Hydration state change of proteins upon unfolding in sugar solutions.


Abstract

Change in hydration number of proteins upon unfolding, Deltan, was obtained from the analysis of thermal unfolding behavior of proteins in various sugar solutions with water activity, a(W), varied. By applying the reciprocal form of Wyman-Tanford equation, Deltan was determined to be 133.9, 124.1, and 139.2 per protein molecule for ribonuclease A at pH=5.5, 4.2, and 2.8, respectively, 201.4 for lysozyme at pH=5.5, and 100.1 for alpha-chymotripnogen A at pH=2.0. Among the sugars tested, reducing sugars gave the lower apparent Deltan as compared with nonreducing sugars probably because of the direct interaction of reducing terminal with amino group of proteins at a high temperature. From the knowledge of Deltan, a new thermodynamic model for protein stability was proposed with explicit consideration for hydration state change of protein upon unfolding. From this model, the contribution of a(W) was proven to be always positive for stabilization of proteins and its effect is not negligible depending on Deltan and a(W). Study holds ProTherm entries: 22921, 22922, 22923, 22924, 22925, 22926, 22927, 22928, 22929, 22930, 22931, 22932, 22933, 22934, 22935, 22936, 22937, 22938, 22939, 22940, 22941, 22942, 22943, 22944, 22945, 22946, 22947, 22948, 22949, 22950, 22951, 22952, 22953, 22954, 22955, 22956, 22957, 22958, 22959, 22960, 22961, 22962, 22963, 22964, 22965, 22966, 22967, 22968, 22969, 22970, 22971, 22972, 22973, 22974, 22975, 22976, 22977, 22978, 22979, 22980, 22981, 22982, 22983, 22984, 22985, 22986, 22987, 22988, 22989, 22990, 22991, 22992, 22993, 22994, 22995, 22996, 22997, 22998, 22999, 23000, 23001, 23002, 23003, 23004, 23005, 23006, 23007, 23008, 23009, 23010, 23011, 23012, 23013, 23014, 23015, 23016, 23017, 23018, 23019, 23020, 23021, 23022, 23023, 23024, 23025, 23026, 23027, 23028, 23029, 23030, 23031, 23032, 23033, 23034, 23035, 23036, 23037, 23038, 23039 Extra Details: Data were obtained in 0 M sucrose Thermal unfolding of protein; Hydration number; Water activity; Free energy for protein stability; Ribonuclease A

Submission Details

ID: sKfHK8YF3

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:54 p.m.

Version: 1

Publication Details
Miyawaki O,Biochim. Biophys. Acta (2007) Hydration state change of proteins upon unfolding in sugar solutions. PMID:17581805
Additional Information

Study Summary

Number of data points 238
Proteins Ribonuclease pancreatic ; Lysozyme C ; Ribonuclease pancreatic ; Chymotrypsinogen A ; Lysozyme C ; Calnexin
Unique complexes 3
Assays/Quantities/Protocols Experimental Assay: Tm details:Additives , pH:2.0, buffers:HCl: 0.01 M ; Experimental Assay: dHvH details:Additives , pH:2.0, buffers:HCl: 0.01 M ; Experimental Assay: Tm details:Additives sucrose (1.9963 M),, pH:2.0, buffers:HCl: 0.01 M ; Experimental Assay: dHvH details:Additives sucrose (1.9963 M),, pH:2.0, buffers:HCl: 0.01 M ; Experimental Assay: Tm details:Additives sucrose (1.5563 M),, pH:2.0, buffers:HCl: 0.01 M ; Experimental Assay: dHvH details:Additives sucrose (1.5563 M),, pH:2.0, buffers:HCl: 0.01 M ; Experimental Assay: Tm details:Additives sucrose (1.0801 M),, pH:2.0, buffers:HCl: 0.01 M ; Experimental Assay: dHvH details:Additives sucrose (1.0801 M),, pH:2.0, buffers:HCl: 0.01 M ; Experimental Assay: Tm details:Additives sucrose (0.5632 M),, pH:2.0, buffers:HCl: 0.01 M ; Experimental Assay: dHvH details:Additives sucrose (0.5632 M),, pH:2.0, buffers:HCl: 0.01 M ; Experimental Assay: Tm details:Additives sucrose (0 M),, pH:2.0, buffers:HCl: 0.01 M ; Experimental Assay: dHvH details:Additives sucrose (0 M),, pH:2.0, buffers:HCl: 0.01 M ; Experimental Assay: Tm details:Additives , pH:2.8, buffers:Glycine-HCl: 0.04 M ; Experimental Assay: dHvH details:Additives , pH:2.8, buffers:Glycine-HCl: 0.04 M ; Experimental Assay: Tm details:Additives sucrose (1.9963 M),, pH:2.8, buffers:Glycine-HCl: 0.04 M ; Experimental Assay: dHvH details:Additives sucrose (1.9963 M),, pH:2.8, buffers:Glycine-HCl: 0.04 M ; Experimental Assay: Tm details:Additives sucrose (1.5563 M),, pH:2.8, buffers:Glycine-HCl: 0.04 M ; Experimental Assay: dHvH details:Additives sucrose (1.5563 M),, pH:2.8, buffers:Glycine-HCl: 0.04 M ; Experimental Assay: Tm pH:2.8, details:Additives sucrose (1.0801 M),, buffers:Glycine-HCl: 0.04 M ; Experimental Assay: dHvH pH:2.8, details:Additives sucrose (1.0801 M),, buffers:Glycine-HCl: 0.04 M ; Experimental Assay: Tm pH:2.8, details:Additives sucrose (0.5632 M),, buffers:Glycine-HCl: 0.04 M ; Experimental Assay: dHvH pH:2.8, details:Additives sucrose (0.5632 M),, buffers:Glycine-HCl: 0.04 M ; Experimental Assay: Tm details:Additives sucrose (0 M),, pH:2.8, buffers:Glycine-HCl: 0.04 M ; Experimental Assay: dHvH details:Additives sucrose (0 M),, pH:2.8, buffers:Glycine-HCl: 0.04 M ; Experimental Assay: Tm pH:4.2, details:Additives , buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: dHvH pH:4.2, details:Additives , buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: Tm pH:4.2, details:Additives sucrose (1.9963 M),, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: dHvH pH:4.2, details:Additives sucrose (1.9963 M),, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: Tm pH:4.2, details:Additives sucrose (1.5563 M),, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: dHvH pH:4.2, details:Additives sucrose (1.5563 M),, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: Tm pH:4.2, details:Additives sucrose (1.0801 M),, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: dHvH pH:4.2, details:Additives sucrose (1.0801 M),, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: Tm pH:4.2, details:Additives sucrose (0.5632 M),, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: dHvH pH:4.2, details:Additives sucrose (0.5632 M),, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: Tm pH:4.2, details:Additives sucrose (0 M),, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: dHvH pH:4.2, details:Additives sucrose (0 M),, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: Tm pH:5.5, details:Additives , buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: dHvH pH:5.5, details:Additives , buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: Tm details:Additives sucrose (1.9963 M),, pH:5.5, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: dHvH details:Additives sucrose (1.9963 M),, pH:5.5, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: Tm details:Additives sucrose (1.5563 M),, pH:5.5, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: dHvH details:Additives sucrose (1.5563 M),, pH:5.5, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: Tm pH:5.5, details:Additives sucrose (1.0801 M),, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: dHvH pH:5.5, details:Additives sucrose (1.0801 M),, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: Tm pH:5.5, details:Additives sucrose (0.5632 M),, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: dHvH pH:5.5, details:Additives sucrose (0.5632 M),, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: Tm details:Additives sucrose (0 M),, pH:5.5, buffers:Acetic acid-Sodium acetate: 0.04 M ; Experimental Assay: dHvH details:Additives sucrose (0 M),, pH:5.5, buffers:Acetic acid-Sodium acetate: 0.04 M
Libraries Mutations for sequence KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL ; Mutations for sequence KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV ; Mutations for sequence SKSKPDTSAPTSPKVTYKAPVPSGEVYFADSFDRGTLSGWILSKAKKDDTDDEIAKYDGKWEVDEMKETKLPGDKGLVLMSRAKHHAISAKLNKPFLFDTKPLIVQYEVNFQNGIECGGAYVKLLSKTPELNLDQFHDKTPYTIMFGPDKCGEDYKLHFIFRHKNPKTGVYEEKHAKRPDADLKTYFTDKKTHLYTLILNPDNSFEILVDQSIVNSGNLLNDMTPPVNPSREIEDPEDQKPEDWDERPKIPDPDAVKPDDWNEDAPAKIPDEEATKPDGWLDDEPEYVPDPDAEKPEDWDEDMDGEWEAPQIANPKCESAPGCGVWQRPMIDNPNYKGKWKPPMIDNPNYQGIWKPRKIPNPDFFEDLEPFKMTPFSAIGLELWSMTSDIFFDNFIVCGDRRVVDDWANDGWGLKKAADGAAEP

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
1JHN 2001-06-28T00:00:00+0000 2.9 Crystal Structure of the Lumenal Domain of Calnexin
2IHL 1993-06-29T00:00:00+0000 1.4 LYSOZYME (E.C.3.2.1.17) (JAPANESE QUAIL)
6QMN 2019-02-07T00:00:00+0000 2.31 Crystal structure of a Ribonuclease A-Onconase chimera
1FBI 1995-01-19T00:00:00+0000 3.0 CRYSTAL STRUCTURE OF A CROSS-REACTION COMPLEX BETWEEN FAB F9.13.7 AND GUINEA-FOWL LYSOZYME
1GHL 1993-05-04T00:00:00+0000 2.1 THE THREE-DIMENSIONAL STRUCTURE OF PHEASANT AND GUINEA-FOWL EGG LYSOZYMES
1HHL 1993-05-04T00:00:00+0000 1.9 THE THREE-DIMENSIONAL STRUCTURE OF PHEASANT AND GUINEA-FOWL EGG LYSOZYMES
1JHL 1993-05-04T00:00:00+0000 2.4 THREE-DIMENSIONAL STRUCTURE OF A HETEROCLITIC ANTIGEN-ANTIBODY CROSS-REACTION COMPLEX
1BQL 1995-02-03T00:00:00+0000 2.6 STRUCTURE OF AN ANTI-HEL FAB FRAGMENT COMPLEXED WITH BOBWHITE QUAIL LYSOZYME
1DKJ 1996-01-10T00:00:00+0000 2.0 BOBWHITE QUAIL LYSOZYME
1DKK 1996-01-10T00:00:00+0000 1.9 BOBWHITE QUAIL LYSOZYME WITH NITRATE

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Ribonuclease pancreatic P61824 RNAS1_BISBI
100.0 Ribonuclease pancreatic P61823 RNAS1_BOVIN
96.8 Ribonuclease pancreatic P67926 RNAS1_CAPHI
96.8 Ribonuclease pancreatic P67927 RNAS1_SHEEP
95.2 Ribonuclease pancreatic P00657 RNAS1_BUBBU
96.0 Ribonuclease pancreatic P07847 RNAS1_AEPME
93.5 Ribonuclease pancreatic P07848 RNAS1_EUDTH
95.2 Ribonuclease pancreatic P00660 RNAS1_CONTA
92.7 Ribonuclease pancreatic P00668 RNAS1_ANTAM
90.3 Ribonuclease pancreatic P00662 RNAS1_GIRCA
96.0 Ribonuclease pancreatic Q29606 RNAS1_ORYLE
100.0 Lysozyme C P00698 LYSC_CHICK
96.9 Lysozyme C P00700 LYSC_COLVI
96.9 Lysozyme C P00699 LYSC_CALCC
96.9 Lysozyme C Q7LZQ0 LYSC_CATWA
96.9 Lysozyme C Q7LZP9 LYSC_LOPIM
96.1 Lysozyme C Q7LZI3 LYSC_TRASA
95.3 Lysozyme C P00701 LYSC_COTJA
96.1 Lysozyme C P19849 LYSC_PAVCR
95.3 Lysozyme C P22910 LYSC_CHRAM
95.3 Lysozyme C Q7LZT2 LYSC_TRATE
95.2 Lysozyme C P00703 LYSC_MELGA
92.2 Lysozyme C P00704 LYSC_NUMME
93.0 Lysozyme C P24364 LYSC_LOPLE
94.6 Lysozyme C P24533 LYSC_SYRRE
93.2 Lysozyme C P00702 LYSC_PHACO
93.0 Lysozyme C P81711 LYSC_SYRSO
92.3 Lysozyme C P49663 LYSC_PHAVE
100.0 Chymotrypsinogen A P00766 CTRA_BOVIN
99.8 Calnexin P24643 CALX_CANLF
96.4 Calnexin Q5R440 CALX_PONAB
96.1 Calnexin P27824 CALX_HUMAN
97.6 Calnexin P35564 CALX_MOUSE
96.4 Calnexin P35565 CALX_RAT