PDBsum entry 2zl1

Protein binding

PDB id: 2zl1

Contents

Protein chains

119 a.a. *

116 a.a. *

Waters ×110

* Residue conservation analysis

PDB id:

2zl1

Name:

Protein binding

Title:

Mp1-p14 scaffolding complex

Structure:

Mitogen-activated protein kinase kinase 1-interacting protein 1. Chain: a. Synonym: mek-binding partner 1, mp1. Engineered: yes. Mutation: yes. Mitogen-activated protein-binding protein-interacting protein. Chain: b.

Source:

Homo sapiens. Human. Gene: map2k1ip1. Expressed in: escherichia coli. Mus musculus. Mouse. Gene: mapbpip.

Resolution:

2.00Å R-factor: 0.205 R-free: 0.256

Authors:

J.D.Schrag,M.Cygler,C.Munger,A.Magloire

Key ref:

Q.Cui et al. (2008). Molecular dynamics-solvated interaction energy studies of protein-protein interactions: the MP1-p14 scaffolding complex. J Mol Biol, 379, 787-802. PubMed id: 18479705

Date:

02-Apr-08 Release date: 24-Jun-08

Protein chain

Q9UHA4  (LTOR3_HUMAN) -  Ragulator complex protein LAMTOR3 from Homo sapiens

Seq: 124 a.a.

Struc: 119 a.a.*

Protein chain

Q9JHS3  (LTOR2_MOUSE) -  Ragulator complex protein LAMTOR2 from Mus musculus

Seq: 125 a.a.

Struc: 116 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.?

J Mol Biol 379:787-802 (2008)

PubMed id: 18479705

Molecular dynamics-solvated interaction energy studies of protein-protein interactions: the MP1-p14 scaffolding complex.

Q.Cui, T.Sulea, J.D.Schrag, C.Munger, M.N.Hung, M.Naïm, M.Cygler, E.O.Purisima.

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.