Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction

Akhila Melarkode Vattekatte; Nicolas Ken Shinada; Tarun J Narwani; Floriane Noël; Olivier Bertrand; Jean-Philippe Meyniel; Alain Malpertuy; Jean-Christophe Gelly; Frédéric Cadet; Alexandre G de Brevern

doi:10.7717/peerj.8408

Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction

PeerJ. 2020 Mar 6:8:e8408. doi: 10.7717/peerj.8408. eCollection 2020.

Authors

Akhila Melarkode Vattekatte^{1

2

3

4}, Nicolas Ken Shinada^{1

2

4

5}, Tarun J Narwani^{1

2

4}, Floriane Noël^{1

2

4

6

7}, Olivier Bertrand^{1

2

4}, Jean-Philippe Meyniel⁸, Alain Malpertuy⁹, Jean-Christophe Gelly^{1

2

4

10}, Frédéric Cadet^{1

2

3

11}, Alexandre G de Brevern^{1

2

3

4

10}

Affiliations

¹ Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.
² Laboratoire d'Excellence GR-Ex, Paris, France.
³ Faculté des Sciences et Technologies, Saint Denis, La Réunion, France.
⁴ Institut National de la Transfusion Sanguine (INTS), Paris, France.
⁵ Discngine SAS, Paris, France.
⁶ PSL Research University, INSERM, UMR 932, Institut Curie, Paris, France.
⁷ Université Paris Sud, Université Paris-Saclay, Orsay, France.
⁸ ISoft, Saint-Aubin, France.
⁹ Atragene, Ivry-sur-Seine, France.
¹⁰ IBL, Paris, France.
¹¹ Peaccel, Protein Engineering Accelerator, Paris, France.

Abstract

Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only three CDR loops from the single variable domain (V_HH) at the N-terminus of each heavy chain. This feature of the V_HH, along with their other important features, e.g., easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better V_HH domains, it is important to thoroughly understand their sequence and structure characteristics and relationship. In this study, sequence characteristics of V_HH domains have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of V_HH domains showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of V_HH, an exciting view of various factors in structure prediction of V_HH, like template framework selection, is also discussed.

Keywords: Antibodies; Complementarity determining regions; Frameworks; Nanobodies; Secondary structure; Sequence structure relationship; Structural alphabet.

Grants and funding

This work was supported by grants from the Ministry of Research (France), University Paris Diderot, Sorbonne, Paris Cité (France), University of La Réunion, Réunion Island, National Institute for Blood Transfusion (INTS, France), National Institute for Health and Medical Research (INSERM, France) and labex GR-Ex. The labex GR-Ex, reference ANR-11-LABX-0051 is funded by the program “Investissements d’avenir” of the French National Research Agency, reference ANR-11-IDEX-0005-02. Tarun J. Narwani and Alexandre G de Brevern received a collaborative grant (number 5302-2) from Indo-French Centre for the Promotion of Advanced Research/CEFIPRA. Nicolas K. Shinada is supported by Discngine, Paris, France and ANRT, France. Akhila Melarkode Vattekatte is supported by Allocation de Recherche Réunion granted by the Conseil Régional de la Réunion and the European Social Fund EU (ESF). The authors were granted access to high performance computing (HPC) resources at the French National Computing Centre CINES under grant no. A0010707621 and A0040710426 funded by the GENCI (Grand Equipement National de Calcul Intensif). Calculations were also performed on an SGI cluster granted by Conseil Régional Ile de France and INTS (SESAME Grant). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.