Our three Most Recent Publications – and interesting “behind the scenes” stories
1) Whitehead, R. III, Teschke, C.M., & Alexandrescu, A.T (2019) “NMR mapping of disordered segments for a viral scaffolding protein encapsulated in a 23 MDa procapsid complex”, Biophysical Journal, in press.
We were stuffing phage capsids full of scaffolding protein anyway for ssNMR, so we decided to also look at them by solution NMR. In analogy to "in cell" NMR, our "in virus" NMR approach shows that the first 40 a,a. of scaffolding protein can be observed inside the virus because this segment is disordered. Disorder in this region is probably important for scaffolding protein to exit through holes in the capsid as it becomes packaged with its dsDNA genome. The experiment illustrates the utility of NMR for identifying intrinsically disordered protein (IDPs) segments - in this case even though we are looking at a 23 MDa complex, which is way beyond the "size limit" of NMR! Richard's first paper.
2) Rebecca L. Newcomer, Jason R. Schrad, Eddie B. Gilcrease, Sherwood R. Casjens, Michael Feig, Carolyn M. Teschke, Andrei T. Alexandrescu & Kristin N. Parent (2019) “The phage L capsid decoration protein has a novel OB-fold and an unusal capsid binding strategy”eLife 8: e45345.
In March 2015, Becca and Andrei were looking at a 5-crosspeak HSQC spectrum of a 45 kDa trimer trying to figure out if this was a viable PhD thesis project. No one sane would have bet on that! About 4 years later through some protein folding magic we don't fully understand, we have a cool structure determined from awesome NMR spectra, and a landscape full of protein folding riddles we are working on sorting out. Oh, and the structure turned out to be an OB-fold, a structural motif that occupied Andrei's research from about 1995-2010, so blast from the past! The whole Dec project is the result of a cool collaboration with Carol Teschke's (website) and Kristin Parent's (website) groups. It's interesting enough to deserve a "highlight", so you can read more about it on the "Research Highlights" section of our web site.
3) Tripler, T.N., Kaplan, A.R., Alexandrescu, A.T, & Teschke, C.M. (2019) “Conservation and divergence of the I-domain inserted into the ubiquitous HK97 coat protein fold in the P22-like bacteriophages” Journal of Virology 93, pii: e00007-19.
Protein structure evolution from the perspecive of a viral coat protein module, called the I-domain. We looked at I-domains from phages P22, CUS-3, and Sf6; representatives of three main homology groups in a gene cluster of over 150 phages. The 6-stranded beta-barrel fold is conserved between the three i-domains. NOT MUCH ELSE IS! Differences include elements of secondary structre at the periphery of the conserved fold, changes in the charge distribution of the docking interface between the I-domains and the correponding coat protein cores, differences in motifs displayed on the capsid surfaces, and changes in dynamic loops that are functionally important in capsid assemly. The last obervation is particularly cute, since a selling point of NMR is the ability to look at intrinsically disordered loops that are often functionally important. In this case, the flexible loops come and go between the three domains, at the expense of secondary structure (basically this is caused by differences in secondary structure propentities between the sequences - in some cases these encode secondary structure, in other cases unstructured loops).