Multiscale Modeling of Dynamin Protein Allostery

Protein Allostery and Conformational Dynamics.

The functions of many proteins are regulated through allostery, whereby effector binding at a distal site changes the functional activity (e.g., substrate binding affinity or catalytic efficiency) at the active site. Most allosteric studies have focused on thermodynamic properties, in particular, substrate binding affinity. Changes in substrate binding affinity by allosteric effectors have gene...

Modeling Spatial Correlation of DNA Deformation: DNA Allostery in Protein Binding Citation

Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Abstract We report a study of DNA deformations using a coarse-grained mechanical model and quantitatively interpret...

Multiscale Design and Modeling of Protein-based Nanomechanisms for Nanorobotics

In this paper, we present a novel approach that makes use of multiscale and multiphysics modeling coupled to virtual reality for nanorobotic prototyping systems. First, a CAD-assisted assembly system that integrates principles for a multiscale approach into a nanorobotics structure design is presented. Then, we focus on the different design levels, more specifically, the optimization of geometr...

Multiscale modeling

Multiscale modeling and simulation of microtubule-motor-protein assemblies.

Microtubules and motor proteins self-organize into biologically important assemblies including the mitotic spindle and the centrosomal microtubule array. Outside of cells, microtubule-motor mixtures can form novel active liquid-crystalline materials driven out of equilibrium by adenosine triphosphate-consuming motor proteins. Microscopic motor activity causes polarity-dependent interactions bet...