2018
DOI: 10.1063/1.5004141
|View full text |Cite
|
Sign up to set email alerts
|

Characterizing protein conformations by correlation analysis of coarse-grained contact matrices

Abstract: We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-… Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
2
1
1
1

Citation Types

0
22
0

Year Published

2018
2018
2023
2023

Publication Types

Select...
7
1

Relationship

6
2

Authors

Journals

citations
Cited by 9 publications
(22 citation statements)
references
References 34 publications
0
22
0
Order By: Relevance
“…The third type of contact matrices \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${u_{ij}}$\end{document} that we studied here is from protein conformations, mostly from atomistic molecular dynamics simulations of nuclear receptor complexes. The detailed system setup and simulation protocol was reported previously ( 23 ). The simulation was performed at constant temperature (300 K) and pressure (1 atm) for 200 ns using NAMD ( 29 ), where we recorded conformations every 1 ps.…”
Section: Methodsmentioning
confidence: 99%
“…The third type of contact matrices \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${u_{ij}}$\end{document} that we studied here is from protein conformations, mostly from atomistic molecular dynamics simulations of nuclear receptor complexes. The detailed system setup and simulation protocol was reported previously ( 23 ). The simulation was performed at constant temperature (300 K) and pressure (1 atm) for 200 ns using NAMD ( 29 ), where we recorded conformations every 1 ps.…”
Section: Methodsmentioning
confidence: 99%
“…Similarly, by combining network analyses with PCA, the computation of allosteric mechanism by evaluating residue-residue associations (CAMERRA) tool aims to capture allosteric motions based on the residue-residue contact analysis of protein dynamics [60,61]. The CAMERRA tool is freely available as a set of Perl scripts.…”
Section: Interaction Network and Correlated Motion Analysesmentioning
confidence: 99%
“…The system setup details have been reported previously for E-PCA analysis (16,17). Here, we focused on conformations from a long-time simulation of the wild-type complex (19). Both protein systems we considered contain a dimer of the ligand binding domains of nuclear hormone receptors.…”
Section: Implicit Contact Correlation Analysis Reveals Consensus Featmentioning
confidence: 99%
“…In recent years, PCA has also been used for the statistical analysis of other degrees of freedom (DOFs), such as torsion angles (13) and residue-residue contacts (14) in the protein system. Particularly, treating each individual contact as a DOF, PCA assisted researchers in identifying regions of protein with concerted dynamics of contact forming and breaking (14)(15)(16)(17)(18)(19)(20).…”
Section: Introductionmentioning
confidence: 99%
See 1 more Smart Citation