Large-Scale Analysis of Protein–Protein Interactions Using Cellulose-Bound Peptide Arrays

2008 ◽  
pp. 115-152 ◽  
Author(s):  
Ulrike Beutling ◽  
Kai Städing ◽  
Theresia Stradal ◽  
Ronald Frank
Keyword(s):  
Protein Interactions ◽  
Large Scale ◽  
Scale Analysis ◽  
Protein Protein Interactions ◽  
Peptide Arrays ◽  
Large Scale Analysis

scholarly journals Reliable identification of protein-protein interactions by crosslinking mass spectrometry

2020 ◽  
Author(s):  
Swantje Lenz ◽  
Ludwig R. Sinn ◽  
Francis J. O’Reilly ◽  
Lutz Fischer ◽  
Fritz Wegner ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Large Scale ◽  
Protein Complexes ◽  
Estimation Procedure ◽  
Scale Analysis ◽  
Protein Protein Interactions ◽  
False Discovery ◽  
Large Scale Analysis ◽  
False Discovery Rate Estimation

Crosslinking mass spectrometry is widening its scope from structural analyzes of purified multi-protein complexes towards systems-wide analyzes of protein-protein interactions. Assessing the error in these large datasets is currently a challenge. Using a controlled large-scale analysis of Escherichia coli cell lysate, we demonstrate a reliable false-discovery rate estimation procedure for protein-protein interactions identified by crosslinking mass spectrometry.

scholarly journals A Large Scale Analysis of Protein-Protein Interactions in the Nitrogen-fixing Bacterium Mesorhizobium loti

DNA Research ◽  
2008 ◽  
Vol 15 (1) ◽  
pp. 13-23 ◽  
Author(s):  
Y. Shimoda ◽  
S. Shinpo ◽  
M. Kohara ◽  
Y. Nakamura ◽  
S. Tabata ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Large Scale ◽  
Scale Analysis ◽  
Nitrogen Fixing ◽  
Protein Protein Interactions ◽  
Mesorhizobium Loti ◽  
Large Scale Analysis

scholarly journals FrustratometeR: an R-package to compute Local frustration in protein structures, point mutants and MD simulations

2020 ◽  
Author(s):  
Atilio O. Rausch ◽  
Maria I. Freiberger ◽  
Cesar O. Leonetti ◽  
Diego M. Luna ◽  
Leandro G. Radusky ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Large Scale ◽  
Protein Structures ◽  
Md Simulations ◽  
R Package ◽  
Protein Protein Interactions ◽  
Large Scale Analysis ◽  
Functional Aspects ◽  
Catalytic Sites ◽  
Polypeptide Chains

Once folded natural protein molecules have few energetic conflicts within their polypeptide chains. Many protein structures do however contain regions where energetic conflicts remain after folding, i.e. they have highly frustrated regions. These regions, kept in place over evolutionary and physiological timescales, are related to several functional aspects of natural proteins such as protein-protein interactions, small ligand recognition, catalytic sites and allostery. Here we present FrustratometeR, an R package that easily computes local energetic frustration on a personal computer or a cluster. This package facilitates large scale analysis of local frustration, point mutants and MD trajectories, allowing straightforward integration of local frustration analysis in to pipelines for protein structural analysis.Availability and implementation: https://github.com/proteinphysiologylab/frustratometeR

scholarly journals Reliable identification of protein-protein interactions by crosslinking mass spectrometry

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Swantje Lenz ◽  
Ludwig R. Sinn ◽  
Francis J. O’Reilly ◽  
Lutz Fischer ◽  
Fritz Wegner ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Large Scale ◽  
Structural Information ◽  
Protein Complexes ◽  
Interaction Network ◽  
Protein Protein Interactions ◽  
False Discovery Rates ◽  
Large Scale Analysis ◽  
Exit Tunnel

AbstractProtein-protein interactions govern most cellular pathways and processes, and multiple technologies have emerged to systematically map them. Assessing the error of interaction networks has been a challenge. Crosslinking mass spectrometry is currently widening its scope from structural analyses of purified multi-protein complexes towards systems-wide analyses of protein-protein interactions (PPIs). Using a carefully controlled large-scale analysis of Escherichia coli cell lysate, we demonstrate that false-discovery rates (FDR) for PPIs identified by crosslinking mass spectrometry can be reliably estimated. We present an interaction network comprising 590 PPIs at 1% decoy-based PPI-FDR. The structural information included in this network localises the binding site of the hitherto uncharacterised protein YacL to near the DNA exit tunnel on the RNA polymerase.

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