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Title: Molecular Dynamics - Solvated Interaction Energy Studies of Protein-Protein Interactions; The MP1-p14 Scaffolding Complex

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-hybridmore » 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.« less

Authors:
; ; ; ; ; ; ;
Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL) National Synchrotron Light Source
Sponsoring Org.:
Doe - Office Of Science
OSTI Identifier:
959727
Report Number(s):
BNL-82713-2009-JA
Journal ID: ISSN 0022-2836; JMOBAK; TRN: US201016%%871
DOE Contract Number:  
DE-AC02-98CH10886
Resource Type:
Journal Article
Journal Name:
Journal of Molecular Biology
Additional Journal Information:
Journal Volume: 379; Journal Issue: 4; Journal ID: ISSN 0022-2836
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; AFFINITY; CRYSTAL STRUCTURE; HOT SPOTS; MUTANTS; MUTATIONS; PHOSPHOTRANSFERASES; PROTEINS; RESIDUES; SURFACE AREA; TRAJECTORIES; YEASTS; national synchrotron light source

Citation Formats

Cui, Q, Sulea, T, Schrag, J, Munger, C, Hung, M, Naim, M, Cygler, M, and Purisima, E. Molecular Dynamics - Solvated Interaction Energy Studies of Protein-Protein Interactions; The MP1-p14 Scaffolding Complex. United States: N. p., 2008. Web. doi:10.1016/j.jmb.2008.04.035.
Cui, Q, Sulea, T, Schrag, J, Munger, C, Hung, M, Naim, M, Cygler, M, & Purisima, E. Molecular Dynamics - Solvated Interaction Energy Studies of Protein-Protein Interactions; The MP1-p14 Scaffolding Complex. United States. https://doi.org/10.1016/j.jmb.2008.04.035
Cui, Q, Sulea, T, Schrag, J, Munger, C, Hung, M, Naim, M, Cygler, M, and Purisima, E. Tue . "Molecular Dynamics - Solvated Interaction Energy Studies of Protein-Protein Interactions; The MP1-p14 Scaffolding Complex". United States. https://doi.org/10.1016/j.jmb.2008.04.035.
@article{osti_959727,
title = {Molecular Dynamics - Solvated Interaction Energy Studies of Protein-Protein Interactions; The MP1-p14 Scaffolding Complex},
author = {Cui, Q and Sulea, T and Schrag, J and Munger, C and Hung, M and Naim, M and Cygler, M and Purisima, E},
abstractNote = {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.},
doi = {10.1016/j.jmb.2008.04.035},
url = {https://www.osti.gov/biblio/959727}, journal = {Journal of Molecular Biology},
issn = {0022-2836},
number = 4,
volume = 379,
place = {United States},
year = {2008},
month = {1}
}