Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis

Normal Mode Analysis Techniques in Structural Biology

The dynamic simulation of macromolecular systems with biologically relevant sizes and time scales is critical for understanding macromolecular function. In this context, normal mode analysis (NMA) approximates the complex dynamicalbehaviourofa macromoleculeas a simple setof harmonic oscillators vibrating around a given equilibrium conformation. This technique, originated from classical mechanic...

Macromolecular Dynamics by Hybrid Electron Microscopy Normal Mode Analysis

Structural changes are critical for biological functions of proteins and describing conformational changes in large macromolecular complexes is a major challenge. To allow full studies of gradual conformational changes, we have recently developed Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) [1]. HEMNMA uses normal modes to elastically align electron microscopy (EM) images with a ref...

Failure Mode and Effects Analysis Using Data Envelopment Analysis

Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme.

We have developed a new method for modelling protein dynamics using normal-mode analysis in internal co-ordinates. This method, normal-mode dynamics, is particularly well suited for modelling collective motion, makes possible direct visualization of biologically interesting modes, and is complementary to the more time-consuming simulation of molecular dynamics trajectories. The essential assump...

Coarse-grained normal mode analysis in structural biology.

The realization that experimentally observed functional motions of proteins can be predicted by coarse-grained normal mode analysis has renewed interest in applications to structural biology. Notable applications include the prediction of biologically relevant motions of proteins and supramolecular structures driven by their structure-encoded collective dynamics; the refinement of low-resolutio...