title: Web-based computational chemistry education with CHARMMing II: Coarse-grained protein folding.
abstract: A lesson utilizing a coarse-grained (CG) Gō-like model has been implemented into the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org) to the Chemistry at HARvard Macromolecular Mechanics (CHARMM) molecular simulation package. While widely used to model various biophysical processes, such as protein folding and aggregation, CG models can also serve as an educational tool because they can provide qualitative descriptions of complex biophysical phenomena for a relatively cheap computational cost. As a proof of concept, this lesson demonstrates the construction of a CG model of a small globular protein, its simulation via Langevin dynamics, and the analysis of the resulting data. This lesson makes connections between modern molecular simulation techniques and topics commonly presented in an advanced undergraduate lecture on physical chemistry. It culminates in a straightforward analysis of a short dynamics trajectory of a small fast folding globular protein; we briefly describe the thermodynamic properties that can be calculated from this analysis. The assumptions inherent in the model and the data analysis are laid out in a clear, concise manner, and the techniques used are consistent with those employed by specialists in the field of CG modeling. One of the major tasks in building the Gō-like model is determining the relative strength of the nonbonded interactions between coarse-grained sites. New functionality has been added to CHARMMing to facilitate this process. The implementation of these features into CHARMMing helps automate many of the tedious aspects of constructing a CG Gō model. The CG model builder and its accompanying lesson should be a valuable tool to chemistry students, teachers, and modelers in the field.
authors: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
authors: Frank C
authors: FC
authors: Pickard
authors: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
authors: Benjamin T
authors: BT
authors: Miller
authors: Department of Natural Sciences, New College of Florida, Sarasota, Florida, United States of America.
authors: Vinushka
authors: V
authors: Schalk
authors: Department of Physics and Astronomy, Earlham College, Richmond, Indiana, United States of America.
authors: Michael G
authors: MG
authors: Lerner
authors: Department of Chemistry, University of South Florida, Tampa, Florida, United States of America.
authors: H Lee
authors: HL
authors: Woodcock
authors: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
authors: Bernard R
authors: BR
authors: Brooks
mesh_terms: D019295:Computational Biology / Q000193:education* / Q000379:methods*; D020407:Internet; D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins