Probing the role of packing specificity in protein design

Abstract

By using a protein-design algorithm that quantitatively considers side-chain packing, the effect of specific steric constraints on protein design was assessed in the core of the streptococcal protein Gβ1 domain. The strength of packing constraints used in the design was varied, resulting in core sequences that reflected differing amounts of packing specificity. The structural flexibility and stability of several of the designed proteins were experimentally determined and showed a trend from well-ordered to highly mobile structures as the degree of packing specificity in the design decreased. This trend both demonstrates that the inclusion of specific packing interactions is necessary for the design of native-like proteins and defines a useful range of packing specificity for the design algorithm. In addition, an analysis of the modeled protein structures suggested that penalizing for exposed hydrophobic surface area can improve design performance.

Submission Details

ID: 26hCGiZi

Submitter: Admin Admin

Submission Date: July 31, 2017, 11:46 a.m.

Version: 2

Publication Details
Dahiyat BI;Mayo SL,Proc Natl Acad Sci U S A (1997) Probing the role of packing specificity in protein design. PMID:9294182
Additional Information

Study Summary

Number of data points 10
Proteins Protein Gβ1
Unique complexes 5
Assays/Quantities/Protocols Experimental Assay: Tm, α = 0.85 ; Experimental Assay: Tm, α = 0.70 ; Experimental Assay: Tm, α = 0.90 ; Experimental Assay: Tm, α = 1.07 ; Computational Protocol: Side chain volume, α = 0.85 ; Computational Protocol: Side chain volume, α = 0.90 ; Computational Protocol: Side chain volume, α = 1.07 ; Computational Protocol: Side chain volume, α = 0.70
Libraries Stability and residue volume of GMEC predicted by core design, α = 0.85; also for 85W43V ; Stability and residue volume of GMEC predicted by core design, α = 0.70 ; Stability and residue volume of GMEC predicted by core design, α = 0.90 ; Stability and residue volume of GMEC predicted by core design, α = 1.07

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)