Evolutionary protein stabilization in comparison with computational design.


Abstract

Two major strategies are currently used for stabilizing proteins: in vitro evolution and computational design. Here, we used gene libraries of the beta1 domain of the streptococcal protein G (Gbeta1) and Proside, an in vitro selection method, to identify stabilized variants of this protein. In the Gbeta1 libraries, the codons for the four boundary positions 16, 18, 25, and 29 were randomized. Many Gbeta1 variants with strongly increased thermal stabilities were found in 11 selections performed with five independent libraries. Previously, Mayo and co-workers used computational design to stabilize Gbeta1 by sequence optimization at the same positions. Their best variant ranked third within the panel of the selected variants. None of the ten computed sequences was found in the Proside selections, because several computed residues for positions 18 and 29 were not optimal for stability. Study holds ProTherm entries: 18767, 18768, 18769, 18770, 18771, 18772, 18773, 18774, 18775, 18776, 18777, 18778, 18779, 18780, 18781, 18782, 18783, 18784, 18785, 18786, 18787, 18788, 18789, 18790, 18791, 18792, 18793, 18794, 18795, 18796, 18797, 18798, 18799, 18800, 18801, 18802, 18803, 18804, 18805, 18806, 18807, 18808, 18809, 18810, 18811, 18812, 18813, 18814, 18815, 18816, 18817, 18818, 18819, 18820, 18821, 18822, 18823, 18824, 18825, 18826 Extra Details: protein stability; in vitro selection; phage display; computational protein design; streptococcal protein G

Submission Details

ID: ouR2hhr34

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:50 p.m.

Version: 1

Publication Details
Wunderlich M;Martin A;Staab CA;Schmid FX,J. Mol. Biol. (2005) Evolutionary protein stabilization in comparison with computational design. PMID:16051264
Additional Information

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)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1EM7 2000-03-16T00:00:00+0000 2.0 HELIX VARIANT OF THE B1 DOMAIN FROM STREPTOCOCCAL PROTEIN G
1GB1 1991-05-15T00:00:00+0000 0 A NOVEL, HIGHLY STABLE FOLD OF THE IMMUNOGLOBULIN BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G
1IGC 1994-08-05T00:00:00+0000 2.6 IGG1 FAB FRAGMENT (MOPC21) COMPLEX WITH DOMAIN III OF PROTEIN G FROM STREPTOCOCCUS
1IGD 1994-08-05T00:00:00+0000 1.1 THE THIRD IGG-BINDING DOMAIN FROM STREPTOCOCCAL PROTEIN G: AN ANALYSIS BY X-RAY CRYSTALLOGRAPHY OF THE STRUCTURE ALONE AND IN A COMPLEX WITH FAB
1LE3 2002-04-09T00:00:00+0000 0 NMR Structure of Tryptophan Zipper 4: A Stable Beta-Hairpin Peptide Based on the C-terminal Hairpin of the B1 Domain of Protein G
1MPE 2002-09-12T00:00:00+0000 0 Ensemble of 20 structures of the tetrameric mutant of the B1 domain of streptococcal protein G
1MVK 2002-09-25T00:00:00+0000 2.5 X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G
1PGA 1993-11-23T00:00:00+0000 2.07 TWO CRYSTAL STRUCTURES OF THE B1 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G AND COMPARISON WITH NMR
1PGB 1993-11-23T00:00:00+0000 1.92 TWO CRYSTAL STRUCTURES OF THE B1 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCCOCAL PROTEIN G AND COMPARISON WITH NMR
1PGX 1992-04-03T00:00:00+0000 1.66 THE 1.66 ANGSTROMS X-RAY STRUCTURE OF THE B2 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G AND COMPARISON TO THE NMR STRUCTURE OF THE B1 DOMAIN

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Immunoglobulin G-binding protein G P06654 SPG1_STRSG
100.0 Immunoglobulin G-binding protein G P19909 SPG2_STRSG