Molecular evolution in shared structural modules within transcriptional co-activators
Eva Nogales, Professor
Molecular and Cell Biology
Applications for Spring 2025 are closed for this project.
The large transcription coactivators TFIID and SAGA play important
roles in the regulation of gene expression. Over a megadalton in size,
each of these complexes contains a number of structural modules with
distinct functionalities. Interestingly, they share one particular
module that plays different roles and that contains a number of
proteins with histone-like folds that interact forming structures that
resemble the histone octamer in nucleosomes. However, unlike histones,
these proteins are not involved in DNA binding. We are taking a
computational approach to investigate the evolutionary origin of these
modules, by modeling structures from the protein family using
experimental structures as templates. By examining the experimental
and model structures, we hope to understand how this family of
proteins has evolved to play distinct functions in transcription.
Role: The student will be involved in modeling protein oligomeric structures
using experimental structures as templates, and comparing these structures
to each other. They will conduct research into the evolution
of the histone-like family of proteins, using research papers and online
databases such as InterPro and SCOPe. The student will maintain a clear record of their work, discuss it with mentors, and attend and present results in group meetings.
Qualifications: The ideal candidate would be interested in computational
biology and programming. Knowledge of protein structures and CS
coursework at Berkeley (e.g., CS61A) are preferred.
Day-to-day supervisor for this project: John-Marc Chandonia, Staff Researcher
Hours: 12 or more hours
Biological & Health Sciences