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


Abstract

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
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