Start2Fold

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

Entry STF0028

Villin 14T

 DOWNLOAD ENTRY IN XML

Protein information

Name of the protein: Villin-1
Organism: Gallus gallus (Chicken)
Number of residues: 126
Related UniProt entry:   P02640 (Fragment: 2 - 127)
Related PDB entry:   2VIL

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

EARLY

Method: Quenched-flow HDX NMR

Conditions: pH 4.1; 21.0 Celsius; Probes: 31

Related publication:
 PMID 9772179

Experiment details: "Quenched-flow experiments were performed using a Biologic QFM-5 rapid mixing module, operated at room temperature (21 °C). For refolding in 2.4 M urea, the lyophilized, 15N-labeled protein was first dissolved (to 40 μM) in 6.5 M urea, 50 mM acetic acid, 15 mM NaCl, and 1 mM DTT (pH 4.1) in D2O (reading unadjusted for isotope effect). This buffer was mixed in a 1:12 ratio with 50 mM acetic acid, 15 mM NaCl, and 2.06 M urea (pH 4.1) in H2O, to produce a refolding environment of 3 μM protein, 2.4 M urea, and pH 4.1. Delays for monitoring the time course of refolding ranged from 6 to 340 ms. To initiate amide hydrogen exchange, the buffer was mixed in a 13:12 ratio with 180 mM glycine and 15 mM NaCl (pH 9.8). The resulting pH was 9.3, which promotes rapid H-D exchange (0.6 ms). The exchange delay was 20 ms. Exchange was quenched by addition in a 25:9 ratio of 1.5 M acetic acid and 15 mM NaCl. The final pH was 3.7, essentially stopping exchange of all interior amides."

Protection threshold: refolding time constant ~60 ms

Sequence: VELSKKVTGKLDKTTPGIQIWRIENMEMVPVPTKSYGNFYEGDCYVLLSTRKTGSGFSYNIHYWLGKNSSQDEQGAAAIYTTQMDEYLGSVAVQHREVQGHESETFRAYFKQGLIYKQGGVASGMK
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

EARLY residues

19: Q; 21: W; 22: R; 23: I; 29: V; 31: V; 45: Y; 46: V; 47: L; 48: L; 49: S; 50: T; 51: R; 60: N; 62: H; 63: Y; 64: W; 65: L; 77: A; 79: I; 80: Y; 82: T; 83: Q; 84: M; 88: L; 97: E; 98: V; 99: Q; 108: A; 109: Y; 110: F;
 CLICK TO DOWNLOAD LIST OF RESIDUES

 Show  Hide

STRONG

Method: Native exchange NMR

Conditions: pH 4.15; 25.0 Celsius; Probes: 116

Related publication:
 PMID 8075541

Experiment details: "The sample was lyophilized from NMR buffer (pH 4.15) and then redissolved in D2O at time zero. 15N HSQC spectra were recorded with 8 scans and 128 tt increments. Experiments were started at times 11, 30, 50, 69, 89, 108, 128, 157, 186, 216, 249, 279, 309, 338, 367, 464, 524, 583, 642, 702, 761, 820, 880, 939, 998, 1058, 1117, 1176, 1236, 1295 and 9920 min, sampling over one 24-h period with an additional experiment one week later. Temperature during exchange was maintained at 298 K. For each residue, peak volumes were measured in FELIX, and the natural logarithms of the peak volumes were plotted as a function of time. This representation gives a line with slope equal to the negative of the exchange rate for that residue."

Protection threshold: no exchange in one week

Sequence: VELSKKVTGKLDKTTPGIQIWRIENMEMVPVPTKSYGNFYEGDCYVLLSTRKTGSGFSYNIHYWLGKNSSQDEQGAAAIYTTQMDEYLGSVAVQHREVQGHESETFRAYFKQGLIYKQGGVASGMK
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

STRONG residues

19: Q; 22: R; 23: I; 29: V; 45: Y; 46: V; 47: L; 48: L; 49: S; 51: R; 60: N; 62: H; 63: Y; 64: W; 65: L; 66: G; 79: I; 80: Y; 84: M; 97: E; 98: V; 107: R; 108: A; 109: Y;
 CLICK TO DOWNLOAD LIST OF RESIDUES

 Show  Hide

MEDIUM

Method: Native exchange NMR

Conditions: pH 4.15; 25.0 Celsius; Probes: 116

Related publication:
 PMID 8075541

Experiment details: "The sample was lyophilized from NMR buffer (pH 4.15) and then redissolved in D2O at time zero. 15N HSQC spectra were recorded with 8 scans and 128 tt increments. Experiments were started at times 11, 30, 50, 69, 89, 108, 128, 157, 186, 216, 249, 279, 309, 338, 367, 464, 524, 583, 642, 702, 761, 820, 880, 939, 998, 1058, 1117, 1176, 1236, 1295 and 9920 min, sampling over one 24-h period with an additional experiment one week later. Temperature during exchange was maintained at 298 K. For each residue, peak volumes were measured in FELIX, and the natural logarithms of the peak volumes were plotted as a function of time. This representation gives a line with slope equal to the negative of the exchange rate for that residue."

Protection threshold: very slow exchange (rate constant < E-04)

Sequence: VELSKKVTGKLDKTTPGIQIWRIENMEMVPVPTKSYGNFYEGDCYVLLSTRKTGSGFSYNIHYWLGKNSSQDEQGAAAIYTTQMDEYLGSVAVQHREVQGHESETFRAYFKQGLIYKQGGVASGMK
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

MEDIUM residues

21: W; 31: V; 43: D; 50: T; 67: K; 74: Q; 77: A; 82: T; 83: Q; 88: L; 99: Q; 101: H; 110: F;
 CLICK TO DOWNLOAD LIST OF RESIDUES