Modeling and designing Bc1-2 family protein interactions using high-throughput interaction data

Protein-protein interactions (PPIs) play a major role in cellular function, mediating signal processing and regulating enzymatic activity. Understanding how proteins interact is essential for predicting new binding partners and engineering new functions. Mutational analysis is one way to study the determinants of protein interaction. Traditionally, the biophysical study of protein interactions has been limited by the number of mutants that could be made and analyzed, but advances in high-throughput sequencing have enabled rapid assessment of thousands of variants. The Keating lab has developed an experimental protocol that can rank peptides based on their binding affinity for a designated receptor. This technique, called SORTCERY, takes advantage of cell sorting and deep-sequencing technologies to provide more binding data at a higher resolution than has previously been achievable. New computational methods are needed to process and analyze the high-throughput datasets. In this thesis, I show how experimental data from SORTCERY experiments can be processed, modeled, and used to design novel peptides with select specificity characteristics. I describe the computational pipeline that I developed to curate the data and regression models that I constructed from the data to relate protein sequence to binding. I applied models trained on experimental data sets to study the peptide-binding specificity landscape of the Bc1-xL, Mc1-1, and Bf1-1 anti-apoptotic proteins, and I designed novel peptides that selectively bind tightly to only one of these receptors, or to a pre-specified combination of receptors. My thesis illustrates how data-driven models combined with high-throughput binding assays provide new opportunities for rational design.

Department dc:contributor.department

Massachusetts Institute of Technology. Computational and Systems Biology Program.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2018

Author dc:creator

• Xue, Vincent

Advisor dc:contributor.advisor

• Amy Keating.

• Computational and Systems Biology Program.

Statement dc:rights

• MIT theses are protected by copyright. They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/120446

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/120446