User:Michael Roberts/BIOL115 Myo: Difference between revisions

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[[Image:1a6m.png|left|150px|thumb|Crystal Structure of myoglobin, [[1a6m]]]]
[[Image:myo.png|left|200px|thumb|Myoglobin with oxygen bound to heme ([[1a6m]])]]




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Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.
Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.


<StructureSection load='1mbo' size='500' side='right' caption='Structure of Myoglobin (PDB entry [[1mbo]])' scene='User:Michael_Roberts/BIOL115_Myo/Start/1'>
<StructureSection load='1mbo' size='600' side='right' caption='Structure of Myoglobin (PDB entry [[1mbo]])' scene='User:Michael_Roberts/BIOL115_Myo/Start/1'>
'''MOLECULAR MODEL:'''
== Molecular model: ==
The initial view here is a ball-and-stick representation of the molecular structure of myoglobin.
The initial view here is a ball-and-stick representation of the molecular structure of myoglobin.




'''SECONDARY STRUCTURE''':
'''SECONDARY STRUCTURE''': This next view simplifies things, and just shows a <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/9'>cartoon representation </scene>of the secondary structure of the protein.
You see how the <scene name='User:Michael_Roberts/BIOL115_Myo/Hbonds/1'>hydrogen bonds</scene> (yellow) that maintain the main secondary structure of the protein are arranged in this next view.
Some amino acids have specific effects on secondary structure. This next view shows the locations of the <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/11'>PROLINE</scene> residues in myoglobin. You can see that they all fall at the end of a stretch of helix. This is because their large, cyclic side chains do not fit within the straight run of α-helix.


This next view simplifies things, and just shows a <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/1'>cartoon representation </scene>of the secondary structure of the protein.


'''THE GLOBIN FOLD''': In this next view, the eight <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/3'>individual alpha-helices </scene>are each coloured differently. This gives you an impression of the classic globin fold. The α-helices pack together tightly, and there is very little space in the centre of the protein.


'''THE GLOBIN FOLD''':
In this next view, the eight <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/3'>individual alpha-helices </scene>are each coloured differently. This gives you an impression of the classic globion fold. The α-helices pack together tightly, and there is very little space in the centre of the protein.




'''HYDROPHOBICITY''':
'''HYDROPHOBICITY''': Globular folds like this are characterised by a polar, <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/4'>hydrophilic exterior</scene>, which interacts with the aqueous solvent, and a hydrophobic core.
 
Globular folds like this are characterised by a polar, <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/4'>hydrophilic exterior</scene>, which interacts with the aqueous solvent, and a hydrophobic core.
{{Template:ColorKey_Hydrophobic}},  {{Template:ColorKey_Polar}}
{{Template:ColorKey_Hydrophobic}},  {{Template:ColorKey_Polar}}


The next view shows a section through the protein that highlights the <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/5'>hydrophobic core </scene>better.
The next view shows a section through the protein that highlights the <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/5'>hydrophobic core </scene>better.
This view has been produced in the software by a process known as 'slabbing'. You can still rotate the molecule around - whatever view you see will the the front part of the view of the protein cut off.
This view has been produced in the software by a process known as 'slabbing'. You can still rotate the molecule around - whatever view you see will have the front part of the view of the protein cut off.




'''THE HEME GROUP''':
== The Heme Group ==
 
Now let's turn our attention to the main function of myoglobin - oxygen binding.
Now let's turn our attention to the main function of myoglobin - oxygen binding.
Oxygen is bound by a <scene name='User:Michael_Roberts/BIOL115_Myo/Heme/1'>heme group</scene>, which sits in a hydrophobic pocket in the myoglobin protein.
Oxygen is bound by a <scene name='User:Michael_Roberts/BIOL115_Myo/Heme/1'>heme group</scene>, (coloured red) which sits in a hydrophobic pocket in the myoglobin protein.


Central to the heme group is an <scene name='User:Michael_Roberts/BIOL115_Myo/Heme/3'>iron (Fe) atom</scene>.
Central to the heme group is an <scene name='User:Michael_Roberts/BIOL115_Myo/Heme/3'>iron (Fe) atom</scene>.




'''PROXIMAL AND DISTAL HISTIDINES''':
'''PROXIMAL AND DISTAL HISTIDINES''': The iron atom sits either side of the side chains of two <scene name='User:Michael_Roberts/BIOL115_Myo/Heme/4'>histidine residues</scene>.
 
One of these (coloured cyan) is attached to the iron atom, and is known as the ''proximal'' histidine. It is also referred to as His F8, because it is the eighth residue of helix F. The other (green) is called the ''distal'' histidine, also referred to as His E7 (7<sup>th</sup> residue of helix E).
The iron atom sits either side of the side chains of two <scene name='User:Michael_Roberts/BIOL115_Myo/Heme/4'>histidine residues</scene>.
Note how the iron is pulled out slightly to one side of the plane of the haem group as a result of it's co-ordination with the side chain of the proximal histidine.
One of these (coloured cyan) is attached to the iron atom, and is known as the ''proximal'' histidine. The other (green) is called the ''distal'' histidine.




'''OXYGEN''':
'''OXYGEN''':
The space between the iron and the distal histidine is where the <scene name='User:Michael_Roberts/BIOL115_Myo/Heme/6'>oxygen </scene>binds.
The space between the iron and the distal histidine is where the <scene name='User:Michael_Roberts/BIOL115_Myo/Heme/6'>oxygen</scene> (pink) binds.
Note the angled orientation of the oxygen relative to the plane of the haem. The oxygen-haem complex is stabilised by the presence of the side chain of the distal His, which contributes a hydrogen atom that hydrogen bonds with the O<sub>2</sub>. The presence of the distal His also reduces the affinity of haem for carbon monoxide, by displacing it from it's more natural position perpendicular to the plane of the haem into a more angled position, similar to bound O<sub>2</sub>.


</StructureSection>
</StructureSection>
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