SEMINAR:Understanding protein evolution: from the concept of fitness...

Guest: Fyodor Kondrashov, Okinawa Institute of Science and Technology Graduate University

Title: Understanding protein evolution: from the concept of fitness landscapes to protein engineering

Date/Time: 30 May 2024, 12:30

Location: FENS G029

Abstract: I will present the general background to the work that we do in our lab at the interface of protein evolution and design. I will start by introducing the concept of fitness landscapes, which forms the basis for thinking about how proteins evolve. I will touch upon the fundamental genetic concepts that determine how evolutionary biologists think about fitness landscapes, but I will mostly skip the mathematics behind complex models. I will then turn to describing our recent experimental work that was done to understand how we can apply empirical data to shaping our understanding of the fitness landscapes. We have mostly worked on GFP as a model protein, which turned out to be a useful starting point to understand the general principles of fitness landscapes for a variety of proteins. Finally, in the last part of my talk I will discuss how our understanding of the fitness landscapes allowed us to create machine-learning models that can predict functional GFP sequences. Our work presents an example of how understanding fundamental concepts typically used to understand evolution of protein sequences can be used to create novel functional proteins.

Bio: Fyodor started his research career in the year 2000 in the lab of Eugene Koonin at NCBI, NIH after his BA degree. The main focus of his research was evolutionary genomics and bioinformatics. In 2003 Fyodor continued on to University of California at Davis graduating with an MA degree. In 2005 with the help of an NSF Graduate Fellowship he started his PhD in University of California at San Diego graduating in 2008. During the course of his PhD, Fyodor became interested in field work in the Arctic working with endangered endemic bird species, which continues to be an important aspect of his research.

After starting his lab in 2008 at the Centre for Genomic Regulation, Fyodor began to combine theoretical, computational and experimental biology. Over the years, Fyodor’s work morphed into an interdisciplinary concoction of interwoven research directions. Combining theory, computation, field work, experimental and synthetic biology approaches, the work of the Evolutionary and Synthetic Biology Unit strives, in equal measure, to understand the evolution of living forms and to use that understanding to design novel biological systems.