Contribution of amino acid substitutions at two different interior positions to the conformational stability of human lysozyme.


Abstract

To elucidate correlative relationships between structural change and thermodynamic stability in proteins, a series of mutant human lysozymes modified at two buried positions (Ile56 and Ile59) were examined. Their thermodynamic parameters of denaturation and crystal structures were studied by calorimetry and X-ray crystallography. The mutants at positions 56 and 59 exhibited different responses to a series of amino acid substitutions. The changes in stability due to substitutions showed a linear correlation with changes in hydrophobicity of substituted residues, having different slopes at each mutation site. However, the stability of each mutant was found to be represented by a unique equation involving physical properties calculated from mutant structures. By fitting present and previous stability data for mutant human lysozymes substituted at various positions to the equation, the magnitudes of the hydrophobicity of a carbon atom and the hydrophobicity of nitrogen and neutral oxygen atoms were found to be 0.178 and -0.013 kJ/mol.A(2), respectively. It was also found that the contribution of a hydrogen bond with a length of 3.0 A to protein stability was 5.1 kJ/mol and the entropy loss of newly introduction of a water molecules was 7.8 kJ/mol. Study holds ProTherm entries: 7046, 7047, 7048, 7049, 7050, 7051, 7052, 7053, 7054, 7055, 7056, 7057, 7058, 7059, 7060, 7061, 7062, 7063, 7064, 7065, 7066, 7067, 7068, 7069, 7070, 7071, 7072, 7073, 7074, 7075, 7076, 7077, 7078, 7079, 7080, 7081, 7082, 7083, 7084, 7085, 7086, 7087, 7088, 7089, 7090, 7091, 7092, 7093, 7094, 7095, 7096, 7097, 7098, 7099, 7100, 7101, 7102, 7103, 7104, 7105, 7106, 7107, 7108, 7109, 7110, 7111, 7112, 7113, 7114, 7115, 7116, 7117, 14376, 14377, 14378, 14379, 14380, 14381, 14382, 14383, 14384, 14385, 14386, 14387, 14388, 14389, 14390 Extra Details: calorimetry; human lysozyme; mutant protein; protein stability;,X-ray structural analysis

Submission Details

ID: eofBZniU3

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:33 p.m.

Version: 1

Publication Details
Funahashi J;Takano K;Yamagata Y;Yutani K,Protein Eng. (1999) Contribution of amino acid substitutions at two different interior positions to the conformational stability of human lysozyme. PMID:10556244
Additional Information

Study Summary

Number of data points 271
Proteins Lysozyme C ; Lysozyme C
Unique complexes 17
Assays/Quantities/Protocols Experimental Assay: ddG ; Experimental Assay: dTm ; Experimental Assay: dCp pH:3.18 ; Experimental Assay: dHcal pH:3.18 ; Experimental Assay: Tm pH:3.18 ; Experimental Assay: dHvH pH:3.18 ; Experimental Assay: dCp pH:2.89 ; Experimental Assay: dHcal pH:2.89 ; Experimental Assay: Tm pH:2.89 ; Experimental Assay: dHvH pH:2.89 ; Experimental Assay: dCp pH:2.71 ; Experimental Assay: dHcal pH:2.71 ; Experimental Assay: Tm pH:2.71 ; Experimental Assay: dHvH pH:2.71 ; Experimental Assay: dCp pH:2.99 ; Experimental Assay: dHcal pH:2.99 ; Experimental Assay: Tm pH:2.99 ; Experimental Assay: dHvH pH:2.99 ; Experimental Assay: dCp pH:2.79 ; Experimental Assay: dHcal pH:2.79 ; Experimental Assay: Tm pH:2.79 ; Experimental Assay: dHvH pH:2.79 ; Experimental Assay: dCp pH:2.62 ; Experimental Assay: dHcal pH:2.62 ; Experimental Assay: Tm pH:2.62 ; Experimental Assay: dHvH pH:2.62 ; Experimental Assay: dCp pH:2.4 ; Experimental Assay: dHcal pH:2.4 ; Experimental Assay: Tm pH:2.4 ; Experimental Assay: dHvH pH:2.4 ; Experimental Assay: dCp pH:3.04 ; Experimental Assay: dHcal pH:3.04 ; Experimental Assay: Tm pH:3.04 ; Experimental Assay: dHvH pH:3.04 ; Experimental Assay: dCp pH:2.84 ; Experimental Assay: dHcal pH:2.84 ; Experimental Assay: Tm pH:2.84 ; Experimental Assay: dHvH pH:2.84 ; Experimental Assay: dCp pH:3.15 ; Experimental Assay: dHcal pH:3.15 ; Experimental Assay: Tm pH:3.15 ; Experimental Assay: dHvH pH:3.15 ; Experimental Assay: dCp pH:3.05 ; Experimental Assay: dHcal pH:3.05 ; Experimental Assay: Tm pH:3.05 ; Experimental Assay: dHvH pH:3.05 ; Experimental Assay: dCp pH:2.9 ; Experimental Assay: dHcal pH:2.9 ; Experimental Assay: Tm pH:2.9 ; Experimental Assay: dHvH pH:2.9 ; Experimental Assay: dCp pH:2.73 ; Experimental Assay: dHcal pH:2.73 ; Experimental Assay: Tm pH:2.73 ; Experimental Assay: dHvH pH:2.73 ; Experimental Assay: dCp pH:3.13 ; Experimental Assay: dHcal pH:3.13 ; Experimental Assay: Tm pH:3.13 ; Experimental Assay: dHvH pH:3.13 ; Experimental Assay: dCp pH:2.95 ; Experimental Assay: dHcal pH:2.95 ; Experimental Assay: Tm pH:2.95 ; Experimental Assay: dHvH pH:2.95 ; Experimental Assay: dCp pH:2.8 ; Experimental Assay: dHcal pH:2.8 ; Experimental Assay: Tm pH:2.8 ; Experimental Assay: dHvH pH:2.8 ; Experimental Assay: dCp pH:2.47 ; Experimental Assay: dHcal pH:2.47 ; Experimental Assay: Tm pH:2.47 ; Experimental Assay: dHvH pH:2.47 ; Experimental Assay: dCp pH:3.17 ; Experimental Assay: dHcal pH:3.17 ; Experimental Assay: Tm pH:3.17 ; Experimental Assay: dHvH pH:3.17 ; Experimental Assay: dCp pH:2.66 ; Experimental Assay: dHcal pH:2.66 ; Experimental Assay: Tm pH:2.66 ; Experimental Assay: dHvH pH:2.66 ; Experimental Assay: dCp pH:2.51 ; Experimental Assay: dHcal pH:2.51 ; Experimental Assay: Tm pH:2.51 ; Experimental Assay: dHvH pH:2.51 ; Experimental Assay: dCp pH:3.06 ; Experimental Assay: dHcal pH:3.06 ; Experimental Assay: Tm pH:3.06 ; Experimental Assay: dHvH pH:3.06 ; Experimental Assay: dCp pH:2.75 ; Experimental Assay: dHcal pH:2.75 ; Experimental Assay: Tm pH:2.75 ; Experimental Assay: dHvH pH:2.75 ; Experimental Assay: dCp pH:3.11 ; Experimental Assay: dHcal pH:3.11 ; Experimental Assay: Tm pH:3.11 ; Experimental Assay: dHvH pH:3.11 ; Experimental Assay: dCp pH:3.02 ; Experimental Assay: dHcal pH:3.02 ; Experimental Assay: Tm pH:3.02 ; Experimental Assay: dHvH pH:3.02 ; Experimental Assay: dCp pH:2.83 ; Experimental Assay: dHcal pH:2.83 ; Experimental Assay: Tm pH:2.83 ; Experimental Assay: dHvH pH:2.83 ; Experimental Assay: dCp pH:2.7 ; Experimental Assay: dHcal pH:2.7 ; Experimental Assay: Tm pH:2.7 ; Experimental Assay: dHvH pH:2.7 ; Experimental Assay: dCp pH:2.54 ; Experimental Assay: dHcal pH:2.54 ; Experimental Assay: Tm pH:2.54 ; Experimental Assay: dHvH pH:2.54 ; Experimental Assay: dCp pH:3.1 ; Experimental Assay: dHcal pH:3.1 ; Experimental Assay: Tm pH:3.1 ; Experimental Assay: dHvH pH:3.1 ; Experimental Assay: dCp pH:2.96 ; Experimental Assay: dHcal pH:2.96 ; Experimental Assay: Tm pH:2.96 ; Experimental Assay: dHvH pH:2.96 ; Experimental Assay: dCp pH:2.65 ; Experimental Assay: dHcal pH:2.65 ; Experimental Assay: Tm pH:2.65 ; Experimental Assay: dHvH pH:2.65 ; Experimental Assay: dCp pH:2.48 ; Experimental Assay: dHcal pH:2.48 ; Experimental Assay: Tm pH:2.48 ; Experimental Assay: dHvH pH:2.48
Libraries Mutations for sequence KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV

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
2MEA 1998-05-02T00:00:00+0000 2.2 CHANGES IN CONFORMATIONAL STABILITY OF A SERIES OF MUTANT HUMAN LYSOZYMES AT CONSTANT POSITIONS
1EQE 2000-04-04T00:00:00+0000 1.8 CRYSTAL STRUCTURES OF SALT BRIDGE MUTANTS OF HUMAN LYSOZYME
1OUI 1996-08-23T00:00:00+0000 1.8 CONTRIBUTION OF HYDROPHOBIC RESIDUES TO THE STABILITY OF HUMAN LYSOZYME: X-RAY STRUCTURE OF THE V93A MUTANT
1OUJ 1996-08-23T00:00:00+0000 1.8 CONTRIBUTION OF HYDROPHOBIC RESIDUES TO THE STABILITY OF HUMAN LYSOZYME: X-RAY STRUCTURE OF THE V99A MUTANT
2ZIJ 2008-02-18T00:00:00+0000 1.9 Crystal Structure of Human Lysozyme Expressed in E. coli.
207L 1996-03-26T00:00:00+0000 1.8 MUTANT HUMAN LYSOZYME C77A
1B5W 1999-01-11T00:00:00+0000 2.17 CONTRIBUTION OF HYDROGEN BONDS TO THE CONFORMATIONAL STABILITY OF HUMAN LYSOZYME: CALORIMETRY AND X-RAY ANALYSIS OF SIX SER->ALA MUTANTS
1B5V 1999-01-11T00:00:00+0000 2.17 CONTRIBUTION OF HYDROGEN BONDS TO THE CONFORMATIONAL STABILITY OF HUMAN LYSOZYME: CALORIMETRY AND X-RAY ANALYSIS OF SIX SER->ALA MUTANTS
2ZIK 2008-02-18T00:00:00+0000 1.81 Crystal Structure of Human Lysozyme from Pichia pastoris
2ZIL 2008-02-18T00:00:00+0000 1.8 Crystal Structure of Human Lysozyme from Urine

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
96.9 Lysozyme C P79180 LYSC_HYLLA
99.2 Lysozyme C P79239 LYSC_PONPY
100.0 Lysozyme C P61628 LYSC_PANTR
100.0 Lysozyme C P61627 LYSC_PANPA
100.0 Lysozyme C P61626 LYSC_HUMAN
100.0 Lysozyme C P79179 LYSC_GORGO