Role of amino acid residues in left-handed helical conformation for the conformational stability of a protein.


Our previous study of six non-Gly to Gly/Ala mutant human lysozymes in a left-handed helical region showed that only one non-Gly residue at a rigid site had unfavorable strain energy as compared with Gly at the same position (Takano et al., Proteins 2001; 44:233-243). To further examine the role of left-handed residues in the conformational stability of a protein, we constructed ten Gly to Ala mutant human lysozymes. Most Gly residues in human lysozyme are located in the left-handed helix region. The thermodynamic parameters for denaturation and crystal structures were determined by differential scanning calorimetry and X-ray analysis, respectively. The difference in denaturation Gibbs energy (DeltaDeltaG) for the ten Gly to Ala mutants ranged from + 1.9 to -7.5 kJ/mol, indicating that the effect of the mutation depends on the environment of the residue. We confirm that Gly in a left-handed region is more favorable at rigid sites than non-Gly, but there is little difference in energetic cost between Gly and non-Gly at flexible sites. The present results indicate that dihedral angles in the backbone conformation and also the flexibility at the position should be considered for analyses of protein stability, and protein structural determination, prediction, and design. Study holds ProTherm entries: 12022, 12023, 12024, 12025, 12026, 12027, 12028, 12029, 12030, 12031, 12032, 12033, 12034, 12035, 12036, 12037, 12038, 12039, 12040, 12041, 12042, 12043, 12044, 12045, 12046, 12047, 12048, 12049, 12050, 12051, 12052, 12053, 12054, 12055, 12056, 12057, 12058, 12059, 12060, 12061, 12062, 12063, 12064, 12065, 12066, 12067 Extra Details: differential scanning calorimetry; X-ray crystallography; mutant protein;,Gibbs energy; Ramachandran map; local constraints

Submission Details

ID: ax45eMFC3

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:43 p.m.

Version: 1

Publication Details
Takano K;Yamagata Y;Yutani K,Proteins (2001) Role of amino acid residues in left-handed helical conformation for the conformational stability of a protein. PMID:11599030
Additional Information

Study Summary

Number of data points 110
Proteins Lysozyme C ; Lysozyme C
Unique complexes 11
Assays/Quantities/Protocols Experimental Assay: dTm ; Experimental Assay: dHvH ; Experimental Assay: dCp temp:64.9 C, units:kcal/mol·K ; Experimental Assay: dCp units:kJ/mol·K, temp:64.9 C ; Experimental Assay: ddG ; Experimental Assay: dCp units:kJ/mol·K ; Experimental Assay: dHcal pH:2.8 ; Experimental Assay: Tm pH:2.8 ; Experimental Assay: dHcal pH:2.79 ; Experimental Assay: Tm pH:2.79 ; Experimental Assay: dHcal pH:2.67 ; Experimental Assay: Tm pH:2.67 ; Experimental Assay: dHcal pH:2.2 ; Experimental Assay: Tm pH:2.2 ; Experimental Assay: dHcal pH:2.65 ; Experimental Assay: Tm pH:2.65 ; Experimental Assay: dHcal pH:2.3 ; Experimental Assay: Tm pH:2.3 ; Experimental Assay: dHcal pH:3.16 ; Experimental Assay: Tm pH:3.16 ; Experimental Assay: dHcal pH:2.64 ; Experimental Assay: Tm pH:2.64 ; Experimental Assay: dHcal pH:3.0 ; Experimental Assay: Tm pH:3.0 ; Experimental Assay: dHcal pH:2.72 ; Experimental Assay: Tm pH:2.72 ; Experimental Assay: dHcal pH:3.2 ; Experimental Assay: Tm pH:3.2 ; Experimental Assay: dHcal pH:2.68 ; Experimental Assay: Tm pH:2.68 ; Experimental Assay: dHcal pH:2.4 ; Experimental Assay: Tm pH:2.4 ; Experimental Assay: dHcal pH:3.18 ; Experimental Assay: Tm pH:3.18 ; Experimental Assay: dHcal pH:2.6 ; Experimental Assay: Tm pH:2.6 ; Experimental Assay: dHcal pH:2.38 ; Experimental Assay: Tm pH:2.38 ; Experimental Assay: dHcal pH:2.7 ; Experimental Assay: Tm pH:2.7

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 UniProtKB Entries

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