Start2Fold

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

Entry STF0016

Turkey ovomucoid third domain (OMTKY3)

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Protein information

Name of the protein: Ovomucoid
Organism: Meleagris gallopavo (Wild turkey)
Number of residues: 56
Related UniProt entry:   P68390 (Fragment: 130 - 185)
Related PDB entry:   1OMU

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Experiment sets

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EARLY

Method: pH-dependent HDX NMR

Conditions: pH 6.0-10.0; 30.0 Celsius; Probes: 13

Related publication:
 PMID 9289014

Experiment details: "Rates of unfolding and folding have been determined by monitoring NH exchange over a range of pH where (1) the free energy of unfolding is insensitive to pH and (2) the mechanism of exchange changes from one governed by a rapid equilibrium preceding the chemistry of exchange (i.e., EX2 exchange) to one where exchange is limited by the rate of unfolding (i.e., EX1 exchange). The pH dependence of exchange has then been fit to a two-state model to obtain the unfolding and folding rates. Exchange samples were prepared by adjusting aliquots of pure OMTKY3 in H2O to the desired experimental pH with potassium hydroxide. Protein solutions were then lyophilized to a constant weight. Exchange buffers, consisting of 10 mM glycine and 10 mM glycyl-glycine in D2O, were also preadjusted to the desired experimental pH by addition of sodium deuterioxide. The final concentration of buffered OMTKY3 was approximately 2 mM for each experiment. Sample pH was measured after each experiment."

Protection threshold: closing rate time constant < 170 microsec

Sequence: LAAVSVDCSEYPKPACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC
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EARLY residues

38: C; 39: N; 40: A; 24: C;
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INTERMEDIATE

Method: pH-dependent HDX NMR

Conditions: pH 6.0-10.0; 30.0 Celsius; Probes: 13

Related publication:
 PMID 9289014

Experiment details: "Rates of unfolding and folding have been determined by monitoring NH exchange over a range of pH where (1) the free energy of unfolding is insensitive to pH and (2) the mechanism of exchange changes from one governed by a rapid equilibrium preceding the chemistry of exchange (i.e., EX2 exchange) to one where exchange is limited by the rate of unfolding (i.e., EX1 exchange). The pH dependence of exchange has then been fit to a two-state model to obtain the unfolding and folding rates. Exchange samples were prepared by adjusting aliquots of pure OMTKY3 in H2O to the desired experimental pH with potassium hydroxide. Protein solutions were then lyophilized to a constant weight. Exchange buffers, consisting of 10 mM glycine and 10 mM glycyl-glycine in D2O, were also preadjusted to the desired experimental pH by addition of sodium deuterioxide. The final concentration of buffered OMTKY3 was approximately 2 mM for each experiment. Sample pH was measured after each experiment."

Protection threshold: 400 < closing rate time constant (microsec) < 1200

Sequence: LAAVSVDCSEYPKPACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC
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INTERMEDIATE residues

25: G; 28: N; 29: K; 31: Y; 33: N; 37: F; 41: V; 51: S;
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LATE

Method: pH-dependent HDX NMR

Conditions: pH 6.0-10.0; 30.0 Celsius; Probes: 13

Related publication:
 PMID 9289014

Experiment details: "Rates of unfolding and folding have been determined by monitoring NH exchange over a range of pH where (1) the free energy of unfolding is insensitive to pH and (2) the mechanism of exchange changes from one governed by a rapid equilibrium preceding the chemistry of exchange (i.e., EX2 exchange) to one where exchange is limited by the rate of unfolding (i.e., EX1 exchange). The pH dependence of exchange has then been fit to a two-state model to obtain the unfolding and folding rates. Exchange samples were prepared by adjusting aliquots of pure OMTKY3 in H2O to the desired experimental pH with potassium hydroxide. Protein solutions were then lyophilized to a constant weight. Exchange buffers, consisting of 10 mM glycine and 10 mM glycyl-glycine in D2O, were also preadjusted to the desired experimental pH by addition of sodium deuterioxide. The final concentration of buffered OMTKY3 was approximately 2 mM for each experiment. Sample pH was measured after each experiment."

Protection threshold: closing rate time constant > 1200 microsec

Sequence: LAAVSVDCSEYPKPACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC
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LATE residues

23: L;
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STRONG

Method: Native exchange NMR

Conditions: pH 3.0; 40.0 Celsius; Probes: >30

Related publication:
 PMID 8555171

Experiment details: "Two-dimensional nuclear magnetic resonance spectroscopy has been used to monitor H/D exchange rates for more than 30 residues in turkey ovomucoid third domain. To test whether exchange is governed by global unfolding, rates were measured over a wide range of pH and temperatures where the change in the free energy of unfolding (ΔG(uf)) is known."

Protection threshold: slowly exchanging amid protons

Sequence: LAAVSVDCSEYPKPACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC
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STRONG residues

23: L; 24: C; 26: S; 28: N; 29: K; 31: Y; 33: N; 35: C; 37: F; 38: C; 39: N; 40: A; 41: V; 51: S;
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