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 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.
Villanueva
Josep
J
Institut de Biotecnologia i de Biomedicina, Departament de Bioquímica, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
Fernández-Ballester
Gregorio
G
Querol
Enrique
E
Aviles
Francesc X
FX
Serrano
Luis
L
D000465:Algorithms; D003373:Coumaric Acids / Q000737:chemistry; D015723:Gene Library; D006801:Humans; D008024:Ligands; D013058:Mass Spectrometry; D008958:Models, Molecular; D019151:Peptide Library; D010455:Peptides / Q000737:chemistry; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000378:metabolism*; D012984:Software; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D018909:src Homology Domains
D003373:Coumaric Acids; D008024:Ligands; D019151:Peptide Library; D010455:Peptides; D011506:Proteins; C073734:sinapinic acid