Evolutionary analysis of host proteins CD4, CXCR4 and CCR5, and ...

Evolutionary analysis of host proteins CD4, CXCR4

and CCR5, and HIV/SIV gp120

An honors thesis presented to theDepartment of Biological Sciences,

University at Albany,State University of New York

in partial fulfillmentof the Honors Program Requirements

Lana Bunning2009

Abstract

The acquired immune deficiency syndrome, AIDS, is a growing epidemic in the United

States and the world. Since its discovery in 1981, the virus that causes AIDS, human

immunodeficiency virus (HIV), has escalated. .Certain African ape (i.e., chimpanzees and

gorillas) and monkey species are known to harbor forms of the virus termed SIV (simian

immunodeficiency virus). Chimpanzees are the natural hosts of the SIV strains from which

HIV-I evolved, but do not rapidly progress to AIDS, unlike their human relatives. In the wild,

gorillas have been observed to harbor SIV, but this species' disease progression is currently

unknown. As the closest living species to humans, the chimpanzee genome is over 95%

identical to the human genorne, yet genetic differences between the species are known to exist

that are thought to play a role in their different responses to SIV/HIV infection. It is posfulated

that African apes and monkeys have co-evolved with SIV for a few million years, and thus have

been able to adapt to, and co-evolve with, this deadly virus. By contrast, the recent cross-over of

HIV to humans would suggest that such adaptive changes are missing from the human genome.

Previous work by this and other labs has identified the T cell surface proteins CD4,

CCR5, and CXCR4 which are involved in HIV infection of these cells potential targets

of selection in the viral-host response. This past year I analyzed the protein-coding exons of the

CD4, CCR5 and CXCR4 genes and their inferred proteins from avariety of primate species. In

addition to the analysis of these host genes, I gathered numerous sequences for the F{IV/SIV

surface protein gpl20 and scanned the translated amino acid sequences for unique changes at

sites of interaction with the host CD4 protein. I found strong evidence for rapid evolution of

CD4 on the chimpanzeehneage, and found no change on the human lineage. Two of the amino

acid replacements on the chimpanzee lineage create two potential N-linked glycosylation sites

which, if glycosylated, would likely interfere with gp120-binding. This finding supports the

thesis that chimpanzees have adapted genetically to SIV.

Introduction

The human immunodeficiency virus (HIV) is known to attack the immune system of its

host, and is a serious threat to the human species. The virus preferentially targets and destroys

CD4n T cells, severely crippling the host's ability to coordinate a successful immune response.

AIDS (acquired immune deficiency syndrome) occurs when the CD4* T cell count drops below

200 cells per microliter of blood. The virus does not discriminate, as males, females,

heterosexuals, and homosexuals from all populations globally are affected by HIV (Wessner

2006).

Chimpanzees (Corbet et a\.2000), and perhaps gorillas (Takehisa et a|.2009), are the

natural hosts of the SIV strains that gave rise to the major HIV-1 strains M, N, and O. Since

chimpanzees typically do not progress to AIDS (Hvilsom et a|.2008), it may be informative to

investigate the genetic differences between humans and these African primates to further

understand SIV and HIV infections. We do know that HIV- 1 and HIV-2 have entered the human

race from two different African primate species. HIV-I came from cross-species transmission

from chimpanzees and HIV-2 came from the sooty mangabey (Wessner 2006). Recent analysis

has shown that gorillas also harbor SIV in the wild (Takehisa et al. 2009). The SIV of gorillas is

most closely related to the O strain of HIV. SIVcpz (Pan troglodfies) is most closely related to

the M strain, which is the most infectious, and the N strain found in central Africa. Although

many believe that sexual.intercourse spread SIV to humans, the most likely cause of the cross-

species infection was from the butchering and consuming of bushmeat (Peeters et a|.2002).

The evolutionary tree in Figure 1 shows the relationship of humans to the African apes,

chimpanzee and gorilla, and the Asian apes, orangutan and gibbon. As indicated on this tree, we

hypothesizethat chimpanzees and gorillas were independently infected by SIV a few million

years ago, which would allow them sufficient time to adapt to the virus at multiple loci. In

contrast, it appears that the human lineage somehow avoided this infection until quite recently. If

?

so, the expectation would be that chimpanzee and gorilla proteins such as the HIV receptors

CD4, CXCR4 and CCR5 would show evidence of adaptation to the virus, whereas the human

proteins would not. Based on this hypothesis, careful phylogenetic analysis was done on CD4,

CXCR4 and CCR5 of the host genomes, as well as gp120 of HIV and SIV.

The CD4, CXCR4 and CCR5 proteins are necessary for the acquisition of HIV and SIV.

CD4 is a major player in the immune system and can be found on T-helper cells. It increases

interactions between the helper T-cells and MHC class II cells by forming the ternary complex

with T-cell receptors (Claphamet a|.2002). CD4 is a member of the immunoglobulin

superfamily, which includes molecules that share structural features with variable (V) or constant

(C) immunoglobulin domains (Brunet et al. 1987). Conformational changes occur within the

four domains (D 1 , D2, D3, D4) that make up CD4. These changes are important for the binding

between CD4 and gp120, discussed below (Ctrapham et a(.2002).

The differences between HIV and SIV infection and diseases progression between the

human and non-human primates depend on pathogenic properties of the viruses and host-specific

factors such as virus-receptor/co-receptor interactions (Hvilsom et al. 2008). CD4 is a main

receptor for HIV infection and is found on the surface of immune system cells (T-cells). The

HIV virion uses its gpI20 to attach itself to CD4 and spill its contents into the host cell with the

help of a chemokine co-receptor such as CCR5 and CXCR4 (Kwong et al. 1998).

The binding of HIV/SN to CD4 occurs through a number of steps; the initial binding of

the virion to CD4 causes a conformational change in gp120 allowing for a binding site for the

chemokine receptors CCR5 and CXCR4. Evidence for these conformational changes is in the

crystal structure's cavity laden CD4-gp120 interface where conserved binding sites were found

for CXCR4 and CCR5 (Kwong et al. 1998). The third variable (V3) region of gp120 loop

determines which chemokine receptor is necessary (Kwong et al. 1998). Specificity is also

based upon time of entry into the cells; CCR5 and CXCR4 are used in the early and late stages of

HIV/sry infection' respectively (Bleul et al. 1gg7). The three amino acids and four sulphated

tyrosines that make up the N terminus of ccR5 are negatively charged. This allows the positive

amino acids on gp120 to interact with cCR5, as well as the negatively charge d,E2loop of

CXCR4 (Clapham et al. 2002).

The gp120 protein has five variable regions when compared among the primate

immunodeficiency viruses (Kwong et al. 1998). The first four of these variable regions form

surface-exposed loops that contain disulphide bonds at their bases (Leonard et al,1gg0). As

stated before, analysis in the Stewart lab found the evolution of two potential N-linked

glycosylation sites in cD4 of chimp anzee which are unique to this species. Leonard et al.( 1990)

found that the conserved and variable regions of gp120 contained glycosylation sites as well.

These regions of glycosylation may provide important clues as to why HIV and SIV infect

humans and chimpanzees so differently. The interaction of cD4 and gp120 is at the forefront of

HIV/Sry research' The crystal structure of these interacting proteins described by Kwong et al.

( 1998) allows us to visualize the interaction between the two, and provides insight to the

potential consequences of glycosylation of cD4.

Just recently, poltions of the gorilla genome have been sequenced and released onto the

public databases' Based on the available sequences and analyses by lab members c.B. Stewart

and S' Bandla, I will discuss the similarities of the amino acid replacements and polymorphisms

that gorillacD4 appears to share with chimpanzee cD4.

Human

Chimpanzee

Gori l la

Orangutan

Gibbon

Figure 1: Phylogenetic relationship of the hominoids. This tree shows the relationshipbetween the human and non-human apes. As seen here, the humans are most closely related to

the chimpanzee, followed by gorilla, orangutan, and gibbon. The arrows indicate the lineagesthat appear to have been infected with SIV for a few million years, which would allow them to

currently harbor SIV without rapidly progressing to AIDS.

Materials and Methods

Creatign of the CD4 Alienment

Using the databases on the NCBI website (http://www.ncbi.nlm.nih.gov/) and Ensembl

Genome Browser (http://www.ensembl.org/index.html), I searched for each protein's nucleotide

sequence. Sequences for human (Homo sapiens), chimpanzee (Pan troglodytes), orangutan

(Pongo pygmaeus), and macaque (Macaca mulatta) were obtained from Ensembl Genome

Browser. Partial sequence of gorilla (Gorilla gorilla) CD4 was mined from the available gorilla

genome sequence by Santhoshi Bandla. The sequences that I was able to find were exported into

the FASTA format and placed into a Se-At lhttp:lltree.bio.ed.ac.ulCsoftware/seal/l document. Se-

Al is a r,rnrltiple sequence alignment software package (http:lltree.bio.ed.ac.uk/softwarelseall). In

the Se-Al program I formatted the nucleotide sequences into amino acids and aligned them

accordingly. After all of the sequences were aligned, I imported them as NEXUS files into

MacClade [Maddison and Maddison 1992], which was used for inference of average numbers of

amino acid replacements per lineage, as well as for identifying the specific amino acid

replacements that likely occurred on each lineage.

Phyloeenetic Analvsis of CD4

The nucleotide sequences were translated into amino acid sequences (see Appendix 1)

and a phylogenic tree was built and rooted by the macaque sequence. Within the MacClade

program I was able to measure the minimum, average, and maximum number of amino acid

replacements per lineage. In doing so, I was able to visualtze the evolutionary changes that

occurred on each linease of the tree.

Creation of the ep120 Alienment

Takehisa et al. (2009) produced new SIVcpz and SIVgor sequences, which I used to

analyze gpl20. I retrieved these sequences from the databases on the NCBI website

(http:llwww.ncbi.nlm.nih.gov/). The sequences were exported into the FASTA format and

imported into Se-Al. I viewed and aligned the sequences as amino acids. I obtained a sequence

of the protein used to create the crystal structure of gpl2lby Kwon get al. [1998] on the PDB

website lhttp: I I www.rcsb. org/pdb/home/home. dol . Using amino acid sequence of this

engineered gp120 protein as a guide, I was able to align the HIV, SIVcpz and SIVgor gp120

sequence s accordingly.

Results

Phyloeeny of CD4

Figure 2 shows the phylogeny of CD4 scaled to average number of amino acid

replacements per lineage. I used macaque as the outgroup to root the tree, and found the

following average of amino acid replacements. The orangutan lineage had 15.6 inferred amino

acid replacements. There is an average of 6.9 amino acid replacements leading to the

chimpanzee and human lineage. There is an additional 6 amino acid replacements on the

chimpanzee lineage. In contrast, no amino acid replacements are inferred upon the human

lineage. Thus, all of the observed sequence differences between the human and chimpanzee

CD4 sequences (Hvilsom et al. 2008) are due to derived amino acid replacement on the

chimpanzeelineage. The sequences can be seen in Appendix 1.

Phvloeeny of CXCR4

Figure 3 shows the phylogeny of CXCR4 scaled to average number of amino acid

replacements. The orangutan lineage has an additional2 amino acid replacements, whereas the

orangutan lineage has none. Gorillas do not have any additional amino acid replacements.

Humans and chimpanzees share I amino acid replacement, and neither have any additional

replacements after their split. Thus, the protein sequence of CXCR4 is highly conserved within

the hominoids, in contrast to CD4. The sequences can be seen in Appendix2.

Phvloeenv of CCR5

The phylogenetic tree of CCR5 is shown in Figure 4, scaled to amino acid replacements.

The orangutan branch does not have any inferred amino acid replacements. Gorilla is shown to

have an average of one more amino acid replacemerit on its lineage. Chimpanzees and humans

share one amino acid replacement. The chimpanzee lineage does not show any further amino

acid replacements. The human lineage shows an additional 2 arrtino acids changes on its lineage.

These changes are occur throughout the sequence and will be discussed further below. The

sequences can be seen in Appendix 3.

Alienment of ep120

The alignment of gpl20 can be seen in Appendix 4. On the top line of this alignment is

the protein sequence of the engineered gpl20 used in producing the crystal structure (Kwonget

al. 1998). Aligned to this sequence are examples of sequences of the M and N strains of HIV- 1 .

The next are sequences of SIVcpzPtt (from Pan troglodytes troglodytes, Ptt), followed by

SIVcpzPts (from P. t. schweiffirthii, Pts). The HIV-I O strains are next inthe alignment

followed, by the SIVgor strains. A majority of these sequences were the same as those used by

Takehisa et al. (2009), as seen Figure 5; however, I included additional examples of M and N

strains to the alignment in Appendix 4 to increase the power of our analysis for detecting

adaptive amino acid replacements. This alignment of gp120 reveals many conserved regions as

well as many variable regions (Appendix 4).

l 0

Chirnpanzee

Orangutan

Figure 2: Phylogenetic analysis of CD4 based on amino acid replacements.

The average number of amino acid replacements was determined for the CD4 protein for the

available hominoid sequences with a parsimony approach. Human and chimpanzee share an

average of 6.9 amino acid replacements, but we see that chimpanzees show an additional 6

amino acid replacements that humans do not share.

1 l

Chimpanzee

Goril la

Gibbon

Figure 3: Phylogenetic analysis of CXCR4 based on amino acid replacements.The average number of amino acid replacements was determined for the CXCR4 chemokine co-receptor for the available hominoid sequences with a parsimony approach. Human andchimpanzee share an average of 1 amino acid replacement. For CXCR4, we do not see additionalreplacements on the chimpanzee lineage as we saw for CD4 sequence.

t 2

Human

Chimpanzee

Gorilla

Figure 4: Phylogenetic analysis of CCR5 based on amino acid replacements.The average number of amino acid replacements was determined for the CCR5 chemokine co-receptor for the available hominoid sequences with a parsimony approach. Human andchimpanzee share an average of I amino acid replacement. Gorilla also expressed 1 amino acidreplacement. Human had an additional 2 amino acid replacements, while the chimpanzee lineageshowed none.

13

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Figure 5: Molecular phylogeny of envelope protein from various SIV and HIV strains.This phylogeny illustrates how it is known that humans got HIV-I from chimps. The numbersabove the lineages indicate the statistical bootstrap support for the clades. The black cladesrepresent SIVcpz, the blue clades represent HIV- I strains M, N, and O. The red clade representsSIVgor. Note that the three human HIV- 1 strains are nested within the chimp and gorilla SIVstrains, providing the evidence that HIV jumped from these apes to humans. SIV strains TANl,TAN2, TAN3 and ANT are found in the Pan troglodytes schweinfurthii sub-species, whereas theremainder of the SIVcpz strains are from Pan troglodytes troglodyles (see Figure 6). fFiguretaken from Takehisa et al. 20091

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Discussion

As shown in Figures 3, phylogenetic analysis revealed no evidence of rapid protein

sequence evolution on the chimpanzee or gorilla CXCR4 lineages. Interestingly, there seem to

be possible amino acid replacements and/or polymorphisms on the gorilla and human lineages of

CCR5. Humans seem to have 2 amino acid replacements. If these are found to be in the regions

that interact with HIV, they might be allowing humans to be more susceptible to HIV infection

than chimpanzees. Perhaps CCR5 plays a bigger role in allowing HIV infection in humans

rather than changes in chimpanzees and gorillas that prevent it. We can see that chimpanzees

have 6 amino acid changes while humans have none as illustrated in Figure 2. This shows that

CDlhas evolved very *rdt, on the chimpan zee,butnot human, lineage.

Then we must ask the question: are these amino acid replacements fixed in chimpanzees?

To answer this question requires understanding the demographics of the chimpanzees and

sequencing the genes of different populations and sub-species.

The map in Figure 6 shows the chimpanzee sub-species and their estimated dates of

divergence. The chimpanzee genome that has been sequenced is from aP.t. verus. Each of the

sub-species has differences in infection rates for SIV. P.t. verus is from western Africa as are the

majority of chimps that are kept in captivity in the USA and used in HIV/AIDS research. This

subspecies has not been found to harbor SIV like chimps from central and eastern Africa (Figure

6). They are extremely difficult to infect with SIV or HIV, and they do not progress to AIDS if

infected experimentally. As the map shows, fuither eastern and central chimps such as P. t.

troglodytes and P. t. schweinfurthii are infected with SIV, but there has been little or no

indication that they die from AIDS. However, recent evidence suggests that,in the wild, Eastern

chimpanzees infected with SIV are less fit than uninfected chimps. Taken together, these data

suggest to us that the differences in SIV infection rates of the different populations is likely due

to differences in levels of adaptation to the virus.

1 5

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P. l. verus

P. l. vel/erosus

WestAfrican Group

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P. t. troglodytes + Central/East

P. t. schweinfufthii * African Group

Bonobo 7

Figure 6: Phylogeny of chimpanzee sub-species indicating SIV infection and geographic

locationThe left side of the figure shows the molecular phylogeny of the chimpanzees and bonobo (Pan

paniscus). The colored circles next to their names indicate their geographical location as shown

on the map to the right. SIVcpz status of these sub-species is indicated by (+) or (-). Note that

only P.t. troglodytes and P. t. schweinfurthii are shown to harbor SIV to this date. The

chimpanzee genome that was secluenced, and thus the one that was used in this study was from

P.t. verus. fFigure made by K. Gonder].

If this were correct, we would expect to see differences in the sequences of host protetns

involved in SIV infection, such as CD4. Indeed, Hvilsom et al. (2003) charactertzed the genetic

diversity of CD4 in all four recognized subspecies of chimpanzees and found variation among

them. They discovered that amino acid replacements in CD4 are conserved in individuals

belonging to the P. t. verus subspecies and divergent from the other three subspecies, which

harbored highly variable CD4 receptors (Hvilsom et a1.,2008). However, these researchers did

not analy ze their data in phylogenetic framework, as we have done in Figure 7. Phylogenetic

analysis reveals that there are 4 amino acid replacements shared by all of the subspecies, and

thus were 'fixed' on the ancestral chimpanzeelineage. One of these is a threonine that replaces

an isoleucine and creates a potential N-linked glycosylation site. For glycosylation to occur the

motif N-X-T/S is needed. P. t. verus has fixed a proline to threonine change, which would create

a second N-linked glycosylation site; this site is polymorphic in the other subspecies. Human

t 6

CD4 has neither of these glycosylation sites. If glycosylation occurs, large and bulky

carbohydrates have the opportunity to be added to CD4, which could hinder the binding of SIV

to the host CD4. P.t. verus has fixed an additional asparagine to aspartic acid replacement not

seen in the other subspecies. Thus, all six replacements inferred to have happened on the

chimpanzee CD4lineage (Figure 2) do appear to have been fixed inP. t. verus, but not the other

subspecies. The other subspecies have additional polymorphic sites not seen in P.t. verus,

however.

P. t. verus

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P. t. traglodytes

v / 1 5 5 v / M 3 3 5

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P. t. schweinfurthii

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Figure 7: Mapping of the CD4 amino acid replacements on a phylogeny of the chimpanzee

sub-species.This tree illustrates the 6 amino acid replacements on the chimpanzee lineage. The amino acid

replacements (arrows) and polymorphisms (slashes) are shown under the lineages in which they

are inferred to have happened, with the exception of the two polymorphisms shown at the

ancestral chimpanzee node (which are found in all subspecies except for P.t. verus). Four of the

amino acid replacements are found in all four of the sub-species, and thus were likely fixed on

the lineage leading to this species. Two additional amino acid replacements are found only in

P.t. verus. The boxes around some of the amino acid replacements indicate those that result in

potential N-linked glycosylation sites.

t 7

Now that we are aware of the 6 amino acid replacements in chimpanzee CD4, it is

important to see where these amino acid replacements occur in the 3D structure of the protein.

Figure 8a is arepresentation of the interaction of Domains 1 and 2 of human CD4 (inyellow)

with a genetically engineered version of 9p120 from HIV-1 (in purple). Note that this gpl20

molecule only interacts with Domain 1. Figure 8b illustrates the amino acid replacements of the

chimpan zeelineage modeled onto the human CD4structure. Note that 4of the 6 replacements

found inP.t. verus CD4 occurred in Domain 1. These include the replacement of an otherwise

conserved glutamate (negative charge) with a glycine (no charge) at the interacting face. They

also include the gain of two threonine residues that create N-glycosylation sites that are not

found in human CDA. If long-chain N-linked carbohydrates were added onto CD4 at these

positions, they likely would hinder the binding of gpl20 to the host cell's CD4. If so, this could

help explain why P.t. verus appears difficult to infect with HIV or SIV experimentally, and

perhaps is part of the reason that this subspecies currently lacks endemic SIV.

As discussed above, recent research has shown that wild gorillas harbor SIV and there is

no evidence that they progress to AIDS (Takehisaet a|.,2009). This led us to wonder whether

CD4 might also be the target of selection by SIV, and to ask what amino acid changes have

occurred on the gorilla CD4lineage. A recent search of the gorilla genome database revealed a

newly-available partialsequence of the CD4 gene. Santhoshi Bandla analyzedthis gene, and

some of her findinss are discussed next.

1 8

(c)(b)(a)

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Figure 8: Host CD4 interacting with SIV/HIV gp120.

(a) This figure shows the interaction of Domains 1 and 2 of human CD4 (in yellow) with a

genetically engineered version of gp120 from HIV-I (in purple). This figure was produced

in VMD (molecular visual ization program for displ aying, animating, and analyzing large

biomolecular systems) by Santhoshi Bandla, usingthe PDB file IGSM from Kwong et al. (1998).

(b) Chimpanzee amino acid replacements mapped onto human CD4.

In this figure, Bandla mapped the amino acid replacements of the chimpanzee CD4 protein onto

human CD4. The bright pink residue is a glycine, which replaced a glutamate. The green one is

a valine, which replaced an alanine. The two threonine replacements are represented in blue.

The asparagine residues that would be glycosylated as a result of these threonine gains (which

create N-X-T sites) are modeled in purple. This structure shows that the possible N-linked

glycosylation sites occur in Domain 1 where CD4 of the host interacts with gpl20 of the virus.

(c) Gorilla amino acid replacements mapped onto human CD4. Gorilla amino acid

replacements mapped onto human CD4, as in (b). The threonine replacement is represented in

blue, and the asparagine residue that would be glycosylated is modeled in purple. The bright pink

residue is a glycine, which in this case replaced an aspartate.

t 9

Seen in Figure 8c, gorillas have similar amino acid replacements as chimpanzees. This

figure shows the amino acid replacements of gorilla CD4 modeled onto human CD4. Once

again, the purple amino acid replacements represent asparagines and blue represents threonine.

The pink amino acids in these figures represent the replacements that caused an independent loss

of a charged residue at the interface. Gorillas have a gained an N-linked glycosylation site on the

same side of CD4as has chimpanzee. Also, the glycosylation site is near the same place on the

crystal structure but at a different position. Thus, this is a case of convergent evolution of

glycosylation sites in these two SlV-endemic species. It is tempting to think that these represent

independent adaptations to SIV infection.

The fact that chimpanzee and gorilla CD4 appear to have adapted to SIV is striking

information and makes us wonder what protein adaptations humans need to evolve in order to

allow us to avoid HIV infection or to harbor HIV without AIDS. We know that HIV evolves

rapidly, allowing the virus to dodge medications like aztdothymidine (AZT). With this rapid

evolution we expect to see co-evolution of the virus especially in HIVgpl2} adapting to humans.

Using the HIV/SIV envelope protein sequences of Takehisa et al. (2009) seen in Figure 5, and

some additional HIV sequences, I aligned the sequences of gp120. In doing so, I was looking for

evidence of adaptive evolution of HIV-I gp120 following the'jumps' of SIV from chimpanzees

to humans. I was also looking for patterns of shared changes among the sequences of the HIV

strains, M, N and O. I found some sites to be conserved and others to be highly variable

(Appendix 4). Some regions were so variable that they were very hard to align. This illustrates

the well-known fact that gpl20 is evolving extremely rapidly.

The amino acid replacements on chimpanzee CD4 in comparison to human CD4 helps to

explain why chimpanzees successfully live without progressing to AIDS, while humans fail to do

so. With new gorilla sequences available, there is more evidence that these African primates

have evolved molecularly to survive with the SIV. The rapid rate of evolution and the

20

'convergence' of the chimpanzee and gorilla CD4 proteins suggest that they have adapted under

positive selection to SIV gpl20. Importantly, both the rapid evolution and the convergence

occurred in the regions of chimparrzee and gorillaCD4 that interact with gpl20. Unfortunately,

it is still unclear whether HIV-1 gp120 has adapted to human CD4 following the cross-species

transmissions.

2 l

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Wessner ,D.2006. HIV and ArDS, The Benjamin Cummings Topics in Biology Series. M'A'

Palladino, Ed. 35 pp. Pearson Education Inc., Benjamin Cummings. San Francisco'

S e - A1. http : I I tr ee. b i o . ed. ac. uk/ s o ftw at e I seal I'

22

Appendix 1: CD4 Alignment

23

l lunl*n

{h rmpan r te

Orangut*n

b!a{.ngue

Hunl&n( | r rmpan, : **

Otangut -*n

L la t*qu*

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t l r rmpant*e

t)r artg utelt

fvlar*qu*

Hu *r;ln(h r rupa* t * *

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*1d l (AqUe

H u n r * n

t l r r m p a n r e *

O r a n q u l t n

. ! tecaqut

f l un rsn

t h rn tpa t r . r * *

( } rangu t * t t

i l a {dque

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0 r a n g u t a *

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f lunr in

Lhrn rpan :e*

Ora t rgu tan

*tac,rqur

I 1_ '

h l N , t L v * , f R H t L t - V L Q L A L t - f A A ' f Q L K K V 1 , ' t - L x K L l l

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24

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t ' e A L f r e t A L : t N L I

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l{ (_ l{ t-r ft x * t Q A L f { [ r 5 { t l

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25

Appendix 2z CXCR4 Alignment

26

t{{.r rxr&n

(h r r l t pan :e*

eorul l " l

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tc l r r l l " r

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Lrb t ron

|.rlac.rqu *

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L r : r t l l a

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L r b b o n

t la l ;qu*

l - lur l lan

L h r n r p a n z r *

t o n l l ;

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t i b b * r t

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. f . L ' 5

tt

R t H L } V

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L L Q I

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L N L T V

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l ' 1 5 { J N Y f

l ! I n I L I L l V I L V I \ , l L Y Q K K L R 5

t - l R l Y r

r\L T L I

\ ' f I t " f ' ; v t ' d v O , , 1 \ . , \ I ' J W Y l t i l l L L t ( ^ \ , 1 - l \ ' I

a

r \ , l l

: i .

Y L " \ IL A * r 5 L $ l { . \ ' t { d , l } r ' } Q t {

l l 4 N t ' : t A u t l R Y t L

r R K

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l P : \ L L t l l { , ' U l

. 1 ,

v t Q t Q t " r t l t l , L r - | ! - F L I

5

' . " , , . , i

L S t Y t l r I l x L 5 l " t S K L f l Q , ( a x\ ' l

27

- ' 1 " - 1 ' - l

l - l u n r a n L N I \ H l t \ t l 5 | t L A L A I l r l L L L l . l P l L Y A f L t A | t ] K l S " A Q H r \

( l r r n t p , r r r l e e

L r r r r l l . r

0 r a n < ; u l a r r

L r b b r i r r

Ul . lc . iqur

r . 1 . 4 ; ' , i

t { u m a n L l 5 \ ' 5 R L } 5 t . X i t S f t L X n L L i l S } \ ' 5 | t S t 5 5 } } r l 5 5

t -h rn rpan ; * *

L o r r l l . r

0 r a t r g u t a t r

L r b b o r r

$ la i . rqu r

28

Appendix 3: CCR5 Atignment

29

firinl &il

Lhi f f r la$r€€

0 r a n q u l a n

Gr;r t i l la

lvt.r<ague

N"{ur?1nfi

Lh rn rpe* l * *

t ) rangu ta t r

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Mar *quc

f i* rn an

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0 r angu{a r t

t * t r l l a

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t l a { i q$ r

l l un l *n

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C r ; r t l l a

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l lunlan

( l r rn tp ; r l r * *

$ r a n q u t a n

L * r t l l a

M a c a q u e

M t ; Y Q \ , 3 t P I

L \ , f I I

t t * i L A l l U t f

, L

f | {, I l

U I I ' I V Y T T L

t]

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r Q K I r . i v

I

x Q t 4 A t { r - L l ' F

ILL Y 5 t ' 1 , ' L N h { L } | L I

. l l '

t't L h ,t t_ li. : t ' l l l l l Y LL I

l lr t t

X5L I . Y

I \ , ' ' \ ! , \ H Y

1 " " '

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, " I ; :

A ^ A Q w L ) * L N t r r t . Q L

A R

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r l

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t 5 t ' r I r l v l A v ' A ! L P t l l l l R S

t . . i

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a :

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Q r \ ! K h r Q t L K I V I

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L t \ , . L T ' Lb Q t L \' fr{

30

t lunran

(t tnrpan;**

0 l a n g u t a t t

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ldurtt *n

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t t t r l l n

t ! . rc . rqu*

H $ m l l r

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O r e n q u t a n

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M a t a q u t

Hun t i r r

Lh rn tpan l * *

{ } r * n g u t e n

L * r r l l a

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\ , I L Y 5 L I L

! t ' A f

A V N L

N f - l t 3 ! 5 t { l {

l t I i , l l V Y lK XK I L t R t r { f t t

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t ' L L l { | R , f ' . } L L \ ' f * Q K

I

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t A l L l ' L l I l l l r l Q f ' l

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L \ \ L \ 5 5 \ R {.} Q

32

1 , j r . " i l t ' , 1 , , i t , f

l lurn&n A MQ \ , ' t t " f L L M 1 Ll L t { i / P I I Y ' \ } \ ,& t X } R t , l Y L L ! f I

L l*nrpantcr

0 r a n g u t a n

L * r u l l a

M a c a q u r

l-{ur}1 An Q K H I A R I T ' L * T C L I I T Q Q T A P L R A 5 ! V Y 1 ' { 5 I L t , Q L

C h r n t p d r r ^ u € r

Ora*qu lan

& o r r l l a

i l1*c*que

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C h r n r p . t n r r e

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L lac . rqu e

J J

Appendix 4z gpl20 Alignment

34

{ c r y s t a l i t { t r r { u r € t L A t l } t ! ' \ , L ! ' \ ! I t { ' \ a f N t l t l / r K l . ' l { J * t \ ' t Q M f i l U l | 5 L l t l - )

i f l , V t { } ' l $ J j l C I } F h t r Q . I t } . t N . l }

i H t \ , L 1 t j . { b 0 l b r p 5 r Q t L t " . a

t l - l l \ ' t t A t l $ { r l i , : ! r h P Q . t i t t I \ ' I

r f t t \ , $ ' t K t l j . l ! 4 ) P t o f Q . | * t N

{ H r u f l l A l l S & C J t r r l ' � h f } Q N , d D . N . A "

iHl \ , ' |1 U*$fr1{ t t ' l { t ' Q . I t i . L N .

{ f l t } L t ' \ ? J J l l 5 s r f ' { . } t } Q . t t L } . N . D .

{ H r u } t 4 } J i t l 5 r i l p ! J } ' � Q . I t l - } . N . l l .

i l - l l ! L l d\ ' l ; iJ l l l Xt t ' f , { t ' Q , I H . r \

i l l l 1 . l ' l u 5 . l i l l l , ' ! ' \ t ' Q . I f l t " f t . a . ! '

{ H l ! b ! A l * , " l . J J { r t l ' l \ l } Q l | r t . U . N . I

{ l l l t | l ! ; \ Y * { i { 9 . * i ] l F } f Q l f ' l [ ' l R N '

' l 5 l v { p t , ' { { L A M S A J I ; l i t } 9 i l ' t u t } Q \ ' t ! P } : N . n A . 5

{ H f V l f d * t r " - { r . ) f 1 t p l d t { : q d t l i : $ l * f ' f r f ' Q P l l . f ' t R ' { f ' Q t

r , f { e n t . ' r l t l ' \ t ' Q . t P K K A A . L

{ t - f l \ ' i l } S f J 0 } l ' f t } ' U . L ? l r t t t A L } A ' t

{ l " l l l q Y $ t l { : } P t u P Q . L t Y L K ' ' 1 A . t

{ l t v { p r f r t t H s b b l f r f t p l I t t } A L N ! N

1 5 l v { r r f t r L X 5 0 5 l P t $ f ' Q , L l l H , t } . N . U a . t

i ! t ! ' { p t r r r ^ l 8 t { 1 J , ' , l ' i \ t ' L I I t " t u 4 . N N . u e . L

, l : t b { p l f q r u . t l ; , ' J t } t f ' u f l ! ' l { { 5 v l t ' A \ ' Y 5 t l l l } a l Q

{ t l v { p r P r r G , , \ S t f ' ! P L | | t V t } , { A . t

{ 5 1 \ i ( p l P r { t A t " ' ! J t Y S f Q Q l P h l I r 1 r ' \ i l

i i l ! ' ( p rP l l l ' 11 t4 \ i t ' I t " Q L P t t l ' l l a t -

{ : l ! ' ( p r f l l r tA*1 l { l l ' \ $ ' t l f 1 l J N . A A ' S

: 5 1 ! ' ( p r P l l L A t s l l l ' \ f ' Q t P | \ N D

{ 5 t v r t } , { t ' t r u } A t l C I i s l t i r t " t { t ' Q t ' l r K D . t h l A a .

{ 5 l v ( p r F l r L S ; ' D Q t i J * t } - ] i F t } t ' K / \ l t : t , t I ' l . Q a ' \ , '

{ } t v r p $ P t s A l d 4 ; ' . r t ' t r P f i \ t ' � t 1 A . } l & . t L 1 ' Q r K L t a

i 5 l \ ' { p r P r s l } Q j / 4 t r 5 t i t * ' n l ' � } t ' l A S t f i L t " l ' x [ h L L f Q

{ 5 1 \ { t } : P t 5 { - X l J l 4 b ! , : t f \ t } Y t ' 4 . I t U { J ' t V t X L L t A

{ t - f i v o l j t l 5 l t ! r f r t ' H t P { , . $ . U l } ' u L

i l i l \ , o l i o 5 8 , r t , ' l F Y I P H . l " ) L i , I l a

l g u r r l l . r ( . P J l j i , } J . { 1 " * $ t 1 * i P 5 P l } f L { U l N f i . D . Q t } .

{ q u r r l l a ( f t } l } { , f ; A i , * l { , r l i F 5 1 ' I 1 L t I D l } ' a .

{ q * n l f a t - P l f J $ A J { l 4 l ( $ 4 r a r t { t " I t P t I t l ' D . Q { " } t '

{ s t l r r l l " s t " P l l 3 ' l / } J " t J 4 $ $ 9 r i } f t t ' l f P l " I I I $ . Q D . !

l E r : r r l l a p 8 t { i , ' f { t ' l ' I f ' L | | Y { J . Q l ) . t r

l -

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{ { r y s l s l 5 1 r u ( l u f * }

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i 5 l ! { p r P l l t A * ' t . J }

t 5 l ! { r } r P { r f 1 f l . t t }

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{ 5 1 ! ' { p r l ' { r u ! A t t 0 : t $ I l * r

i \ lvr t ) rPt{ tS ; DC J ,1 J Ot ' "1I

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Evolutionary analysis of host proteins CD4, CXCR4 and CCR5, and ...

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