Immune Receptor Patches Analysis

Overview

Electrostatic interactions play an important role in numerous processes within antibodies and it is important to understand this further. EMLy is capable of helping with this by highlighting and displaying the electrostatic patches on a diagram of the molecule.

Inputs

• The structure to analyse (must be paired antibody or TCR structure)

• Name of PDB file to analyse

• To run the function if the sequence is invalid (true), or not to run (false), default value is false

Output

• Sentence about whether or not the alignment was successful

• Patch summary detailing the location of heavy and light chain patches, and key information

• Annotated molecule is now visible in the 3D Viewer tab

Description

The output in the 3D Viewer shows the CDR 1 loops coloured gold, CDR2 loops magenta, and CDR3 loops teal. The central residue for each patch is shown in stick representation (carbon is grey, nitrogen is blue, sulfur is yellow).

EMLy obtains this information by using ANARCI to number the amino acids. Its own LLM is used to get the information.

Electrostatic interactions play an important role in numerous processes within antibodies so it is important to understand these interactions so proteins can be successfully engineered.

AggScore (https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.25594

) - Agg score is a method of identifying aggregation prone regions in proteins. This is important as protein aggregation can lead to protein liabilities so it is best to find them early to stop this from happening. AggScore uses 3D input, taking the 3D surface of the protein and analysing the distribution of hydrophobic and electrostatic patches on its surface to identify these regions. It can accurately identify aggregation behaviour upon residue mutation. The method can be applied to globular proteins, small peptides, and antibodies. The AggScore of an input protein is expressed as the sum of aggregation propensity values at each residue.