X-ray crystallographic studies of Fab fragments of various neutralizing antibodies in complex with V3 loop peptides have shown that the V3 loop can adopt at least two different conformations for the highly conserved

1
Evolution of the Conserved Region of the gp120
Loop and Its Affect on HIV Disease
Progression Drew Foy, Rebecca Roberts.
Departments of Biochemistry and Molecular
Biology, Ursinus College 601 E. Main St.
Collegeville, PA 19426-1000. 
INTRODUCTION
Evolution of gp120
Representative Data of Intervisit Comparisons
Between Clones from Rapid, Moderate, and
Nonprogressors

• Due to the importance of the V3 loop in virus
  infectivity its evolution has been the subject of
  intense study and it has been suggested that
  mutations in this region correlate with the
  degree of disease development in its hosts. (3)
• Markham et al. has found that different patterns
  of selection in the env V3 sequence are observed
  between nonprogressor and moderately or rapidly
  progressing subjects and that attainment of
  higher levels of genetic diversity was most
  frequently associated with more rapid CD4 T-cell
  decline (Figure 5). (3)
• However, despite the wealth of nucleotide
  sequence data in patients infected with HIV
  obtained from Markham, the corresponding peptide
  sequences have not been subject to critical
  analysis.

Table 2 This figure represents changes between
visits for 4 subjects in the Markham et al.
study. Blue highlighted residues represent
residues that have been changed from the previous
visit.
Mechanism of HIV entry into host T-cells
Data Analysis and Discussion

• As expected, the intervisit diversity between the
  amino acid sequences of the critical 12-residue
  sections varied significantly for rapid and
  moderate progressors versus nonprogressors.
• Subjects 10 and 7 represent fast progressors by
  measurement of their CD4 declines of -363 and
  -392/yr respectively. Each of these subjects
  initially contained 3 variations in the critical
  12-residue section. However, the initial
  variations differed significantly. Subject 7
  contained the variations R1S, H/S3P, and G12A
  while subject 10 contained the variations H/S3N,
  I4M, and G12T.
• The initial variations corresponding to H/S3P and
  H/S3N in subjects 7 and 10 respectively, could
  play a large role in altering the conformation of
  the V3 loop and hence, disease progression
  because both of these variations occur in the
  third amino acid residue in the conserved region
  and continue to show variations over the
  visitation period. Therefore, variation at the
  third site in the conserved region could play a
  large role in affecting the loop and hence
  disease progression. However, data from other
  subjects seems to nullify this observation.
• Subject 5 represents a moderate progressor with a
  CD4 decline of -41/yr. Like the rapid
  progressors, subject 5 contains 3 initial
  variations, which are R1S, H/S3L, and G12T.
  Similar to subject 7, subject 5 showed initial
  variation from the conserved sequence at residues
  1, 3, and 12. However, subject 5s CD4 decline
  was much less dramatic. Therefore, it is hard to
  characterize these sites as sites that
  significantly affect disease progression.
• It is also interesting to note that subjects 7
  and 5 showed intervisit variation in amino acids
  that did not originally vary from the conserved
  sequence. However, with the current data it is
  not possible to draw a connection between these
  variations and their effect on disease
  progression.
• Subject 13 represents a nonprogressor with a CD4
  increase of 53/yr. Subject 13s initial
  variations are R1S, H/S3N, I4M, and G12A. Like
  the other subjects, subject 13 contains
  variations at sites 1, 3, and 12 in addition to
  variation at site 4. Unlike subjects 7 and 5,
  subject 13 does not show significant intervisit
  diversity.
• Although it is not possible to predict the
  conformation of the V3 loop in the subjects,
  there are differences between rapid and moderate
  progressors versus nonprogressors in intervisit
  diversity. Table 2 shows that in fast and
  moderate progressors, significant changes occur
  per visit in the amino acid sequences of the
  critical 12-residue section. However, it is not
  possible to characterize these changes into a
  pattern of how they contribute to the fast,
  moderate, or non-progression of disease.
  Therefore, further data analysis should be done
  in an attempt to characterize these changes and
  their effect, if there is one, on disease
  progression.
• Even though this study only focused on the
  critical 12-residue section of the V3 loop
  implicated in chemokine receptor binding and
  macrophage recognition, it is a possibility that
  changes distal to this 12-residue section had a
  major affect on disease progression (i.e.) it can
  be seen from the similarity data compiled in
  Table 2 that rapid progressor S7 had
  significantly lower similarities in subsequent
  amino acid sequences to S13 even though its
  critical 12 residue section stayed relatively
  constant.

Figure 5 Comparison among different progressor
groups of the mean slope per year of intravisit
viral genetic diversity and the percent of
nucleotides that diverged from the original
postseroconversion consensus sequence (Markham et
al., PNAS 1998).
Figure 3 Structure of HIV-1 gp120 bound to CD4
T-cell receptor and 17b antibody. The V3 loop is
sandwiched between the CD4 T-cell receptor and
the top of the 17b antibody

• X-ray crystallographic studies of Fab fragments
  of various neutralizing antibodies in complex
  with V3 loop peptides have shown that the V3 loop
  can adopt at least two different conformations
  for the highly conserved
• Gly-Pro-Gly-Arg sequence (GPGR) at the tip of the
  loop (Figure 4). (2)
• The high degree of conservation of the GPGR
  motif, surrounded by regions of high sequence
  diversity suggests this structural conservation
  is related to biological function. (2)
• For Fab-V3 X-ray crystal structures it has been
  determined that a 12-residue section of the V3
  loop (Table 1) including the GPGR tip, plays a
  critical role in chemokine receptor binding and
  macrophage recognition properties. (2)
• This peptide sequence, depending on the amino
  acid composition of the amino acids flanking the
  GPGR tip, can be represented by two possible
  conformations of the V3 loop. (2)

• Once an individual is infected with HIV he or she
  may live for up to ten years or more without any
  noticeable medical problems.
• The lesions of Kaposi's sarcoma are sometimes the
  first physical sign that a person with HIV
  infection has developed AIDS. There is no test to
  identify people who have KS before lesions
  develop (Figure 2).

Intervisit variation of V3 peptide
sequences between rapid, moderate, and
nonprogressors
Table 1 Section of the V3 loop critical in
determining its conformation, which in general
contains a ß turn followed by a double bend
.
Figure 2 The lesions of Kaposi's sarcoma are
sometimes the first physical sign that a person
with HIV infection has developed AIDS.

• References
• Kwong et al. (1998). Structure of an HIV gp120
  envelope glycoprotein in complex with the CD4
  receptor and a neutralizing human antibody.
  Nature 393 648-659.
• Stanfield et al. (1999). Dual conformations for
  the HIV-1 gp120 V3 loop in complexes with
  different neutralizing Fabs. Structure 7
  131-142.
• Markham et al. (1998). Patterns of HIV-1
  evolution in individuals with differing rates of
  CD4 T cell decline. PNAS 95 12568-12573.

Figure 4 Dual conformations of the V3 loop
(Stanfield et al. Structure 1999).