Start2Fold

The database of hydrogen/deuterium exchange data on protein folding and stability

Entry STF0042

Hen egg-white lysozyme

 DOWNLOAD ENTRY IN XML

Protein information

Name of the protein: Lysozyme C
Organism: Escherichia coli (strain K12)
Number of residues: 129
Related UniProt entry:   P00698 (Fragment: 19 - 147)
Related PDB entry:   1HEL

Visualize the data

 Click here or on the image on the right to visualize the residues using JSmol. Warning: JSmol is known to load slowly on certain browsers, depending on the size of the macromolecule. The applet is optimized for Chrome, other browsers have limited support.

Experiment sets

 Show  Hide

STRONG

Method: Native exchange NMR

Conditions: pH 7.5; 30.0 Celsius; Probes: 68

Related publication:
 PMID 1409571

Experiment details: "Exchange was carried out at 30°C in a D2O incubation mixture containing 0.1 M NaC1, 3 mM sodium azide, and 20 mM sodium phosphate buffer, pH 7.5. (uncorrected). Hydrogen exchange was initiated by dissolution of lyophilized protein in the exchange buffer to give a protein concentration of 2.5 mg/ml (0.17 mM). This protein concentration was chosen so that aggregation of lysozyme was negligible. Sixteen samples were withdrawn from the incubation mixture after time intervals ranging from 40 sec to 70 days and the exchange quenched by addition of 2.3 ml of 240 mM deuterated sodium acetate buffer, pH 3.6, giving a final pH of 3.8."

Protection threshold: very slowly exchanging amide protons; k(ex) < E-07

Sequence: KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

STRONG residues

12: M; 28: W; 29: V; 30: C; 31: A; 58: I; 95: A; 96: K; 98: I;
 CLICK TO DOWNLOAD LIST OF RESIDUES

 Show  Hide

EARLY

Method: HDX-folding competition by NMR

Conditions: pH 4.5-9.5; None Celsius; Probes: 65

Related publication:
 PMID 2000138

Experiment details: "Refolding experiments were carried out between pH values of 4.5 and 9.5."

Protection threshold: high degree of protection relative to exchange (% exchange < 30)

Sequence: KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

EARLY residues

8: L; 9: A; 10: A; 11: A; 12: M; 13: K; 15: H; 17: L; 23: Y; 27: N; 28: W; 29: V; 30: C; 31: A; 32: A; 33: K; 34: F; 35: E; 63: W; 64: C; 78: I; 92: V; 93: N; 94: C; 95: A; 96: K; 97: K; 98: I; 99: V; 108: W; 111: W; 112: R; 115: C; 123: W; 124: I; 125: R;
 CLICK TO DOWNLOAD LIST OF RESIDUES

 Show  Hide

EARLY

Method: Pulse labeling HDX NMR

Conditions: pH 5.5; 20.0 Celsius; Probes: 48

Related publication:
 PMID 1641003

Experiment details: "Experiments were done at 20 °C using a Biologic QFM5 rapid mixing quench flow apparatus. Lysozyme (20 mg/ml) was initially dissolved in 6M GdnDCl in D2O at pH 6, leading to complete denaturation and substitution of all exchangeable hydrogens by deuterium. Refolding was initiated by dilution of this solution 10-fold into 20 mM sodium acetate, pH 5.5 in H2O. At the resulting pH of 5.2 the half life for amide exchange is about 16 s, so that negligible labelling occurred during this phase. After variable refolding times (3.5-2000 ms) the solution was diluted again with a volume five times that of the initial protein solution of 0.2 M sodium borate, pH 10.0. This initiated labelling at a pH of 9.5. After 8.4 ms the labelling pulse was terminated by further dilution, with a volume again five times that of the initial volume of protein solution, of 0.5 M acetic acid in H2O. The final pH was about 4, at which exchange in the native protein of the investigated amides is very slow."

Protection threshold: refolding time constant < 3 ms

Sequence: KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

EARLY residues

12: M; 29: V; 63: W; 78: I; 96: K; 99: V; 124: I;
 CLICK TO DOWNLOAD LIST OF RESIDUES

 Show  Hide

INTERMEDIATE

Method: Pulse labeling HDX NMR

Conditions: pH 5.5; 20.0 Celsius; Probes: 48

Related publication:
 PMID 1641003

Experiment details: "Experiments were done at 20 °C using a Biologic QFM5 rapid mixing quench flow apparatus. Lysozyme (20 mg/ml) was initially dissolved in 6M GdnDCl in D2O at pH 6, leading to complete denaturation and substitution of all exchangeable hydrogens by deuterium. Refolding was initiated by dilution of this solution 10-fold into 20 mM sodium acetate, pH 5.5 in H2O. At the resulting pH of 5.2 the half life for amide exchange is about 16 s, so that negligible labelling occurred during this phase. After variable refolding times (3.5-2000 ms) the solution was diluted again with a volume five times that of the initial protein solution of 0.2 M sodium borate, pH 10.0. This initiated labelling at a pH of 9.5. After 8.4 ms the labelling pulse was terminated by further dilution, with a volume again five times that of the initial volume of protein solution, of 0.5 M acetic acid in H2O. The final pH was about 4, at which exchange in the native protein of the investigated amides is very slow."

Protection threshold: 3 ms < refolding time constant < 6 ms

Sequence: KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

INTERMEDIATE residues

8: L; 10: A; 11: A; 28: W; 31: A; 64: C; 92: V; 94: C; 95: A; 108: W; 111: W; 112: R; 123: W; 125: R;
 CLICK TO DOWNLOAD LIST OF RESIDUES