Experimental verification of the 'stability profile of mutant protein' (SPMP) data using mutant human lysozymes.


Abstract

The stability profile of mutant protein (SPMP) (Ota,M., Kanaya,S. and Nishikawa,K., 1995, J. Mol. Biol., 248, 733-738) estimates the changes in conformational stability due to single amino acid substitutions using a pseudo-energy potential developed for evaluating structure-sequence compatibility in the structure prediction method, the 3D-1D compatibility evaluation. Nine mutant human lysozymes expected to significantly increase in stability from SPMP were constructed, in order to experimentally verify the reliability of SPMP. The thermodynamic parameters for denaturation and crystal structures of these mutant proteins were determined. One mutant protein was stabilized as expected, compared with the wild-type protein. However, the others were not stabilized even though the structural changes were subtle, indicating that SPMP overestimates the increase in stability or underestimates negative effects due to substitution. The stability changes in the other mutant human lysozymes previously reported were also analyzed by SPMP. The correlation of the stability changes between the experiment and prediction depended on the types of substitution: there were some correlations for proline mutants and cavity-creating mutants, but no correlation for mutants related to side-chain hydrogen bonds. The present results may indicate some additional factors that should be considered in the calculation of SPMP, suggesting that SPMP can be refined further. Study holds ProTherm entries: 6650, 6651, 6652, 6653, 6654, 6655, 6656, 6657, 6658, 6659, 6660, 6661, 6662, 6663, 6664, 6665, 6666, 6667, 6668, 6669, 6670, 6671, 6672, 6673, 6674, 6675, 6676, 6677, 6678, 6679, 6680, 6681, 6682, 6683, 6684, 6685, 6686, 6687, 6688, 6689, 6690, 6691, 6692, 6693, 6694, 6695, 6696, 14361, 14362, 14363, 14364, 14365, 14366, 14367, 14368, 14369 Extra Details: 3D-1D compatibility evaluation; human lysozyme;,mutant stability; pseudo-energy potential; stability profile

Submission Details

ID: X5RHA2S23

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:32 p.m.

Version: 1

Publication Details
Takano K;Ota M;Ogasahara K;Yamagata Y;Nishikawa K;Yutani K,Protein Eng. (1999) Experimental verification of the 'stability profile of mutant protein' (SPMP) data using mutant human lysozymes. PMID:10469827
Additional Information

Study Summary

Number of data points 138
Proteins Lysozyme C ; Lysozyme C
Unique complexes 11
Assays/Quantities/Protocols Experimental Assay: ddG ; Experimental Assay: dTm ; Experimental Assay: dCp ; Experimental Assay: dHcal pH:2.7 ; Experimental Assay: dHcal pH:3.26 ; Experimental Assay: Tm pH:3.26 ; Experimental Assay: dHvH pH:3.26 ; Experimental Assay: dHcal pH:2.62 ; Experimental Assay: Tm pH:2.62 ; Experimental Assay: dHvH pH:2.62 ; Experimental Assay: dHcal pH:3.19 ; Experimental Assay: Tm pH:3.19 ; Experimental Assay: dHvH pH:3.19 ; Experimental Assay: dHcal pH:2.77 ; Experimental Assay: Tm pH:2.77 ; Experimental Assay: dHvH pH:2.77 ; Experimental Assay: dHcal pH:3.1 ; Experimental Assay: Tm pH:3.1 ; Experimental Assay: dHvH pH:3.1 ; Experimental Assay: dHcal pH:2.75 ; Experimental Assay: Tm pH:2.75 ; Experimental Assay: dHvH pH:2.75 ; Experimental Assay: dHcal pH:2.53 ; Experimental Assay: Tm pH:2.53 ; Experimental Assay: dHvH pH:2.53 ; Experimental Assay: dHcal pH:3.28 ; Experimental Assay: Tm pH:3.28 ; Experimental Assay: dHvH pH:3.28 ; Experimental Assay: dHcal pH:3.15 ; Experimental Assay: Tm pH:3.15 ; Experimental Assay: dHvH pH:3.15 ; Experimental Assay: dHcal pH:2.59 ; Experimental Assay: Tm pH:2.59 ; Experimental Assay: dHvH pH:2.59 ; Experimental Assay: dHcal pH:3.11 ; Experimental Assay: Tm pH:3.11 ; Experimental Assay: dHvH pH:3.11 ; Experimental Assay: dHcal pH:2.78 ; Experimental Assay: Tm pH:2.78 ; Experimental Assay: dHvH pH:2.78 ; Experimental Assay: dHcal pH:2.58 ; Experimental Assay: Tm pH:2.58 ; Experimental Assay: dHvH pH:2.58 ; Experimental Assay: dHcal pH:3.09 ; Experimental Assay: Tm pH:3.09 ; Experimental Assay: dHvH pH:3.09 ; Experimental Assay: dHcal pH:2.73 ; Experimental Assay: Tm pH:2.73 ; Experimental Assay: dHvH pH:2.73 ; Experimental Assay: dHcal pH:2.48 ; Experimental Assay: Tm pH:2.48 ; Experimental Assay: dHvH pH:2.48 ; Experimental Assay: dHcal pH:3.25 ; Experimental Assay: Tm pH:3.25 ; Experimental Assay: dHvH pH:3.25 ; Experimental Assay: dHcal pH:2.56 ; Experimental Assay: Tm pH:2.56 ; Experimental Assay: dHvH pH:2.56 ; Experimental Assay: dHcal pH:3.23 ; Experimental Assay: Tm pH:3.23 ; Experimental Assay: dHvH pH:3.23 ; Experimental Assay: dHcal pH:2.83 ; Experimental Assay: Tm pH:2.83 ; Experimental Assay: dHvH pH:2.83 ; Experimental Assay: dHcal pH:2.61 ; Experimental Assay: Tm pH:2.61 ; Experimental Assay: dHvH pH:2.61 ; Experimental Assay: Tm pH:2.7
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