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IDP Pedagogy, Part I

This article is the first in a series of articles illustrating how IDPs are taught across the discipline. Look for subsequent installments in
future Newsletters.
 
Ryan Hoffman, IDP Postdoctoral Representative, interviewed Gary Daughdrill, Associate Professor at the University of South Florida, regarding his approaches to teaching about IDPs.
 

What types of students do you usually teach?

All types, it does not really matter. It is best if they have a good foundation in chemistry.

When you introduce students to IDPs, are the students usually already aware of protein structure, or do you get to introduce both subjects?

Now I teach an introductory Cell Biology class, so I start with the sequence-to-structure paradigm. Once the polypeptide is synthesized, we
talk about multiple fates, depending on the sequence characteristics of the polypeptide and interactions with water.

If the students are already products of the “traditional” protein structural pedagogy (primary–tertiary structure, heme-globins as paradigmatic globular proteins) does that act as an impediment? What misconceptions about proteins do students most often need to unlearn?

I have not experienced a lot of students that fall into this category. Even the graduate students that I teach have typically had a fairly light introduction to protein structure and function. I think the fundamental impediment for any person to understand this problem is imagination. You have to be able to imagine what the molecule is doing. Simple movies can help in this area but you have to be careful to not present images that are physically unrealistic.

Do you look at IDPs as a kind of scientific revolution (in the Kuhnsian sense)? Do you emphasize that to your students?

Not really, and I think it is important for progress in the fi eld that we move beyond this notion. IDPs are just proteins that have evolved a particular set of characteristics. I do think that the human brain has more difficulty processing the notion of disorder than it does order and this combined with how much 3-D structures of ordered proteins were able to impact understanding of function was part of the reason for the lag in focusing attention on these proteins. I also think that the lack of a consensus description of the equilibrium ensembles of IDPs is inhibiting
progress in the fi eld. I am not sure how much longer it is going to take to get to this point, but it does not help when some groups claim to have already solved the problem.

There are multiple devices for describing the protein universe. Do you have more success with a particular approach?

I do like the energy landscape and actually have a standard figure that I use in my conference talks to compare energy landscapes for ordered
and disordered proteins. For the students I teach now, we are not getting into the problem this deeply.

Structure-activity relationships are almost always described in ordered systems. What are your favorite—putative or accepted—structure-activity relationships for disordered proteins?

The two that I think are the simplest to conceptually display and that we have the most data on are coupled folding and binding, and flexible linkers.
 
Jianhan Chen, IDP Secretary/Treasurer
 

BIV

We are excited to announce the Biopolymers in vivo (BIV) subgroup plans for the next Biophysical Society Meeting in San Diego in 2012.
 
The theme of the Biopolymers in Vivo Symposium will be “Bridging in vivo and in vitro studies.” We are pleased to have secured a stellar list of speakers, including experimentalists and theorists at the forefront of this emerging field. The keynote talk will be delivered by Tom Record, University of Wisconsin. Other invited talks will be given by Christine D. Keating, Pennsylvania State University; Sarah Woodson, Johns Hopkins University; Huan-Xiang Zhou, Florida State University, Gary J. PielakUniversity of North Carolina; and Jeffrey Skolnick, Georgia Institute of Technology. To give young researchers an opportunity to present exciting new research, two slots will be reserved for postdoctoral or graduate student presentations. Look for more information about these in subsequent Newsletters.
 
We are again planning a group dinner, taking place on Saturday, February 26, 2012, to conclude the Symposium. Please plan to attend! 
 
We look forward to seeing all of you in San Diego in 2012!
 
— Joan-Emma Shea, Biopolymers in vivo
Member at Large