User:Amy Kerzmann/Sandbox 3
From Proteopedia
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| - | {{STRUCTURE_1bl8| PDB=1bl8 | SCENE=User:Amy_Kerzmann/Sandbox_2/Potassium_ions/5}} | + | {{STRUCTURE_1bl8 | PDB=1bl8 | SCENE=User:Amy_Kerzmann/Sandbox_2/Potassium_ions/5}} |
| - | =='''Background'''== | + | =='''Background Information'''== |
Initial observations of the extraordinary selectivity of some ion-conducting channels for potassium baffled many scientists. How could such proteins permit the passage of potassium ions while restricting smaller sodium ions from being transferred across the membrane? | Initial observations of the extraordinary selectivity of some ion-conducting channels for potassium baffled many scientists. How could such proteins permit the passage of potassium ions while restricting smaller sodium ions from being transferred across the membrane? | ||
The crystal structure of the ''Streptomyces lividans'' potassium channel illuminated the principles of ion selectivity when it was solved in 1998 (PDB:1bl8).<ref name="Doyle">PMID:9525859</ref> To further demonstrate the importance of this structure, the [http://nobelprize.org/nobel_prizes/chemistry/laureates/2003 2003 Nobel Prize in Chemistry] was awarded to Roderick MacKinnon for the work performed in his HHMI laboratory at Rockefeller University. | The crystal structure of the ''Streptomyces lividans'' potassium channel illuminated the principles of ion selectivity when it was solved in 1998 (PDB:1bl8).<ref name="Doyle">PMID:9525859</ref> To further demonstrate the importance of this structure, the [http://nobelprize.org/nobel_prizes/chemistry/laureates/2003 2003 Nobel Prize in Chemistry] was awarded to Roderick MacKinnon for the work performed in his HHMI laboratory at Rockefeller University. | ||
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=='''Channel Structure'''== | =='''Channel Structure'''== | ||
| - | <applet load='1bl8' size='300' frame='true' align='left' caption='This Streptomyces lividans protein was the first potassium channel to be crystallized.' /> | + | <applet load='1bl8' size='300' frame='true' align='left' scene='User:Amy_Kerzmann/Sandbox_3/Spacefill/1' target='1' caption='This Streptomyces lividans protein was the first potassium channel to be crystallized.' /> |
| - | As described by Doyle, ''et al'' in their original paper, the potassium channel forms an "inverted teepee, or cone" with the widest portion facing the extracellular space.<ref name="Doyle" /> Almost the entire structure is buried within the lipid bilayer, which is evident when the | + | As described by Doyle, ''et al'' in their original paper, the potassium channel forms an "inverted teepee, or cone" with the widest portion facing the extracellular space.<ref name="Doyle" /> Almost the entire crystalized structure is buried within the lipid bilayer, which is evident when the spacefill structure is colored according to the <scene name='User:Amy_Kerzmann/Sandbox_2/Hydrophobicity/1'>hydrophobicity</scene> of each sidechain (residues are indicated as: {{Template:ColorKey_Hydrophobic}} or {{Template:ColorKey_Polar}}). The protein spans approximately 34 angstroms of the lipid bilayer <ref name="Doyle" />, based on the distance between the <scene name='User:Amy_Kerzmann/Sandbox_3/Bilayer_thickness/1'>aromatic amino acids</scene> highlighted in black. |
The potassium channel is also a homotetramer, which means that it is comprised of <scene name='User:Amy_Kerzmann/Sandbox_3/Original_scene/1'>four</scene> identical protein chains or monomers, each shown in a different color. These monomeric units assemble to form a functional protein with <scene name='User:Amy_Kerzmann/Sandbox_3/Four-fold_symmetry/1'>four-fold rotational symmetry</scene> around the longitudinal axis, which is best viewed from either membrane surface. As a result, each of the channel-lining residues appears as a ring of four identical sidechains. This principle is represented by the conserved <scene name='User:Amy_Kerzmann/Sandbox_2/Tyrosine_symmetry/1'>tyrosine</scene> amino acids that function as selectivity filters within the cavity. Additional <scene name='User:Amy_Kerzmann/Sandbox_2/Aspartate_symmetry/1'>aspartate</scene>, <scene name='User:Amy_Kerzmann/Sandbox_2/Threonine_symmetry/2'>threonine</scene> and <scene name='User:Amy_Kerzmann/Sandbox_3/Glycine_symmetry/1'>glycine</scene> sidechains line the channel. We will examine each of these conserved sites in greater detail under the "Channel Function" heading. It is also important to note that analysis of a <scene name='User:Amy_Kerzmann/Sandbox_3/Channel-lining_residues/2'>composite scene</scene> of these residues reveals some hydrophobic patches within the cavity. | The potassium channel is also a homotetramer, which means that it is comprised of <scene name='User:Amy_Kerzmann/Sandbox_3/Original_scene/1'>four</scene> identical protein chains or monomers, each shown in a different color. These monomeric units assemble to form a functional protein with <scene name='User:Amy_Kerzmann/Sandbox_3/Four-fold_symmetry/1'>four-fold rotational symmetry</scene> around the longitudinal axis, which is best viewed from either membrane surface. As a result, each of the channel-lining residues appears as a ring of four identical sidechains. This principle is represented by the conserved <scene name='User:Amy_Kerzmann/Sandbox_2/Tyrosine_symmetry/1'>tyrosine</scene> amino acids that function as selectivity filters within the cavity. Additional <scene name='User:Amy_Kerzmann/Sandbox_2/Aspartate_symmetry/1'>aspartate</scene>, <scene name='User:Amy_Kerzmann/Sandbox_2/Threonine_symmetry/2'>threonine</scene> and <scene name='User:Amy_Kerzmann/Sandbox_3/Glycine_symmetry/1'>glycine</scene> sidechains line the channel. We will examine each of these conserved sites in greater detail under the "Channel Function" heading. It is also important to note that analysis of a <scene name='User:Amy_Kerzmann/Sandbox_3/Channel-lining_residues/2'>composite scene</scene> of these residues reveals some hydrophobic patches within the cavity. | ||
| - | Each <scene name='User:Amy_Kerzmann/Sandbox_2/Chain_a/3'>monomer</scene> is predominantly <scene name='User:Amy_Kerzmann/Sandbox_2/Chain_a/4'>alpha helical</scene> and lacks beta strands. When viewed in <scene name='User:Amy_Kerzmann/Sandbox_2/Chain_a/5'>N->C color coding</scene> (where the N-terminus is | + | Each <scene name='User:Amy_Kerzmann/Sandbox_2/Chain_a/3'>monomer</scene> is predominantly <scene name='User:Amy_Kerzmann/Sandbox_2/Chain_a/4'>alpha helical</scene> and lacks beta strands. |
| + | Secondary structure is coded by the following, if present: {{Template:ColorKey_Helix}}, {{Template:ColorKey_Strand}}, and {{Template:ColorKey_Turn}}. | ||
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| + | When viewed in <scene name='User:Amy_Kerzmann/Sandbox_2/Chain_a/5'>N->C color coding</scene> (where the <FONT COLOR="blue">'''N-terminus'''</FONT> is gradually shaded into the <FONT COLOR="red">'''C-terminus'''</FONT> according to the scale below), one can see that both termini are located on the cytosolic side of the membrane. Note that the two C-terminal helices form the central core of the channel and that the region between them lines the cavity, making contacts with the migrating potassium ions. {{Template:ColorKey_N2CRainbow}} | ||
=='''Selectivity Filter'''== | =='''Selectivity Filter'''== | ||
| - | <applet load='1bl8' size='300' frame='true' align='left' caption='The structure of this channel revealed how potassium selectivity is attained.' /> | + | <applet load='1bl8' size='300' frame='true' align='left' scene='User:Amy_Kerzmann/Sandbox_3/Carbonyls/2' target='2' caption='The structure of this channel revealed how potassium selectivity is attained.' /> |
| - | The selectivity filter of the channel is formed from the strand that connects the second and third helices of each monomer, as briefly described above. In this case, the <scene name='User:Amy_Kerzmann/Sandbox_3/Carbonyls/1'>carbonyl groups</scene> of the backbone that span residues 74-79 make direct contact with potassium ions. The partial negative charge supplied by these carbonyl groups repel negatively charged ions that approach the channel. These carbonyl-ion contacts are clearer when <scene name='User:Amy_Kerzmann/Sandbox_3/Carbonyls_-_two_chains/2'>only two protein chains</scene> are visualized. A conserved <scene name='User:Amy_Kerzmann/ | + | |
| + | The selectivity filter of the channel is formed from the strand that connects the second and third helices of each monomer, as briefly described above. In this case, the <scene name='User:Amy_Kerzmann/Sandbox_3/Carbonyls/1'>carbonyl groups</scene> of the backbone that span residues 74-79 make direct contact with potassium ions. The partial negative charge supplied by these carbonyl groups repel negatively charged ions that approach the channel. These carbonyl-ion contacts are clearer when <scene name='User:Amy_Kerzmann/Sandbox_3/Carbonyls_-_two_chains/2'>only two protein chains</scene> are visualized. Note that the lower two potassium ions in this view overlap in such a manner to suggest that both ions are not present concurrently. It is more likely that they represent an average of electron density from two or more distinct binding sites which are in steady exchange due to sufficiently similar affinity. A conserved <scene name='User:Amy_Kerzmann/Sandbox_3/Carbonyls_-_two_chains-y78/1'>tyrosine</scene> (Y78) forms the narrowest portion of the selectivity filter, with the carbonyl oxygen atoms pointed toward the core. | ||
In addition to the partial negative charges from the carbonyl oxygens that line the core of the channel, the passage of cations is further stabilized by the <scene name='User:Amy_Kerzmann/Sandbox_3/Helix_dipole/1'>dipole moments</scene> of the four central helices. In each case, the partial negative charge is directed toward the central cavity. | In addition to the partial negative charges from the carbonyl oxygens that line the core of the channel, the passage of cations is further stabilized by the <scene name='User:Amy_Kerzmann/Sandbox_3/Helix_dipole/1'>dipole moments</scene> of the four central helices. In each case, the partial negative charge is directed toward the central cavity. | ||
| - | It is apparent from these images that potassium must be completely stripped of its waters of hydration to pass through the channel. This observation was the key finding from the crystal structure that lead to an understanding of the channel selectivity. While hydrated potassium and sodium ions are approximately the same size, the unsolvated ions have significantly different diameters. The larger potassium ion can shed its coordinated water molecules (an unfavorable process) because contacts with carbonyl oxygens within the channel are suitable substitutes. On the other hand, sodium is too small to form these compensatory bonds with the protein channel. Therefore, since the hydrated | + | It is apparent from these images that potassium must be completely stripped of its waters of hydration to pass through the channel. This observation was the key finding from the crystal structure that lead to an understanding of the channel selectivity. While hydrated potassium and sodium ions are approximately the same size, the unsolvated ions have significantly different diameters (Na+ is 1.90 Å, K+ is 2.66 Å). The larger potassium ion can shed its coordinated water molecules (an unfavorable process) because contacts with carbonyl oxygens within the channel are suitable substitutes. On the other hand, sodium is too small to form these compensatory bonds with the protein channel. Therefore, since the hydrated sodium is too large and the dehydrated sodium is too small, the potassium channel seems to be another example of the [http://en.wikipedia.org/wiki/Goldilocks_Principle "Goldilocks Principle"], in which only the desolvated form of potassium is "just right" for passage. |
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| + | =='''Channel Function'''== | ||
| + | As the potassium ions move past the selectivity filter, they are exposed to an aqueous cavity lined with relatively hydrophobic residues. In this cavity, the potassium ions become rehydrated, driving their movement out of the channel and into the cytosol. This arrangement is efficient for rapid passage of ions, as a channel entirely lined with negative charge would provide too many contacts and potential thermodynamic wells. | ||
Current revision
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| 1bl8, resolution 3.20Å () | |||||||||
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| Ligands: | |||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Contents |
Background Information
Initial observations of the extraordinary selectivity of some ion-conducting channels for potassium baffled many scientists. How could such proteins permit the passage of potassium ions while restricting smaller sodium ions from being transferred across the membrane?
The crystal structure of the Streptomyces lividans potassium channel illuminated the principles of ion selectivity when it was solved in 1998 (PDB:1bl8).[1] To further demonstrate the importance of this structure, the 2003 Nobel Prize in Chemistry was awarded to Roderick MacKinnon for the work performed in his HHMI laboratory at Rockefeller University.
Channel Structure
|
As described by Doyle, et al in their original paper, the potassium channel forms an "inverted teepee, or cone" with the widest portion facing the extracellular space.[1] Almost the entire crystalized structure is buried within the lipid bilayer, which is evident when the spacefill structure is colored according to the of each sidechain (residues are indicated as: Hydrophobic or Polar). The protein spans approximately 34 angstroms of the lipid bilayer [1], based on the distance between the highlighted in black.
The potassium channel is also a homotetramer, which means that it is comprised of identical protein chains or monomers, each shown in a different color. These monomeric units assemble to form a functional protein with around the longitudinal axis, which is best viewed from either membrane surface. As a result, each of the channel-lining residues appears as a ring of four identical sidechains. This principle is represented by the conserved amino acids that function as selectivity filters within the cavity. Additional , and sidechains line the channel. We will examine each of these conserved sites in greater detail under the "Channel Function" heading. It is also important to note that analysis of a of these residues reveals some hydrophobic patches within the cavity.
Each is predominantly and lacks beta strands. Secondary structure is coded by the following, if present: Alpha Helices, Beta Strands , and Turns.
| N | C |
Selectivity Filter
|
The selectivity filter of the channel is formed from the strand that connects the second and third helices of each monomer, as briefly described above. In this case, the of the backbone that span residues 74-79 make direct contact with potassium ions. The partial negative charge supplied by these carbonyl groups repel negatively charged ions that approach the channel. These carbonyl-ion contacts are clearer when are visualized. Note that the lower two potassium ions in this view overlap in such a manner to suggest that both ions are not present concurrently. It is more likely that they represent an average of electron density from two or more distinct binding sites which are in steady exchange due to sufficiently similar affinity. A conserved (Y78) forms the narrowest portion of the selectivity filter, with the carbonyl oxygen atoms pointed toward the core.
In addition to the partial negative charges from the carbonyl oxygens that line the core of the channel, the passage of cations is further stabilized by the of the four central helices. In each case, the partial negative charge is directed toward the central cavity.
It is apparent from these images that potassium must be completely stripped of its waters of hydration to pass through the channel. This observation was the key finding from the crystal structure that lead to an understanding of the channel selectivity. While hydrated potassium and sodium ions are approximately the same size, the unsolvated ions have significantly different diameters (Na+ is 1.90 Å, K+ is 2.66 Å). The larger potassium ion can shed its coordinated water molecules (an unfavorable process) because contacts with carbonyl oxygens within the channel are suitable substitutes. On the other hand, sodium is too small to form these compensatory bonds with the protein channel. Therefore, since the hydrated sodium is too large and the dehydrated sodium is too small, the potassium channel seems to be another example of the "Goldilocks Principle", in which only the desolvated form of potassium is "just right" for passage.
Channel Function
As the potassium ions move past the selectivity filter, they are exposed to an aqueous cavity lined with relatively hydrophobic residues. In this cavity, the potassium ions become rehydrated, driving their movement out of the channel and into the cytosol. This arrangement is efficient for rapid passage of ions, as a channel entirely lined with negative charge would provide too many contacts and potential thermodynamic wells.
Gating Mechanism
Details of the voltage-gated mechanism go here.
References
