Analysis of ligand binding to a ribose biosensor using site-directed mutagenesis and fluorescence spectroscopy.


Abstract

Computational design of proteins with altered ligand specificity is an emerging method for the creation of new biosensing systems. In this work, we investigated the outcome of site-directed mutagenesis on the Escherichia coli ribose binding protein (RBP), which is frequently used as a design scaffold for computational searches. A ribose biosensor was first constructed whereby an environmentally sensitive fluorescent probe was covalently attached to RBP at position S265C. This protein conjugate displayed a 54% decrease in emission intensity upon the addition of saturating ribose concentrations and exhibited an apparent dissociation constant (K(d) ) of 3.4 microM. Site-directed mutants within the RBP binding pocket were created and examined for ribose binding ability and overall structural stability. Because as many as 12 mutations are needed to alter ligand specificity in RBP, we measured the effect of single and multiple alanine mutations on stability and signal transduction potential of the ribose biosensor. Single alanine mutations had significant impact on both stability and signaling. Mutations of N190A and F214A each produced melting temperatures >8 degrees C below those observed for the wild-type protein. Residue Q235, located in the hinge region of RBP, appeared to be a hot spot for global protein stability as well. Additional single alanine mutations demonstrated as much as 200-fold increase in apparent K(d) but retained overall protein stability. The data collected from this study may be incorporated into design algorithms to help create more stable biosensors and optimize signal transduction properties for a variety of important analytes. Study holds ProTherm entries: 22848, 22849, 22850, 22851, 22852, 22853, 22854, 22855, 22856, 22857, 22858, 22859, 22860, 22861, 22862, 22863, 22864, 22865, 22866, 22867, 22868, 22869, 22870, 22871, 22872, 22873, 22874, 22875, 22876, 22877, 22878, 22879, 22880, 22881, 22882, 22883 Extra Details: mutants were constructed with L265C background and labeled with ABD-F. biosensor; periplasmic binding proteins; ribose binding protein; fluorescence

Submission Details

ID: v9BaQSVg

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:53 p.m.

Version: 1

Publication Details
Vercillo NC;Herald KJ;Fox JM;Der BS;Dattelbaum JD,Protein Sci. (2007) Analysis of ligand binding to a ribose biosensor using site-directed mutagenesis and fluorescence spectroscopy. PMID:17242374
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
2DRI 1995-01-26 1.6 PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS
2GX6 2007-03-20 1.97 Rational stabilization of E. coli ribose binding protein
1DRK 1995-01-26 2.0 PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE-BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS
1BA2 1998-07-15 2.1 D67R MUTANT OF D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI
1DBP 1994-05-31 2.2 IDENTICAL MUTATIONS AT CORRESPONDING POSITIONS IN TWO HOMOLOGOUS PROTEINS WITH NON-IDENTICAL EFFECTS
1URP 1998-06-17 2.3 D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI
1DRJ 1995-01-26 2.5 PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE-BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
97.3 Ribose import binding protein RbsB P0A2C5 RBSB_SALTY
97.3 Ribose import binding protein RbsB P0A2C6 RBSB_SALTI
100.0 Ribose import binding protein RbsB P02925 RBSB_ECOLI