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Free Energy Perturbation Calculation of Relative Binding Free Energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1

View Article: PubMed Central - PubMed

ABSTRACT

Direct calculation of relative binding affinities between antibodies and antigens is a long-sought goal. However, despite substantial efforts, no generally applicable computational method has been described. Here, we describe a systematic free energy perturbation (FEP) protocol and calculate the binding affinities between the gp120 envelope glycoprotein of HIV-1 and three broadly neutralizing antibodies (bNAbs) of the VRC01 class. The protocol has been adapted from successful studies of small molecules to address the challenges associated with modeling protein–protein interactions. Specifically, we built homology models of the three antibody–gp120 complexes, extended the sampling times for large bulky residues, incorporated the modeling of glycans on the surface of gp120, and utilized continuum solvent-based loop prediction protocols to improve sampling. We present three experimental surface plasmon resonance data sets, in which antibody residues in the antibody/gp120 interface were systematically mutated to alanine. The RMS error in the large set (55 total cases) of FEP tests as compared to these experiments, 0.68 kcal/mol, is near experimental accuracy, and it compares favorably with the results obtained from a simpler, empirical methodology. The correlation coefficient for the combined data set including residues with glycan contacts, R2 = 0.49, should be sufficient to guide the choice of residues for antibody optimization projects, assuming that this level of accuracy can be realized in prospective prediction. More generally, these results are encouraging with regard to the possibility of using an FEP approach to calculate the magnitude of protein–protein binding affinities.

No MeSH data available.


First and last frames of the (a to b) wild-type and (c to d) mutant phases for the VRC-PG04 G54 mutation using the PLOP-predicted starting structure. (b) The wild-type phase regains the contact with the gp120 residue shown, which is found for the crystal structure-based homology model and wild-type loop prediction. (c and d) The mutant phase system maintains the contact between R73 and the gp120 residue because the contact involving R71 is now prevented by the alanine side chain.
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f0025: First and last frames of the (a to b) wild-type and (c to d) mutant phases for the VRC-PG04 G54 mutation using the PLOP-predicted starting structure. (b) The wild-type phase regains the contact with the gp120 residue shown, which is found for the crystal structure-based homology model and wild-type loop prediction. (c and d) The mutant phase system maintains the contact between R73 and the gp120 residue because the contact involving R71 is now prevented by the alanine side chain.

Mentions: However, using the prediction for the mutant as the starting configuration for the FEP/REST run, we found that the mutant system stabilizes into a configuration where R73 replaces R71 in the contact with the gp120, approximately canceling the effect of breaking the contact with R71 (see Fig. 5). The barrier to the R73 crossing into this configuration is sufficiently large that a 100-ns trial is not sufficient to observe it, and it is doubtful that it will be accessible to any tractable simulation length. The large number of atoms involved in the barrier likely also makes it inaccessible to inclusion in the REST region. These results suggest that in prospective predictions going forward that involve larger additive mutations, applying the PLOP protocol to predict the conformation of the mutant state will be a useful adjunct in achieving robust, accurate relative binding affinity prediction. The net RMSE of the four CDR H2 loop cases was reduced from 1.78 kcal/mol using the default protocol to 0.89 kcal/mol. The remaining glycine-to-alanine cases on the CDR H3 and CDR L1 loops of VRCPG-04 mutations are identified as moderate or strong glycan contacts. Loop predictions for these cases were performed, with the glycan fragment present and included in the final protocol, and these are the values reported for the cases in Table 3. The difference from the result using the crystal structure loop was negligible in these cases.


Free Energy Perturbation Calculation of Relative Binding Free Energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1
First and last frames of the (a to b) wild-type and (c to d) mutant phases for the VRC-PG04 G54 mutation using the PLOP-predicted starting structure. (b) The wild-type phase regains the contact with the gp120 residue shown, which is found for the crystal structure-based homology model and wild-type loop prediction. (c and d) The mutant phase system maintains the contact between R73 and the gp120 residue because the contact involving R71 is now prevented by the alanine side chain.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5383735&req=5

f0025: First and last frames of the (a to b) wild-type and (c to d) mutant phases for the VRC-PG04 G54 mutation using the PLOP-predicted starting structure. (b) The wild-type phase regains the contact with the gp120 residue shown, which is found for the crystal structure-based homology model and wild-type loop prediction. (c and d) The mutant phase system maintains the contact between R73 and the gp120 residue because the contact involving R71 is now prevented by the alanine side chain.
Mentions: However, using the prediction for the mutant as the starting configuration for the FEP/REST run, we found that the mutant system stabilizes into a configuration where R73 replaces R71 in the contact with the gp120, approximately canceling the effect of breaking the contact with R71 (see Fig. 5). The barrier to the R73 crossing into this configuration is sufficiently large that a 100-ns trial is not sufficient to observe it, and it is doubtful that it will be accessible to any tractable simulation length. The large number of atoms involved in the barrier likely also makes it inaccessible to inclusion in the REST region. These results suggest that in prospective predictions going forward that involve larger additive mutations, applying the PLOP protocol to predict the conformation of the mutant state will be a useful adjunct in achieving robust, accurate relative binding affinity prediction. The net RMSE of the four CDR H2 loop cases was reduced from 1.78 kcal/mol using the default protocol to 0.89 kcal/mol. The remaining glycine-to-alanine cases on the CDR H3 and CDR L1 loops of VRCPG-04 mutations are identified as moderate or strong glycan contacts. Loop predictions for these cases were performed, with the glycan fragment present and included in the final protocol, and these are the values reported for the cases in Table 3. The difference from the result using the crystal structure loop was negligible in these cases.

View Article: PubMed Central - PubMed

ABSTRACT

Direct calculation of relative binding affinities between antibodies and antigens is a long-sought goal. However, despite substantial efforts, no generally applicable computational method has been described. Here, we describe a systematic free energy perturbation (FEP) protocol and calculate the binding affinities between the gp120 envelope glycoprotein of HIV-1 and three broadly neutralizing antibodies (bNAbs) of the VRC01 class. The protocol has been adapted from successful studies of small molecules to address the challenges associated with modeling protein–protein interactions. Specifically, we built homology models of the three antibody–gp120 complexes, extended the sampling times for large bulky residues, incorporated the modeling of glycans on the surface of gp120, and utilized continuum solvent-based loop prediction protocols to improve sampling. We present three experimental surface plasmon resonance data sets, in which antibody residues in the antibody/gp120 interface were systematically mutated to alanine. The RMS error in the large set (55 total cases) of FEP tests as compared to these experiments, 0.68 kcal/mol, is near experimental accuracy, and it compares favorably with the results obtained from a simpler, empirical methodology. The correlation coefficient for the combined data set including residues with glycan contacts, R2 = 0.49, should be sufficient to guide the choice of residues for antibody optimization projects, assuming that this level of accuracy can be realized in prospective prediction. More generally, these results are encouraging with regard to the possibility of using an FEP approach to calculate the magnitude of protein–protein binding affinities.

No MeSH data available.