Autostery, Quasi-equivalence, and Procapsid Assembly. From Brandeis to MIT.
Peter E. Prevelige Jr.
Dept. of Microbiology, BBRB 416/6
Univ. of Alabama @ Birmingham
845 19th St. South
Birmingham AL. 35294-2170
Phone 205 266-8383
My interest in biological self-assembly was nucleated in college when I was assigned to write a paper for a course entitled “Physical Chemistry for Biological Sciences”. Seeking a topic that would be interesting to a biology major I stumbled on the literature pertaining to the assembly of microtubules. I was fascinated by the notion that complex biological processes could be described by relatively simple physics. While my graduate training at Brandeis focused on histone acetylation and not biological assembly, I was afforded the unique opportunity of taking a course on Biological Assembly taught by Don Caspar. I was the only student in the class which consisted of regular one-on-one lunch time meetings at which we discussed (meaning Don discoursed on) whatever aspects of assembly he found interesting and important. At one of our meetings, Don pronounced that Jonathan King was doing some of the most interesting work in assembly and we (meaning I) should read his papers. Unsurprisingly, I found that Jon’s experimental work on tail assembly dovetailed quite nicely with Don’s notions of autostery. In my thesis work on histone acetylation I was frustrated by the current inability to marry biochemistry and genetics to test hypotheses. Jon’s work and the phage assembly literature in general led me to appreciate the (awesome) power of phage genetics which allowed for the in situ dissection of the role of individual structural components in assembly. Importantly, the genetics made possible the discovery of molecules such as scaffolding which played a necessary though transient role in assembly, and more generally the potential for unanticipated discovery.
As I was finishing up my thesis work, as I suspect is the case with many PhD candidates, I found myself exhausted by vagaries of experimental science and intrigued by simple logic of computer programming. I was actively interviewing for positions writing code when my thesis advisor, Gerald Fasman, posted a letter from Jon seeking postdoctoral applications. I knew his work from my course with Don and thought MIT would probably be an interesting place to check out, so I applied. At my interview I met Chris Bazinet, Bentley Fane, Meyong He-Yu, Cammie Hase-Pettingell, and Erica Hartweig. They seemed a lively, motivated, and approachable crew and when I was awarded the position, I accepted the offer and appropriately started on May 1 of 1985.
My initial project in Jon’s lab was to study the re-entry of scaffolding protein into empty coat protein shells. I didn’t know how to approach this experimentally (ultimately Trevor Douglas’ lab elegantly approached this problem ) and turned my attention to building on Minx Fuller’s work on in vitro capsid assembly with the goal of developing a system suitable for kinetic analysis of assembly. After a short bit, Dennis Thomas joined our team and Dennis and I systematically picked apart the steps involved in nucleation and growth of P22 procapsids primarily using light scattering and electron microscopy. One of the highlights of my career as a postdoc was when Dennis and I presented the work at the 1988 Phage Assembly meeting in Asilomar. There was such enthusiasm and so many questions after our back-to-back talks that a special session was added. Unfortunately, Dennis, myself, and several others were drawn by the lure of Big Sur and upon our late return to the session were nonplussed to see Jon holding court in a large armchair in the center of the chapel. This series of experiments was perhaps most important for its demonstration that capsid assembly follows a nucleation limited/rapid growth process , a conclusion supported by the recent single particle assembly studies of Garman and Manoharan .
The question that most intrigued me was how scaffolding protein could direct the high fidelity assembly of the coat protein into T=7 icosahedra. Jon’s laboratory had a long tradition of using electron microscopy to analyze structure and assembly, and upon hearing a talk by Wah Chiu I realized that the ability to see inside capsids with cryo-EM would be critical to understanding the role of scaffolding protein in directing high fidelity capsid assembly. With Jon’s enthusiastic support, I approached Wah about a collaboration which yielded a number of defining, cutting-edge structures. These studies yielded insight into P22 assembly and function including the mechanism of capsid expansion upon DNA packaging [4, 5] but did little to clarify at the molecule level how scaffolding protein directs assembly.
I framed the question as: “given a partially built T=7 shell, how does the next subunit know which of the quasi-equivalent states it should adopt”. This seemed formally similar to John Conway’s “Game of Life” and Jon and I approached Bonnie Berger and Russell Schwartz about modeling the system. Despite computational limitations, we were able to generate a computationally tractable kinetic model  and to demonstrate the therapeutic potential of capsid assembly mis-directors , an approach that has subsequently been well studied by Adam Zlotnick for hepatitis B assembly . I believe this was some of the earliest work on simulating the process of capsid assembly.
My training in biophysics at Brandeis left me well positioned to apply physical biochemistry to capsid assembly but poorly versed in the scientific method. During my tenure in Jon’s lab I learned about the importance of alternative hypotheses, positive and negative controls, to take all results seriously, and how to apply the scientific method to the endeavor of science itself. Through Jon, I came to a deeper understanding of what it means to be a scientist, the role of human progress, and the responsibility of scientists to act in the public interest.
Those lessons are part of what drove me to move to the University of Alabama at Birmingham which had an extremely strong virology group and Center for AIDS Research (CFAR). I was quickly draw into and accepted by the laboratory of Eric Hunter who was the CFAR director. In collaboration with Eric’s lab I initiated studies on the assembly of HIV in parallel with my ongoing studies on P22. In Jon’s lab Carol Teschke and I had explored the notion of inhibiting assembly as a therapeutic approach . This proof-of-concept with P22 garnered relatively little interest. At UAB, building on the approach we had perfected in Jon’s lab we developed a means to follow the kinetics of assembly of HIV capsid protein  and used the system to screen for small molecule assembly inhibitors. These studies of course had greater impact and contributed in part to the development of the current family of HIV capsid inhibitors .
I was fortunate enough to be in Jon’s lab from 1985 until 1992. During that period, Jon supported me both intellectually and financially. I benefited immensely not just from the training he provided but also from the intellectual environment within the lab. His lab attracted outstanding students, postdocs, and visitors including: Julyet Benbaset, Jean-Michelle Betton, Bao-lu Chen, Patricia Clark, Bertrand Friguet, Maria Galisteo, Carl Gordon, Barrie Greene, Dasa Lipovsek, Anna Mitraki, Steve Raso, Susan Sather, Margaret Speed, Carol Teschke, Bob Villafane, and Richard Willson.
When I decided to accept a position in Jon’s lab, Don Caspar was delighted and said something to the effect of “these days people just want to clone an oncogene”. While I have largely retired, the mechanistic basis of form determination in iscosahedral, fullerene, and the recently described oddly shaped capsids still remains unresolved and no less intellectually intriguing.
- Selivanovitch E, LaFrance B, Douglas T. Molecular exclusion limits for diffusion across a porous capsid. Nat Commun. 2021;12(1):2903. doi: 10.1038/s41467-021-23200-1. PubMed PMID: 34006828.
- Prevelige PE, Jr., Thomas D, King J. Nucleation and growth phases in the polymerization of coat and scaffolding subunits into icosahedral procapsid shells. Biophys J. 1993;64(3):824-35. PubMed PMID: 8471727.
- Garmann RF, Goldfain AM, Manoharan VN. Measurements of the self-assembly kinetics of individual viral capsids around their RNA genome. Proc Natl Acad Sci U S A. 2019;116(45):22485-90. doi: 10.1073/pnas.1909223116. PubMed PMID: 31570619.
- Jiang W, Li Z, Zhang Z, Baker ML, Prevelige PE, Jr., Chiu W. Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions. Nat Struct Biol. 2003;10(2):131-5. PubMed PMID: 12536205.
- Prasad BV, Prevelige PE, Marietta E, Chen RO, Thomas D, King J, Chiu W. Three-dimensional transformation of capsids associated with genome packaging in a bacterial virus. J Mol Biol. 1993;231(1):65-74. PubMed PMID: 8496966.
- Schwartz R, Shor PW, Prevelige PE, Jr., Berger B. Local rules simulation of the kinetics of virus capsid self-assembly. Biophys J. 1998;75(6):2626-36. PubMed PMID: 9826587.
- Prevelige P. Inhibiting virus-capsid assembly by altering the polymerisation pathway. Trends Biotechnol. 1998;16:61-5.
- Schlicksup CJ, Zlotnick A. Viral structural proteins as targets for antivirals. Curr Opin Virol. 2020;45:43-50. doi: 10.1016/j.coviro.2020.07.001. PubMed PMID: 32777753.
- Teschke CM, King J, Prevelige PE, Jr. Inhibition of viral capsid assembly by 1,1′-bi(4-anilinonaphthalene-5-sulfonic acid). Biochemistry. 1993;32(40):10658-65. PubMed PMID: 8399211.
- Lanman J, Sexton J, Sakalian M, Prevelige PE, Jr. Kinetic analysis of the role of intersubunit interactions in human immunodeficiency virus type 1 capsid protein assembly in vitro. J Virol. 2002;76(14):6900-8. PubMed PMID: 12072491.
- Link JO, Rhee MS, Tse WC, Zheng J, Somoza JR, Rowe W, Begley R, Chiu A, Mulato A, Hansen D, Singer E, Tsai LK, Bam RA, Chou CH, Canales E, Brizgys G, Zhang JR, Li J, Graupe M, Morganelli P, Liu Q, Wu Q, Halcomb RL, Saito RD, Schroeder SD, Lazerwith SE, Bondy S, Jin D, Hung M, Novikov N, Liu X, Villasenor AG, Cannizzaro CE, Hu EY, Anderson RL, Appleby TC, Lu B, Mwangi J, Liclican A, Niedziela-Majka A, Papalia GA, Wong MH, Leavitt SA, Xu Y, Koditek D, Stepan GJ, Yu H, Pagratis N, Clancy S, Ahmadyar S, Cai TZ, Sellers S, Wolckenhauer SA, Ling J, Callebaut C, Margot N, Ram RR, Liu YP, Hyland R, Sinclair GI, Ruane PJ, Crofoot GE, McDonald CK, Brainard DM, Lad L, Swaminathan S, Sundquist WI, Sakowicz R, Chester AE, Lee WE, Daar ES, Yant SR, Cihlar T. Clinical targeting of HIV capsid protein with a long-acting small molecule. Nature. 2020;584(7822):614-8. doi: 10.1038/s41586-020-2443-1. PubMed PMID: 32612233.