In many virus families, replication requires that hundreds to thousands of proteins assemble around the viral nucleic acid (NA) to form a protein shell called a capsid. Furthermore, many animal viruses use protein assembly to drive budding of the capsid from a cell membrane. Understanding the mechanisms that control assembly around NAs and on membranes would identify targets for novel antivirus therapies that inhibit NA packaging or budding, and would guide efforts to exploit viruses as targeted transport vehicles. Assembly mechanisms inferred from experiments alone are incomplete because intermediates are transient. Therefore, this project develops and applies computational models for capsid proteins, NAs, and lipids that reveal details of assembly and membrane budding not accessible to experiments. To understand how the properties of viral NAs facilitate assembly, models are developed for capsid proteins and NAs that begin with a linear polyelectrolyte (without base-pairing) and then systematically add the geometric and electrostatic features of NAs that arise due to base-pairing. Comparison of predicted assembly kinetics and thermodynamics for each model identifies the contributions of base-pairing to assembly. Predictions for each model are tested against experiments performed by collaborating labs on capsid assembly around corresponding molecules (e.g., synthetic polyelectrolytes, heterologous NAs, and viral genomic NAs). The mechanism by which capsids form different icosahedral morphologies to accommodate NAs with different sizes is also studied. Employed simulation techniques include Brownian dynamics and equilibrium calculations. For some enveloped viruses (e.g., HIV) capsid assembly drives budding from a cell membrane, while for others (e.g., alphaviruses) assembly of membrane proteins drives budding of a pre-assembled capsid. Simulations are used to investigate how these two classes of assembly-driven budding processes depend on properties such as protein interactions and membrane rigidity, and why many viruses preferentially bud from particular membrane microdomains. Predictions will be compared to experiments on alphavirus budding. In addition to identifying factors that can be manipulated to prevent or exploit viral assembly, the proposed simulations will elucidate how biology employs membranes and filamentous scaffolds to assemble multi- macromolecular complexes. The research combines coarse-grained models that are informed by atomistic simulations and experiments with recent advances in GPUs and distributed computing to simulate relevant time and length scales. A new method to apply Markov state models to assembly reactions is developed.

Public Health Relevance

Viral diseases and acquired drug resistance by viruses are major biomedical challenges. The most effective antiviral treatments fight acquired resistance by using multiple drugs to target several steps in the infection process, but relatively few treatment target viral assembly. By understanding how viruses assemble around nucleic acids and on membranes, we can learn to block these processes, identifying new targets for antiviral research.

Agency
National Institute of Health (NIH)
Type
Research Project (R01)
Project #
5R01GM108021-07
Application #
8729612
Study Section
Modeling and Analysis of Biological Systems Study Section (MABS)
Program Officer
Lyster, Peter
Project Start
Project End
Budget Start
Budget End
Support Year
7
Fiscal Year
2014
Total Cost
Indirect Cost
Name
Brandeis University
Department
Physics
Type
Schools of Arts and Sciences
DUNS #
City
Waltham
State
MA
Country
United States
Zip Code
02453
Perkett, Matthew R; Hagan, Michael F (2014) Using Markov state models to study self-assembly. J Chem Phys 140:214101
Perlmutter, Jason D; Perkett, Matthew R; Hagan, Michael F (2014) Pathways for virus assembly around nucleic acids. J Mol Biol 426:3148-65