Within this component of our core research project on long timescale/length scale sampling for protein and peptide folding, we have developed """"""""minimalist"""""""" representations of protein topologies and sequences based on simplified Ca-based interaction models. The development of these models has been automated allowing one to construct such a representation of a protein structure and carry out folding studies on this representation given a PDB file. We are in the process of providing an automated means of producing these models for scientists over the WWW, thus allowing scientists within the broad community to investigate the folding aspects of their particular protein sequences/topologies. Our protocol produces CHARMM topology and parameter files appropriate for studies of the thermodynamics and kinetics of folding of these models. We have used such minimalist models together with theoretical developments to explore the """"""""optimization"""""""" of such minimalist models for protein folding. Our studies have demonstrated that we can explore a rather large range of the underlying energy function space using these methods and hence significantly reduce the computational cost of developing representative minimalist models for protein folding. We anticipate these ideas will be transferable to studies of DNA and RNA models as well as questions involving virus assembly. Our first paper on this topic has been recently accepted for publication in the Journal of Chemical Physics. The full title and references are: Exploring the Space of Protein Folding Hamiltonians: The Balance of Forces in a Minimalist b-Barrel Model. J.-E. Shea, Y. D. Nochomovitz, Z. Guo and C. L. Brooks III, J. Chem. Phys., accepted for publication (1998). Frontiers of Science 1997 - Chemical Physics of Protein Folding. C. L. Brooks III, M. Gruebele, J. N. Onuchic and P. G. Wolynes PNAS, in press (1998).
| 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 |
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