Positive contribution of hydration structure on the surface of human lysozyme to the conformational stability.


Abstract

Water molecules make a hydration structure with the network of hydrogen bonds, covering on the surface of proteins. To quantitatively estimate the contribution of the hydration structure to protein stability, a series of hydrophilic mutant human lysozymes (Val to Ser, Tyr, Asp, Asn, and Arg) 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. The introduced polar residues made hydrogen bonds with protein atoms and/or water molecules, sometimes changing the hydration structure around the mutation site. Changes in the stability of the mutant proteins can be evaluated by a unique equation that considers the conformational changes resulting from the substitutions. Using this analysis, the relationship between the changes in the stabilities and the hydration structures for mutant human lysozymes substituted on the surface could be quantitatively estimated. The analysis indicated that the hydration structure on protein surface plays an important role in determining the conformational stability of the protein. Study holds ProTherm entries: 15282, 15283, 15284, 15285, 15286, 15287, 15288, 15289, 15290, 15291, 15292, 15293, 15294, 15295, 15296, 15297, 15298, 15299, 15300, 15301, 15302, 15303, 15304, 15305, 15306, 15307, 15308, 15309, 15310, 15311, 15312, 15313, 15314, 15315, 15316, 15317, 15318, 15319, 15320, 15321, 15322, 15323, 15324, 15325, 15326, 15327, 15328, 15329, 15330, 15331, 15332, 15333, 15334, 15335, 15336, 15337, 15338, 15339, 15340, 15341, 15342, 15343, 15344, 15345, 15346, 15347, 15348, 15349, 15350, 15351, 15352, 15353, 15354, 15355, 15356, 15357, 15358, 15359, 15360, 15361, 15362, 15363, 15364, 15365, 15366, 15367, 15368, 15369, 15370, 15371, 15372, 15373 Extra Details: hydration structure; surface; alpha-helix; beta-sheet;

Submission Details

ID: gSPsC2ZW4

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:46 p.m.

Version: 1

Publication Details
Funahashi J;Takano K;Yamagata Y;Yutani K,J. Biol. Chem. (2002) Positive contribution of hydration structure on the surface of human lysozyme to the conformational stability. PMID:11927576
Additional Information

Study Summary

Number of data points 260
Proteins Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C ; Lysozyme C
Unique complexes 15
Assays/Quantities/Protocols Experimental Assay: dCp temp:64.9 C ; Experimental Assay: dHcal pH:2.7, temp:64.9 C ; Experimental Assay: ddG ; Experimental Assay: dTm ; Experimental Assay: dCp ; Experimental Assay: dHcal pH:2.7 ; Experimental Assay: Tm pH:2.7 ; Experimental Assay: dHcal pH:2.8 ; Experimental Assay: Tm pH:2.8 ; Experimental Assay: dHvH pH:2.8 ; Experimental Assay: dHcal pH:2.72 ; Experimental Assay: Tm pH:2.72 ; Experimental Assay: dHvH pH:2.72 ; Experimental Assay: dHcal pH:3.04 ; Experimental Assay: Tm pH:3.04 ; Experimental Assay: dHvH pH:3.04 ; Experimental Assay: dHcal pH:2.64 ; Experimental Assay: Tm pH:2.64 ; Experimental Assay: dHvH pH:2.64 ; Experimental Assay: dHcal pH:3.34 ; Experimental Assay: Tm pH:3.34 ; Experimental Assay: dHvH pH:3.34 ; Experimental Assay: dHcal pH:3.13 ; Experimental Assay: Tm pH:3.13 ; Experimental Assay: dHvH pH:3.13 ; Experimental Assay: dHcal pH:2.63 ; Experimental Assay: Tm pH:2.63 ; Experimental Assay: dHvH pH:2.63 ; Experimental Assay: dHcal pH:3.38 ; Experimental Assay: Tm pH:3.38 ; Experimental Assay: dHvH pH:3.38 ; Experimental Assay: dHcal pH:3.22 ; Experimental Assay: Tm pH:3.22 ; Experimental Assay: dHvH pH:3.22 ; Experimental Assay: dHcal pH:3.0 ; Experimental Assay: Tm pH:3.0 ; Experimental Assay: dHvH pH:3.0 ; Experimental Assay: dHcal pH:2.85 ; Experimental Assay: Tm pH:2.85 ; Experimental Assay: dHvH pH:2.85 ; Experimental Assay: dHcal pH:3.18 ; Experimental Assay: Tm pH:3.18 ; Experimental Assay: dHvH pH:3.18 ; Experimental Assay: dHcal pH:2.84 ; Experimental Assay: Tm pH:2.84 ; Experimental Assay: dHvH pH:2.84 ; Experimental Assay: dHcal pH:3.25 ; Experimental Assay: Tm pH:3.25 ; Experimental Assay: dHvH pH:3.25 ; Experimental Assay: dHcal pH:3.1 ; Experimental Assay: Tm pH:3.1 ; Experimental Assay: dHvH pH:3.1 ; Experimental Assay: dHcal pH:2.98 ; Experimental Assay: Tm pH:2.98 ; Experimental Assay: dHvH pH:2.98 ; Experimental Assay: dHcal pH:3.26 ; Experimental Assay: Tm pH:3.26 ; Experimental Assay: dHvH pH:3.26 ; Experimental Assay: dHcal pH:3.02 ; Experimental Assay: Tm pH:3.02 ; Experimental Assay: dHvH pH:3.02 ; Experimental Assay: dHcal pH:2.67 ; Experimental Assay: Tm pH:2.67 ; Experimental Assay: dHvH pH:2.67 ; Experimental Assay: dHcal pH:3.28 ; Experimental Assay: Tm pH:3.28 ; Experimental Assay: dHvH pH:3.28 ; Experimental Assay: dHcal pH:2.61 ; Experimental Assay: Tm pH:2.61 ; Experimental Assay: dHvH pH:2.61 ; Experimental Assay: dHcal pH:3.15 ; Experimental Assay: Tm pH:3.15 ; Experimental Assay: dHvH pH:3.15 ; Experimental Assay: dHcal pH:2.99 ; Experimental Assay: Tm pH:2.99 ; Experimental Assay: dHvH pH:2.99 ; Experimental Assay: dHcal pH:2.88 ; Experimental Assay: Tm pH:2.88 ; Experimental Assay: dHvH pH:2.88 ; Experimental Assay: dHcal pH:2.82 ; Experimental Assay: Tm pH:2.82 ; Experimental Assay: dHvH pH:2.82 ; Experimental Assay: dHcal pH:2.6 ; Experimental Assay: Tm pH:2.6 ; Experimental Assay: dHvH pH:2.6 ; Experimental Assay: dHcal pH:3.3 ; Experimental Assay: Tm pH:3.3 ; Experimental Assay: dHvH pH:3.3 ; Experimental Assay: dHcal pH:3.14 ; Experimental Assay: Tm pH:3.14 ; Experimental Assay: dHvH pH:3.14 ; Experimental Assay: dHcal pH:3.01 ; Experimental Assay: Tm pH:3.01 ; Experimental Assay: dHvH pH:3.01 ; Experimental Assay: dHcal pH:2.96 ; Experimental Assay: Tm pH:2.96 ; Experimental Assay: dHvH pH:2.96 ; Experimental Assay: dHcal pH:2.66 ; Experimental Assay: Tm pH:2.66 ; Experimental Assay: dHvH pH:2.66 ; Experimental Assay: dHcal pH:3.21 ; Experimental Assay: Tm pH:3.21 ; Experimental Assay: dHvH pH:3.21 ; Experimental Assay: dHcal pH:3.2 ; Experimental Assay: Tm pH:3.2 ; Experimental Assay: dHvH pH:3.2 ; Experimental Assay: dHcal pH:2.91 ; Experimental Assay: Tm pH:2.91 ; Experimental Assay: dHvH pH:2.91 ; Experimental Assay: dHcal pH:3.45 ; Experimental Assay: Tm pH:3.45 ; Experimental Assay: dHvH pH:3.45 ; Experimental Assay: dHcal pH:3.24 ; Experimental Assay: Tm pH:3.24 ; Experimental Assay: dHvH pH:3.24 ; Experimental Assay: dHcal pH:3.09 ; Experimental Assay: Tm pH:3.09 ; Experimental Assay: dHvH pH:3.09 ; Experimental Assay: dHcal pH:2.83 ; Experimental Assay: Tm pH:2.83 ; Experimental Assay: dHvH pH:2.83 ; Experimental Assay: dHcal pH:2.65 ; Experimental Assay: Tm pH:2.65 ; Experimental Assay: dHvH 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
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 P61628 LYSC_PANTR
100.0 Lysozyme C P61627 LYSC_PANPA
100.0 Lysozyme C P61626 LYSC_HUMAN
100.0 Lysozyme C P79179 LYSC_GORGO