.s lk1dop 3.

IO3;i 1Ol-c.

Song, H. 1’. & (‘ranter. L\‘. A. (1991). ,IlrmbranrTopography of’ (‘oNI gent’ producnts- the immrmit~

protein .I. IZnctrriol. 173, 835-2948.van Hrijntx. (:. (1986). ‘I? IP distribution of positivt)l?

caharged residues in bacterial inner mc~rnbratx~ ]m,~teins (*orrelates with thtb tram-membranr topology.

ENI~O ./ . 5, 3021 -3027.van Heijne. (:. (1989). C’ontrol of topology ant1 moth. of

assrtnbl?. of a polytopiv membrane protein by posi-tiv rl! charged rrsidurs. Srrt~r~ ~lonrlor/ 1, 341.

15tibkr,x.van Hri,jncs. (:. & (:aveI, Y. (19%). ‘I’c,])ogrnic. signals in

integral mC~mt)rattt~ proteins. E/c/. . ./. fjioChr,rr/. 174.671 6iX.

van Heijnr. (:. & Manoil. C’. (1990). Membrane proteins

--from sequence to structure. Protein En,g . 4.

109- I I”.

MTeiss. M. S.. Kreuscsh, A.. Schiltz. E., Nested. I’.. \Yt~lt~r.iv. . \Vrckrssrr. J. & Schulz. (:. E. (1991). ‘l ’hv strucmturn of porin from Rl~odobfrct~~r rupxulatcf at I .X,i

resolution. PEES Lrtters. 280. 379 382.

Vessels, H. 1’. & Spiess. M. (1988). Insertion of a multi-spanning membrane protein occurs sequentially and

requires only one signal sequence. (‘ell, 55, 61- 70.Yamant,. K.. Akivama. \‘.. Ito. K. & Mizushim:i. S.

(1990). ;\ positi vely vhargrd regiotl is a dett~tmirtatrt

of the orientat,ion of c~ytoplastnic membrane lnvteinsin Esrhrrichin coli. ./. Niol. C’hun. 265. “1 I66 11 171.

Edifrd by K. IT. J!!atthru~.s

Membrane protein structure prediction Hydrophobicity analysis and the positive-inside rule

Documents

Transcript of Membrane protein structure prediction Hydrophobicity analysis and the positive-inside rule