We present a new method to incorporate electrostatic interactions in coarse-grained representations of proteins. The model is based on a topologically reconstructed multipolar expansion of the all-atom centers of charge, specifically of the backbone dipoles and the polar or charged side chains. The reliability of the model is checked by studying different test cases, namely protein-cofactor/substrate interactions, protein large conformational changes, and protein-protein complexes. In all cases, the model quantitatively reproduces the all-atom electrostatic field in both a static and a dynamic framework. The model is of general applicability and can be used to improve both full coarse-grained simulations and hybrid all-atom/coarse-grained multiscale approaches.
Topologically based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins
2008
Abstract
We present a new method to incorporate electrostatic interactions in coarse-grained representations of proteins. The model is based on a topologically reconstructed multipolar expansion of the all-atom centers of charge, specifically of the backbone dipoles and the polar or charged side chains. The reliability of the model is checked by studying different test cases, namely protein-cofactor/substrate interactions, protein large conformational changes, and protein-protein complexes. In all cases, the model quantitatively reproduces the all-atom electrostatic field in both a static and a dynamic framework. The model is of general applicability and can be used to improve both full coarse-grained simulations and hybrid all-atom/coarse-grained multiscale approaches.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
