Stability enhancement of cytochrome c through heme deprotonation and mutations.
Abstract
The chemical denaturation of Pseudomonas aeruginosa cytochrome c(551) variants was examined at pH 5.0 and 3.6. All variants were stabilized at both pHs compared with the wild-type. Remarkably, the variants carrying the F34Y and/or E43Y mutations were more stabilized than those having the F7A/V13M or V78I ones at pH 5.0 compared with at pH 3.6 by ~3.0-4.6 kJ/mol. Structural analyses predicted that the side chains of introduced Tyr-34 and Tyr-43 become hydrogen donors for the hydrogen bond formation with heme 17-propionate at pH 5.0, but less efficiently at pH 3.6, because the propionate is deprotonated at the higher pH. Our results provide an insight into a stabilization strategy for heme proteins involving variation of the heme electronic state and introduction of appropriate mutations. Study holds ProTherm entries: 24920, 24921, 24922, 24923, 24924, 24925, 24926, 24927, 24928, 24929, 24930, 24931, 24932, 24933, 24934, 24935, 24936, 24937, 24938, 24939 Extra Details: Circular dichroism spectroscopy; Cytochrome c; Hydrogen bond; Protein stability; Heme propionate
Submission Details
ID: FB65dEC54
Submitter: Connie Wang
Submission Date: April 24, 2018, 8:55 p.m.
Version: 1
Publication Details
Sonoyama T;Hasegawa J;Uchiyama S;Nakamura S;Kobayashi Y;Sambongi Y,Biophys. Chem. (2009) Stability enhancement of cytochrome c through heme deprotonation and mutations. PMID:18957274Additional Information
Study Summary
| Number of data points | 78 |
| Proteins | Cytochrome c-551 ; Cytochrome c-551 |
| Unique complexes | 10 |
| Assays/Quantities/Protocols | Experimental Assay: Cm pH:3.6 ; Experimental Assay: m pH:3.6 ; Experimental Assay: dG_H2O pH:3.6 ; Experimental Assay: Cm pH:5.0 ; Experimental Assay: m pH:5.0 ; Experimental Assay: dG_H2O pH:5.0 ; Derived Quantity: ddG_H2O pH:3.6 ; Derived Quantity: ddG_H2O pH:5.0 |
| Libraries | Mutations for sequence EDPEVLFKNKGCVACHAIDTKMVGPAYKDVAAKFAGQAGAEAELAQRIKNGSQGVWGPIPMPPNAVSDDEAQTLAKWVLSQK |
Structure view and single mutant data analysis
Study data
| 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 |
|---|---|---|---|
| 1DVV | 2000-01-22T00:00:00+0000 | 0 | SOLUTION STRUCTURE OF THE QUINTUPLE MUTANT OF CYTOCHROME C-551 FROM PSEUDOMONAS AERUGINOSA |
| 2EXV | 2005-11-09T00:00:00+0000 | 1.86 | Crystal structure of the F7A mutant of the cytochrome c551 from Pseudomonas aeruginosa |
| 2PAC | 1993-05-05T00:00:00+0000 | 0 | SOLUTION STRUCTURE OF FE(II) CYTOCHROME C551 FROM PSEUDOMONAS AERUGINOSA AS DETERMINED BY TWO-DIMENSIONAL 1H NMR |
| 351C | 1981-07-20T00:00:00+0000 | 1.6 | STRUCTURE OF CYTOCHROME C551 FROM P. AERUGINOSA REFINED AT 1.6 ANGSTROMS RESOLUTION AND COMPARISON OF THE TWO REDOX FORMS |
| 3X39 | 2015-01-16T00:00:00+0000 | 1.5 | Domain-swapped dimer of Pseudomonas aeruginosa cytochrome c551 |
| 451C | 1981-07-20T00:00:00+0000 | 1.6 | STRUCTURE OF CYTOCHROME C551 FROM P. AERUGINOSA REFINED AT 1.6 ANGSTROMS RESOLUTION AND COMPARISON OF THE TWO REDOX FORMS |
| 5XEC | 2017-04-04T00:00:00+0000 | 1.1 | Heterodimer constructed from PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins |
| 5XEC | 2017-04-04T00:00:00+0000 | 1.1 | Heterodimer constructed from PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins |
| 5XED | 2017-04-04T00:00:00+0000 | 1.55 | Heterodimer constructed from M61A PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins |
| 5XED | 2017-04-04T00:00:00+0000 | 1.55 | Heterodimer constructed from M61A PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins |
Relevant UniProtKB Entries
| Percent Identity | Matching Chains | Protein | Accession | Entry Name |
|---|---|---|---|---|
| 100.0 | Cytochrome c-551 | P00099 | CY551_PSEAE |