During the replication of many viruses, hundreds to thousands of protein subunits assemble around the viral nucleic acid to form a protein shell called a capsid. Within their host organism, most viruses form one particular structure with astonishing fidelity;yet, recent experiments demonstrate that capsids can assemble with different sizes and morphologies to accommodate nucleic acids, inorganic nanoparticles, and polyanions with different sizes. This project will use computational models to determine the features of viral proteins and their cargoes that enable assembly to be so precise and yet so adaptable. We develop simplified representations of viral proteins and cargoes that range from rigid spheres to fluctuating polymers to model nucleic acids. With these models we will develop experimentally testable predictions for the mechanisms by which viral proteins dynamically encapsidate these objects, and which factors direct the assembly process towards a particular size and morphology. These coarse-grained models of the overall assembly process will be validated and guided by atomic-resolution simulations that examine the dynamic conformations of viral proteins.

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 use multiple drugs to target several steps in the infection process, but relatively few treatments target viral assembly. By identifying the features that make viral assembly successful, we can learn to block it and thereby create novel antivirus therapies.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI080791-04
Application #
8196801
Study Section
Modeling and Analysis of Biological Systems Study Section (MABS)
Program Officer
Park, Eun-Chung
Project Start
2008-12-01
Project End
2013-11-30
Budget Start
2011-12-01
Budget End
2012-11-30
Support Year
4
Fiscal Year
2012
Total Cost
$228,304
Indirect Cost
$81,289
Name
Brandeis University
Department
Physics
Type
Schools of Arts and Sciences
DUNS #
616845814
City
Waltham
State
MA
Country
United States
Zip Code
02454
Patel, Amish J; Varilly, Patrick; Jamadagni, Sumanth N et al. (2012) Sitting at the edge: how biomolecules use hydrophobicity to tune their interactions and function. J Phys Chem B 116:2498-503
Ni, Peng; Wang, Zhao; Ma, Xiang et al. (2012) An examination of the electrostatic interactions between the N-terminal tail of the Brome Mosaic Virus coat protein and encapsidated RNAs. J Mol Biol 419:284-300
Hagan, Michael F; Elrad, Oren M; Jack, Robert L (2011) Mechanisms of kinetic trapping in self-assembly and phase transformation. J Chem Phys 135:104115
Giomi, L; Mahadevan, L; Chakraborty, B et al. (2011) Excitable patterns in active nematics. Phys Rev Lett 106:218101
Sumedha; Hagan, Michael F; Chakraborty, Bulbul (2011) Prolonging assembly through dissociation: a self-assembly paradigm in microtubules. Phys Rev E Stat Nonlin Soft Matter Phys 83:051904
Yang, Yasheng; Meyer, Robert B; Hagan, Michael F (2010) Self-limited self-assembly of chiral filaments. Phys Rev Lett 104:258102
Kivenson, Aleksandr; Hagan, Michael F (2010) Mechanisms of capsid assembly around a polymer. Biophys J 99:619-28
Hagan, Michael F; Elrad, Oren M (2010) Understanding the concentration dependence of viral capsid assembly kinetics--the origin of the lag time and identifying the critical nucleus size. Biophys J 98:1065-74
Hagan, Michael F (2009) A theory for viral capsid assembly around electrostatic cores. J Chem Phys 130:114902
Hagan, Michael F (2008) Controlling viral capsid assembly with templating. Phys Rev E Stat Nonlin Soft Matter Phys 77:051904

Showing the most recent 10 out of 11 publications