Ligand Screening by Exoproteolysis and Mass Spectrometry in Combination With Computer Modelling

Here, we present a new approach for protein ligand screening based on the use of limited exoproteolysis coupled to MALDI-TOF mass spectrometry, combined with computational modelling and prediction of binding energies. As a test for this combined approach, we have screened a combinatorial library con...

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Bibliographic Details
Published in:Journal of molecular biology 2003-07, Vol.330 (5), p.1039-1048
Main Authors: Villanueva, Josep, Fernández-Ballester, Gregorio, Querol, Enrique, Aviles, Francesc X., Serrano, Luis
Format: Article
Language:English
Subjects:
Algorithms
binding constant
computer design
Coumaric Acids - chemistry
Gene Library
Humans
ligand screening
Ligands
Mass Spectrometry
Models, Molecular
Peptide Library
Peptides - chemistry
Protein Binding
Protein Structure, Tertiary
Proteins - metabolism
SH3 domain
Software
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
src Homology Domains
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Summary:Here, we present a new approach for protein ligand screening based on the use of limited exoproteolysis coupled to MALDI-TOF mass spectrometry, combined with computational modelling and prediction of binding energies. As a test for this combined approach, we have screened a combinatorial library containing 8000 peptides (organized in 60 peptide samples) based on positional scanning format. This library is attached to a poly-Pro framework, and screened against the Abl-SH3 domain. The results obtained demonstrated the validity of the experimental and theoretical approaches in identifying better ligands and in rationalizing the changes in affinity. Exoproteolysis coupled to MALDI-TOF mass spectrometry could be used to screen complex libraries in a fast and efficient way.
ISSN:0022-2836
1089-8638
DOI:10.1016/S0022-2836(03)00664-8