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Antibody Numbering

Introduction​

An important prerequisite for antibody humanization is a standardized numbering method, It is possible to precisely define complementary determining regions that affect antibody-antigen interaction, CDRs）, frameworks, and light and heavy chain residues (VH residues and VL residues) that affect binding affinity and specificity.

Antibody engineering methods require the accurate identification of regions in an antibody that have a critical influence on the interaction or affinity of its target antigen. For example, CDR-grafting reduces the immunogenicity of non-human antibodies by engineering variable regions against target antigens, and residues from framework regions may also have a strong effect on antibody affinity. Therefore, detailed alignment of antibody sequences from human and non-human species to accurately identify the corresponding positions in human and animal immunoglobulin chains is essential.

The Antibody Numbering module of the Hermite ® platform provides the ability to number antibodies based on three numbering schemes (IMGT, Kabat, and Chothia) to help you complete antibody numbering quickly and easily.

1IGM is the three-dimensional structure of human lgM immunoglobulin Fv region. In this tutorial, the sequence of 1IGM is numbered based on the Antibody Numbering module. The sequence information is as follows:


>Heavy Chain
EVHLLESGGNLVQPGGSLRLSCAASGFTFNIFVMSWVRQAPGKGLEWVSGVFGSGGNTDYADAVKGRFTITRDNSKNTLYLQMNSLRAEDTAIYYCAKHRVSYVL TGFDSWGQGTLVTVSSGSASAPTL


>Light Chain DIQMTQSPSSLSASVGDRVTITCQASQDISNYLAWYQQKPGKAPELRIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYQNLPLTFGPGTKVDIKRTVAAPSV|

1. How to use​

1.1 Entrance​

  • The left general menu bar is Menu → Function → Biomacromolecule → Antibody Numbering.

import_structure

  • The interface of 'Antibody Numbering' (shown in the red box) appears on the right side, and the overall interface is as follows:

import_structure

1.2 Operation​

  • Input Sequence: Input the sequence of the variable region of the antibody

    • Enter the variable region sequence of the antibody heavy chain in the sequence box under Variable Region of Heavy Chain (VH);

    • Enter the variable region sequence of the antibody light chain in the sequence box under Variable Region of Light Chain (VL).

  • Numbering & CDR Definition, select the definition method, here select 'Kabat'.

import_structure

  • The job is named '1igm_AN' at the 'Job Name'.

  • Click 'Submit' to submit the task.

2. Analysis of results​

2.1 Entrance​

  • General menu bar on the left: Job → Find the required task.

import_structure

2.2 Operation​

2.2.1 Presentation of results​

  • Select '1igm_AN' task and click 'Show' in the Operation column to display the results of the task. The interface is shown in the figure below.
import_structureimport_structure

2.2.2 Explanation of results​

  • The heavy chain of the antibody sequence is marked in light blue, the light chain in light green, and the CDR region in blue-violet.
import_structureimport_structure