[Identification of
variable regions in HIV1-PR molecules]
In identification of variable regions in HIV1-PR moleclules, the
D2 code (ProteinEncoder)
is compared with two existing methods: a (Phi, Psi) dihedral angle-based
method and the PB block
method (structural alphabet).
(1) About HIV1-PR
For comparative performance analysis, we use
72 crystal
structures (
142
chains) of the N37S mutant and the
28
NMR models (
56
chains) of a
mutant (1bve).
Variable regions are identified as the region where more than one type
of
D2
codes or
PB
blocks are assigned.
Shown below are their amino acid sequences:
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1
2
3
4
5
6
7
8
9
10
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890 |
N37S
mutant
1bve
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PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF
x
x
PQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
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<=> Active
site (Res.25-27)
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[MEMO] The list of the N37S mutants: click_here. Among
the 72 PDB
entries, the chains of 1hxb are a {I3V, N37S}
mutant. Their amino acid sequence is the following:
PQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF
[MEMO] 1bve is a {I3V, N37S, C95A} mutant.
Shown below are superimposition of the structures, which are
the 'master-slave' alignments by DALI with 1d4jA (or model26A for NMR
models) as master:
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(A)
N37S (P21212) |
(B) N37S
(P212121)
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(C) N37S
(P61) |
(D)
1bve (NMR)
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'Master-slave' alignments by
DALI,
where the
master is
1d4jA
for crystal structures and
model26-A
for NMR
models.
In the figure, top and front views are given, where yellow
spheres indicate the position of the residues that assume
a "minority"
D2
code (i.e.,
D2-variable
residues).
(A)
49
crystal structures (
98
chains) of space group P2
12
12
of the N37S mutant.
(B)
12
crystal structures (
24
chains) of space group P2
12
12
1
of the N37S mutant.
(C) 9
crystal structures (
18
chains) of space group P6
1
of the N37S mutant.
(D)
28 NMR
models (
56
chains) of a mutant.
(2) Averaged structure of HIV1-PR
(2.1)
Most frequentry occured D2 code assignment
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1
2
3
4
5
6
7
8
9
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1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890 |
N37S
mutant
NMR models
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--001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG000000000R0R00000GAAAAABR000--
x
x
--00RR00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000--
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<=> Active site
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*You could use program
NtileCodePredictor
to obtain the most frequentry occured
D2 code assignment:
% NtileCodePredictor -t
frag_code5_HIV1PR_ID.tbl filename.pdb
Conversion table
frag_code5_HIV1PR_ID.tbl
(
sample),
which is compiles from the
142
chains of the N37S mutan, is available from the
PROGRAM>NtileCodePredictor>DOWNLOADS
section.
*See the bottom for description of the
D2 codes.
[MEMO]
NtileCodePredictor
computes the most frequentry occurred
D2 code (the major D2
code) for each five-residue fragment based on the "fragment-to-D2 code"
conversion table.
(2.2)
Most frequentry occured PB block assignment
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1
2
3
4
5
6
7
8
9
10
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890 |
N37S
mutant
NMR models
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ZZDFKBCCDDDDDEEHIACDDDDDFKBMBDCDDDDDDEHJACDDDDDFKNOIACDDDDEHIACDEEHIACDFBLCDFKLCBDCDFKLMMMMNOPACDZZ
xxxxxxx x
xxxxx xxxx
xx x xx xxxx
ZZFKLMBLCDDDDEHHIACDDDDDFKBCKLPCDDFBLCHJMMDFDDDFBGOIACFBLCEHIACDEEHIACDFBLCDFKLCBDCDFKLMMMMNOPACDZZ
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<=> Active site
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*See the bottom for description of
PB blocks.
(2.3)
Average of (Phi, Psi)-dihedral angles
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1 |
2 |
3 |
4 |
... |
39 |
40 |
41 |
... |
72 |
73 |
74 |
... |
97 |
98 |
99 |
N37S(PHI)
N37S(PSI)
NMR(PHI)
NMR(PSI)
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---
135
---
135 |
-112
123
-86
134 |
-112
122
-132
114 |
-83
165
-110
-28 |
...
...
...
... |
-77
149
-80
35 |
98
-49
18
-54 |
-87
156
2
84 |
...
...
...
... |
-132
126
-95
144 |
-33
-165
-79
-98 |
-78
135
-96
104 |
...
...
...
... |
-100
136
-91
98 |
-136
137
-104
126 |
-162
---
-139
--- |
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*Dihedral angles are calculated in degrees, using
the DSSPcont
server.[2]
*The values are average over the
142 chains in the
case of the N37S mutant, and the
56 chains in the case of the NMR models of 1BVE.
(3) Identification of
variable regions in HIV1-PR
The bar
graphs below show the
spatial distribution of the occurrence of (1) large deviation of
dihedral
angles from the average, (2) minority
D2
code assignment (i.e.,
D2-variable
residues), and (3) minority
PB-block
assignment (i.e.,
PB-variable
residues).
The first row shows the residues whose
phi or
psi angle is away
from the average by more than
30°.
Recall that,
due
to the anticorrelation between Phi and Psi angles, dihedral
angle fluctuations may represent a change not
in backbone conformation but in side-chain
reorientation. [1]
Crystal
Structures: The
phi
or
psi angles
of
residues 40, 50, 51, 73, 78, and 86 are almost always deviated from the
average more than
30° (See (4) Discussion below for detailed discussion).
NMR
models: Variable regions of the NMR models are more widely
distributed than that of crystal structures.
The second row shows spatial distributions of the
occurrence of
minority
D2
code assignment.
Crystal Structures: 348
residues of the
142
chains are assigned a minority
D2
code.
40%
of the minority
D2
codes are assinged at residue 50 or 51 and
15% are assigned at
residue 5. The deformations are provably explained by
crystal packing
and
variation
of the size of the ligands bound.
NMR
models: 480
residues of the
56 chains
are assigned a minority
D2
code.
22%
of the minority
D2
codes are assinged at the loop around residue 40 and
10% are assinged at
the loop around residue 60. The deformations are provably explained by
collision with another
molecule. Note that no minority
D2
code is assinged at the loop around residue 50.
The third row shows spatial distributions of the
occurrence of
minority
PB-block assignment.
Crystal Structures: Not
only around residue 50, but also residue 30, 40, and 71-80 often assume
minority PB block.
NMR
models: Variable regions of the NMR models are more widely
distributed than that of crystal structures.
|
Crystals
of the N37S mutant |
NMR
models (1bve) |
Residue with
dPHIi > 30° or
dPSIi > 30°
|
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D2-variable
residue
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PB-variable
residue
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* [Definition]
dPHIi :=
PHIi - <PHIi>, where PHIi is the
phi
dihedral angle of the i-the residue and
<PHIi> is the
average
over the chains (142 chains in the case of the N37S mutant,
and 56 chains
in the case of the NMR models of 1BVE).
dPSIi is also
defined similarly. That is, the first row shows the residues whose
phi or
psi angle is away from the average by more than
30°.
[MEMO] Gray bars and dark gray bars in the background indicate the
position of minor and major drug resistance mutations, respectively.
The phi or psi angles of residues 40, 50, 51, 73, 78, and 86 are almost always deviated from the average more than 30°. In particular, the phi or psi angles of residues 40 and 73 are almost always deviated from the average more than 110° because chain A and chain B of the HIV-1 PR dimer have different average values (for example, X and X + 340) on these residues (Data not shown).
Recall that,
because of periodicity, the dihedral angles X and X+360° are identical. Therefore, the difference between two dihedral angles X and X+340° is 20°, which means the HIV-1 PR molecules have similar local structures around the residues.
As an example, let's consider the local structure of
1ajx chain A and chain B around residue 73 (Figure 4.1 bottom). The phi angles of residue 73 of 1ajxA and 1ajxB are 177.6° and -170.2° respectively. Because of periodicity, the difference between them is 12.2°.
Figure 4.1 bottom is the result of the alignment computed by the
DALI server, which shows fragments from residue 58 to residue 88 of 1ajxA and 1ajxB are in very similar conformations (RMSD
0.3Angstrom). T
he fragments have an identical
D2 code sequence but different PB block assignments: "Ccap-beta-beta-Ncap" and "beta-Ccap-Ncap-alpha" around residue 73.
On
the other hand, because of anticorrelation, a big change in dihedral angles does not
necessary mean a change in the Ca backbone, but a reorientation of
the peptide in question. [1]
As an example, let's consider the local structure of
1ajx chain A and chain B around residue 40 (Figure 4.1 top). The phi angles of residue 40 of 1ajxA and 1ajxB are 133.7° and 101.5° respectively, that is, their difference is 32.2°. The difference of psi angles is 15.0°. Figure 4.1 top is the result of the alignment computed by the
DALI server, which shows fragments from residue 25 to residue 55 of 1ajxA and 1ajxB are also in very similar conformations (RMSD
0.5Angstrom). T
he fragments have an identical
D2 code sequence around residue 40 but different PB block assignments: "coil-Ncap-beta" and "coil'-Ncap-Ncap'" around residue 41.
Residue 40
Residue 73
|
<
Around res. 40>
39 PRO
A -84.3
137.6 175.5
40
GLY
A 133.7
175.5
178.0
41
ARG
A -86.4
147.5 176.9
39 PRO
B -88.8
150.0 176.9
40 GLY
B 101.5
-169.5 180.0
41 ARG
B -90.1
156.3 176.8
<
Around res. 73>
72 ILE
A -123.8
139.4 177.8
73
GLY A 177.6
-177.8 178.1
74 THR
A -77.1
144.8 -179.6
72
ILE B -132.3
115.5 179.8
73 GLY
B -170.2 -161.5 -177.2
74
THR B
-80.0 129.3 -179.3
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Around res. 40
Around res. 73
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Around res. 40
Around res. 73
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(A)
Location of residue 40 and 73 |
(B)
Dihedral angles (phi,psi,omega) of 1ajxA and 1ajxB |
(C) 1ajxA
and 1ajxB |
(D)
NMR models |
Figure 4-1.
(A) Location
of residue 40 and 73.
(B) Dihedral
angles (phi,psi,omega) of 1ajxA and 1ajxB.
(C)
Alignments of backbone
fragments of 1ajxA and 1ajxB: residues 35-45 (top) and
residues
68-78 (bottom). They are the 'master-slave' alignments by
DALI
with 1d4jA as master. 1d4jA is not shown in the figure.
(D) The
'master-slave' alignments of fragments of 56 NMR chains by
DALI
with model26-A as master: residues 35-45 (top) and residues 68-78
(bottom). Residues are colored according to thier D2 code:
'0'
in
blue, 'A' in red, 'B' and 'Q' in orange, 'G' in green, and 'R' in
yellow.
DALI pairwise alignment:
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DALI score |
DALI alignment |
Fragment
res.25-55
of
1ajxA and 1ajxB
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Z-value:
4.9
RMSD: 0.5
LALI: 31
NRES: 31
%ID: 100
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Fragment
res.58-88
of
1ajxA and 1ajxB
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Z-value: 5.8
RMSD: 0.3
LALI: 31
NRES: 31
%ID: 100
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Figure 4-2.
(1)
DALI score shows values returned by the
DALI server, where
Z-value: Z-score of the match
RMSD: RMSD of the match
LALI: Number of aligned positions
NRES: Number of residues in matched structure
%ID: Sequence identity of aligned positions.
(2)
DALI alignment shows alignment of fragment pairs computed by
the DALI server: res.25-55 of 1ajxA and 1ajxB (top) and res.58-88 of 1ajxA and 1ajxB (bottom).
Large black spheres in the figure are residue 40 and 73 of 1ajxA.
Large white spheres in the figure are residue 40 and 73 of 1ajxB.
[NOTE] Chains shorter than 30 residues are ignored by the
DALI server.
D2
code assignment:
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1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890 |
1ajxA
1ajxB
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--00RR00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG000000000R0R00000QA2AAABR000--
x
x
x
--001R00R000000RRG00000R0QBGR00000000000000000000QR000000000R00000RRG000000000R0R00000QAAAAABR000--
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<=> Active site
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PB
block assignment:
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1
2
3
4
5
6
7
8
9
10
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890 |
1ajxA
1ajxB
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ZZDFKBCCDDDDDEEHIACDDDDDFKBMBACDDDDDDEHIADDDDDDFBGOIACDDDDEHIACDEEHIACEHJACDFKLCBDCDFKLMMMMNOPACDZZ
x x xx
x
xxxx x
ZZDFKBCCDDDDDEEHIACDDDDDFKBMBACDDDDDDEHJACDDDDDFKNOPACDDDDEHIACDEEHIACDFBLCDFBLCBDCDFKLMMMMNOPACDZZ
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<=> Active site
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(Phi,
Psi, Omega)-dihedral angles:
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1 |
2 |
3 |
4 |
... |
35 |
36 |
37 |
38 |
39 |
40 |
41 |
42 |
43 |
44 |
45 |
... |
68 |
69 |
70 |
71 |
72 |
73 |
74 |
75 |
76 |
77 |
78 |
... |
97 |
98 |
99 |
PHI(1ajxA)
PSI(1ajxA)
Omega(1ajxA)
PHI(1ajxB)
PSI(1ajxB)
Omega(1ajxB)
|
---
153
178
---
170
178 |
-115
111
-176
-115
135
-178 |
-103
118
173
-122
129
-179 |
-74
159
-174
-95
173
-175 |
···
···
···
···
···
··· |
-42
125
178
-43
124
179 |
-163
167
-180
-161
172
179 |
-113
134
-180
-103
129
180 |
-122
157
180
-126
161
-180 |
-84
138
176
-89
151
177 |
134
175
178
101
-170
180 |
-86
148
177
-90
156
177 |
-135
161
-177
-130
159
-180 |
-124
140
179
-120
156
-180 |
-74
149
-180
-85
148
-180 |
-151
155
176
-154
146
-179 |
···
···
···
···
···
··· |
85
-8
178
-84
-4
179 |
-105
119
177
-100
126
179 |
-66
149
177
-86
124
178 |
-151
149
179
-124
155
176 |
-124
139
178
-133
116
-180 |
178
-178
178
-170
-162
-177 |
-77
145
-180
-80
129
-179 |
-136
130
177
-128
138
178 |
-103
135
180
-108
145
-179 |
-121
124
180
-124
131
-178 |
-173
-167
-179
-175
-175
-179 |
···
···
···
···
···
··· |
-104
133
-178
-104
136
-179
|
-136
129
177
-133
130
174 |
-153
---
---
-151
---
--- |
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*http://swift.cmbi.ru.nl/servers/html/index.html
<FOR REFERENCE>
SA-Encode
(SA-27):
|
1
2
3
4
5
6
7
8
9
10
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890 |
1ajxA
1ajxB
|
NMPOIYHSXKNMXUFSLXLXKPRGBQPILNTKYXLTLJJNMLXMNNXFCRJTLXLLNNUSLXMTFFQLXMJJNMNJFSPIKNMNYEZZWVWDSXLX
x
x x
xx xxx
x x xx xxxx
xx x x x
x xxxx x
NMPEIYHSXKNMXUFQLXLXLPRGBQPIKTTKYXKXJJJNMKXMNLXYZRJTLXKNTLUSLXMNUFSLXMJJTMMJFSPIKNMNYBZWAAADSXLN
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<=> Active site
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*http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Encode
DSSP
assignment:
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1
2
3
4
5
6
7
8
9
10
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890 |
1ajxA
1ajxB
|
TTT SSSSSSTTSSSSSSS TT TT SS T
TT SSSSSSSTTSSSSSSSSSSSSSSSTTSSSSSSSSST TT SS
HHHHTTTT
TTT SSSSSSTTSSSSSSS TT TT SS
T TT
SSSSSSSTTSSSSSSSSSSSSSSSTTSSSSSSSSST TT SS HHHHTTTT
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<=> Active site
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*http://swift.cmbi.ru.nl/servers/html/index.html
References
- McCammon JA, Gelin
BR, Karplus M. 1977. Dynamics of folded
proteins. Nature 267:585-590.
- Carter P, Andersen CA, Rost B. DSSPcont: Continuous
secondary structure assignments for proteins. Nucleic Acids Res. 2003
Jul 1;31(13):3293-5.
[The D
2 codes]
- 0 =
DDDDD (Extended
strand, small
blue
spheres)
- 1 = DDDDU
- 2 = DDDUD
- 3 = DDDUU
- 8 = DUDDD
- 9 = DUDDU
- A =
DUDUD (Helix, large
red
spheres)
- B =
DUDUU (C-cap, large
orange
spheres)
- G =
UDDDD (Large green spheres)
- H = UDDDU
- I = UDDUD
- J = UDDUU
- O = UUDDD
- P = UUDDU
- Q =
UUDUD (N-cap,
large orange spheres)
- R =
UUDUU (Turn,
large yellow spheres)
[The PB label]
- A = N-cap beta
- B = N-cap beta
- C = N-cap beta
- D = beta
- E = C-cap beta
- F = C-cap beta
- G = mainly coil
- H = mainly coil
- I = mainly coil
- J = mainly coil
- K = N-cap alpha
- L = N-cap alpha
- M = alpha
- N = C-cap alpha
- O = C-cap alpha
- P = C-cap alpha to N-cap beta
[The DSSP code]
- H = alpha helix
- B = residue in isolated beta-bridge
- E = extended strand, participates in beta
ladder
- G = 3-helix (3/10 helix)
- I = 5 helix (pi helix)
- T = hydrogen bonded turn
- S = bend
- _ = no assigned structure