IDP Pedagogy, Part II

This article is the second in a series of articles illustrating how IDPs are taught across the discipline. Look for subsequent installments, as well as a continuation of this article in future Newsletters.

Richard Kriwacki, St. Jude Children’s Research Hospital, routinely teaches structural biology. He was interviewed by Ryan Hoffman, IDP Subgroup Postdoctoral Representative, focusing on expository strategies.

How do you introduce students to IDPs?

It depends on the level of the students. I lecture to [University of Tennessee] health science students; they’re graduate students primarily. They’re oftentimes incomplete in terms of knowledge of protein structure, and concepts relating to structure-function relationships. I teach anywhere from a half-dozen to thirty students. I have to tailor my lectures to the whole group, and not teach to the top 5%. I basically have to explain how they should be thinking about the physical properties of proteins and the functions they perform. I have to teach them the importance of knowing where the atoms are located in a structure and what the importance of that knowledge is in the context of enzyme function, protein-protein interactions, functional mechanisms, and so on. At the same time that I’m teaching these concepts in the context of folded proteins, I also introduce examples where dynamics are critical for function. Sometimes I build a bridge from folded proteins to dynamics within folded proteins and then move to more dramatic examples of dynamics that are involved in function.

So you primarily motivate IDPs through their biological relevance?

I don’t introduce the topic [of ] IDPs by showing them an ensemble representation of protein structure. I start with function. In the case of p27, I start with, “p27 is a potent inhibitor of the cell cycle. But the kinases that are bound by p27 can be made partially active through post-translational modifi cations to p27, and p27 participates in a signaling cascade that leads to its eventual ubiquitination and degradation. This sounds really cool. How do you think this works?” So then I’ll show them a movie illustrating p27’s dynamic structure in isolation and I’ll say, “We’ve measured this. Th is movie is the result of MD and it’s in agreement with physical measurements of real samples by NMR. So this is the way the protein looks. How is this related to its kinase regulatory function?” Then I’ll show them a cartoon that illustrates what we understand about the sequential folding upon binding mechanism. Then I’ll make a few comments about how binding first to a cyclin isimportant for mediating specificity for particular cyclin-kinase complexes and that’s what this aspect of the mechanism has evolved to do. So I’m constantly making references to the  biology and disease-relatedness to keep their attention.

You mostly use examples of biological relevance from your own work?

I often use p53 to illustrate [IDP structure-function] because most of the students are familiar with the name and it’s kind of attention-getting, but I very often use examples from our own work. In particular, [our] best-studied protein is p27 and it exhibits a lot of cool relationships between dynamics and function. And since we’ve published in some good journals, oftentimes I’ll say to them, “What I’m about to present to you may seem sort of bizarre; you’ve never heard of this before. We’ve been able to publish this work in [top] journals. We’re not just making this up; other people think this is important.” I find I’m fairly successful even with what you may call a somewhat naive student audience based on exam question grading, getting across to them the importance of fl exibility within proteins, [detailed in] a few case studies where it can be seen that function is dependent on flexibility and dynamics.

This interview will be continued in the next installment of IDP Pedagogy.

Jianhan Chen, IDP Secretary/Treasurer

Biopolymers in vivo

Based on BIV’s recommendation, the BPS has added two new abstract categories to the 2012 BPS conference program:

  • 1Q Protein Biophysics In Vivo
  • 2I Nucleic Acid Biophysics In Vivo

If you did not submit an abstract in time for the October 2 deadline, we encourage you to submit a late abstract!

Joan-Emma Shea, BIV, Member-at-Large




October 2011 Table of Contents