Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six Ser --> Ala mutants.


Abstract

To further examine the contribution of hydrogen bonds to the conformational stability of the human lysozyme, six Ser to Ala mutants were constructed. The thermodynamic parameters for denaturation of these six Ser mutant proteins were investigated by differential scanning calorimetry (DSC), and the crystal structures were determined by X-ray analysis. The denaturation Gibbs energy (DeltaG) of the Ser mutant proteins was changed from 2.0 to -5.7 kJ/mol, compared to that of the wild-type protein. With an analysis in which some factors that affected the stability due to mutation were considered, the contribution of hydrogen bonds to the stability (Delta DeltaGHB) was extracted on the basis of the structures of the mutant proteins. The results showed that hydrogen bonds between protein atoms and between a protein atom and a water bound with the protein molecule favorably contribute to the protein stability. The net contribution of one intramolecular hydrogen bond to protein stability (DeltaGHB) was 8.9 +/- 2.6 kJ/mol on average. However, the contribution to the protein stability of hydrogen bonds between a protein atom and a bound water molecule was smaller than that for a bond between protein atoms. Study holds ProTherm entries: 5735, 5736, 5737, 5738, 5739, 5740, 5741, 5742, 5743, 5744, 5745, 5746, 5747, 5748, 5749, 5750, 5751, 5752, 5753, 5754, 5755, 5756, 5757, 5758, 5759, 5760, 5761, 5762, 5763, 5764, 5765 Extra Details: hydrogen bonds; conformational stability; Gibbs energy;,bound water molecule

Submission Details

ID: TH723k9d3

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:30 p.m.

Version: 1

Publication Details
Takano K;Yamagata Y;Kubota M;Funahashi J;Fujii S;Yutani K,Biochemistry (1999) Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six Ser --> Ala mutants. PMID:10350481
Additional Information

Study Summary

Number of data points 123
Proteins Lysozyme C ; Lysozyme C
Unique complexes 7
Assays/Quantities/Protocols Experimental Assay: dTm ; Experimental Assay: dCp ionic:: , pH:2.7 ; Experimental Assay: dHcal ionic:: , pH:2.7 ; Experimental Assay: Tm ionic:: , pH:2.7 ; Experimental Assay: dHvH ionic:: , pH:2.7 ; Experimental Assay: dCp ionic:: , pH:3.12 ; Experimental Assay: dHcal ionic:: , pH:3.12 ; Experimental Assay: Tm ionic:: , pH:3.12 ; Experimental Assay: dHvH ionic:: , pH:3.12 ; Experimental Assay: dCp pH:2.5, ionic:: ; Experimental Assay: dHcal pH:2.5, ionic:: ; Experimental Assay: Tm pH:2.5, ionic:: ; Experimental Assay: dHvH pH:2.5, ionic:: ; Experimental Assay: dCp ionic:: , pH:2.85 ; Experimental Assay: dHcal ionic:: , pH:2.85 ; Experimental Assay: Tm ionic:: , pH:2.85 ; Experimental Assay: dHvH ionic:: , pH:2.85 ; Experimental Assay: dCp pH:2.71, ionic:: ; Experimental Assay: dHcal pH:2.71, ionic:: ; Experimental Assay: Tm pH:2.71, ionic:: ; Experimental Assay: dHvH pH:2.71, ionic:: ; Experimental Assay: dCp pH:3.1, ionic:: ; Experimental Assay: dHcal pH:3.1, ionic:: ; Experimental Assay: Tm pH:3.1, ionic:: ; Experimental Assay: dHvH pH:3.1, ionic:: ; Experimental Assay: dCp ionic:: , pH:2.51 ; Experimental Assay: dHcal ionic:: , pH:2.51 ; Experimental Assay: Tm ionic:: , pH:2.51 ; Experimental Assay: dHvH ionic:: , pH:2.51 ; Experimental Assay: dCp pH:2.69, ionic:: ; Experimental Assay: dHcal pH:2.69, ionic:: ; Experimental Assay: Tm pH:2.69, ionic:: ; Experimental Assay: dHvH pH:2.69, ionic:: ; Experimental Assay: dCp ionic:: , pH:2.86 ; Experimental Assay: dHcal ionic:: , pH:2.86 ; Experimental Assay: Tm ionic:: , pH:2.86 ; Experimental Assay: dHvH ionic:: , pH:2.86 ; Experimental Assay: dCp ionic:: , pH:3.11 ; Experimental Assay: dHcal ionic:: , pH:3.11 ; Experimental Assay: Tm ionic:: , pH:3.11 ; Experimental Assay: dHvH ionic:: , pH:3.11 ; Experimental Assay: dCp pH:2.47, ionic:: ; Experimental Assay: dHcal pH:2.47, ionic:: ; Experimental Assay: Tm pH:2.47, ionic:: ; Experimental Assay: dHvH pH:2.47, ionic:: ; Experimental Assay: dCp ionic:: , pH:2.67 ; Experimental Assay: dHcal ionic:: , pH:2.67 ; Experimental Assay: Tm ionic:: , pH:2.67 ; Experimental Assay: dHvH ionic:: , pH:2.67 ; Experimental Assay: dCp pH:2.84, ionic:: ; Experimental Assay: dHcal pH:2.84, ionic:: ; Experimental Assay: Tm pH:2.84, ionic:: ; Experimental Assay: dHvH pH:2.84, ionic:: ; Experimental Assay: dCp ionic:: , pH:3.09 ; Experimental Assay: dHcal ionic:: , pH:3.09 ; Experimental Assay: Tm ionic:: , pH:3.09 ; Experimental Assay: dHvH ionic:: , pH:3.09 ; Experimental Assay: dCp pH:2.46, ionic:: ; Experimental Assay: dHcal pH:2.46, ionic:: ; Experimental Assay: Tm pH:2.46, ionic:: ; Experimental Assay: dHvH pH:2.46, ionic:: ; Experimental Assay: dCp pH:2.66, ionic:: ; Experimental Assay: dHcal pH:2.66, ionic:: ; Experimental Assay: Tm pH:2.66, ionic:: ; Experimental Assay: dHvH pH:2.66, ionic:: ; Experimental Assay: dCp pH:2.82, ionic:: ; Experimental Assay: dHcal pH:2.82, ionic:: ; Experimental Assay: Tm pH:2.82, ionic:: ; Experimental Assay: dHvH pH:2.82, ionic:: ; Experimental Assay: dCp ionic:: --, pH:3.09 ; Experimental Assay: dHcal ionic:: --, pH:3.09 ; Experimental Assay: Tm ionic:: --, pH:3.09 ; Experimental Assay: dHvH ionic:: --, pH:3.09
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
133L 1993-06-01T00:00:00+0000 1.77 ROLE OF ARG 115 IN THE CATALYTIC ACTION OF HUMAN LYSOZYME. X-RAY STRUCTURE OF HIS 115 AND GLU 115 MUTANTS
134L 1993-06-01T00:00:00+0000 1.77 ROLE OF ARG 115 IN THE CATALYTIC ACTION OF HUMAN LYSOZYME. X-RAY STRUCTURE OF HIS 115 AND GLU 115 MUTANTS
1B5U 1999-01-11T00:00:00+0000 1.8 CONTRIBUTION OF HYDROGEN BONDS TO THE CONFORMATIONAL STABILITY OF HUMAN LYSOZYME: CALORIMETRY AND X-RAY ANALYSIS OF SIX SER->ALA MUTANT
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
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
1B5X 1999-01-11T00:00:00+0000 2.0 Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and x-ray analysis of six ser->ala mutants
1B5Y 1999-01-11T00:00:00+0000 2.2 CONTRIBUTION OF HYDROGEN BONDS TO THE CONFORMATIONAL STABILITY OF HUMAN LYSOZYME: CALORIMETRY AND X-RAY ANALYSIS OF SIX SER->ALA MUTANTS
1B5Z 1999-01-11T00:00:00+0000 2.2 CONTRIBUTION OF HYDROGEN BONDS TO THE CONFORMATIONAL STABILITY OF HUMAN LYSOZYME: CALORIMETRY AND X-RAY ANALYSIS OF SIX SER->ALA MUTANTS
1B7L 1999-01-24T00:00:00+0000 1.8 VERIFICATION OF SPMP USING MUTANT HUMAN LYSOZYMES
1B7M 1999-01-24T00:00:00+0000 2.2 VERIFICATION OF SPMP USING MUTANT HUMAN LYSOZYMES

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 P79179 LYSC_GORGO
100.0 Lysozyme C P61628 LYSC_PANTR
100.0 Lysozyme C P61627 LYSC_PANPA
100.0 Lysozyme C P61626 LYSC_HUMAN