Start2Fold

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

Entry STF0003

Horse apo-myoglobin

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Protein information

Name of the protein: Myoglobin
Organism: Equus caballus (Horse)
Number of residues: 153
Related UniProt entry:   P68082 (Fragment: 2 - 154)
Related PDB entry:   1YMB

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Experiment sets

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EARLY

Method: Pulse labeling HDX MS

Conditions: pH 2.0-10.0; 0.0 Celsius; Probes: every amide site

Related publication:
 PMID 20849085

Experiment details: "Protein refolding and pulsed HDX were carried out using a custom-made four-syringe continuous-flow setup with three sequential mixing steps. Syringe 1 was filled with an aqueous solution of 75 μM acid-unfolded aMb and 30 μM bradykinin in 10 mM HCl. Syringe 2 contained water with dilute ammonium hydroxide. Both syringes were connected to mixer M1 via fused silica capillaries. Refolding was initiated by mixing the contents of syringes 1 and 2 at M1 in a 1:1 volume ratio at a flow rate of 5 μl/min each, resulting in a pH jump from 2 to 10. The outlet of M1 was connected to a folding capillary. Depending on the folding time different capillary i.d. values and lengths were used (10 ms: i.d. 20 μm, l 5 mm; 100 ms: i.d. 50 μm, l 8.5 mm; 1 s: i.d. 75 μm, l 38 mm)."

Protection threshold: amide deuteration level <0.5 at 10ms of folding time

Sequence: GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG
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EARLY residues

107: I; 108: S; 109: D; 110: A; 111: I; 112: I; 113: H; 114: V; 115: L; 116: H; 133: K; 134: A; 135: L; 136: E; 137: L;
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INTERMEDIATE

Method: Pulse labeling HDX MS

Conditions: pH 2.0-10.0; 0.0 Celsius; Probes: every amide site

Related publication:
 PMID 20849085

Experiment details: "Protein refolding and pulsed HDX were carried out using a custom-made four-syringe continuous-flow setup with three sequential mixing steps. Syringe 1 was filled with an aqueous solution of 75 μM acid-unfolded aMb and 30 μM bradykinin in 10 mM HCl. Syringe 2 contained water with dilute ammonium hydroxide. Both syringes were connected to mixer M1 via fused silica capillaries. Refolding was initiated by mixing the contents of syringes 1 and 2 at M1 in a 1:1 volume ratio at a flow rate of 5 μl/min each, resulting in a pH jump from 2 to 10. The outlet of M1 was connected to a folding capillary. Depending on the folding time different capillary i.d. values and lengths were used (10 ms: i.d. 20 μm, l 5 mm; 100 ms: i.d. 50 μm, l 8.5 mm; 1 s: i.d. 75 μm, l 38 mm)."

Protection threshold: amide deuteration level 0.5-0.75 at 10ms of folding time

Sequence: GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG
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INTERMEDIATE residues

138: F; 139: R; 142: I; 146: Y; 148: E;
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STRONG

Method: Native exchange MS

Conditions: pH 10.0; 0.0 Celsius; Probes: every amide site

Related publication:
 PMID 20849085

Experiment details: "Protein refolding and pulsed HDX were carried out using a custom-made four-syringe continuous-flow setup with three sequential mixing steps. Syringe 1 was filled with an aqueous solution of 75 μM acid-unfolded aMb and 30 μM bradykinin in 10 mM HCl. Syringe 2 contained water with dilute ammonium hydroxide. Both syringes were connected to mixer M1 via fused silica capillaries. Refolding was initiated by mixing the contents of syringes 1 and 2 at M1 in a 1:1 volume ratio at a flow rate of 5 μl/min each, resulting in a pH jump from 2 to 10. The outlet of M1 was connected to a folding capillary. Depending on the folding time different capillary i.d. values and lengths were used (10 ms: i.d. 20 μm, l 5 mm; 100 ms: i.d. 50 μm, l 8.5 mm; 1 s: i.d. 75 μm, l 38 mm). Exchange was measured after one hour folding time."

Protection threshold: amide deuteration level < 0.25

Sequence: GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

STRONG residues

8: Q; 9: Q; 10: V; 11: L; 12: N; 13: V; 14: W; 15: G; 16: K; 17: V; 18: E; 25: G; 26: Q; 27: E; 28: V; 29: L; 30: I; 31: R; 32: L; 33: F; 34: T; 35: G; 36: H; 40: L; 41: E; 45: K; 54: E; 55: M; 56: K; 67: V; 68: V; 69: L; 70: T; 128: Q; 129: G; 131: M; 133: K; 134: A; 135: L; 136: E; 137: L; 143: A; 146: Y;
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MEDIUM

Method: Native exchange MS

Conditions: pH 10.0; 0.0 Celsius; Probes: every amide site

Related publication:
 PMID 20849085

Experiment details: "Protein refolding and pulsed HDX were carried out using a custom-made four-syringe continuous-flow setup with three sequential mixing steps. Syringe 1 was filled with an aqueous solution of 75 μM acid-unfolded aMb and 30 μM bradykinin in 10 mM HCl. Syringe 2 contained water with dilute ammonium hydroxide. Both syringes were connected to mixer M1 via fused silica capillaries. Refolding was initiated by mixing the contents of syringes 1 and 2 at M1 in a 1:1 volume ratio at a flow rate of 5 μl/min each, resulting in a pH jump from 2 to 10. The outlet of M1 was connected to a folding capillary. Depending on the folding time different capillary i.d. values and lengths were used (10 ms: i.d. 20 μm, l 5 mm; 100 ms: i.d. 50 μm, l 8.5 mm; 1 s: i.d. 75 μm, l 38 mm). Exchange was measured after one hour folding time."

Protection threshold: amide deuteration level 0.25-0.50

Sequence: GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

MEDIUM residues

6: E; 7: W; 23: G; 24: H; 43: F; 44: D; 61: L; 62: K; 63: K; 106: F; 107: I; 108: S; 109: D; 110: A; 111: I; 112: I; 113: H; 114: V; 115: L; 116: H; 130: A; 132: T; 140: N; 142: I;
 CLICK TO DOWNLOAD LIST OF RESIDUES

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WEAK

Method: Native exchange MS

Conditions: pH 10.0; 0.0 Celsius; Probes: every amide site

Related publication:
 PMID 20849085

Experiment details: "Protein refolding and pulsed HDX were carried out using a custom-made four-syringe continuous-flow setup with three sequential mixing steps. Syringe 1 was filled with an aqueous solution of 75 μM acid-unfolded aMb and 30 μM bradykinin in 10 mM HCl. Syringe 2 contained water with dilute ammonium hydroxide. Both syringes were connected to mixer M1 via fused silica capillaries. Refolding was initiated by mixing the contents of syringes 1 and 2 at M1 in a 1:1 volume ratio at a flow rate of 5 μl/min each, resulting in a pH jump from 2 to 10. The outlet of M1 was connected to a folding capillary. Depending on the folding time different capillary i.d. values and lengths were used (10 ms: i.d. 20 μm, l 5 mm; 100 ms: i.d. 50 μm, l 8.5 mm; 1 s: i.d. 75 μm, l 38 mm). Exchange was measured after one hour folding time."

Protection threshold: amide deuteration level more than 0.50

Sequence: GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

WEAK residues

2: L; 3: S; 4: D; 5: G; 19: A; 20: D; 21: I; 22: A; 37: P; 38: E; 39: T; 42: K; 46: F; 47: K; 48: H; 49: L; 50: K; 51: T; 52: E; 53: A; 57: A; 58: S; 59: E; 60: D; 64: H; 65: G; 66: T; 71: A; 72: L; 73: G; 74: G; 75: I; 76: L; 77: K; 78: K; 79: K; 80: G; 81: H; 82: H; 83: E; 84: A; 85: E; 86: L; 87: K; 88: P; 89: L; 90: A; 91: Q; 92: S; 93: H; 94: A; 95: T; 96: K; 97: H; 98: K; 99: I; 100: P; 101: I; 102: K; 103: Y; 104: L; 105: E; 117: S; 118: K; 119: H; 120: P; 121: G; 122: D; 123: F; 124: G; 125: A; 126: D; 127: A; 138: F; 139: R; 141: D; 144: A; 145: K; 147: K; 148: E; 149: L; 150: G; 151: F; 152: Q; 153: G;
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