3CPT

MP1-p14 Scaffolding complex

Summary for 3CPT

• Entry DOI: 10.2210/pdb3cpt/pdb
• Related: 2ZL1
• Descriptor: Mitogen-activated protein kinase kinase 1-interacting protein 1, Mitogen-activated protein-binding protein-interacting protein (3 entities in total)
• Functional Keywords: scaffold, complex, alpha/beta, endosome, membrane, lysosome, protein binding
• Biological source: Homo sapiens (Human); More
• Cellular location: Late endosome membrane; Peripheral membrane protein; Cytoplasmic side (By similarity): Q9UHA4; Late endosome membrane; Peripheral membrane protein; Cytoplasmic side: Q9JHS3
• Total number of polymer chains: 2
• Total formula weight: 30140.26

Authors

Schrag, J.D.,Cygler, M.,Munger, C.,Magloire, A. (deposition date: 2008-04-01, release date: 2008-07-01, Last modification date: 2024-05-29)

Primary citation

Cui, Q.,Sulea, T.,Schrag, J.D.,Munger, C.,Hung, M.N.,Naim, M.,Cygler, M.,Purisima, E.O.
Molecular dynamics-solvated interaction energy studies of protein-protein interactions: the MP1-p14 scaffolding complex.
J.Mol.Biol., 379:787-802, 2008

PubMed Abstract: Using the MP1-p14 scaffolding complex from the mitogen-activated protein kinase signaling pathway as model system, we explored a structure-based computational protocol to probe and characterize binding affinity hot spots at protein-protein interfaces. Hot spots are located by virtual alanine-scanning consensus predictions over three different energy functions and two different single-structure representations of the complex. Refined binding affinity predictions for select hot-spot mutations are carried out by applying first-principle methods such as the molecular mechanics generalized Born surface area (MM-GBSA) and solvated interaction energy (SIE) to the molecular dynamics (MD) trajectories for mutated and wild-type complexes. Here, predicted hot-spot residues were actually mutated to alanine, and crystal structures of the mutated complexes were determined. Two mutated MP1-p14 complexes were investigated, the p14(Y56A)-mutated complex and the MP1(L63A,L65A)-mutated complex. Alternative ways to generate MD ensembles for mutant complexes, not relying on crystal structures for mutated complexes, were also investigated. The SIE function, fitted on protein-ligand binding affinities, gave absolute binding affinity predictions in excellent agreement with experiment and outperformed standard MM-GBSA predictions when tested on the MD ensembles of Ras-Raf and Ras-RalGDS protein-protein complexes. For wild-type and mutant MP1-p14 complexes, SIE predictions of relative binding affinities were supported by a yeast two-hybrid assay that provided semiquantitative relative interaction strengths. Results on the MP1-mutated complex suggested that SIE predictions deteriorate if mutant MD ensembles are approximated by just mutating the wild-type MD trajectory. The SIE data on the p14-mutated complex indicated feasibility for generating mutant MD ensembles from mutated wild-type crystal structure, despite local structural differences observed upon mutation. For energetic considerations, this would circumvent costly needs to produce and crystallize mutated complexes. The sensitized protein-protein interface afforded by the p14(Y56A) mutation identified here has practical applications in screening-based discovery of first-generation small-molecule hits for further development into specific modulators of the mitogen-activated protein kinase signaling pathway.

PubMed: 18479705
DOI: 10.1016/j.jmb.2008.04.035

Experimental method

X-RAY DIFFRACTION (1.9 Å)