Merlin Li

Deciphering Protein Evolution – Evidence of Negative Cooperativity in Cytosolic Taurocyamine Kinase from Arenicola brasiliensis and its evolutionary implication

April 2, 2021   /  

Name: Mingyuan “Merlin” Li
Major: Biochemistry and Molecular Biology
Advisors: Dr. Mark Snider, Dr. Dean Fraga

The study of biological evolution-how and why biological traits change over generations—enables us to understand the history of life on Earth. From a molecular perspective, the evolution of species along the life history can be attributed to the evolution of proteins. Phosphagen kinases (PK) belong to a family of important enzymes that facilitate energy balance. Since different phosphagen kinases are present in all living forms, they provide an excellent model for studying protein evolution. Even though there are different proposed models for phosphagen kinase evolution, the exact path remains unknown. What can clarify the evolutionary relationship is a careful comparison of structures and functionalities among members of PK. This study focuses on negative cooperativity, an interesting structural feature where the binding of substrates in one subunit of the enzyme hinders the binding of the other subunit.

To better understand the evolutionary context for this negative cooperativity, the cytosolic taurocyamine kinase (CytoTK) from a sea worm species, was purified and examined for negativity cooperativity in forming a quaternary transition state analogue complex (TK –MgADP –NO3-–taurocyamine). Both fluorescent quenching and isothermal titration showed the presence of negative cooperativity. The results of this study provide insights into the possible evolutionary trajectories within the PK family.

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Mingyuan “Merlin” Li will be online to field comments on April 16:
8-10am EDT (Asia: evening, Africa/Europe: afternoon)

45 thoughts on “Deciphering Protein Evolution – Evidence of Negative Cooperativity in Cytosolic Taurocyamine Kinase from Arenicola brasiliensis and its evolutionary implication”

  1. The fluorescence quenching titration is a very elegant assay. It is neat to see that works well in TK. Nice work as the experiment takes careful attention. It was nice to have you in your first chemistry class at Wooster. Good luck in the future!

    1. Thank you, Dr. Edmiston! I was surprised this MitoTK also has Trp residues in its substrate-binding site!

  2. Very impressive Merlin, great job!! What was the most interesting part of your research to you? Was there anything that stood out to you during your research that you didn’t expect going into this project?

    1. Thank you, Michael! I would say the most interesting/exciting part is that there are always different directions to approach the same question, and it’s nice to see all data are consistent with each other. When I did my first experiment, I just wanted to get an experimental parameter for another experiment, but it actually supports my hypothesis indirectly. That was one thing really surprising. Also, in order to do all these binding assays/titrations, I had to express and purify TONS of protein, which took me almost 80% of the time figuring out how to optimize the yield during the whole time. That was unexpected and really stood out.

  3. Nice work Merlin! Do you know if the negative cooperatively is mainly a result of a structural change or if there is chemical release or change that leads to it?

    1. Thank you, Dr. Sobeck! I would say, it’s both. Since negative cooperativity is defined as “the binding of substrate(s) on one subunit will hinder the binding of the other, forming a reciprocating subunit binding mechanism”, negative cooperativity is a reflection and induction of substrate binding (chemical change) and structural changes.

  4. Hi Merlin! Great project and congratulations on completing your IS! I am curious: what made you decide to use sea worms for your study this year?

    1. Thank you, Justin! I chose sea worm A. brasiliensis because the taurocyamine kinase (TK) isolated from this species has an intriguing evolutionary relationship with other proteins in the same protein family.

  5. Congratulations, Merlin! You’ve clearly done an excellent job. I wish you luck in your future endeavors!

  6. Great work Merlin – it’s amazing to see this research area carried through the years at Wooster! Reach out if you ever want to talk about grad school or science careers (logdrews@gmail.com).

    1. Hi Logan,
      Thank you for your comments! I will attend graduate school pursuing a Ph.D. this fall. I will definitely reach out to you to learn more about grad school and science careers!

  7. Congratulations, Merlin! It has been a pleasure to work with you during your time at Wooster. I wish you much success in your future, you will do awesome things, no doubt!

    1. Thank you, Marylou! It’s been great working with you. Thank you for all the help on resumes, cover letters, and all other things!

  8. Merlin, you are doomed to be an excellent researcher in yoir beloved area! Stick to your great idea of being a good scientist!

  9. Merlin, your work is so impressive. Now, all the time spent in lab has paid off! I’m proud of you for finIShing and am excited to see what’s next for you in your career. Great job.

    1. Thank you, Emmalee! Our discussions and work on PK have been great this year! Thanks for the help on NMR. I wish you all the best in your future endeavors!

  10. Mingyuan,Today is the first step toward maturity. May you walk steadily and steadily along a path full of flowers.congratulations.

  11. I know that you have set up a lofty ideal, so I firmly believe that you can create a brilliant tomorrow!

  12. Hi Merlin! Congratulations! Seeing how you went through this massive project is impressive. You will be brilliant.

  13. Great stuff, Merlin. Thanks for reminding us again about the role of kinases and proteins in how we came to be. So interesting, and best wishes in your future explorations!

  14. Fantastic work Merlin! It’s so wonderful to see your hard work at Wooster paying off. So excited to see how you thrive beyond Woo!

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