PDBsum entry 2q7c

Viral protein

PDB id: 2q7c

Contents

Protein chains

46 a.a.

Metals

_CL ×4

Waters ×84

References listed in PDB file

Key reference

Title

Inhibiting HIV-1 entry: discovery of d-Peptide inhibitors that target the gp41 coiled-Coil pocket.

Authors

D.M.Eckert, V.N.Malashkevich, L.H.Hong, P.A.Carr, P.S.Kim.

Ref.

Cell, 1999, 99, 103-115. [DOI no: 10.1016/S0092-8674(00)80066-5]

PubMed id

10520998

Abstract

The HIV-1 gp41 protein promotes viral entry by mediating the fusion of viral and cellular membranes. A prominent pocket on the surface of a central trimeric coiled coil within gp41 was previously identified as a potential target for drugs that inhibit HIV-1 entry. We designed a peptide, IQN17, which properly presents this pocket. Utilizing IQN17 and mirror-image phage display, we identified cyclic, D-peptide inhibitors of HIV-1 infection that share a sequence motif. A 1.5 A cocrystal structure of IQN17 in complex with a D-peptide, and NMR studies, show that conserved residues of these inhibitors make intimate contact with the gp41 pocket. Our studies validate the pocket per se as a target for drug development. IQN17 and these D-peptide inhibitors are likely to be useful for development and identification of a new class of orally bioavailable anti-HIV drugs.

Figure 1.
Figure 1. Model of HIV Membrane Fusion and Structure of the gp41 CoreSchematic representation of a working model for HIV membrane fusion (for review[9]). In the native state of the trimeric gp120/gp41 complex (“Native”), the fusion peptide and N-peptide regions of gp41 are not exposed. Following interaction with cellular receptors (CD4 and coreceptor), a conformational change results in formation of the transient prehairpin intermediate (“Pre-Hairpin”), in which the fusion peptide regions (red lines) are inserted into the cell membrane and the coiled coil of the N-peptide region of gp41 (indicated as “N”) is exposed. However, the C-peptide region of gp41 (indicated as “C”) is constrained and unavailable for interaction with the coiled coil. Thus, exogenous C-peptides can bind to the prehairpin intermediate and inhibit fusion in a dominant-negative manner (“Inhibited”). In the absence of inhibitors, the prehairpin intermediate resolves to the hairpin structure and membrane fusion results (“Hairpin/Fusion”), although it is not known whether hairpin formation precedes membrane fusion per se. The C-peptides discussed in this paper (and corresponding residues in gp41, numbered according to their position in gp160 of the HXB2 HIV-1 strain) are as follows: C34 [628–661]; DP178, also called T-20 [638–673]; and T649 [628–663]. Adapted from [9].The inset depicts the 2.0 Å X-ray crystal structure of N36/C34, a peptide version of the HIV-1 gp41 core ([10]). Three central N-peptides form a coiled coil, shown here as a surface representation, and three helical C-peptides pack along conserved grooves on the surface of the coiled-coil trimer. There are three symmetry-related hydrophobic pockets on the surface of the N-peptide coiled coil (shaded). The pocket region is highly conserved among HIV-1 isolates. There are 11 residues that comprise the lining of the hydrophobic pocket (see Figure 7 of [10]): Leu-565, Leu-566, Leu-568, Thr-569, Val-570, Trp-571, Gly-572, Ile-573, Lys-574, Leu-576, and Gln-577 of HXB2. These 11 residues are completely conserved in 158 of 202 fully sequenced M group HIV-1 strains (HIV Sequence Database [1998/1999 alignments], Los Alamos National Laboratory, ). Of the remaining 44 isolates, 33 possess only a single conservative methionine substitution for Leu-565.

Figure 5.
Figure 5. Crystal Structure of a D-Peptide Bound to the gp41 Pocket(A) Ribbon representation of the overall structure of the IQN17/D10-p1 complex. The GCN4-pI[Q]I′ part of the chimera (dark blue) and the HIV-1 gp41 hydrophobic segment (gray) form a continuous three-stranded coiled coil. Three D10-p1 inhibitors (purple and green) bind solely to the hydrophobic pocket. The six residues of the D-peptide that make direct contact with IQN17 are shown in green (Gly-1, Ala-2, Trp-10, Trp-12, Leu-13, and Ala-16). Figure drawn with Insight II 98.0 (Molecular Simulations Inc.).(B) Stereo view of the IQN17/D10-p1 complex in which IQN17 is represented as a molecular surface and D10-p1 is represented with sticks. The color scheme is as in (A). The four conserved residues of the EWXWL motif (Glu-9, Trp-10, Trp-12, and Leu-13) are labeled. Figure drawn with Insight II 98.0 (Molecular Simulations Inc.).(C) Stereo view of a region of the final 1.5 Å 2Fo-Fc map, contoured at 2.1σ, superimposed on the final model. The view is approximately the same orientation as in (B). Figure drawn with O ([26]).

The above figures are reprinted by permission from Cell Press: Cell (1999, 99, 103-115) copyright 1999.

Secondary reference #1

Title

Crystal structure of gcn4-Piqi, A trimeric coiled coil with buried polar residues.

Authors

D.M.Eckert, V.N.Malashkevich, P.S.Kim.

Ref.

J Mol Biol, 1998, 284, 859-865. [DOI no: 10.1006/jmbi.1998.2214]

PubMed id

9837709

Figure 1.
Figure 1. Helial wheel representation of the GCN4-pI[Q]I trimer. Residues in the first heptad, corresponding to the first two helical turns, are circled. The positions in the heptad repeat are labeled in lower case letters. The boxed residue indicates the Ile16Gln mutation from GCN4-pII to GCN4-pI[Q]I. Broken lines from one subunit to another represent the potential salt bridges that characteristically form between the g residue of one heptad (g[n]) and the e residue of the next heptad in the neighboring strand (e'[n + 1]). The sequence of GCN4-pI[Q]I is Ac-R Image KQ Image EDK Image EE Image LSK Image YH Image ENE Image AR Image KKL Image GE Image , with a positions singly underlined and d positions doubly underlined. GCN4-pI[Q]I was synthesized by solid-phase FMOC peptide synthesis as described previously [Lockhart and Kim 1992] . After cleavage from the resin, the peptide was desalted over a Sephadex G-25 column (Pharmacia) in 5% (v/v) acetic acid. Following lyophilization, the peptide was resuspended in 5% acetic acid and purified by reverse-phase high performance liquid chromatography (Waters, Inc.) using a Vydac C18 preparative column and a water/acetonitrile gradient with 0.1% (v/v) trifluoroacetic acid. The peptide elutes at approximately 36% acetonitrile. The identity of the peptide was confirmed by MALDI-TOF mass spectrometry on a Voyager Elite mass spectrometer (PerSeptive Biosystems).

Figure 4.
Figure 4. Crystal structure of GCN4-pI[Q]I. a, A portion of the 20.0 to 1.8 Å 2F[o] - F[c] electron density map contoured at 1.5s is superposed on the final model. The side view of the helix covers residues 16 to 23. b, Another region of the same map, superposed on the final model, showing the cross section of the trimer at residue 16. A chloride ion (green sphere) is located in the center of the trimer, on the crystallographic 3-fold axis, 3.35 Å from the N epsilon 2 atom of Gln16. The O epsilon 1 atom of Gln16 forms a hydrogen bond with a water molecule (red sphere). c, A view of the GCN4-pI[Q]I structure, looking down the helices from the N to the C terminus. All side-chains are displayed and the chloride ion is depicted as a yellow ball in the center of the trimer. GCN4-pI[Q]I is a trimeric coiled coil with three right-handed a-helices wrapped around each other in a left-handed superhelical twist. d, A side, stereo view of GCN4-pI[Q]I. Side-chains of the residues in the a and d positions are displayed. The chloride ion is represented as a yellow ball. Figures a and b were generated with O [Jones et al 1991], and Figures c and d were generated with InsightII (Biosym).

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #2

Title

Core structure of gp41 from the HIV envelope glycoprotein.

Authors

D.C.Chan, D.Fass, J.M.Berger, P.S.Kim.

Ref.

Cell, 1997, 89, 263-273. [DOI no: 10.1016/S0092-8674(00)80205-6]

PubMed id

9108481

Figure 1.

Figure 8.
Figure 8. Comparison of Influenza HA[2], HIV gp41, and Mo-MLV TM StructuresThe top panel shows an end-on view of the three structures from the top, as in the left panel of Figure 3. The bottom panel shows a side view. The three monomers forming the central coiled coil of each structure are colored yellow, green, and blue. Supporting structures are colored purple. Residues 40–129 of HA[2] ([6]) and 45–98 of Mo-MLV TM ( [26]) are included. The figure was generated using the program Insight (Biosym).

The above figures are reproduced from the cited reference with permission from Cell Press