Structural and Thermodynamic Characterization of PolyGly, a protein backbone model

Bernard Pettitt, University of Texas Medical Branch at Galveston

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Evolution has favored the incorporation of homopolymeric amino acid repeats (i.e. tracts of the same amino acid) or low complexity sequences in human transcription factors. Events that expand or shorten these tracts often abrogate the transcription factor's function and lead to diseases such as Alzheimer's and various cancers. In some cases the length of these tracts are only altered by a few amino acids with considerable effects on protein function.

We hypothesize that homopolymeric tracts will have unique structural and thermodynamic properties determined by their length and that changes in these properties due to events that alter the length of the tract may be the driving force in disease pathogenesis. These peptide tracts are often disordered and pose problems to experimental methods due to their propensity to aggregate. Single molecule techniques, which operate in extremely low concentrations, have been successful in probing the conformational ensemble of disordered structures, but these methods typically rely on attachment of large fluorescent probes that could alter the native protein's conformation. To circumvent these problems and test our hypothesis we will use all-atom molecular dynamics (MD) simulations of polyglycine chains (polyGly), a model disordered peptide, of various lengths. 
 
Current force fields used for MD simulations are primarily designed for proteins with secondary and tertiary structure and maintain distributions of conformations close to the native folded protein. When the protein or peptide of interest lacks stable secondary structure elements, the conformational  distributions become very important and the differences in conformational sampling between the different force fields may be more pronounced. To obtain detailed comparative structural analyses for our model system, polyGly, we first performed all-atom molecular dynamics simulations of Gly3 and Gly10 using three commonly used protein force fields, CHARMM274, CHARMM365, and Amber ff12SB6. A variety of methods were used to evaluate and characterize the structural manifolds (end-to-end distance, radius of gyration, and dihedral angle distributions) and we discovered that each force field samples conformational space differently.

To further elucidate how the conformations of these "structureless" domains and how they fold and unfold we will investigate the free energy and entropy versus chain length of our polyglycine model systems as a function of the number of residues and with and without end-to-end distance constraints. Metadynamics will be performed using the NAMD7  program. This allocation will be used to perform the initial calculations for the Gly10 (CHARMM36) system.