. Addition of more Fab8066 at 1:2 and 1:3 coreS:Fab ratios does not result in the binding of additional Fab8066 molecules to coreS, as evidenced by the presence of an excess Fab8066 band in the native-PAGE lanes. A similar 1:1 mixture of coreS and Fab8062 barely shows any shift on native-PAGE and elutes on SEC-MALS mainly in free form with masses of,52 and 26 kDa, corresponding to Fab8062 and coreS, respectively. In the case of Sc66, both 1:1 and 1:3 coreS:Sc66 complexes are apparent on both native-PAGE and SECMALS. That the peaks seen in SEC-MALS correspond to the same compositions as observed by native-PAGE was verified by subjecting peak fractions from the SEC-MALS column to native and SDS-PAGE. In contrast, Sc62 binds only very weakly to coreS and only a very small amount of 1:1 complex is apparent by either native-PAGE or SEC-MALS. Similar results are seen with the ScFv mutants: the behavior of the neutralizing mutants Sc66I53L and Sc66T57A is very similar to Sc66, while the 6 Antibody Binding to gp41 non-neutralizing mutants Sc66T56F and Sc66N58V behave like Sc62. Binding of Fabs and ScFvs to the six-helix bundle mimetics coresp and 6-helix The binding of Fab8066 and Sc66 to coreS does not allow one to distinguish PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19661824 whether binding occurs directly to the surface accessible region of the N-HR MedChemExpress PG-490 helices between the surrounding CHR helices in the six-helix bundle conformation, or whether binding involves displacement of one or more C-HR helices in the six-helix bundle permitting interaction with the resulting fully exposed epitope on the trimeric N-HR coiled coil. To this end we investigated the binding of Fab8066 and Sc66 to coreSP and 6-helix. In the case of coreSP, displacement of the C-HR would result in dissociation of the CHR helix into free solution, while for 6-helix only a single C-HR could be displaced without unraveling the protein. The SEC-MALS profiles observed for 1:1 mixtures of Fab8066 and Sc66 with coreSP are similar to those obtained with coreS. Specifically, a 1:1 complex is observed for the interaction of Fab8066 with coreSP while 1:1 and 1:3 antigen:ScFv complexes are observed for the interaction of Sc66 with coreSP. SDSPAGE of the elution fractions indicate that the 1:1 and 1:3 antigen:antibody complexes contain N-HR and C-HR peptides together with heavy and light chains for Fab8066 and a single chain for Sc66. In addition, circular dichroism of 1:1 mixtures of coreSP and Fab8066 or Sc66 indicates that the helicity of coreSP remains unchanged upon complexation with antibodies. Likewise, native-PAGE and SEC-MALS of a 1:1 mixture of Sc66 
and 6-helix reveal the presence of 1:1 and 1:3 antigen:ScFv complexes with no change in helicity of 6-helix upon complexation with Sc66 as monitored by CD. Thus, one can conclude unambiguously that no displacement of the C-HR is involved upon binding of Fab8066 Antibody Binding to gp41 and Sc66 to 6-helix bundle mimetics, and therefore the mode of interaction of these antibodies with the 6-helix bundle mimetics must be slightly different from that observed by crystallography with pre-hairpin intermediate mimetics to avoid steric clash between the CDR-H1 and CDR-H2 loops of the antibodies and one of the C-HR helices. 8 Antibody Binding to gp41 Estimating the binding affinity of Fab8066 to Cores by native-PAGE and SEC-MALS Since we were unable to successfully use ITC to quantitatively determine the binding affinities of our neutralizing antibodies in either Fab or ScFv formats to the si