PDBsum entry 4d8h

De novo protein

PDB id: 4d8h

Contents

Protein chain

124 a.a.

Ligands

TRS

SO4

Waters ×177

PDB id:

4d8h

Name:

De novo protein

Title:

Crystal structure of symfoil-4p/pv2: de novo designed beta-trefoil architecture with symmetric primary structure, primitive version 2 (6xleu / pv1)

Structure:

De novo protein. Chain: a. Engineered: yes. Other_details: f22l/f44l/f64l/f85l/f108l/f132l hissymfoil-4p/pv1 (6xleu pv1) de novo designed beta-trefoil architecture with symmetric primary structure enriched for pre-biotic amino acids

Source:

Synthetic. Organism_taxid: 32630. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: synthetic sequence derived from human acidic fibroblast growth factor with symmetric deconstruction method and enriched for pre-biotic amino acids.

Resolution:

1.90Å R-factor: 0.167 R-free: 0.214

Authors:

M.Blaber,L.Longo

Key ref:

L.M.Longo et al. (2013). Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein. Proc Natl Acad Sci U S A, 110, 2135-2139. PubMed id: 23341608

Date:

10-Jan-12 Release date: 16-Jan-13

Protein chain

No UniProt id for this chain

Struc: 124 a.a.

Proc Natl Acad Sci U S A 110:2135-2139 (2013)

PubMed id: 23341608

Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein.

L.M.Longo, J.Lee, M.Blaber.

ABSTRACT

A compendium of different types of abiotic chemical syntheses identifies a consensus set of 10 "prebiotic" α-amino acids. Before the emergence of biosynthetic pathways, this set is the most plausible resource for protein formation (i.e., proteogenesis) within the overall process of abiogenesis. An essential unsolved question regarding this prebiotic set is whether it defines a "foldable set"-that is, does it contain sufficient chemical information to permit cooperatively folding polypeptides? If so, what (if any) characteristic properties might such polypeptides exhibit? To investigate these questions, two "primitive" versions of an extant protein fold (the β-trefoil) were produced by top-down symmetric deconstruction, resulting in a reduced alphabet size of 12 or 13 amino acids and a percentage of prebiotic amino acids approaching 80%. These proteins show a substantial acidification of pI and require high salt concentrations for cooperative folding. The results suggest that the prebiotic amino acids do comprise a foldable set within the halophile environment.