Sandbox 11: Difference between revisions
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One of the major features of NAPase is that each protease has two domains, an N domain and a C domain. In this <scene name='Sandbox_11/Ntocrotatingone/1'>N to C Rainbow</scene>, one can see the N domain (red, orange, yellow), so-called because it contains the N-terminal amino acid, is connected covalently through the protein to the C domain (green, blue, violet). The horizontal axis of this scene is the main dividing line between the domains, with few chains crossing the barrier. | One of the major features of NAPase is that each protease has two domains, an N domain and a C domain. In this <scene name='Sandbox_11/Ntocrotatingone/1'>N to C Rainbow</scene>, one can see the N domain (red, orange, yellow), so-called because it contains the N-terminal amino acid, is connected covalently through the protein to the C domain (green, blue, violet). The horizontal axis of this scene is the main dividing line between the domains, with few chains crossing the barrier. | ||
Kelch (2007)<ref>PMID:17382344</ref>, looks at the differences between NAPase and <i>alpha</i>-lytic protease to try to understand what causes NAPase to be more acid resistant that <i>alpha</i>-lytic protease. It is found that they form a similar number of salt-bridges (7 in NAPase, 8 in <i>alpha</i>-lytic protease), but the salt bridges are in different places. Two of these bridges are conserved between the two, so there are five salt bridges that could be considered as important for acid resistance in NAPase. The important difference between the location of bridges is that <i>alpha</i>-lytic protease has three bridges that span the N and C domains, while NAPase has none that span the domains. (It is important to note here that research suggests that the first step to unfolding is when the two domains split.<ref>PMID:20195497</ref> Just ask Professor Jaswal, or look at reference 2.) <scene name='Sandbox_11/Two_salt_bridges/2'>This picture</scene> shows the charged residues of Glutamate and Arginine, with red representing a negative charge, and blue representing a positive charge. The distance between these residues is relatively small(avg. distance = 20 residues), when compared to the large distance between the residues in <i>alpha</i>-lytic protease (avg. distance = 78 residues).< | Kelch (2007)<ref>PMID:17382344</ref>, looks at the differences between NAPase and <i>alpha</i>-lytic protease to try to understand what causes NAPase to be more acid resistant that <i>alpha</i>-lytic protease. It is found that they form a similar number of salt-bridges (7 in NAPase, 8 in <i>alpha</i>-lytic protease), but the salt bridges are in different places. Two of these bridges are conserved between the two, so there are five salt bridges that could be considered as important for acid resistance in NAPase. The important difference between the location of bridges is that <i>alpha</i>-lytic protease has three bridges that span the N and C domains, while NAPase has none that span the domains. (It is important to note here that research suggests that the first step to unfolding is when the two domains split.<ref>PMID:20195497</ref> Just ask Professor Jaswal, or look at reference 2.) <scene name='Sandbox_11/Two_salt_bridges/2'>This picture</scene> shows the charged residues of Glutamate and Arginine, with red representing a negative charge, and blue representing a positive charge. The distance between these residues is relatively small(avg. distance = 20 residues), when compared to the large distance between the residues in <i>alpha</i>-lytic protease (avg. distance = 78 residues). So, at low pH, the domain bridging salt bridges of <i>alpha</i>-lytic protease break or weaken enough that the N and C domains split apart enough for <i>alpha</i>-lytic protease to be protealyzed. NAPase avoids this with its alternately placed salt bridges. This is not to say that the only reason NAPase is more stabilized at low pH is due to the placement of the salt bridges. | ||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 22:08, 23 June 2010
Please do NOT make changes to this sandbox. Sandboxes 10-30 are currently reserved by Prof. Sheila Jaswal at Amherst College.
Note to the reader: This is a really boring sandbox. I left all of my toys at home. Sorry.
NAPase
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| 2oua, resolution 1.85Å () | |||||||||
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| Ligands: | , , , | ||||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Nocardiopsis alba Protease A, or NAPase, is an acid-resistant homolog of alpha-lytic protease. As such, NAPase and alpha-lytic protease are both kinetically stable proteases, meaning it is the large barrier to unfolding that keeps this protease in its folded, active state. This is different from most other proteins, which stay in their folded, or native, state because of the energy difference between their native and unfolded states, with the native state being lower in energy. These proteases gain a significant advantage in half-life because of their kinetic stability, but it comes with a price. The barrier to folding is large, with alpha-lytic protease's half life for folding around 1800 years. Luckily, these proteases have coevolved a pro region that can assist with folding while covalently attached, or while in solution with the unfolded protease. Once the protease has been guided to its native state by the pro region, it mercilessly proteolyzes the pro region that helped it gain its protein-degrading ability.
The NAPase molecule provided shows two NAPase molecules that are mirror images, so here is just . NAPase, along with the rest of the trypsin family, has an active site that consists of the "catalytic triad." This is made up of three amino acid residues (H57, D102, and S195) that play a major role in binding the substrate and catalyzing proteolysis. The distance between these residues on the protein chain, and the complexity of folding one might imagine is occurring, help to demonstrate the value of the Pro region.
One of the major features of NAPase is that each protease has two domains, an N domain and a C domain. In this , one can see the N domain (red, orange, yellow), so-called because it contains the N-terminal amino acid, is connected covalently through the protein to the C domain (green, blue, violet). The horizontal axis of this scene is the main dividing line between the domains, with few chains crossing the barrier.
Kelch (2007)[1], looks at the differences between NAPase and alpha-lytic protease to try to understand what causes NAPase to be more acid resistant that alpha-lytic protease. It is found that they form a similar number of salt-bridges (7 in NAPase, 8 in alpha-lytic protease), but the salt bridges are in different places. Two of these bridges are conserved between the two, so there are five salt bridges that could be considered as important for acid resistance in NAPase. The important difference between the location of bridges is that alpha-lytic protease has three bridges that span the N and C domains, while NAPase has none that span the domains. (It is important to note here that research suggests that the first step to unfolding is when the two domains split.[2] Just ask Professor Jaswal, or look at reference 2.) shows the charged residues of Glutamate and Arginine, with red representing a negative charge, and blue representing a positive charge. The distance between these residues is relatively small(avg. distance = 20 residues), when compared to the large distance between the residues in alpha-lytic protease (avg. distance = 78 residues). So, at low pH, the domain bridging salt bridges of alpha-lytic protease break or weaken enough that the N and C domains split apart enough for alpha-lytic protease to be protealyzed. NAPase avoids this with its alternately placed salt bridges. This is not to say that the only reason NAPase is more stabilized at low pH is due to the placement of the salt bridges.
ReferencesReferences
- ↑ Kelch BA, Eagen KP, Erciyas FP, Humphris EL, Thomason AR, Mitsuiki S, Agard DA. Structural and mechanistic exploration of acid resistance: kinetic stability facilitates evolution of extremophilic behavior. J Mol Biol. 2007 May 4;368(3):870-83. Epub 2007 Feb 22. PMID:17382344 doi:10.1016/j.jmb.2007.02.032
- ↑ Salimi NL, Ho B, Agard DA. Unfolding simulations reveal the mechanism of extreme unfolding cooperativity in the kinetically stable alpha-lytic protease. PLoS Comput Biol. 2010 Feb 26;6(2):e1000689. PMID:20195497 doi:10.1371/journal.pcbi.1000689