Squishy Physics


Next seminar: 5/18/2022

Evolution of Protein Dynamics - Time Travel to the Past and Future


Dorothee Kern

Brandeis UniversityDeptartment of Biochemistry



The essential role of protein dynamics for enzyme catalysis has become more generally accepted. Since evolution is driven by organismal fitness hence the function of proteins, we are asking the question of how enzymatic efficiency has evolved. First, I will address the evolution of enzyme catalysis in response to one of the most fundamental evolutionary drivers, temperature. Using Ancestral Sequence Reconstruction (ASR), we answer the question of how enzymes coped with an inherent drop in catalytic speed caused as the earth cooled down over 3.5 billion years. Tracing the evolution of enzyme activity and stability from the hot-start towards modern hyperthermophilic, mesophilic and psychrophilic organisms illustrates active pressure versus passive drift in evolution on a molecular level (1). Second, I will share a novel approach to visualize the structures of transition-state ensembles (TSEs), that has been stymied due to their fleeting nature despite their crucial role in dictating the speed of biological processes.  We determined the transition-state ensemble in the enzyme adenylate kinase by a synergistic approach between experimental high-pressure NMR relaxation during catalysis and molecular dynamics simulations (2). Third, a novel general method to determine high resolution structures of high-energy states that are often the biologically reactive species will be described (3). With the ultimate goal to apply this new knowledge about energy landscapes in enzyme catalysis for designing better biocatalysts, in “forward evolution” experiments, we discovered how directed evolution reshapes energy landscapes in enzymes to boost catalysis by nine orders of magnitude relative to the best computationally designed biocatalysts. The underlying molecular mechanisms for directed evolution, despite its success, had been illusive, and the general principles discovered here (dynamic properties) open the door for large improvements in rational enzyme design (4). Finally, visions (and success) for putting protein dynamics at the heart of drug design are discussed.




Squishy Physics & Pizza Seminar Series

When: Wednesday Evenings at 6pm. Pizza served after the talk.

Where: Room 301, Pierce Hall, 29 Oxford St, on the Harvard Campus. Directions and parking instructions are here.

What: These talks are informal, with emphasis on new results and ideas, rather than polished presentations. The Squishy audience members typically include soft matter scientists, physicists, engineers, chemists, and biologists.  The goal is to stimulate discussion with the audience.  Talks are typically about 45 minutes long, with lots of questions along the way.

Pizza: Only the finest! 

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Parking: Metered parking is available on Oxford Street.  Speakers, please contact Matthew Zahnzinger to obtain a parking permit.  

Squishy Physics is sponsored by the Cabot Corporation, Dean Cherry Murray and the Weitz Research Group.

If you have comments or suggestions or would like to give a talk, please contact Karla Ilic Durdic, Bobby Haney or Thomas Litschel.

Here is the upcoming schedule