Bottom-Up Coarse-Graining of Peptide Ensembles and Helix-Coil Transitions

作者：Rudzinski Joseph F; Noid William G^*

来源：Journal of Chemical Theory and Computation, 2015, 11(3): 1278-1291.

DOI：10.1021/ct5009922

This work investigates, the capability of bottom-up methods for parametrizing minimal coarse-grained (CG) models of disordered and helical peptides. We consider four high-resolution, peptide, ensembles that demonstrate varying degrees of complexity, For each high-resolution ensemble, we parametrize a CG model via the multiscale coarse-graining (MS-CG) method, which employs a generalized Yvon-Born-Green (g-YBG) relation to determine potentials directly (i.e., without iteration) from the high-resolution ensemble: The MS-CG, method accurately describes high-resolution models that fluctuate about a single conformation. However, given the minimal resolution and simple molecular mechanics potential, the MS-CG method provides a less accurate description for a high-resolution peptide model that Samples a disordered ensemble with multiple distinct conformations. We employ an iterative g-YBG method to develop a CG model that more accurately describes the relevant distribution functions and free energy surfaces for this disordered ensemble. Nevertheless, this more accurate model does not reproduce the cooperative helix-coil transition that is sampled by the high resolution model. By comparing the different models, we demonstrate that the errors in the MS-CG model primarily stem from the lack of cooperative interactions afforded by the minimal representation and molecular mechanics potential. This work demonstrates the potential of the MS-CG method for accurately modeling complex biomolecular structures, but also highlights the importance of more complex potentials for modeling cooperative transitions with a minimal CG representation.

• 出版日期2015-3