4IWW : Computational Design of an Unnatural Amino Acid Metalloprotein with Atomic Level Accuracy

  • Jill M. Bolduc (Contributor)
  • Sagar D. Khare (Contributor)
  • Jeremy Mills (Contributor)
  • David Baker (Contributor)
  • David Baker (Contributor)
  • Barry L. Stoddard (Contributor)
  • Jeremy Mills (Contributor)

Dataset

Description

Experimental Technique/Method:X-RAY DIFFRACTION
Resolution:2.3
Classification:METAL BINDING PROTEIN
Release Date:2013-08-21
Deposition Date:2013-01-24
Revision Date:2013-09-04#2013-09-25
Molecular Weight:60530.61
Macromolecule Type:Protein
Residue Count:516
Atom Site Count:4035
DOI:10.2210/pdb4iww/pdb

Abstract:
Genetically encoded unnatural amino acids could facilitate the design of proteins and enzymes of novel function, but correctly specifying sites of incorporation and the identities and orientations of surrounding residues represents a formidable challenge. Computational design methods have been used to identify optimal locations for functional sites in proteins and design the surrounding residues but have not incorporated unnatural amino acids in this process. We extended the Rosetta design methodology to design metalloproteins in which the amino acid (2,2'-bipyridin-5yl)alanine (Bpy-Ala) is a primary ligand of a bound metal ion. Following initial results that indicated the importance of buttressing the Bpy-Ala amino acid, we designed a buried metal binding site with octahedral coordination geometry consisting of Bpy-Ala, two protein-based metal ligands, and two metal-bound water molecules. Experimental characterization revealed a Bpy-Ala-mediated metalloprotein with the ability to bind divalent cations including Co(2+), Zn(2+), Fe(2+), and Ni(2+), with a Kd for Zn(2+) of ∼40 pM. X-ray crystal structures of the designed protein bound to Co(2+) and Ni(2+) have RMSDs to the design model of 0.9 and 1.0 Å respectively over all atoms in the binding site.
Date made availableAug 21 2013
PublisherRCSB-PDB

Cite this