Over the past few years, a wealth of new data has become available on the structure of the ribosome. Of particular importance are the crystal structures of several ribosomal proteins and cryoelectron microscopic images with a resolution of about 15?. The new data have validated some aspects of earlier models for the structure of the ribosome, but they have also revealed a number of problems with those models. The quality and quantity of these data offer opportunities for the development of better and more accurate models of the ribosome. In addition, the improved methods that we have developed -- particularly the generation of starting models for YAMMP refinement using distance geometry, and the addition of new descriptions of proteins, transfer RNA, and messenger RNA -- will enable us to generate the next generation of ribosome models much more rapidly and with fewer problems than in the past. We have evaluated all the available data, established a suitable set of constraints from the data, and generated preliminary models using the combined distance geometry / YAMMP refinement approach. We expect to complete these second generation efforts during the next year of the grant.
| 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 |
| Taylor, Kenneth A; Feig, Michael; Brooks 3rd, Charles L et al. (2014) Role of the essential light chain in the activation of smooth muscle myosin by regulatory light chain phosphorylation. J Struct Biol 185:375-82 |
| Zeng, Xiancheng; Chugh, Jeetender; Casiano-Negroni, Anette et al. (2014) Flipping of the ribosomal A-site adenines provides a basis for tRNA selection. J Mol Biol 426:3201-3213 |
| 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 |
Showing the most recent 10 out of 176 publications
