Primary Citation PubMed: 23340338
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PUMA binding induces partial unfolding within BCL-xL to disrupt p53 binding and promote apoptosis.
(2013) Nat Chem Biol 9
PubMed: 23340338 | PubMedCentral: PMC3683295 | DOI: 10.1038/nchembio.1166
Database Depositions The atomic coordinates (or 20 lowest-energy structures) and structure factors (or NMR assignments) for the X-ray-derived (NMR-derived) models described in this manuscript have bee... deposited in the PDB (NMR assignments deposited in the BioMAgRes Databank): solution structure of apo BCL-xLΔLΔC: 2M03 (BMRB #18792); solution structure of monomeric, 1:1 BCL-xLΔLΔC·PUMA BH3 complex: 2M04 (BMRB #18793); and X-ray structure of domain-swapped, 2:2 dimeric BCL-xLΔC·PUMA BH3 complex: 4HNJ.
Publication Year: 2013
Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces.
(2014) PLoS Comput Biol 10
PubMed: 25275445 | PubMedCentral: PMC4183424 | DOI: 10.1371/journal.pcbi.1003872
The accession codes are 1z1m, 1ycr, 1rv1, 2lzg, 1iu2, 1rgr, 2kpk, 2kpl, 4a53, 4a54, 2m03, 2yxj, and 1bxl.
Table S9 Binding site hit rates and bound state similarity coefficients (BSSCs) for the ensemble of ligand-free Bcl-xL structures (PDB ID 2m03).
Mapping the NMR ensemble of ligand-free structures (PDB ID 2m03), the interaction site with the BAK peptide occurs as the top ranked binding site in only 6 of the 20 structures, and a different site is ranked first in the highest number of times (in 9 of the 20 structures).
g005 Figure 5 Binding site hit rates (blue columns, left axis) and BSSC (bound-state similarity coefficient) values (red lines, right axis) for the Bcl-xL ensemble (PDB ID 2m03, 20 models).
B. Ligand-free Bcl-xL structure (2m03, green), with BAK peptide (cyan) from structure 1bxl, inhibitor ABT-737 (red sticks) from structure 2yxj, and the BIH SAHB peptide (magenta) binding to the close Bcl-xL homologue BAX (2k7w).
The top predicted binding site (brown mesh) overlaps with the BAK peptide and ABT-737 in 6 of the 20 structures in 2m03, and with the BIH SAHB site in 9 of the 20 structures.
Protein-Protein Complex Receptor/Ligand Structures in PDB Model with highest BSSC c R d Unbound a Bound (Ligand) b MDM2/p53 1z1m (24) 1ycr (p53 peptide) Model 19 (2 nd ) 0.78 1rv1 (Nutlin-2) Model 19 (2 nd) 0.72 2lzg (piperidinone) Model 9 (1 st ) 0.77 PSD-95 PDZ1/CRIPT 1iu2 (50) 1rgr (peptide) Model 23 (1 st ) 0.92 MAGI-1 PDZ1/HPV16 E6 2kpk (20) 2kpl (peptide) Model 9 (3 rd ) 0.77 EDC3/DCP2 4a53 (20) 4a54 (peptide) Model 16 (2 nd ) 0.60 Bcl-xL/BAK, BAX, PUMA, BAD, etc. 2m03 (20) 2yxj (ABT-737) Model 3 (1 st ) 0.85 1bxl (BAK peptide) Model 3 (1 st ) 0.72 a The number in parenthesis indicates the number of structures in the NMR ensemble.
Publication Year: 2014
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