Approaching Elastic Network Models to Molecular Dynamics Flexibility

Citations Over TimeTop 12% of 2010 papers

Abstract

Elastic network models (ENMs) are coarse-grained descriptions of proteins as networks of coupled harmonic oscillators. However, despite their widespread application to study collective movements, there is still no consensus parametrization for the ENMs. When compared to molecular dynamics (MD) flexibility in solution, the ENMs tend to disperse the important motions into multiple modes. We present here a new ENM, trained against a database of atomistic MD trajectories. The role of residue connectivity, the analytical form of the force constants, and the threshold for interactions were systematically explored. We found that contacts between the three nearest sequence neighbors are crucial determinants of the fundamental motions. We developed a new general potential function including both the sequential and spatial relationships between interacting residue pairs which is robust against size and fold variations. The proposed model provides a systematic improvement compared to standard ENMs: Not only do its results match the MD results-even for long time scales-but also the model is able to capture large X-ray conformational transitions as well as NMR ensemble diversity.

Related Papers

• → A new parametrization for the radiative properties of ice crystals: Comparison with existing schemes and impact in a GCM(2006)102 cited
• → Parametrization of effective sizes of cirrus‐cloud particles and its verification against observations(1999)73 cited
• → An improvement of parametrization of short-wave radiation at the sea surface on the basis of direct measurements in the Atlantic(2007)34 cited
• → Parametrization of effective sizes of cirrus-cloud particles and its verification against observations(1999)18 cited
• Parametrization of indecomposable modules(2011)