Role of surface hydrophobic residues in the conformational stability of human lysozyme at three different positions.


Abstract

To evaluate the contribution of the amino acid residues on the surface of a protein to its stability, a series of hydrophobic mutant human lysozymes (Val to Gly, Ala, Leu, Ile, Met, and Phe) modified at three different positions on the surface, which are located in the alpha-helix (Val 110), the beta-sheet (Val 2), and the loop (Val 74), were constructed. Their thermodynamic parameters of denaturation and crystal structures were examined by calorimetry and by X-ray crystallography at 100 K, respectively. Differences in the denaturation Gibbs energy change between the wild-type and the hydrophobic mutant proteins ranged from 4.6 to -9.6 kJ/mol, 2.7 to -1.5 kJ/mol, and 3.6 to -0.2 kJ/mol at positions 2, 74, and 110, respectively. The identical substitution at different positions and different substitutions at the same position resulted in different degrees of stabilization. Changes in the stability of the mutant proteins could be evaluated by a unique equation considering the conformational changes due to the substitutions [Funahashi et al. (1999) Protein Eng. 12, 841-850]. For this calculation, secondary structural propensities were newly considered. However, some mutant proteins were not adapted to the equation. The hydration structures around the mutation sites of the exceptional mutant proteins were affected due to the substitutions. The stability changes in the exceptional mutant proteins could be explained by the formation or destruction of the hydration structures. These results suggest that the hydration structure mediated via hydrogen bonds covering the protein surface plays an important role in the conformational stability of the protein. Study holds ProTherm entries: 9650, 9651, 9652, 9653, 9654, 9655, 9656, 9657, 9658, 9659, 9660, 9661, 9662, 9663, 9664, 9665, 9666, 9667, 9668, 9669, 9670, 9671, 9672, 9673, 9674, 9675, 9676, 9677, 9678, 9679, 9680, 9681, 9682, 9683, 9684, 9685, 9686, 9687, 9688, 9689, 9690, 9691, 9692, 9693, 9694, 9695, 9696, 9697, 9698, 9699, 9700, 9701, 9702, 9703, 9704, 9705, 9706, 9707, 9708, 9709, 9710, 9711, 9712, 9713, 9714, 9715, 9716, 9717, 9718, 9719, 9720, 9721, 9722, 9724, 9725, 9726, 9727, 9728, 9730, 9731, 9732, 9733, 9734, 9735, 9736, 9737, 9738, 9739, 9740, 9741, 9742, 9743, 9744, 9745, 9746, 9747, 9748, 9749, 14497, 14498, 14499, 14500, 14501, 14502, 14503, 14504, 14505, 14506, 14507, 14508, 14509, 14510, 14511 Extra Details:

Submission Details

ID: i5k76m7B

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:38 p.m.

Version: 1

Publication Details
Funahashi J;Takano K;Yamagata Y;Yutani K,Biochemistry (2000) Role of surface hydrophobic residues in the conformational stability of human lysozyme at three different positions. PMID:11087397
Additional Information

Study Summary

Number of data points 226
Proteins Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Endoglucanase G ; Lysozyme C ; Beta-lactamase ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C
Unique complexes 16
Assays/Quantities/Protocols Experimental Assay: ddG ; Experimental Assay: dTm ; Experimental Assay: dCp ; Experimental Assay: dHcal pH:3.04 ; Experimental Assay: Tm pH:3.04 ; Experimental Assay: dHcal pH:2.72 ; Experimental Assay: Tm pH:2.72 ; Experimental Assay: dHcal pH:3.06 ; Experimental Assay: Tm pH:3.06 ; Experimental Assay: dHcal pH:2.85 ; Experimental Assay: Tm pH:2.85 ; Experimental Assay: dHcal pH:2.48 ; Experimental Assay: Tm pH:2.48 ; Experimental Assay: dHcal pH:3.25 ; Experimental Assay: Tm pH:3.25 ; Experimental Assay: dHcal pH:3.03 ; Experimental Assay: Tm pH:3.03 ; Experimental Assay: dHcal pH:2.82 ; Experimental Assay: Tm pH:2.82 ; Experimental Assay: dHcal pH:2.9 ; Experimental Assay: Tm pH:2.9 ; Experimental Assay: dHcal pH:3.11 ; Experimental Assay: Tm pH:3.11 ; Experimental Assay: dHcal pH:2.6 ; Experimental Assay: Tm pH:2.6 ; Experimental Assay: dHcal pH:3.23 ; Experimental Assay: Tm pH:3.23 ; Experimental Assay: dHcal pH:2.84 ; Experimental Assay: Tm pH:2.84 ; Experimental Assay: dHcal pH:3.2 ; Experimental Assay: Tm pH:3.2 ; Experimental Assay: dHcal pH:3.1 ; Experimental Assay: Tm pH:3.1 ; Experimental Assay: dHcal pH:3.15 ; Experimental Assay: Tm pH:3.15 ; Experimental Assay: dHcal pH:3.0 ; Experimental Assay: Tm pH:3.0 ; Experimental Assay: dHcal pH:2.8 ; Experimental Assay: Tm pH:2.8 ; Experimental Assay: dHcal pH:2.67 ; Experimental Assay: Tm pH:2.67 ; Experimental Assay: dHcal pH:3.3 ; Experimental Assay: Tm pH:3.3 ; Experimental Assay: dHcal pH:2.95 ; Experimental Assay: Tm pH:2.95 ; Experimental Assay: dHcal pH:2.78 ; Experimental Assay: Tm pH:2.78 ; Experimental Assay: dHcal pH:2.53 ; Experimental Assay: Tm pH:2.53 ; Experimental Assay: dHcal pH:3.22 ; Experimental Assay: Tm pH:3.22 ; Experimental Assay: dHcal pH:2.87 ; Experimental Assay: Tm pH:2.87 ; Experimental Assay: dHcal pH:2.68 ; Experimental Assay: Tm pH:2.68 ; Experimental Assay: dHcal pH:3.31 ; Experimental Assay: Tm pH:3.31 ; Experimental Assay: dHcal pH:3.09 ; Experimental Assay: Tm pH:3.09 ; Experimental Assay: dHcal pH:2.94 ; Experimental Assay: Tm pH:2.94 ; Experimental Assay: dHcal pH:2.73 ; Experimental Assay: Tm pH:2.73 ; Experimental Assay: dHcal pH:2.52 ; Experimental Assay: Tm pH:2.52 ; Experimental Assay: dHcal pH:3.05 ; Experimental Assay: Tm pH:3.05 ; Experimental Assay: dHcal pH:2.49 ; Experimental Assay: Tm pH:2.49 ; Experimental Assay: dHcal pH:3.13 ; Experimental Assay: Tm pH:3.13 ; Experimental Assay: dHcal pH:2.92 ; Experimental Assay: Tm pH:2.92 ; Experimental Assay: dHcal pH:2.7 ; Experimental Assay: Tm pH:2.7 ; Experimental Assay: dHcal pH:2.5 ; Experimental Assay: Tm pH:2.5 ; Experimental Assay: dHcal pH:3.4 ; Experimental Assay: Tm pH:3.4 ; Experimental Assay: dHcal pH:3.19 ; Experimental Assay: Tm pH:3.19 ; Experimental Assay: dHcal pH:3.08 ; Experimental Assay: Tm pH:3.08 ; Experimental Assay: dHcal pH:2.83 ; Experimental Assay: Tm pH:2.83 ; Experimental Assay: dHcal pH:2.65 ; Experimental Assay: Tm pH:2.65
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
1G87 2000-11-16T00:00:00+0000 1.6 THE CRYSTAL STRUCTURE OF ENDOGLUCANASE 9G FROM CLOSTRIDIUM CELLULOLYTICUM
1GA2 2000-11-29T00:00:00+0000 1.7 THE CRYSTAL STRUCTURE OF ENDOGLUCANASE 9G FROM CLOSTRIDIUM CELLULOLYTICUM COMPLEXED WITH CELLOBIOSE
1K72 2001-10-18T00:00:00+0000 1.8 The X-ray Crystal Structure Of Cel9G Complexed With cellotriose
1KFG 2001-11-20T00:00:00+0000 1.9 The X-ray Crystal Structure of Cel9G from Clostridium cellulolyticum complexed with a Thio-Oligosaccharide Inhibitor
1BLS 1993-12-17T00:00:00+0000 2.3 CRYSTALLOGRAPHIC STRUCTURE OF A PHOSPHONATE DERIVATIVE OF THE ENTEROBACTER CLOACAE P99 CEPHALOSPORINASE: MECHANISTIC INTERPRETATION OF A BETA-LACTAMASE TRANSITION STATE ANALOG
1GCE 1999-05-17T00:00:00+0000 1.8 STRUCTURE OF THE BETA-LACTAMASE OF ENTEROBACTER CLOACAE GC1
1RGZ 2003-11-13T00:00:00+0000 1.37 Enterobacter cloacae GC1 Class C beta-Lactamase Complexed with Transition-State Analog of Cefotaxime
1XX2 2004-11-03T00:00:00+0000 1.88 Refinement of P99 beta-lactamase from Enterobacter cloacae
1Y54 2004-12-02T00:00:00+0000 2.1 Crystal structure of the native class C beta-lactamase from Enterobacter cloacae 908R complexed with BRL42715
2Q9M 2007-06-13T00:00:00+0000 2.05 4-Substituted Trinems as Broad Spectrum-Lactamase Inhibitors: Structure-based Design, Synthesis and Biological Activity

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
90.8 Lysozyme C P61634 LYSC_ERYPA
90.8 Lysozyme C P61633 LYSC_CHLAE
100.0 Endoglucanase G P37700 GUNG_CLOCE
98.6 Beta-lactamase P05364 AMPC_ENTCL