Viral capids are comprised of multiple copies of a few proteins organized as icosahedral shells. These shells undergo significant changes in shape and size during the virus life cycle - as they assemble, mature and ultimately release their genetic material. This process in a number of viruses involves pH-mediated changes in radius, and sometimes shape, e.g., as in HK97, which swells and transforms from a highly rounded to a highly faceted shape. The pH-induced changes arise from protonation equilibrium of ionizable side chains and the concomitant loss/gain of bound ions. While structural biology, via X-ray crystallography and cryo-EM, has provided glimpses of stable structural states and occasionally intermediates, little is known in detail about specific residues that are responsible for the pH-induced changes or the energetic landscape that connects the two stable states. These studies are directed toward establishing detailed atomic-level pathways and free energy landscapes for pH-mediated shape/size changes in viral capsids of T number varying from 3-7. Three systems that have been characterized from a structural standpoint: CCMV (T=3), N(omega)V (T=4) and HK97 (T=7) will be examined with the objective of: i) deriving pKa values of ionizable residues for the normal and swollen states of these capsids using novel constant pH molecular dynamics methods, ii) calculating the swelling conformational transition pathway, and iii) deriving the pH-dependent free energy landscapes through simulation methods. The resulting free energy pathways will reveal key interactions that facilitate or hinder swelling and further understanding of the biophysical forces that underlie this complex process. Additionally, driven by growing interest in the physical and material properties of viral capsids, and desire to understand these properties during the virus life cycle, which will inform applications from biotechnology and material science to imaging and single molecule manipulations, a new multi-scale computational method to calculate elastic moduli that characterize viral capsids will be developed and applied to the three systems noted above. This combination elasticity calculations and studies of pH-dependent transition pathways will elucidate the elastic character of the capsid during pH-mediated structural transitions, making connections to ongoing single molecule experiments and development of finite element models.
Broader Impact: The calculations and model development described above will yield significant new information about the forces and processes that control virus capsid swelling and shape changes of viral capsids during the virus life-cycle. Furthermore, the calculated pH-mediated free energy landscapes will provide vital information on lynchpin residues and interactions for biophysicists and physical virologists. The unique combination of landscape sampling and constant pH MD will establish new approaches to study pH-mediated conformational transitions, and the development and application of a novel multi-scale approach will inform and extend single molecule measurements and finite element modeling. The resultant software and models will be made available to the simulation and modeling community.
The PI will engage in the development and teaching of training workshops for students and postdoctoral researchers and also conduct research training for undergraduate students working on this project.