Molecular evolution in shared structural modules in transcriptional co-activators
Eva Nogales, Professor
Molecular and Cell Biology
Closed. This professor is continuing with Fall 2023 apprentices on this project; no new apprentices needed for Spring 2024.
The large transcription coactivators TFIID and SAGA play importan roles in the regulation of gene expression. Over a megadalton in size,each of these complexes contains a number of structural modules wit 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 tha 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 thesemodules, 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 structure 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 present results to mentors and potentially draft a manuscript describing their findings.
Qualifications: The ideal candidate is willing to learn and knows how to write programs (in any language); knowledge of protein structures is a plus. Applicants with GPA under 3.6 will be considered only in exceptional circumstances. Candidates must track research using weekly notebooks and a final semester report, and register for credits, regardless of program-specific requirements
Day-to-day supervisor for this project: John-Marc Chandonia, Staff Researcher
Hours: 12 or more hours
Related website: https://biosciences.lbl.gov/profiles/john-marc-chandonia-2/
Related website: https://biosciences.lbl.gov/profiles/john-marc-chandonia-2/