This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. For about half of the known virus families, the coat that protects their genome in the form of DNA or RNA is a spherical or icosahedral capsid. These capsids are composed of hundreds of copies of individual proteins that must assemble correctly, rapidly, and reproducibly on a biological timescale in order to propagate an infection in vivo. Once assembled, capsid proteins undergo a rearrangement process in which large-scale conformational changes take place to achieve their functionalities such as catalysis and regulation of activity. Elucidating the self-assembly and stability of viruses may have the potential to assist in developing novel approaches to interfere with viral infection. We have three specific projects: (i) to learn the basic physical principles governing the self-assembly of empty virus capsids by simulating large systems containing multiple capsid subunits with our newly-developed coarse-grained geometric models, (ii) to perform structural studies to investigate assembly mechanisms using our newly-developed intermediate-resolution crystal-structure-based C? model, (iii) to examine physical properties such as elastic behavior, capsid expansion / buckling transition and to explore the initial stages of virus capsid assembly by using all-atom CHARMM.
| Salmon, Loïc; Ahlstrom, Logan S; Horowitz, Scott et al. (2016) Capturing a Dynamic Chaperone-Substrate Interaction Using NMR-Informed Molecular Modeling. J Am Chem Soc 138:9826-39 |
| Bruno, Paul A; Morriss-Andrews, Alex; Henderson, Andrew R et al. (2016) A Synthetic Loop Replacement Peptide That Blocks Canonical NF-?B Signaling. Angew Chem Int Ed Engl 55:14997-15001 |
| Montiel-García, Daniel J; Mannige, Ranjan V; Reddy, Vijay S et al. (2016) Structure based sequence analysis of viral and cellular protein assemblies. J Struct Biol 196:299-308 |
| Rosen, Laura E; Kathuria, Sagar V; Matthews, C Robert et al. (2015) Non-native structure appears in microseconds during the folding of E. coli RNase H. J Mol Biol 427:443-53 |
| Cheng, Shanshan; Brooks 3rd, Charles L (2015) Protein-Protein Interfaces in Viral Capsids Are Structurally Unique. J Mol Biol 427:3613-3624 |
| Carrillo-Tripp, Mauricio; Montiel-García, Daniel Jorge; Brooks 3rd, Charles L et al. (2015) CapsidMaps: protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps. J Struct Biol 190:47-55 |
| Ahlstrom, Logan S; Law, Sean M; Dickson, Alex et al. (2015) Multiscale modeling of a conditionally disordered pH-sensing chaperone. J Mol Biol 427:1670-80 |
| Mustoe, Anthony M; Brooks, Charles L; Al-Hashimi, Hashim M (2014) Hierarchy of RNA functional dynamics. Annu Rev Biochem 83:441-66 |
| Nobrega, R Paul; Arora, Karunesh; Kathuria, Sagar V et al. (2014) Modulation of frustration in folding by sequence permutation. Proc Natl Acad Sci U S A 111:10562-7 |
| Arthur, Evan J; King, John T; Kubarych, Kevin J et al. (2014) Heterogeneous preferential solvation of water and trifluoroethanol in homologous lysozymes. J Phys Chem B 118:8118-27 |
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