Hidden Complexity of Protein Free-Energy Landscapes Revealed by Principal Component Analysis by Parts

2010 ◽  
Vol 1 (19) ◽  
pp. 2769-2773 ◽  
Author(s):  
Abhinav Jain ◽  
Rainer Hegger ◽  
Gerhard Stock
Keyword(s):  
Principal Component Analysis ◽  
Free Energy ◽  
Principal Component ◽  
Component Analysis ◽  
Energy Landscapes ◽  
Free Energy Landscapes

Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis

2008 ◽  
Vol 128 (24) ◽  
pp. 245102 ◽  
Author(s):  
Alexandros Altis ◽  
Moritz Otten ◽  
Phuong H. Nguyen ◽  
Rainer Hegger ◽  
Gerhard Stock
Keyword(s):  
Principal Component Analysis ◽  
Free Energy ◽  
Dihedral Angle ◽  
Energy Landscape ◽  
Principal Component ◽  
Component Analysis ◽  
Free Energy Landscape

scholarly journals Comparison between slow, anisotropic LE4PD fluctuations and the Principal Component Analysis modes of Ubiquitin

2021 ◽  
Author(s):  
Eric R Beyerle ◽  
Marina G Guenza
Keyword(s):  
Principal Component Analysis ◽  
Free Energy ◽  
Protein Dynamics ◽  
Large Scale ◽  
Principal Component ◽  
Component Analysis ◽  
Hydrodynamic Interactions ◽  
Complete Analysis ◽  
Energy Barriers ◽  
Protein Motion

Proteins' biological function and folding mechanisms are often guided by large-scale, slow motions, which involve crossing high energy barriers. In a simulation trajectory, these slow fluctuations are commonly identified using a principal component analysis (PCA). Despite the popularity of this method, a complete analysis of its predictions based on the physics of protein motion has been so far limited. This study formally connects the PCA to a Langevin model of protein dynamics and analyzes the contributions of energy barriers and hydrodynamic interactions to the slow PCA modes of motion. To do so, we introduce an anisotropic extension of the Langevin Equation for Protein Dynamics, called the LE4PD-XYZ, which formally connects to the PCA 'essential dynamics'. The LE4PD-XYZ is an accurate coarse-grained diffusive method to model protein motion, which describes anisotropic fluctuations in the protein's alpha-carbons. The LE4PD accounts for hydrodynamic effects and mode-dependent free-energy barriers. This study compares large-scale anisotropic fluctuations identified by the LE4PD-XYZ to the mode-dependent PCA's predictions, starting from a microsecond-long alpha-carbon molecular dynamics atomistic trajectory of the protein ubiquitin. We observe that the inclusion of free-energy barriers and hydrodynamic interactions has important effects on the identification and timescales of ubiquitin's slow modes.

scholarly journals Exploring Protein Energy Landscapes with Time-Dependent Principal Component Analysis

2013 ◽  
Vol 104 (2) ◽  
pp. 171a
Author(s):  
Andreas Volkhardt ◽  
Tim Meyer ◽  
Helmut Grubmüller
Keyword(s):  
Principal Component Analysis ◽  
Principal Component ◽  
Component Analysis ◽  
Time Dependent ◽  
Energy Landscapes ◽  
Protein Energy
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