Normal modes and essential dynamics.

  title={Normal modes and essential dynamics.},
  author={Steven Hayward and B. L. de Groot},
  journal={Methods in molecular biology},
Normal mode analysis and essential dynamics analysis are powerful methods used for the analysis of collective motions in biomolecules. Their application has led to an appreciation of the importance of protein dynamics in function and the relationship between structure and dynamical behavior. In this chapter, the methods and their implementation are introduced and recent developments such as elastic networks and advanced sampling techniques are described. 

MAVENs: Motion analysis and visualization of elastic networks and structural ensembles

The new software, MAVEN, aims to bring ENMs and their analysis to a broader audience by integrating methods for their generation and analysis into a user friendly environment that automates many of the steps.

Oscillatory Diffusion and Second-Order Cyclostationarity in Alanine Tripeptide from Molecular Dynamics Simulation.

Nonstationarity in the form of pure oscillatory instantaneous variance exists in the signed dihedral angular accelerations (SDAA) along the main chain of alanine tripeptide in MD simulations by power spectrum, corrected squared envelope spectrum (CSES), and cross-CSES.

Analysis of changes of cavity volumes in predefined directions of protein motions and cavity flexibility

An updated and improved version of ANA is presented that expands it use to quantify changes in cavity features, like volume and flexibility, due to protein structural distortions performed on predefined biologically relevant directions obtained by MD simulations or ensembles of NMR structures, collective NMA modes or any other direction of motion associated with specific conformational changes.

Exploring free energy landscapes of large conformational changes: molecular dynamics with excited normal modes.

The MDeNM (molecular dynamics with excited normal modes) method presented here consists of multiple-replica short MD simulations in which motions described by a given subset of low-frequency NMs are kinetically excited, thus allowing an efficient coupling between slow and fast motions.

An Atomistic View of DNA Dynamics and Its Interaction with Small Binders: Insights from Molecular Dynamics and Principal Component Analysis

DNA oligomers are promising building blocks for the development of bottom-up nano-devices and molecular logic machines. To control and exploit their unique capabilities of self-assembling and

Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models

Two alternative approaches to the coarse-grained modeling of dynamic properties of protein systems are presented, including two CG representations of polypeptide chains used for Monte Carlo dynamics simulations of protein local dynamics and conformational transitions and highly simplified structure-based elastic network models of protein flexibility.

Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure

Methods in the latter class - including Monte Carlo methods, harmonic approximations, and coarse graining - many of which yield valuable conformational insights into biomolecular structure and flexibility, despite altered kinetics are surveyed.

Molecular Dynamics Computations for Proteins: A Case Study in Membrane Ion Permeation

This chapter demonstrates how molecular dynamics (MD) simulation can reveal the microscopic mechanisms of biomolecular activity by exploring ion channel proteins that allow selective permeation of charged molecules across cell membranes to control the authors' nervous systems and chemical activity in the body.

Elements and modulation of functional dynamics.

  • A. Gibbs
  • Chemistry, Biology
    Journal of medicinal chemistry
  • 2014
The existing structure-function paradigm of drug discovery has been evolving toward the essential incorporation of dynamics data. This new functional dynamics paradigm emphasizes conformational



A comparison of techniques for calculating protein essential dynamics

It is shown that it is possible to perform essential dynamics using different subsets of atoms and compared to the basic C-a analysis, and the stability of the essential space during a simulation is investigated by comparing the two halves of a trajectory.

Investigating protein dynamics in collective coordinate space.

Principal Component Analysis and Long Time Protein Dynamics

It has been suggested that principal component analysis can identify slow modes in proteins and, thereby, facilitate the study of long time dynamics. However, sampling errors due to finite simulation

A kinetic model for the internal motions of proteins: Diffusion between multiple harmonic wells

It was found that a limited set of harmonic wells can be used to approximate the configurational fluctuations of these proteins, although any single harmonic approximation cannot properly describe their dynamics.

Similarities between principal components of protein dynamics and random diffusion

  • Hess
  • Biology
    Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
  • 2000
This work derives the principal components for high-dimensional random diffusion, which are almost perfect cosines, which implies that for many proteins the time scales of current simulations are too short to obtain convergence of collective motions.

Large-amplitude nonlinear motions in proteins.

  • García
  • Physics, Chemistry
    Physical review letters
  • 1992
A molecular-dynamics calculation on a hydrated protein, crambin, demonstrates that (i) neighboring dihedral angles are correlated to local transitions in the protein backbone, and that (ii) the

Coarse-grained normal mode analysis in structural biology.

On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations

Using a detailed analysis of long molecular dynamics trajectories in combination with a statistical assessment of the significance of the measured convergence, it is obtained that simulations of a few hundreds of picoseconds are in general sufficient to provide a stable and statistically reliable definition of the essential and near constraints subspaces.

A sampling problem in molecular dynamics simulations of macromolecules.

Three different representations of the fluctuations in a macromolecule are shown: the reciprocal space of crystallography using diffuse x-ray scattering data, real three-dimensional Cartesian space using covariance matrices of the atomic displacements, and the 3N-dimensional configuration space of the protein using dimensionally reduced projections to visualize the extent to which phase space is sampled.