The Impact of Proline Isomerization on Antigen Binding and the Analytical Profile of a Trispecific Anti-HIV Antibody

Overview

Journal MAbs

Specialty Allergy & Immunology

Date 2019 Dec 4

PMID 31791173

Citations 8

Authors

Alessandro Masiero

Lechat Nelly

Gentric Marianne

Sourrouille Christophe

Laville Florian

Crepin Ronan

Borel Claire

Ziegler Cornelia

Bisch Gregoire

Leclerc Eric

Laurent Ludovic

Brault Dominique

Alexandre Sylvie

Gagnaire Marie

Duffieux Francis

Soubrier Fabienne

Capdevila Cecile

Arnould Isabelle

Dumas Jacques

Dabin Jerome

Genet Bruno

Radosevic Katarina

Menet Jean-Michel

Prades Catherine

Affiliations

Soon will be listed here.

Abstract

Proline conformational isomerization is a mechanism that affects different types of protein functions and behaviors. Using analytical characterization, structural analysis, and molecular dynamics simulations, we studied the causes of an aberrant two-peak size-exclusion chromatography profile observed for a trispecific anti-HIV antibody. We found that proline isomerization in the tyrosine-proline-proline (YPP) motif in the heavy chain complementarity-determining region (CDR)3 domain of one of the antibody arms (10e8v4) was a component of this profile. The pH effect on the conformational equilibrium that led to these two populations was presumably caused by a histidine residue (H147) in the light chain that is in direct contact with the YPP motif. Finally, we demonstrated that, due to chemical equilibrium between the and proline conformers, the antigen-binding potency of the trispecific anti-HIV antibody was not significantly affected in spite of a potential structural clash of 10e8v4 YPP conformers with the membrane-proximal ectodomain region epitope in the GP41 antigen. Altogether, these results reveal at mechanistic and molecular levels the effect of proline isomerization in the CDR on the antibody binding and analytical profiles, and support further development of the trispecific anti-HIV antibody.

Citing Articles

The functionality of a therapeutic antibody candidate restored by a single mutation from proline to threonine in the variable region.

Hautiere M, Maffucci I, Costa N, Herbet A, Essono S, Padiolleau-Lefevre S Hum Vaccin Immunother. 2023; 19(3):2279867.

PMID: 38012091 PMC: 10760395. DOI: 10.1080/21645515.2023.2279867.

Combination of IM-Based Approaches to Unravel the Coexistence of Two Conformers on a Therapeutic Multispecific mAb.

Desligniere E, Ollivier S, Ehkirch A, Martelet A, Ropartz D, Lechat N Anal Chem. 2022; 94(22):7981-7989.

PMID: 35604400 PMC: 9178554. DOI: 10.1021/acs.analchem.2c00928.

An Unbound Proline-Rich Signaling Peptide Frequently Samples Conformations in Gaussian Accelerated Molecular Dynamics Simulations.

Alcantara J, Stix R, Huang K, Connor A, East R, Jaramillo-Martinez V Front Mol Biosci. 2021; 8:734169.

PMID: 34869581 PMC: 8634643. DOI: 10.3389/fmolb.2021.734169.

Roles of key residues and lipid dynamics reveal pHLIP-membrane interactions at intermediate pH.

Otieno S, Qiang W Biophys J. 2021; 120(21):4649-4662.

PMID: 34624273 PMC: 8595900. DOI: 10.1016/j.bpj.2021.10.001.

Structures of HIV-1 Neutralizing Antibody 10E8 Delineate the Mechanistic Basis of Its Multi-Peak Behavior on Size-Exclusion Chromatography.

Kwon Y, Wang X, Bender M, Yang R, Li Y, McKee K Antibodies (Basel). 2021; 10(2).

PMID: 34200826 PMC: 8293163. DOI: 10.3390/antib10020023.

References

Nath P, Isakov N . Insights into peptidyl-prolyl cis-trans isomerase structure and function in immunocytes. Immunol Lett. 2014; 163(1):120-31. DOI: 10.1016/j.imlet.2014.11.002. View

Humphrey W, Dalke A, Schulten K . VMD: visual molecular dynamics. J Mol Graph. 1996; 14(1):33-8, 27-8. DOI: 10.1016/0263-7855(96)00018-5. View

Reimer U, Scherer G, Drewello M, Kruber S, Schutkowski M, Fischer G . Side-chain effects on peptidyl-prolyl cis/trans isomerisation. J Mol Biol. 1998; 279(2):449-60. DOI: 10.1006/jmbi.1998.1770. View

Chen Y, Wu Y, Yang H, Li X, Jie M, Hu C . Prolyl isomerase Pin1: a promoter of cancer and a target for therapy. Cell Death Dis. 2018; 9(9):883. PMC: 6115400. DOI: 10.1038/s41419-018-0844-y. View

Nicholson L, Lu K . Prolyl cis-trans Isomerization as a molecular timer in Crk signaling. Mol Cell. 2007; 25(4):483-5. DOI: 10.1016/j.molcel.2007.02.005. View

Pegu A, Yang Z, Boyington J, Wu L, Ko S, Schmidt S . Neutralizing antibodies to HIV-1 envelope protect more effectively in vivo than those to the CD4 receptor. Sci Transl Med. 2014; 6(243):243ra88. PMC: 4562469. DOI: 10.1126/scitranslmed.3008992. View

Sok D, van Gils M, Pauthner M, Julien J, Saye-Francisco K, Hsueh J . Recombinant HIV envelope trimer selects for quaternary-dependent antibodies targeting the trimer apex. Proc Natl Acad Sci U S A. 2014; 111(49):17624-9. PMC: 4267403. DOI: 10.1073/pnas.1415789111. View

Chen S, Li L, Zhang F, Wang Y, Hu Y, Zhao L . Immunoglobulin Gamma-Like Therapeutic Bispecific Antibody Formats for Tumor Therapy. J Immunol Res. 2019; 2019:4516041. PMC: 6388348. DOI: 10.1155/2019/4516041. View

Wu X, Yang Z, Li Y, Hogerkorp C, Schief W, Seaman M . Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1. Science. 2010; 329(5993):856-61. PMC: 2965066. DOI: 10.1126/science.1187659. View

10.

Skjaerven L, Yao X, Scarabelli G, Grant B . Integrating protein structural dynamics and evolutionary analysis with Bio3D. BMC Bioinformatics. 2014; 15:399. PMC: 4279791. DOI: 10.1186/s12859-014-0399-6. View

11.

Shinoda K, Fujitani H . Initiation of prolyl cis-trans isomerisation in the CDR-H3 loop of an antibody in response to antigen binding. Sci Rep. 2017; 7(1):16964. PMC: 5717248. DOI: 10.1038/s41598-017-16766-8. View

12.

Jager M, Pluckthun A . The rate-limiting steps for the folding of an antibody scFv fragment. FEBS Lett. 1997; 418(1-2):106-10. DOI: 10.1016/s0014-5793(97)01350-1. View

13.

Cao W, Yao J, Feng S, He Y, Jiang E, Zhang R . BCR-ABL enhances the prolyl isomerase activity of Pin 1 by interacting with DAPK1 in ph ALL. Cancer Med. 2018; 7(6):2530-2540. PMC: 6010889. DOI: 10.1002/cam4.1478. View

14.

Wernisch S, Trapp O, Lindner W . Application of cinchona-sulfonate-based chiral zwitterionic ion exchangers for the separation of proline-containing dipeptide rotamers and determination of on-column isomerization parameters from dynamic elution profiles. Anal Chim Acta. 2013; 795:88-98. DOI: 10.1016/j.aca.2013.08.004. View

15.

Glykos N . Software news and updates. Carma: a molecular dynamics analysis program. J Comput Chem. 2006; 27(14):1765-8. DOI: 10.1002/jcc.20482. View

16.

Feige M, Hendershot L, Buchner J . How antibodies fold. Trends Biochem Sci. 2009; 35(4):189-98. PMC: 4716677. DOI: 10.1016/j.tibs.2009.11.005. View

17.

Chen S, Wulf G, Zhou X, Rubin M, Lu K, Balk S . Activation of beta-catenin signaling in prostate cancer by peptidyl-prolyl isomerase Pin1-mediated abrogation of the androgen receptor-beta-catenin interaction. Mol Cell Biol. 2006; 26(3):929-39. PMC: 1347015. DOI: 10.1128/MCB.26.3.929-939.2006. View

18.

Hamelberg D, Mongan J, McCammon J . Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys. 2004; 120(24):11919-29. DOI: 10.1063/1.1755656. View

19.

Vogel M, Bukau B, Mayer M . Allosteric regulation of Hsp70 chaperones by a proline switch. Mol Cell. 2006; 21(3):359-67. DOI: 10.1016/j.molcel.2005.12.017. View

20.

Chennamsetty N, Voynov V, Kayser V, Helk B, Trout B . Prediction of aggregation prone regions of therapeutic proteins. J Phys Chem B. 2010; 114(19):6614-24. DOI: 10.1021/jp911706q. View