Product# 1081 HIV-1 gp120 (ADA)
Product# 1011 HIV-1 gp120 (subtype C)
Product# 1031 HIV-1 gp120 (YU2)
Broadly neutralizing antibodies (bnAbs) to HIV delineate vaccine targets and are prophylactic and therapeutic agents. Some of the most potent bnAbs target a quaternary epitope at the apex of the surface HIV envelope (Env) trimer. Using cryo-electron microscopy, we solved the atomic structure of an apex bnAb, PGT145, in complex with Env. We showed that the long anionic HCDR3 of PGT145 penetrated between glycans at the trimer 3-fold axis, to contact peptide residues from all three Env protomers, and thus explains its highly trimer-specific nature. Somatic hypermutation in the other CDRs of PGT145 were crucially involved in stabilizing the structure of the HCDR3, similar to bovine antibodies, to aid in recognition of a cluster of conserved basic residues hypothesized to facilitate trimer disassembly during viral entry. Overall, the findings exemplify the creative solutions that the human immune system can evolve to recognize a conserved motif buried under a canopy of glycans.
Numerous antibodies that target and neutralize a broad range of different human immunodeficiency virus (HIV) isolates have been found in chronically infected HIV donors. Some of these bnAbs inhibit HIV Env with remarkable breadth and potency by recognizing conserved “supersites” of vulnerability (Burton and Hangartner, 2016). One of these epitope clusters is located at the trimer apex, consisting of the variable loops 1 and 2 (V1/V2) that hold together the gp120 subunits of the trimer through inter-protomer interactions (Doria-Rose et al., 2014, McLellan et al., 2011, Sok et al., 2014, Walker et al., 2009).
True to its name, the V1/V2 region varies greatly in sequence and length. All HIV isolates nevertheless retain two notable features in this region. The V2 contains N-linked glycosylation sites at positions N160 and N156 (or the less common compensatory position N173), and a cluster of positively charged amino acids around the trimer 3-fold symmetry axis (Andrabi et al., 2015). In this manner, the trimer apex forms an immunogenic, structurally conserved motif consisting of an electropositive hole surrounded by N-linked glycans. Examples of patient-derived bnAbs that belong to this class include PG9, PG16, CH01-CH04, the CAP256-VRC26 lineage, PGT141-145, and PGDM1400-1412 (Doria-Rose et al., 2014, McLellan et al., 2011, Sok et al., 2014, Walker et al., 2011, Walker et al., 2009). PGDM1400 (83% breadth, 0.003 μg/mL median IC50) and CAP256-VRC26.25 (57% breadth, 0.001 μg/mL median IC50), in particular, are remarkably potent (Doria-Rose et al., 2015, Sok et al., 2014).
Partial descriptions of paratope-epitope interactions have been obtained using epitope scaffolds with PG9 (McLellan et al., 2011), PG16 (Pancera et al., 2013), and the CH01-CH04 apex bnAbs (Gorman et al., 2016). Hybrid-modeling approaches employing low-resolution negative-stain EM (Julien et al., 2013b) and X-ray structures of scaffolds indicate these bnAbs bind at or near the trimer 3-fold axis with a binding stoichiometry of one antigen-binding fragment (Fab) per trimer. This binding mode results in a symmetry mismatch, unique to this class of antibodies, and glycan heterogeneity makes them difficult targets for structural studies (Sok et al., 2014). All characterized apex bnAbs, except for some CAP256-VRC26 lineage antibodies (Doria-Rose et al., 2014), depend on glycans at N160 and N156/N173, and often fail to bind viruses produced in the presence of α-mannosidase-I inhibitor kifunensine (Kif) that results in homogeneous oligomannose glycans with 8-9 mannose (Man) residues (Andrabi et al., 2015, Sok et al., 2014). The structural basis of Env recognition for the PGT145-class of antibodies is highly sought after because its quaternary specificity is now widely exploited to detect and isolate properly formed Env trimers (de Taeye et al., 2015, Pugach et al., 2015), including under GMP conditions for human vaccine trials. Using cryo-electron microscopy (cryoEM), we determined the structure of PGT145 Fab in complex with the soluble, recombinant Env trimer, BG505 SOSIP.664 (Sanders et al., 2013) to elucidate key molecular interactions at the Env apex. Our structural and biochemical analyses revealed that PGT145-class bnAbs utilize their CDR loops, especially HCDR2 to stabilize a long anti-parallel β-hairpin HCDR3. This structural rigidity allows the antibody to penetrate through the tightly packed N160 glycan shield network, to recognize the electropositive sink generated by the protein elements at the core of the trimer apex. Therefore, despite nearly all epitope contacts coming from the HCDR3, additional maturation of the remaining CDR loops influences the HCDR3 and is crucial for generating a potent PGT145-like antibody.
PGT145 Recognizes a Quaternary Epitope at the Apical 3-fold Symmetry Axis of the Env TrimerApex bnAbs discovered so far can be grouped according to their heavy chain (HC) complementarity determining region (CDR) 3 topology: (1) PG9-like with—or predicted to have—a hammerhead motif (Doria-Rose et al., 2015, Doria-Rose et al., 2014, Gorman et al., 2016, McLellan et al., 2011, Pancera et al., 2013); or (2) PGT145-like with a long, anti-parallel β-hairpin (McLellan et al., 2011, Sok et al., 2014). Here, we solved X-ray structures of unliganded PGT143 and PGT144 Fabs, and they too exhibit the β-hairpin HCDR3 motif as expected (Figure 1A, Table 1, Figure S1). The elongated HCDR3 conformation of this PGT145-class bnAbs results in a paratope that projects a long distance away from the surface of the Fab and enables epitope recognition at the C3 axis of the trimer apex via a long-range interaction (Figures 1B and 1C, S2A) (Sok et al., 2014). To define the molecular interactions of an apex antibody, we generated the structures of BG505 SOSIP.664-3BNC117-PGT145 and BG505 SOSIP.664-3BNC117 by single particle cryoEM at global resolutions of ∼4.3 Å and ∼4.4 Å, respectively (Figures 1B, S2B–S2G). The PGT145 HCDR3 inserted perpendicularly to the V1/V2 β sheets between the triad of N160 glycans into a pocket formed at the trimer apex, to simultaneously engage all three gp120s (Figures 1B–1D). This quaternary epitope is only present in the correctly folded pre-fusion Env conformation (Sok et al., 2014).
|APS 23ID-B||APS 23-ID-D|
|Unit cell a, b, c (Å)||70.9, 97.6, 126.2||57.6, 67.6, 69.6|
|α, β, γ (°)||90.00, 90.00, 90.00||82.01, 74.97, 81.28|
|Resolution (Å)||48.8 – 2.40 (2.44 – 2.40)a||40 – 2.9 (3.0 – 2.9)a|
|Completeness||95.1 (87.4)a||96.6 (96.9)a|
|Redundancy||3.5 (2.5)a||2.1 (2.1)a|
|No. total reflections||113,011||45,828|
|No. unique reflections||32,477||21,292|
|I/σ||9.6 (2.2)a||5.5 (1.9)a|
|Rsym||0.11 (0.49)a,b||0.16 (0.39)a,b|
|Rpim||0.06 (0.36)a||0.14 (0.35)a|
|CC1/2||97.0 (90.0)a||94.8 (59.1)a|
|Resolution (Å)||48.8-2.4||40 – 2.9|
|No. reflections total/Rfree||30,746/1,652||21,284/1,064|
|RMSD Bond Length (Å)||0.003||0.0025|
|RMSD Bond Angles (°)||0.900||0.620|
|Wilson B-value (Å2)||46.6||38.6|
|Overall average B-value (Å2)||38.6||42.5|
|MolProbity all-atom clashscore||7.4e||8.7e|
The trimer-specific PGT145 is one of the few antibodies with which we could previously extract cleaved wild-type JR-FL E168K EnvΔCT trimers from cell membranes (Figure S2A) (Blattner et al., 2014). PGT145 also increases the thermal stability of BG505 SOSIP.664 upon binding (Cheng et al., 2015) and is predicted to neutralize HIV by stabilizing the prefusion conformation of the Env trimer. However, surface plasmon resonance (SPR) showed improved binding of the Env-receptor mimic CD4-IgG2 (Liu et al., 2008), when PGT145 Fab had pre-bound the trimer (Figures 1E, S3A). A subtle opening of the trimer apex induced by PGT145 HCDR3 (Figure 1F) might improve access to the CD4-binding site, albeit shown only in vitro with soluble components. In vivo, PGT145 IgG binding at the Env apex would however provide a steric block to CD4 binding on the host cell membrane.
In the BG505-3BNC117 complex, we also observed a subtle opening of the trimer apex (Kwon et al., 2015) (Figure 1F) that appeared to be mediated by HC framework region 3 (HFR3) of 3BNC117. 3BNC117 and its clonal relative, 3BNC60, have a 71dWDFD74 insertion in HFR3, which is critical for neutralizing activity (Klein et al., 2013). In 3BNC117, the HFR3 interacts with the N-acetylglucosamine (GlcNAc) core of the N197 glycan with H71a, and residue W71d interacted with V3 R308 of the adjacent gp120 (Figure 1G). Env residue 308 is typically Arg or His (Arg: 32%, His: 39%), both of which provide favorable interactions with tryptophan. Thus, while PGT145 recognizes the closed conformation of the Env trimer, the trimer apex is very subtly open in the PGT145 bound conformation. Induced allosteric effects, such as 3BNC117 binding at the CD4 binding site, that lead to an increase in spacing between the N160 glycan triad, likely make the apical binding site more accessible to PGT145.
PGT145 Recognizes Oligomannose Glycans
The glycoforms to which apex antibodies bind have been a matter of debate. Studies have shown that apex antibodies such as PG16 bind sialylated hybrid glycans with much higher affinity than oligomannose glycans (Andrabi et al., 2015, Pancera et al., 2013). Similarly, PG9 showed increased binding affinity, neutralization potency, and maximum percentage neutralization (MPN) in the presence of complex/hybrid glycans (Figure 2A). PGT145-family antibodies have also been shown to preferentially bind to wild-type viruses and trimers compared to Kif treated Envs (Sok et al., 2014). However, SPR analysis of PGT145 Fab binding to BG505 SOSIP.664 trimers demonstrated that PGT145 has the highest affinity for glucose N-acetyltransferase 1 (GnT1)-deficient 293S-produced trimers that only have oligomannose Man5-9 glycans, although the larger Man8-9 glycans in the +Kif condition are somewhat inhibitory (Figures 2B, S3B and S3C). Further, a 31-pseudovirus neutralization panel showed a ∼3.5-fold improved median IC50 of PGT145 in 293S compared to wild-type glycan producing 293T cell produced pseudoviruses (Figure 2A), suggesting that, while PGT145 can accommodate glycan heterogeneity, there is a preference for oligomannose forms.
A Network of HCDR3 Stabilizing Interactions Is Found in Multiple PGT145-Class bnAbs
Inter-CDR stabilizing interactions (dashed lines, numbers corresponding to measured distance in Å) shown in Figure 5B are also present in the following unliganded X-ray Fab structures:
CDR loops are colored as in Figure 1A.
We found a 52aH-D/E-X-D/Q53 motif in HCDR2 that appeared to stabilize the HCDR3 stalk (Figures 5B, B,6,6, S1A). PGT143-PGT145 and PGDM1400 all contained extensive electrostatic interactions between the HCDR2 and 3, such as the interaction between R99HCDR3 with D53HCDR2 (Q53 in PGDM1403-6) and D100rHCDR3. The R99A paratope substitution had the second largest increase in PGT145 IC50 against all three pseudoviruses tested (Figure 5C). The D100rAHCDR3 or D53AHCDR2 substitutions also reduced potency, although not as severely as a single R99A substitution, which simultaneously ablates two electrostatic interactions. K97HCDR3 formed electrostatic interactions with E52bHCDR2 and D33HCDR1, where H52aHCDR2, a residue that contacted the N160glycan1 also played a role in orienting the side chain of E52bHCDR2. K97 is conserved across all PGT145-family mAbs except for PGDM1411, a weak neutralizer that has K98 in place of K97 and R99, thereby incompletely substituting for two basic residues. Further, introduction of the 4- (52aH-E-G-D53) or 6-residue HCDR2 (52S-H-E-G-D-K54) stabilization motif back into inferred-germline (iGL; germine reversion with the exception of HCDR3) PGT145 partially rescued the neutralizing activity of PGT145 iGL variants (Figures 5D and 5E). LCDR1 exhibited the greatest variability in CDR length and sequence (Figure S1B). Nevertheless, a semi-conserved Y32LCDR1 (9 of 18 MAbs) when mutated to alanine in PGT145 resulted in a large drop in neutralization (Figure 5C). In our four Fab structures, Y32LCDR1 hydrogen bonded with the π-nitrogen of conserved H98HCDR3 (Figures 5B and 5C). The remaining nine PGDM14XX MAbs had an F32LCDR1-F98HCDR3 interaction pair instead that plausibly stabilizes the HCDR3 by π-stacking.
Based on the SHM patterns, B cell affinity selection during the Ab maturation process led to four distinct PGT145 Ab sub-lineages (Figures S1A and S1B), reminiscent of a fork, which contains a “shaft” consisting of mutations that accumulated early to give rise to the most recent common ancestor (MRCA) Ab. These mutations are shared across all the Ab lineage members, and the four “prongs” represent the sub-lineages. Conservation of the 52aH-D/E-X-D/Q53 motif suggests that certain HCDR2 mutations arose in the MRCA Ab and were critical for stabilizing a given HCDR3, then further diversified as the Ab sub-lineages diverged. Most of the prong mutations occurred in the C-term half of HCDR2, HCDR3, and LCDR1, likely due to strong viral selection pressure. The insertions in LCDR1 likely correspond to different N160glycan2 recognition strategies.
The overall matured HCDR3 β-motif in the PGT145 family is similar to bovine antibodies, which form an anti-parallel β sheet “stalk” (Wang et al., 2013) that support a globular domain at the turn of the β sheet, thought to recognize antigen. In humans, a cross-reactive influenza antibody called C05 uses a HCDR3 β-hairpin to bind the hemagglutinin receptor binding site and was shown to contain potential HCDR3 stabilizing mutations in HCDR1 and HCDR2 (Ekiert et al., 2012); although its HCDR3 reflects the hammerhead shape of PG9, rather than the long β sheet stalks in bovine antibodies and PGT145. Therefore the structural and sequence analysis reveals that the evolution of these types of antibodies is driven by somatic hypermutation in which substitutions stabilize an extended HCDR, thereby reducing the entropy for binding antigen.
HIV Env is remarkable in its ability to substantially alter its sequence and accommodate a high density of surface glycans and yet still fold and retain its conserved receptor binding and fusion functions. Here we described the structural basis of recognition and neutralization by a class of trimer apex-targeting bnAbs that exploit the intrinsic conservation in the trimer apex that enables Env to undergo receptor-induced conformational changes to attain its fusion active configuration. In the trimer ground state, the V1/V2 regions of the three protomers interact at the trimer apex to hold the gp120 subunits together and mask the co-receptor binding site. These interactions, however, cannot be overly stabilizing, as the V1/V2 region must remodel to enable the V3 base to bind the negatively charged N terminus of the CCR5/CXCR4 co-receptor for viral fusion to proceed (Liu et al., 2008, Rizzuto et al., 1998, Wu et al., 1996). We hypothesize that Env achieves this meta-stable balance by enriching the apex in basic amino acids, a subset of which are also important for co-receptor engagement. The PGT145-family bnAbs then exploit this cationic apex through extended, unusually stabilized HCDR3 loops that contain acidic residues and sulfated tyrosines distributed along the length of the β-hairpin loop, with most charge localized to the apical tip. The HCDR3 stalk is structurally conserved across the PGT145 family yet primarily interacts with a single glycan at N160. The stalk, stabilized by tertiary and quaternary interactions with the other CDR loops, serves as a platform to insert the somewhat variable tip of the β-hairpin into the glycan-shielded trimer apex. The 3-fold axis at the trimer apex comprises a large deep pocket that is permissive to a variety of negatively charged residues at the apical tip of the β-hairpin. This type of Env recognition is unique to this class of antibodies as most bnAb families, such as the VRC01-class (Scharf et al., 2016, Yacoob et al., 2016), PGT121-124 family (Steichen et al., 2016), or even PG9/PG16 (Andrabi et al., 2015), retain a few key specific peptide interactions that are conserved. Overall, our observations demonstrate that the potency of PGT145 is highly dependent on the CDR-stabilized HCDR3 structure and the acidic charge localization in the HCDR3 β-turn. We hypothesize that apex-directed bnAbs like PGT145 require less SHM to achieve breadth and potency because of the less-specific nature of binding to the apex; that is, the specific molecular determinants of binding are less stringent than for other bnAb classes. The steep angle of approach made possible by the long rigidified β-hairpin of HCDR3 also minimizes potential steric block by the hypervariable V1 and V2 loops. Viral fitness relies on preserving a fine balance between the closed and open conformations of the meta-stable, charged apical region of the Env trimer. By targeting these conserved properties, rather than sparsely conserved residues on the surface of Env, the PGT145-family of bnAbs have solved the HIV neutralization puzzle in a particularly creative fashion.
Our structural description of Env in complex with an apex targeting bnAb highlights the importance of an intact trimer apex for eliciting an appropriate immune response to this region. As germline targeting strategies gain more popularity the apex will likely require a trimeric immunogen that has the correct disposition of glycans and positive charges rather than a monomeric scaffold. Most rational vaccine design approaches involve engagement of appropriate germline precursors and biasing SHM to evolve specific molecular contacts with the antigen. The trimer apex presents a different challenge. Here, several mutations that do not contact the antigen are critical for bnAb evolution. One strategy for analyzing germline antibodies capable of evolving these types of responses would be to search for homologous HCDR3-stabilizing residues that reside in the other CDRs. These mutations can also act as early guideposts for evaluating if an immune response is going down the right path.
Protein Expression and Purification
Untagged or C-term His6-tagged BG505 SOSIP.664 trimers were expressed in HEK293S or 293F cells and affinity purified using a 2G12 IgG cross-linked Sepharose column as described previously (Julien et al., 2013a). The affinity-purified trimers were size exclusion purified using a HiLoad 26/600 Superdex 200 pg column in 20 mM Tris pH 7.4, 150 mM NaCl (1× TBS), unless stated otherwise. The JR-FL EnvΔCT-PGT145 Fab complex was purified as described using PGT145 as the pull-down reagent (Blattner et al., 2014). Antibody IgGs and Fabs were expressed in 293F cells and purified as previously described (Sok et al., 2014) (Supplemental Experimental Procedures).
Negative Stain EM Data Collection and Processing
All negative stain grids were prepared using 400 Cu mesh carbon coated grids as previously described (Julien et al., 2013b). PGT145 bound complexes were stained using NanoW for ∼30 s, and unliganded trimers were stained using 2% uranyl formate for 45 s to 1 min. The EnvΔCT-PGT145 Fab complex was imaged on a Tecnai T12 coupled with a Tietz PXL 2k × 2k CCD camera, at a magnification of 52,000× resulting in 2.65 Å/pix images. Images were collected using Leginon (Suloway et al., 2005). Particles were processed as previously described (Blattner et al., 2014). Unliganded trimer mutants were imaged on a Tecnai T12 microscope coupled with a Tietz TemCam F416 CMOS detector, at a magnification of 52,000× resulting in 2.05 Å/pix on the specimen plane. Reference-free 2D classes were generated using MSA/MRA (Ogura et al., 2003) to sort the different trimer forms. Because these trimers were SEC purified over a Superdex 200 Increase 10/300 GL column, a large number of the mutants contained a significant portion of particles corresponding to monomers and dimers. Thus monomer and dimer populations were included in the analysis. In the first round of classification, all classes that had more than one particle in the boxed class average were eliminated. From a second round of 2D classification, reference-free 2D class averages were sub-grouped into three populations; (1) “non-native” that includes monomers, dimers, and badly assembled trimers, (2) “native-like closed,” and (3) “native-like total” that includes both the closed (population ) and “breathing” (“native-like” but open) trimers (Pugach et al., 2015) (Supplemental Experimental Procedures).
CryoEM Data Collection and Processing
BG505 SOSIP.664 trimers produced in 293F cells were pre-complexed with 6-molar excess of 3BNC117 Fab overnight at 4°C, and size exclusion purified. To break the pseudo-symmetry of PGT145, PGT145 Fab was pre-complexed with a mouse Fab obtained from a commercial hybridoma cell line ATCC CRL-1757 (1757) that binds the HC of human Fabs (Figures S2A and S2B). To make the BG505 SOSIP.664-3BNC117-PGT145-1757 complex, PGT145 was combined with 1757 Fab (1:2 molar ratio) and size exclusion purified. The PGT145-1757 complex was then incubated with the purified BG505 SOSIP-3BNC117 complex and size exclusion purified. Samples were concentrated and manually frozen in liquid ethane. Data were collected via Leginon (Suloway et al., 2005) on an FEI Titan Krios electron microscope operating at 300 KeV coupled with a K2 Summit direct electron detector camera (Gatan) in counting mode at a magnification of 22,500× resulting in a pixel size of 1.31 Å/pixel, using a total dose of ∼32 e−/Å2. Data were processed using RELION 1.4b1 (Scheres, 2012). The BG505 SOSIP.664-3BNC117 complex was refined using 22,625 particles with C3 symmetry imposed, to ∼4.4 Å resolution at a Fourier shell correlation (FSC) cut-off of 0.143. 1757 was found to be specific for the constant region of the Fab HC, near the protein G binding site (Derrick and Wigley, 1994) (Figure S2F) allowing for confidence in the PGT145 Fab orientation. The BG505 SOSIP.664-3BNC117-PGT145-1757 and BG505 SOSIP.664-3BNC117-PGT145 classes from 3D sorting were combined, resulting in a total of 65,060 particles that were refined without imposing symmetry to 4.7 Å resolution (FSC = 0.143). A soft edge mask masking out 1757 Fab and PGT145 Fab constant domains was applied for one additional iteration of focused refinement, resulting in the ∼4.3 Å resolution model (FSC = 0.143) (Figure S2D) (Supplemental Experimental Procedures).
Model Building and Refinement into the CryoEM Maps
The crystal structures of BG505 SOSIP.664 (4TVP) and 3BNC117 Fab (4JPV) were used as templates to generate an initial atomic model using the Modeller plug-in in UCSF Chimera (Pettersen et al., 2004, Webb and Sali, 2016). The resulting model was iteratively fixed and refined in Coot (Emsley et al., 2010) and RosettaRelax (DiMaio et al., 2009) employing Ramachandran constraints. Final models were chosen based on a combination of the Rosetta energy score, MolProbity and clash scores (Chen et al., 2010), and EMRinger score (Barad et al., 2015). Glycans were modeled into the finalized protein model as previously described (Lee et al., 2015), with all glycans being modeled as oligomannose. The protein structure in the BG505-3BNC117 model was used as an initial model to refine the PGT145-bound structure. The sulfated tyrosines in the PGT145 Fab X-ray structure were replaced with regular tyrosines because Rosetta fails to recognize sulfated tyrosines. The complete BG505-3BNC117-PGT145 complex was refined and followed by glycan modeling as was done for the BG505-3BNC117 complex (Supplemental Experimental Procedures).
Crystallization and X-ray Data Collection
PGT143 and PGT144 Fabs were concentrated to 4-24 mg/mL. Fab samples were screened for crystallization using the 384 conditions of the JCSG Core Suite at both 277 and 293 K using the TSRI/IAVI/JCSG robotic Crystalmation system as described previously (McLellan et al., 2011). Data collection was performed at cryogenic temperature (100 K) at beamline 23-ID of the Argonne Photon Source (APS), using a beam wavelength of 1.033 Å. The diffraction data were indexed, processed and scaled with HKL-2000 (Otwinowski and Minor, 1997) or XDS. Both structures were determined by molecular replacement using Phaser (McCoy et al., 2007) with PGT145 Fab as an initial model (3U1S). Model building and refinement was carried out using Coot-0.7 (Emsley et al., 2010) and Phenix (Adams et al., 2010) (Supplemental Experimental Procedures).
Surface Plasmon Resonance
SPR analysis of PGT145 Fab binding to His-tagged BG505 SOSIP trimers was analyzed on a Biacore 3000 instrument at 25°C. Glycan knockout mutants were expressed in HEK293F cells unless otherwise indicated. All trimers were immobilized on the chip by His-tag capture, as previously described (Yasmeen et al., 2014). To study interference or enhancement of CD4 and PGT145 binding, sequential binding analyses were also performed as stated previously (Derking et al., 2015) (Supplemental Experimental Procedures).
For pseudovirus production, we cotransfected HEK293T or 293S cells with an Env encoding and an Env-deficient backbone (pSG3DEnv) plasmids using Fugene 6 (1:2 ratio). Pseudoviruses were harvested 48–72 hr post-transfection, filtered, and titrated for use in neutralization assays. Neutralization was measured in TZM-bl target cells, as described previously (Andrabi et al., 2015) (Supplemental Experimental Procedures).
Glycan Array Assays
mAbs were screened on a custom high mannose array, consisting of 9 mannosides and 1 control sialylated N-glycan. The 10 amine-linked glycans were covalently immobilized onto custom NHS-ester dendron functionalized glass microscope slides (G3 and G4, ZBiotech). To assess mAb binding, the antibodies were pre-mixed with the detection antibody (anti-human-IgG R-PE). Following 15 min, the pre-complexed antibodies were applied directly to the slide surface and allowed to incubate for 1 hr and then washed. Washed arrays were dried by centrifugation and then scanned for RPE signal on a confocal microarray scanner (Supplemental Experimental Procedures).
Identification of Key Residues by Regression Analysis
TZM-bl neutralization assay derived IC50 values of PGT145 from 135 strains was employed for linear regression analysis. Strains with IC50 > 10 μg/mL were classified as escape. Multiple sequence alignment was performed by MUSCLE using default parameters (Edgar, 2004). By comparing the amino acid identity of each residue of interest in each strain to that of BG505, a numeric value was assigned based on an adjusted BLOSUM62 matrix (Henikoff and Henikoff, 1992). For each substitution relative to a given amino acid at BG505, the numeric value was computed by subtracting the substitution score from the self-substitution score. No substitution is represented by a value of 0. A negative value would represent the conservativeness of the substitution, with less conservative being more negative. As a result, the amino-acid sequence for each strain was converted to a list of integers. Combining these sequences in the integer representation generated a matrix. A logistic regression model with L1 regularization was then fit to the matrix with the escape phenotype as the targets. Logistic regression was performed using “linear_model.LogisticRegressionCV” in scikit-learn (Pedregosa et al., 2011) in python. Each residue of interest would be assigned a coefficient. A larger magnitude of coefficient a residue implied more influence it has on the escape phenotype. The absolute value of the coefficient was reported (Supplemental Experimental Procedures).
J.H.L, R.A., and J.-P.J. designed the project. J.H.L. performed the EM work and structural analysis. J.-P.J. and L.K. performed the crystallization studies. J.H.L. and C.A.C. performed atomic modeling of the EM structures. R.A., C.S., D.S., and M.P. performed the neutralization assays. A.Y. and P.J.K. performed the SPR studies. R.M. performed the glycan array assays. N.C.W. performed the linear regression analysis. T.N. and C.B. provided reagents. J.H.L., R.A., P.J.K., D.R.B., and A.B.W. analyzed the data. R.A. contributed to figure generation. J.H.L., A.B.W., D.R.B., and I.A.W. wrote the manuscript. All authors were asked to comment on the manuscript.
This work was supported by the California HIV/AIDS Research Program Dissertation Award D12-SRI-353 (to J.H.L.), the Scripps CHAVI-ID (UM1 AI100663), P01 AI110657, International AIDS Vaccine Initiative, and the Bill and Melinda Gates Foundation CAVD (OPP1115782 and OPP1084519). GM/CA@APS has been funded in whole or in part with Federal funds from the National Cancer Institute (ACB-12002) and the National Institute of General Medical Sciences (AGM-12006). This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. This is manuscript number 29440 from the Scripps Research Institute.
Published: April 18, 2017
Supplemental Information includes seven figures and Supplemental Experimental Procedures and can be found with this article online at http://dx.doi.org/10.1016/j.immuni.2017.03.017.
Atomic coordinates and structure factors for the X-ray structures have been deposited with the Protein Data Bank under accession codes 5UXQ (PGT143) and 5UY3 (PGT144). The cryoEM maps and models have been deposited with the Electron Microscopy Data Bank and the Protein Data Bank under accession codes EMD-8644, 5V8M (BG505 SOSIP.664-3BNC117) and EMD-8643, 5V8L (BG505 SOSIP.664-3BNC117-PGT145).
Document S1. Figures S1–S7 and Supplemental Experimental Procedures:
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Document S2. Article plus Supplemental Information:
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