Discovery of ABT-263, a Bcl-family protein inhibitor: observations on targeting a large protein–protein interaction

2008 ◽  
Vol 3 (9) ◽  
pp. 1123-1143 ◽  
Author(s):  
Michael D Wendt
Keyword(s):  
Protein Interaction ◽  
Protein Inhibitor ◽  
Large Protein ◽  
Protein Protein Interaction ◽  
Family Protein

scholarly journals Photocatalytic Proximity Labelling of MCL-1 by a BH3 Ligand

2019 ◽  
Author(s):  
Hester Beard ◽  
Rachel George ◽  
Andrew Wilson ◽  
Robin Bon
Keyword(s):  
Visible Light ◽  
Dynamic Analysis ◽  
Protein Interaction ◽  
Affinity Purification ◽  
Cysteine Residue ◽  
Tandem Ms ◽  
Dependent Manner ◽  
Protein Protein Interaction ◽  
Apoptotic Protein ◽  
Family Protein

Ligand-directed protein labelling can be used to introduce diverse chemical functionalities onto proteins without the need for incorporation of genetically encoded tags. Here we report a method for the rapid and efficient labelling of a protein using a ruthenium-bipyridyl (Ru(II)(bpy)3) modified peptide designed to mimic an interacting BH3 ligand within a BCL-2 family protein-protein interaction (PPI). Using sub-stoichiometric quantities of (Ru(II)(bpy)3)-modified NOXA-B and irradiation with visible light for 1 minute, the anti-apoptotic protein MCL-1 was photolabelled in a ligand-dependent manner with a variety of functional tags, as determined by in-gel fluorescence, affinity purification, and ESIMS analysis. In contrast with previous reports on Ru(II)(bpy)3-catalysed photolabelling, tandem MS experiments revealed that the dominant labelling occurred on a cysteine residue of MCL-1. Labelling of MCL-1 occurred selectively in mixtures with other proteins, including the structurally related BCL-2 member, BCL-xL. These results improve methodology for proximity-induced photolabelling of proteins, demonstrate the approach is applicable to interfaces that mediate PPIs, and pave the way towards future use of ligand-directed proximity labelling for dynamic analysis of the localisation and interactome of BCL-2 family proteins.<br>

scholarly journals Photocatalytic Proximity Labelling of MCL-1 by a BH3 Ligand

2019 ◽  
Author(s):  
Hester Beard ◽  
Rachel George ◽  
Andrew Wilson ◽  
Robin Bon
Keyword(s):  
Visible Light ◽  
Dynamic Analysis ◽  
Protein Interaction ◽  
Affinity Purification ◽  
Cysteine Residue ◽  
Tandem Ms ◽  
Dependent Manner ◽  
Protein Protein Interaction ◽  
Apoptotic Protein ◽  
Family Protein

Ligand-directed protein labelling can be used to introduce diverse chemical functionalities onto proteins without the need for incorporation of genetically encoded tags. Here we report a method for the rapid and efficient labelling of a protein using a ruthenium-bipyridyl (Ru(II)(bpy)3) modified peptide designed to mimic an interacting BH3 ligand within a BCL-2 family protein-protein interaction (PPI). Using sub-stoichiometric quantities of (Ru(II)(bpy)3)-modified NOXA-B and irradiation with visible light for 1 minute, the anti-apoptotic protein MCL-1 was photolabelled in a ligand-dependent manner with a variety of functional tags, as determined by in-gel fluorescence, affinity purification, and ESIMS analysis. In contrast with previous reports on Ru(II)(bpy)3-catalysed photolabelling, tandem MS experiments revealed that the dominant labelling occurred on a cysteine residue of MCL-1. Labelling of MCL-1 occurred selectively in mixtures with other proteins, including the structurally related BCL-2 member, BCL-xL. These results improve methodology for proximity-induced photolabelling of proteins, demonstrate the approach is applicable to interfaces that mediate PPIs, and pave the way towards future use of ligand-directed proximity labelling for dynamic analysis of the localisation and interactome of BCL-2 family proteins.<br>

scholarly journals Protein complex prediction for large protein protein interaction networks with the Core&Peel Method

2016 ◽  
Author(s):  
Marco Pellegrini ◽  
Miriam Baglioni ◽  
Filippo Geraci
Keyword(s):  
Protein Interaction ◽  
State Of The Art ◽  
Protein Complexes ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Medium Size ◽  
Large Protein ◽  
Running Time ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Networks

AbstractMotivations.Biological networks play an increasingly important role in the exploration of functional modularity and cellular organization at a systemic level. Quite often the first tools used to analyze these networks are clustering algorithms. We concentrate here on the specific task of predicting protein complexes (PC) in large protein-protein interaction networks (PPIN). Currently, many state-of-the-art algorithms work well for networks of small or moderate size. However, their performance on much larger networks, which are becoming increasingly common in modern proteome-wise studies, needs to be re-assessed. Our aim is to push forward the state-of the-art in PPIN clustering providing an algorithmic solution with polynomial running time that attains experimentally demonstrable good output quality and speed on challenging large real networks.Results.We present a new fast algorithm for clustering large sparse networks: Core&Peel, which runs essentially in time and storage O(a(G)m+n) for a network G of n nodes and m arcs, where a(G) is the arboricity of G (which is roughly proportional to the maximum average degree of any induced subgraph in G). We evaluated Core&Peel on five PPI networks of large size and one of medium size from both yeast and homo sapiens, comparing its performance against those of ten state-of-the-art methods. We demonstrate that Core&Peel consistently outperforms the ten competitors in its ability to identify known protein complexes and in the functional coherence of its predictions. Our method is remarkably robust, being quite insensible to the injection of random interactions. Core&Peel is also empirically efficient attaining the second best running time over large networks among the tested algorithms.Availabilityhttp://bioalgo.iit.cnr.it (via web interface)[email protected]

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