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Molecular Dynamics—Solvated Interaction Energy Studies of Protein–Protein Interactions: The MP1–p14 Scaffolding Complex

Cui, Qizhi, Sulea, Traian, Schrag, Joseph D., Munger, Christine, Hung, Ming-Ni, Naïm, Marwen, Cygler, Miroslaw, Purisima, Enrico O.·2008·Journal of Molecular Biology

DOI 10.1016/j.jmb.2008.04.035

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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.

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Authors: Cui, Q., Sulea, T., Schrag, J. D., Munger, C., Hung, M.-N., Naïm, M., Cygler, M., & Purisima, E. O.
Affiliations: Biotechnology Research Institute (CA)
McGill University (CA)
Corresponding author: Purisima, Enrico O.
ORCID: Sulea, Traian
Purisima, Enrico O.
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 2008-06
Volume: 379
Issue: 4
Pages: 787-802
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1016/j.jmb.2008.04.035
OpenAlex: W2071919488
Cited by: 162
References: 56
Citations by year: 2026: 3 · 2025: 5 · 2024: 13 · 2023: 9 · 2022: 10 · 2021: 4 · 2020: 8 · 2019: 5 · 2018: 7 · 2017: 8 · 2016: 5 · 2015: 10 · 2014: 16 · 2013: 14 · 2012: 9
FWCI: 5.08
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Journal of Molecular Biology (publishedVersion)
PubMed (publishedVersion)
NPARC (submittedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
Keywords: protein-protein interaction, MAPK signaling, alanine scanning, MM-GBSA, yeast two-hybrid, small molecule hits
MeSH terms: Binding Sites, Models, Molecular, Proteins, Recombinant Proteins, Thermodynamics, Mutagenesis, Site-Directed, Crystallography, X-Ray, Amino Acid Substitution, Two-Hybrid System Techniques, MAP Kinase Signaling System, Multiprotein Complexes, Adaptor Proteins, Signal Transducing, Protein Interaction Domains and Motifs

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Molecular Dynamics—Solvated Interaction Energy Studies of Protein–Protein Interactions: The MP1–p14 Scaffolding Complex

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