Design of Peptoid Analogue Dimers and Measure of Their Affinity for Grb2 SH3 Domains
- 21 May 2004
- journal article
- Published by American Chemical Society (ACS) in Biochemistry
- Vol. 43 (23) , 7336-7344
- https://doi.org/10.1021/bi030252n
Abstract
This paper describes the design of the highest affinity ligands for Grb2 SH3 domains reported so far. These compounds were designed by combining N-alkyl amino acid incorporation in a proline-rich sequence with subsequent dimerization of the peptoid sequence based on structural data and molecular modeling. Optimization of the linker size is discussed, and the N-alkyl amino acid incorporation into both monomeric halves is reported. Because the affinity for Grb2 of the optimized compounds was too high to be measured using the fluorescent modifications that they induce on the Grb2 emission spectrum, a competition assay was developed. In this test, Grb2 is pulled down from a cellular extract by the initial VPPPVPPRRR peptide bound to Sepharose beads. In the presence of competitors, the test quantifies the amount of Grb2 displaced from the beads. It has enabled us to determine a Ki value in the 10-10 M range for the highest affinity Grb2 peptoid analogue dimer.Keywords
This publication has 15 references indexed in Scilit:
- Design of N-substituted Peptomer Ligands for EVH1 DomainsJournal of Biological Chemistry, 2003
- Crystal structures of the SH2 domain of grb2: highlight on the binding of a new high-affinity inhibitorJournal of Molecular Biology, 2002
- GRB2 Links Signaling to Actin Assembly by Enhancing Interaction of Neural Wiskott-Aldrich Syndrome Protein (N-WASp) with Actin-related Protein (ARP2/3) ComplexJournal of Biological Chemistry, 2000
- Solution structure of the Grb2 N-terminal SH3 domain complexed with a ten-residue peptide derived from SOS: direct refinement against NOEs, J-couplings and 1H and 13C chemical shiftsJournal of Molecular Biology, 1997
- Grb2 SH3 binding to peptides from Sos: evaluation of a general model for SH3-ligand interactionsChemistry & Biology, 1995
- Discovery of Nanomolar Ligands for 7-Transmembrane G-Protein-Coupled Receptors from a Diverse N-(Substituted)glycine Peptoid LibraryJournal of Medicinal Chemistry, 1994
- Grb2 mediates the EGF-dependent activation of guanine nucleotide exchange on RasNature, 1993
- The SH2 and SH3 domains of mammalian Grb2 couple the EGF receptor to the Ras activator mSos1Nature, 1993
- Hot gas and dark matter in a compact galaxy groupNature, 1993
- An all atom force field for simulations of proteins and nucleic acidsJournal of Computational Chemistry, 1986