PDBsum entry 4hop

Membrane protein/oxidoreductase

PDB id: 4hop

Contents

Protein chains

87 a.a.

120 a.a.

Waters ×501

PDB id:

4hop

Name:

Membrane protein/oxidoreductase

Title:

Crystal structure of the computationally designed nnos-syntrophin complex

Structure:

Alpha-1-syntrophin. Chain: a, c, e. Fragment: pdz domain (residues 77-162). Synonym: 59 kda dystrophin-associated protein a1 acidic component 1, syntrophin-1. Engineered: yes. Mutation: yes. Nitric oxide synthase, brain. Chain: b, d, f.

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: snt1, snta1. Expressed in: escherichia coli. Expression_system_taxid: 469008. Rattus norvegicus. Brown rat,rat,rats. Organism_taxid: 10116.

Resolution:

2.29Å R-factor: 0.226 R-free: 0.273

Authors:

I.M.Harwood,C.Melero,N.Ollikainen,T.Kortemme

Key ref:

C.Melero et al. (2014). Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition. Proc Natl Acad Sci U S A, 111, 15426-15431. PubMed id: 25313039 DOI: 10.1073/pnas.1410624111

Date:

22-Oct-12 Release date: 06-Nov-13

Protein chains

Q61234  (SNTA1_MOUSE) -  Alpha-1-syntrophin from Mus musculus

Seq: 503 a.a.

Struc: 87 a.a.*

Protein chains

P29476  (NOS1_RAT) -  Nitric oxide synthase 1 from Rattus norvegicus

Seq: 1429 a.a.

Struc: 120 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains B, D, F: E.C.1.14.13.39 - nitric-oxide synthase (NADPH).
• Reaction: 2 L-arginine + 3 NADPH + 4 O2 + H⁺ = 2 L-citrulline + 2 nitric oxide + 3 NADP⁺ + 4 H2O

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.1410624111

Proc Natl Acad Sci U S A 111:15426-15431 (2014)

PubMed id: 25313039

Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition.

C.Melero, N.Ollikainen, I.Harwood, J.Karpiak, T.Kortemme.

ABSTRACT

Reengineering protein-protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of "second-site suppressors," where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein-protein interfaces. To extend this approach, it would be advantageous to be able to "transplant" existing engineered and experimentally validated specificity changes to other homologous protein-protein complexes. Here, we test this strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain-peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein-protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. Although the context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein-protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context.