Genetic and structural analyses of affinity maturation in the humoral response to HIV-1

Abstract

Most broadly neutralizing antibodies (BNAbs) elicited in response to HIV-1 infection are extraordinarily mutated. One goal of HIV-1 vaccine development is to induce antibodies that are similar to the most potent and broad BNAbs isolated from infected subjects. The most effective BNAbs have very high mutation frequencies, indicative of the long periods of continual activation necessary to acquire the BNAb phenotype through affinity maturation. Understanding the mutational patterns that define the maturation pathways in BNAb development is critical to vaccine design efforts to recapitulate through vaccination the successful routes to neutralization breadth and potency that have occurred in natural infection. Studying the mutational changes that occur during affinity maturation, however, requires accurate partitioning of sequence data into B-cell clones and identification of the starting point of a B-cell clonal lineage, the initial V(D)J rearrangement. Here, we describe the statistical framework we have used to perform these tasks. Through the recent advancement of these and similar computational methods, many HIV-1 ancestral antibodies have been inferred, synthesized and their structures determined. This has allowed, for the first time, the investigation of the structural mechanisms underlying the affinity maturation process in HIV-1 antibody development. Here, we review what has been learned from this atomic-level structural characterization of affinity maturation in HIV-1 antibodies and the implications for vaccine design.

Keywords: HIV-1; affinity maturation; broadly neutralizing antibodies; computational immunology.

Figure 1. Estimation of recombination parameters

a) A mature heavy chain VRG (c662) is shown aligned against the maximum likelihood V, D, and J gene segments, with the maximum likelihood recombination points (r_V, r_D1, r_D2, r_J) shown along with the N regions. Dots indicate nucleotide identity. C₂ and W indicate the codons for the invariant second cysteine and tryptophan, which mark the outside boundaries of CDR3. b) and c) show alternative classifications for the 3′ end with slightly lower likelihoods. d) Alignment of heavy chain CDR3 of VRC01 against its maximum-likelihood gene segments.

Figure 2. Two simple phylogenetic models for determining clonal kinship of two sequences

S₁ and S₂. On the left, the sequences are related through their most recent common ancestor I1, and the founding ancestor a. On the left, each sequence arises by affinity maturation from independent founding ancestors.

Figure 3. Dual Mechanisms for Improving Affinity During Maturation of an HIV-1 Antibody

Antibodies mature by improving their affinity either by increasing enthalpy by adding favorable interactions at the antibody-antigen interface or by decreasing the entropic penalty paid upon complexation. The HIV-1 antibody CH58 (heavy chains colored beige and light chains colored gray unless otherwise noted) utilized both mechanisms in order to increase affinity to a V2 peptide (green). A) The CDR L3 in the unliganded CH58 UA structure (blue) adopts a different conformation (magenta) in the CH58 UA/V2 peptide complex suggesting that the paratope is flexible prior to maturation. The CDR L3 in the unliganded matured CH58 structure (orange) adopts a highly similar conformation as the CDR L3 in the matured CH58/V2 peptide complex structure (red) demonstrating that after maturation the CDR L3 is no longer flexible. Thus, the rigidification of the CDR L3 loop results in a decrease in the entropy penalty and, in turn, an increase in affinity. B) The maturation mutation S28R (shown in stick representation) in the CDR H1 of the matured CH58 heavy chain (magenta) resulted in the gain of a salt bridge to D180 in the V2 peptide. C) An additional salt bridge to K171 (sticks) in the V2 peptide was formed during maturation upon the acquisition of the mutation N31D (sticks) in the CDR L1 of the matured CH58 light chain (magenta). These two additional salt bridges in the matured CH58 antibody greatly contribute to favorable enthalpic interactions and thus increase affinity. Salt bridges are shown as yellow dashed lines. PDB codes: unliganded CH58 UA (4RIR), CH58 UA/V2 peptide complex (4RIS), unliganded matured CH58 (4HQQ); matured CH58/V2 peptide complex (4HPO).

Figure 4. Large Insertions in CD4 Binding Site Targeting Antibodies Contact a Secondary Epitope Between gp120 Subunits

Structural modeling of three matured VRC01-like class HIV-1 antibodies (matured heavy chain colored in blue; GL heavy chain in light blue; all light chains in white) in complex with monomeric gp120 by superposition onto the SOSIP Env trimer structure (surface representation; gp120 in green shades; gp41 in orange shades; glycans shown in stick representation) suggested that large insertions may be contacting a secondary epitope in the cleft between two gp120 subunits. A) An insertion in CDR H1 (red) in VRC-CH31 is directed towards the inter-protomer cleft. Dashed lines indicate the CDR H1 was not completely resolved in the crystal structure. B) An insertion in the framework region 3 (FWR3; red) of VRC03 may allow extension into the inter-subunit cleft. C) An insertion in the FWR3 of 3BNC117 may play a similar role. The addition of a secondary epitope involving a neighboring gp120 in the Env trimer structure suggests affinity maturation in the VRC01-like class of HIV-1 BNAbs may utilize insertions to increase the size of the paratope in order to strengthen binding to Env. The N276 and N332 glycan representations have been removed from view for clarity.

Figure 5. Large Insertions and Deletions in HIV-1 BNAbs Mediate Glycan Interactions

Most large insertions and deletions observed in the structures of HIV-1 BNAbs are involved in mediating glycan interactions. Many of the large deletions that have been observed in crystal structures contribute to maturation by providing steric clearance to nearby glycans such as with A) VRC01 in which a 2 aa deletion in CDR L1 from GL (cyan) to matured VRC01 (red) allows for accommodation of the N276 glycan (yellow sticks). B) Large insertions tend to be employed for penetrating between glycans such as in the maturation of PGT128 where a 6 aa insertion (magenta) in the CDR H2 (red) allowed for the loop to extend between the N301 and N332 glycans (yellow sticks). In both panels, the Env trimer is shown in surface representation with gp120 in green shades and gp41 in orange shades. Glycans are shown as sticks. Antibody heavy chains are colored blue and light chains colored gray.