6GWX | pdb_00006gwx

Stabilising and Understanding a Miniprotein by Rational Design.

• PDB DOI: https://doi.org/10.2210/pdb6GWX/pdb
• BMRB: 34295

• Classification: STRUCTURAL PROTEIN
• Organism(s): Streptococcus mutans
• Mutation(s): No 


• Deposited: 2018-06-26 Released: 2019-07-10 
• Deposition Author(s): Porter Goff, K.L., Williams, C., Baker, E.G., Nicol, D., Samphire, J.L., Zieleniewski, F.L., Crump, M.P., Woolfson, D.N.
• Funding Organization(s): Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 250 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

Stabilizing and Understanding a Miniprotein by Rational Redesign.

Porter Goff, K.L., Nicol, D., Williams, C., Crump, M.P., Zieleniewski, F., Samphire, J.L., Baker, E.G., Woolfson, D.N.

(2019) Biochemistry 58: 3060-3064

• PubMed: 31251570 
• DOI: https://doi.org/10.1021/acs.biochem.9b00067
• Primary Citation Related Structures: 
  6GWX


• PubMed Abstract: 
  

  Miniproteins reduce the complexity of the protein-folding problem allowing systematic studies of contributions to protein folding and stabilization. Here, we describe the rational redesign of a miniprotein, PPα, comprising a polyproline II helix, a loop, and an α helix. The redesign provides a de novo framework for interrogating noncovalent interactions. Optimized PPα has significantly improved thermal stability with a midpoint unfolding temperature ( T _M ) of 51 °C. Its nuclear magnetic resonance structure indicates a density of stabilizing noncovalent interactions that is higher than that of the parent peptide, specifically an increased number of CH-π interactions. In part, we attribute this to improved long-range electrostatic interactions between the two helical elements. We probe further sequence-stability relationships in the miniprotein through a series of rational mutations.

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Organizational Affiliation: 
• School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K.
BrisSynBio , University of Bristol , Life Sciences Building, Tyndall Avenue , Bristol BS8 1TQ , U.K.
School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , U.K.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 3.79 kDa 
• Atom Count: 269 
• Modeled Residue Count: 36 
• Deposited Residue Count: 36 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Optimised PPa-TYR	A	36	Streptococcus mutans	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 250 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Porter Goff, K.L., Williams, C., Baker, E.G., Nicol, D., Samphire, J.L., Zieleniewski, F.L., Crump, M.P., Woolfson, D.N.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/G036764/1

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2019-07-24
  Changes: Data collection, Database references
• Version 1.2: 2023-06-14
  Changes: Database references, Other
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary