This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor 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 processes 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. This subproject holds three specific aims: (i) to explore the basic physical principles governing the self-assembly of empty virus capsids by simulating large systems containing multiple capsid subunits utilizing a novel coarse-grained geometric model for the capsid proteins, (ii) to perform structural studies to investigate assembly mechanisms using a newly-developed intermediate-resolution crystal-structure-based Ca 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.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 |
| Vashisth, Harish; Skiniotis, Georgios; Brooks 3rd, Charles Lee (2014) Collective variable approaches for single molecule flexible fitting and enhanced sampling. Chem Rev 114:3353-65 |
| King, John T; Arthur, Evan J; Brooks 3rd, Charles L et al. (2014) Crowding induced collective hydration of biological macromolecules over extended distances. J Am Chem Soc 136:188-94 |
| Mustoe, Anthony M; Brooks, Charles L; Al-Hashimi, Hashim M (2014) Hierarchy of RNA functional dynamics. Annu Rev Biochem 83:441-66 |
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