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https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Michael+Roberts Proteopedia - User contributions [en] 2026-09-16T00:48:01Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=User:Michael_Roberts&diff=2683581 User:Michael Roberts 2016-10-20T15:22:31Z

<p>Michael Roberts: </p> <hr /> <div>*[[User:Michael Roberts/Sandbox1]]<br /> <br /> * Full Real Name: Michael Roberts<br /> <br /> * Position: Senior Lecturer<br /> <br /> * Institution (NO ABBREVIATIONS): Lancaster University<br /> <br /> * City, State/Province, Country: Lancaster, Lancashire, UK<br /> <br /> * Field of Expertise or Study: Plant molecular biology & signalling</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2683573 User:Michael Roberts/Open-Day Demo 2016-10-20T11:39:07Z

<p>Michael Roberts: </p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> <br /> <StructureSection load='1afq' size='600' side='right' caption=' ' scene='70/703491/Basic_representations/1'><br /> ==Representing protein structures==<br /> '''Spacefill model'''<br /> <br /> The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called <scene name='70/703491/Basic_representations/1'>'spacefill'</scene> view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> <br /> <br /> <br /> '''Ball-and-stick molecular model'''<br /> This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example. <br /> <br /> <br /> <br /> '''Amino acid trace'''<br /> Here's a much more simplified view that <scene name='70/703491/Basic_representations/4'>shows a trace of the backbone</scene> of the amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!<br /> <br /> One question this view does raise, is how the three separate chains are held together in the right way? The answer is the <scene name='70/703491/Basic_representations/5'>presence of disulphide bridges</scene> that link the chains together to form the correct overall structure.<br /> <br /> <br /> What we really need to do next is to have a basic introduction to protein structure. The section that follows is based on the [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure Introduction to Protein Structure] Proteopedia page.<br /> <br /> <br /> == Levels of Protein Structure ==<br /> '''Primary structure'''<br /> <br /> Proteins are polymers of amino acids joined together in linear chains. There are four recognised levels of structural organisation for proteins.<br /> The first, referred to as the <scene name='57/575866/Primary_sequence/2'>primary structure</scene>, is simply the amino acid sequence, from the N terminus (start) to the C terminus (end) of the protein.<br /> <br /> <br /> '''Secondary Structure'''<br /> <br /> The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances. This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/1'>hydrogen bonds</scene> along the amino acid backbone. There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta strands, a planar (flat) arrangement of amino acids which often line up together to from so-called beta sheets.<br /> <br /> <br /> '''Tertiary Structure'''<br /> <br /> These secondary structures <scene name='57/575866/Global_secondary_structures/1'>pack together</scene> to form the overall form of the entire peptide chain, called the <scene name='57/575866/Tertiary/1'>tertiary structure</scene>.<br /> <br /> <br /> '''Quaternary Structure'''<br /> <br /> Some proteins, such as the hemoglobin molecule displayed here, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called <scene name='57/575866/Tertiary/2'>quaternary structure</scene>.<br /> <br /> <br /> == Secondary Structure in chymotrypsin ==<br /> Now that we know something about the structural organisation of proteins, let's go back to our chymotrypsin molecule and have another look.<br /> <br /> This time, we'll display a <scene name='User:Michael_Roberts/BIOL115_Chymo/2ndry_structure/1'>cartoon representation</scene> indicating the main secondary structural elements. We can see that the main structural form in chymotrypsin is the beta strand, with only a small amount of α-helix.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> <br /> We can also see that the protein is organised into two structurally-similar domains. Each domain contains a group of beta strands arranged as anti-parallel sheets forming a circular structure known as a beta barrel. You can rotate the molecule so that you can see down through each of the two beta barrels in turn.<br /> <br /> <br /> Finally, here's chymotrypsin with a molecule of <scene name='70/703491/Substrate/3'>substrate</scene> bound in its active site. Note how the substrate fits into a pocket on the surface of the enzyme.<br /> <br /> <br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2683572 User:Michael Roberts/Open-Day Demo 2016-10-20T11:38:16Z

<p>Michael Roberts: </p> <hr /> <div><scene name='70/703491/Basic_representations/4'>Text To Be Displayed</scene>==Interactive visualisation of 3D protein structures==<br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> <br /> <StructureSection load='1afq' size='600' side='right' caption=' ' scene='70/703491/Basic_representations/1'><br /> ==Representing protein structures==<br /> '''Spacefill model'''<br /> <br /> The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called <scene name='70/703491/Basic_representations/1'>'spacefill'</scene> view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> <br /> <br /> <br /> '''Ball-and-stick molecular model'''<br /> This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example. <br /> <br /> <br /> <br /> '''Amino acid trace'''<br /> Here's a much more simplified view that <scene name='70/703491/Basic_representations/4'>shows a trace of the backbone</scene> of the amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!<br /> <br /> One question this view does raise, is how the three separate chains are held together in the right way? The answer is the <scene name='70/703491/Basic_representations/5'>presence of disulphide bridges</scene> that link the chains together to form the correct overall structure.<br /> <br /> <br /> What we really need to do next is to have a basic introduction to protein structure. The section that follows is based on the [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure Introduction to Protein Structure] Proteopedia page.<br /> <br /> <br /> == Levels of Protein Structure ==<br /> '''Primary structure'''<br /> <br /> Proteins are polymers of amino acids joined together in linear chains. There are four recognised levels of structural organisation for proteins.<br /> The first, referred to as the <scene name='57/575866/Primary_sequence/2'>primary structure</scene>, is simply the amino acid sequence, from the N terminus (start) to the C terminus (end) of the protein.<br /> <br /> <br /> '''Secondary Structure'''<br /> <br /> The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances. This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/1'>hydrogen bonds</scene> along the amino acid backbone. There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta strands, a planar (flat) arrangement of amino acids which often line up together to from so-called beta sheets.<br /> <br /> <br /> '''Tertiary Structure'''<br /> <br /> These secondary structures <scene name='57/575866/Global_secondary_structures/1'>pack together</scene> to form the overall form of the entire peptide chain, called the <scene name='57/575866/Tertiary/1'>tertiary structure</scene>.<br /> <br /> <br /> '''Quaternary Structure'''<br /> <br /> Some proteins, such as the hemoglobin molecule displayed here, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called <scene name='57/575866/Tertiary/2'>quaternary structure</scene>.<br /> <br /> <br /> == Secondary Structure in chymotrypsin ==<br /> Now that we know something about the structural organisation of proteins, let's go back to our chymotrypsin molecule and have another look.<br /> <br /> This time, we'll display a <scene name='User:Michael_Roberts/BIOL115_Chymo/2ndry_structure/1'>cartoon representation</scene> indicating the main secondary structural elements. We can see that the main structural form in chymotrypsin is the beta strand, with only a small amount of α-helix.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> <br /> We can also see that the protein is organised into two structurally-similar domains. Each domain contains a group of beta strands arranged as anti-parallel sheets forming a circular structure known as a beta barrel. You can rotate the molecule so that you can see down through each of the two beta barrels in turn.<br /> <br /> <br /> Finally, here's chymotrypsin with a molecule of <scene name='70/703491/Substrate/3'>substrate</scene> bound in its active site. Note how the substrate fits into a pocket on the surface of the enzyme.<br /> <br /> <br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2683571 User:Michael Roberts/Open-Day Demo 2016-10-20T11:17:37Z

<p>Michael Roberts: </p> <hr /> <div><scene name='70/703491/Basic_representations/4'>Text To Be Displayed</scene>==Interactive visualisation of 3D protein structures==<br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> <br /> <StructureSection load='1afq' size='600' side='right' caption=' ' scene='70/703491/Basic_representations/1'><br /> ==Representing protein structures==<br /> '''Spacefill model'''<br /> <br /> The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called <scene name='70/703491/Basic_representations/1'>'spacefill'</scene> view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> <br /> <br /> <br /> '''Ball-and-stick molecular model'''<br /> This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example. <br /> <br /> <br /> <br /> '''Amino acid trace'''<br /> Here's a much more simplified view that <scene name='70/703491/Basic_representations/4<scene name='70/703491/Basic_representations/5'>Text To Be Displayed</scene>'>traces the chains</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!<br /> <br /> One question this view does raise, is how the three separate chains are held together in the right way? The answer is the <scene name='70/703491/Basic_representations/5'>presence of disulphide bridges</scene> that link the chains together to form the correct overall structure.<br /> <br /> <br /> What we really need to do next is to have a basic introduction to protein structure. The section that follows is based on the [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure Introduction to Protein Structure] Proteopedia page.<br /> <br /> <br /> == Levels of Protein Structure ==<br /> '''Primary structure'''<br /> <br /> Proteins are polymers of amino acids joined together in linear chains. There are four recognised levels of structural organisation for proteins.<br /> The first, referred to as the <scene name='57/575866/Primary_sequence/2'>primary structure</scene>, is simply the amino acid sequence, from the N terminus (start) to the C terminus (end) of the protein.<br /> <br /> <br /> '''Secondary Structure'''<br /> <br /> The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances. This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/1'>hydrogen bonds</scene> along the amino acid backbone. There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta strands, a planar (flat) arrangement of amino acids which often line up together to from so-called beta sheets.<br /> <br /> <br /> '''Tertiary Structure'''<br /> <br /> These secondary structures <scene name='57/575866/Global_secondary_structures/1'>pack together</scene> to form the overall form of the entire peptide chain, called the <scene name='57/575866/Tertiary/1'>tertiary structure</scene>.<br /> <br /> <br /> '''Quaternary Structure'''<br /> <br /> Some proteins, such as the hemoglobin molecule displayed here, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called <scene name='57/575866/Tertiary/2'>quaternary structure</scene>.<br /> <br /> <br /> == Secondary Structure in chymotrypsin ==<br /> Now that we know something about the structural organisation of proteins, let's go back to our chymotrypsin molecule and have another look.<br /> <br /> This time, we'll display a <scene name='User:Michael_Roberts/BIOL115_Chymo/2ndry_structure/1'>cartoon representation</scene> indicating the main secondary structural elements. We can see that the main structural form in chymotrypsin is the beta strand, with only a small amount of α-helix.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> <br /> We can also see that the protein is organised into two structurally-similar domains. Each domain contains a group of beta strands arranged as anti-parallel sheets forming a circular structure known as a beta barrel. You can rotate the molecule so that you can see down through each of the two beta barrels in turn.<br /> <br /> <br /> Finally, here's chymotrypsin with a molecule of <scene name='70/703491/Substrate/3'>substrate</scene> bound in its active site. Note how the substrate fits into a pocket on the surface of the enzyme.<br /> <br /> <br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2607518 User:Michael Roberts/Open-Day Demo 2016-06-16T16:20:53Z

<p>Michael Roberts: Structure of Hemoglobin</p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> <br /> <StructureSection load='1afq' size='600' side='right' caption=' ' scene='70/703491/Basic_representations/1'><br /> ==Representing protein structures==<br /> '''Spacefill model'''<br /> <br /> The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called <scene name='70/703491/Basic_representations/1'>'spacefill'</scene> view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> <br /> <br /> <br /> '''Ball-and-stick molecular model'''<br /> This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example. <br /> <br /> <br /> <br /> '''Amino acid trace'''<br /> Here's a much more simplified view that <scene name='70/703491/Basic_representations/3'>traces the chains</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!<br /> <br /> <br /> What we really need to do next is to have a basic introduction to protein structure. The section that follows is based on the [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure Introduction to Protein Structure] Proteopedia page.<br /> <br /> <br /> == Levels of Protein Structure ==<br /> '''Primary structure'''<br /> <br /> Proteins are polymers of amino acids joined together in linear chains. There are four recognised levels of structural organisation for proteins.<br /> The first, referred to as the <scene name='57/575866/Primary_sequence/2'>primary structure</scene>, is simply the amino acid sequence, from the N terminus (start) to the C terminus (end) of the protein.<br /> <br /> <br /> '''Secondary Structure'''<br /> <br /> The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances. This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/1'>hydrogen bonds</scene> along the amino acid backbone. There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta strands, a planar (flat) arrangement of amino acids which often line up together to from so-called beta sheets.<br /> <br /> <br /> '''Tertiary Structure'''<br /> <br /> These secondary structures <scene name='57/575866/Global_secondary_structures/1'>pack together</scene> to form the overall form of the entire peptide chain, called the <scene name='57/575866/Tertiary/1'>tertiary structure</scene>.<br /> <br /> <br /> '''Quaternary Structure'''<br /> <br /> Some proteins, such as the hemoglobin molecule displayed here, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called <scene name='57/575866/Tertiary/2'>quaternary structure</scene>.<br /> <br /> <br /> == Secondary Structure in chymotrypsin ==<br /> Now that we know something about the structural organisation of proteins, let's go back to our chymotrypsin molecule and have another look.<br /> <br /> This time, we'll display a <scene name='User:Michael_Roberts/BIOL115_Chymo/2ndry_structure/1'>cartoon representation</scene> indicating the main secondary structural elements. We can see that the main structural form in chymotrypsin is the beta strand, with only a small amount of α-helix.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> <br /> We can also see that the protein is organised into two structurally-similar domains. Each domain contains a group of beta strands arranged as anti-parallel sheets forming a circular structure known as a beta barrel. You can rotate the molecule so that you can see down through each of the two beta barrels in turn.<br /> <br /> <br /> Finally, here's chymotrypsin with a molecule of <scene name='70/703491/Substrate/3'>substrate</scene> bound in its active site. Note how the substrate fits into a pocket on the surface of the enzyme.<br /> <br /> <br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2433424 User:Michael Roberts/Open-Day Demo 2015-09-05T13:40:31Z

<p>Michael Roberts: </p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> <br /> <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'><br /> ==Representing protein structures==<br /> '''Spacefill model'''<br /> <br /> The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called <scene name='70/703491/Basic_representations/1'>'spacefill'</scene> view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> <br /> <br /> <br /> '''Ball-and-stick molecular model'''<br /> This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example. <br /> <br /> <br /> <br /> '''Amino acid trace'''<br /> Here's a much more simplified view that <scene name='70/703491/Basic_representations/3'>traces the chains</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!<br /> <br /> <br /> What we really need to do next is to have a basic introduction to protein structure. The section that follows is based on the [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure Introduction to Protein Structure] Proteopedia page.<br /> <br /> <br /> == Levels of Protein Structure ==<br /> '''Primary structure'''<br /> <br /> Proteins are polymers of amino acids joined together in linear chains. There are four recognised levels of structural organisation for proteins.<br /> The first, referred to as the <scene name='57/575866/Primary_sequence/2'>primary structure</scene>, is simply the amino acid sequence, from the N terminus (start) to the C terminus (end) of the protein.<br /> <br /> <br /> '''Secondary Structure'''<br /> <br /> The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances. This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/1'>hydrogen bonds</scene> along the amino acid backbone. There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta strands, a planar (flat) arrangement of amino acids which often line up together to from so-called beta sheets.<br /> <br /> <br /> '''Tertiary Structure'''<br /> <br /> These secondary structures <scene name='57/575866/Global_secondary_structures/1'>pack together</scene> to form the overall form of the entire peptide chain, called the <scene name='57/575866/Tertiary/1'>tertiary structure</scene>.<br /> <br /> <br /> '''Quaternary Structure'''<br /> <br /> Some proteins, such as the hemoglobin molecule displayed here, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called <scene name='57/575866/Tertiary/2'>quaternary structure</scene>.<br /> <br /> <br /> == Secondary Structure in chymotrypsin ==<br /> Now that we know something about the structural organisation of proteins, let's go back to our chymotrypsin molecule and have another look.<br /> <br /> This time, we'll display a <scene name='User:Michael_Roberts/BIOL115_Chymo/2ndry_structure/1'>cartoon representation</scene> indicating the main secondary structural elements. We can see that the main structural form in chymotrypsin is the beta strand, with only a small amount of α-helix.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> <br /> We can also see that the protein is organised into two structurally-similar domains. Each domain contains a group of beta strands arranged as anti-parallel sheets forming a circular structure known as a beta barrel. You can rotate the molecule so that you can see down through each of the two beta barrels in turn.<br /> <br /> <br /> Finally, here's chymotrypsin with a molecule of <scene name='70/703491/Substrate/3'>substrate</scene> bound in its active site. Note how the substrate fits into a pocket on the surface of the enzyme.<br /> <br /> <br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2409100 User:Michael Roberts/Open-Day Demo 2015-06-03T14:21:30Z

<p>Michael Roberts: </p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> <br /> <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'><br /> ==Representing protein structures==<br /> '''Spacefill model'''<br /> <br /> The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> <br /> <br /> <br /> '''Ball-and-stick molecular model'''<br /> This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example. <br /> <br /> <br /> <br /> '''Amino acid trace'''<br /> Here's a much more simplified view that <scene name='70/703491/Basic_representations/3'>traces the chains</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!<br /> <br /> <br /> What we really need to do next is to have a basic introduction to protein structure. The section that follows is based on the [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure Introduction to Protein Structure] Proteopedia page.<br /> <br /> <br /> == Levels of Protein Structure ==<br /> '''Primary structure'''<br /> <br /> Proteins are polymers of amino acids joined together in linear chains. There are four recognised levels of structural organisation for proteins.<br /> The first, referred to as the <scene name='57/575866/Primary_sequence/2'>primary structure</scene>, is simply the amino acid sequence, from the N terminus (start) to the C terminus (end) of the protein.<br /> <br /> <br /> '''Secondary Structure'''<br /> <br /> The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances. This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/1'>hydrogen bonds</scene> along the amino acid backbone. There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta strands, a planar (flat) arrangement of amino acids which often line up together to from so-called beta sheets.<br /> <br /> <br /> '''Tertiary Structure'''<br /> <br /> These secondary structures <scene name='57/575866/Global_secondary_structures/1'>pack together</scene> to form the overall form of the entire peptide chain, called the <scene name='57/575866/Tertiary/1'>tertiary structure</scene>.<br /> <br /> <br /> '''Quaternary Structure'''<br /> <br /> Some proteins, such as the hemoglobin molecule displayed here, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called <scene name='57/575866/Tertiary/2'>quaternary structure</scene>.<br /> <br /> <br /> == Secondary Structure in chymotrypsin ==<br /> Now that we know something about the structural organisation of proteins, let's go back to our chymotrypsin molecule and have another look.<br /> <br /> This time, we'll display a <scene name='User:Michael_Roberts/BIOL115_Chymo/2ndry_structure/1'>cartoon representation</scene> indicating the main secondary structural elements. We can see that the main structural form in chymotrypsin is the beta strand, with only a small amount of α-helix.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> <br /> We can also see that the protein is organised into two structurally-similar domains. Each domain contains a group of beta strands arranged as anti-parallel sheets forming a circular structure known as a beta barrel. You can rotate the molecule so that you can see down through each of the two beta barrels in turn.<br /> <br /> <br /> Finally, here's chymotrypsin with a molecule of <scene name='70/703491/Substrate/3'>substrate</scene> bound in its active site. Note how the substrate fits into a pocket on the surface of the enzyme.<br /> <br /> <br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2409099 User:Michael Roberts/Open-Day Demo 2015-06-03T14:19:38Z

<p>Michael Roberts: </p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> <br /> <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'><br /> ==Representing protein structures==<br /> '''Spacefill model'''<br /> <br /> The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> <br /> <br /> <br /> '''Ball-and-stick molecular model'''<br /> This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example. <br /> <br /> <br /> <br /> '''Amino acid trace'''<br /> Here's a much more simplified view that <scene name='70/703491/Basic_representations/3'>traces the chains</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!<br /> <br /> <br /> What we really need to do next is to have a basic introduction to protein structure. The section that follows is based on the [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure Introduction to Protein Structure] Proteopedia page.<br /> <br /> <br /> == Levels of Protein Structure ==<br /> '''Primary structure'''<br /> <br /> Proteins are polymers of amino acids joined together in linear chains. There are four recognised levels of structural organisation for proteins.<br /> The first, referred to as the <scene name='57/575866/Primary_sequence/2'>primary structure</scene>, is simply the amino acid sequence, from the N terminus (start) to the C terminus (end) of the protein.<br /> <br /> <br /> '''Secondary Structure'''<br /> <br /> The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances. This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/1'>hydrogen bonds</scene> along the amino acid backbone. There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta strands, a planar (flat) arrangement of amino acids which often line up together to from so-called beta sheets.<br /> <br /> <br /> '''Tertiary Structure'''<br /> <br /> These secondary structures <scene name='57/575866/Global_secondary_structures/1'>pack together</scene> to form the overall form of the entire peptide chain, called the <scene name='57/575866/Tertiary/1'>tertiary structure</scene>.<br /> <br /> <br /> '''Quaternary Structure'''<br /> <br /> Some proteins, such as the hemoglobin molecule displayed here, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called <scene name='57/575866/Tertiary/2'>quaternary structure</scene>.<br /> <br /> <br /> == Secondary Structure in chymotrypsin ==<br /> Now that we know something about the structural organisation of proteins, let's go back to our chymotrypsin molecule and have another look.<br /> <br /> This time, we'll display a <scene name='User:Michael_Roberts/BIOL115_Chymo/2ndry_structure/1'>cartoon representation</scene> indicating the main secondary structural elements. We can see that the main structural form in chymotrypsin is the beta strand, with only a small amount of α-helix.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> <br /> We can also see that the protein is organised into two structurally-similar domains. Each domain contains a group of beta strands arranged as anti-parallel sheets forming a circular structure known as a beta barrel. You can rotate the molecule so that you can see down through each of the two beta barrels in turn.<br /> <br /> <br /> Finally, here's chymotrypsin with a molecule of <scene name='70/703491/Substrate/2'>substrate</scene> bound in its active site. Note how the substrate fits into a pocket on the surface of the enzyme.<br /> <br /> <br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2408949 User:Michael Roberts/Open-Day Demo 2015-06-03T12:45:34Z

<p>Michael Roberts: </p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> <br /> <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'><br /> ==Representing protein structures==<br /> '''Spacefill model'''<br /> <br /> The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> <br /> <br /> <br /> '''Ball-and-stick molecular model'''<br /> This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example. <br /> <br /> <br /> <br /> '''Amino acid trace'''<br /> Here's a much more simplified view that <scene name='70/703491/Basic_representations/3'>traces the chains</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!<br /> <br /> <br /> What we really need to do next is to have a basic introduction to protein structure. The section that follows is based on the [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure Introduction to Protein Structure] Proteopedia page.<br /> <br /> <br /> == Levels of Protein Structure ==<br /> '''Primary structure'''<br /> <br /> Proteins are polymers of amino acids joined together in linear chains. There are four recognised levels of structural organisation for proteins.<br /> The first, referred to as the <scene name='57/575866/Primary_sequence/2'>primary structure</scene>, is simply the amino acid sequence, from the N terminus (start) to the C terminus (end) of the protein.<br /> <br /> <br /> '''Secondary Structure'''<br /> <br /> The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances. This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/1'>hydrogen bonds</scene> along the amino acid backbone. There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta strands, a planar (flat) arrangement of amino acids which often line up together to from so-called beta sheets.<br /> <br /> <br /> '''Tertiary Structure'''<br /> <br /> These secondary structures <scene name='57/575866/Global_secondary_structures/1'>pack together</scene> to form the overall form of the entire peptide chain, called the <scene name='57/575866/Tertiary/1'>tertiary structure</scene>.<br /> <br /> <br /> '''Quaternary Structure'''<br /> <br /> Some proteins, such as the hemoglobin molecule displayed here, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called <scene name='57/575866/Tertiary/2'>quaternary structure</scene>.<br /> <br /> <br /> == Secondary Structure in chymotrypsin ==<br /> Now that we know something about the structural organisation of proteins, let's go back to our chymotrypsin molecule and have another look.<br /> <br /> This time, we'll display a <scene name='User:Michael_Roberts/BIOL115_Chymo/2ndry_structure/1'>cartoon representation</scene> indicating the main secondary structural elements. We can see that the main structural form in chymotrypsin is the beta strand, with only a small amount of α-helix.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> <br /> We can also see that the protein is organised into two structurally-similar domains. Each domain contains a group of beta strands arranged as anti-parallel sheets forming a circular structure known as a beta barrel. You can rotate the molecule so that you can see down through each of the two beta barrels in turn.<br /> <br /> <br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2408937 User:Michael Roberts/Open-Day Demo 2015-06-03T12:44:57Z

<p>Michael Roberts: </p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> <br /> <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'><br /> ==Representing protein structures==<br /> '''Spacefill model'''<br /> <br /> The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> <br /> <br /> <br /> '''Ball-and-stick molecular model'''<br /> This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example. <br /> <br /> <br /> <br /> '''Amino acid trace'''<br /> Here's a much more simplified view that <scene name='70/703491/Basic_representations/3'>traces the chains</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!<br /> <br /> <br /> What we really need to do next is to have a basic introduction to protein structure. The section that follows is based on the [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure Introduction to Protein Structure] Proteopedia page.<br /> <br /> <br /> == Levels of Protein Structure ==<br /> '''Primary structure'''<br /> <br /> Proteins are polymers of amino acids joined together in linear chains. There are four recognised levels of structural organisation for proteins.<br /> The first, referred to as the <scene name='57/575866/Primary_sequence/2'>primary structure</scene>, is simply the amino acid sequence, from the N terminus (start) to the C terminus (end) of the protein.<br /> <br /> <br /> '''Secondary Structure'''<br /> <br /> The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances. This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/1'>hydrogen bonds</scene> along the amino acid backbone. There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta strands, a planar (flat) arrangement of amino acids which often line up together to from so-called beta sheets.<br /> <br /> <br /> '''Tertiary Structure'''<br /> <br /> These secondary structures <scene name='57/575866/Global_secondary_structures/1'>pack together</scene> to form the overall form of the entire peptide chain, called the <scene name='57/575866/Tertiary/1'>tertiary structure</scene>.<br /> <br /> <br /> '''Quaternary Structure'''<br /> <br /> Some proteins, such as the hemoglobin molecule displayed here, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called <scene name='57/575866/Tertiary/2'>quaternary structure</scene>.<br /> <br /> <br /> == Secondary Structure in chymotrypsin ==<br /> Now that we know something about the structural organisation of proteins, let's go back to our chymotrypsin molecule and have another look.<br /> This time, we'll display a <scene name='User:Michael_Roberts/BIOL115_Chymo/2ndry_structure/1'>cartoon representation</scene> indicating the main secondary structural elements. We can see that the main structural form in chymotrypsin is the beta strand, with only a small amount of α-helix.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> We can also see that the protein is organised into two structurally-similar domains. Each domain contains a group of beta strands arranged as anti-parallel sheets forming a circular structure known as a beta barrel. You can rotate the molecule so that you can see down through each of the two beta barrels in turn.<br /> <br /> <br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2408916 User:Michael Roberts/Open-Day Demo 2015-06-03T12:43:55Z

<p>Michael Roberts: </p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> <br /> <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'><br /> ==Representing protein structures==<br /> '''Spacefill model'''<br /> <br /> The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> <br /> <br /> <br /> '''Ball-and-stick molecular model'''<br /> This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example. <br /> <br /> <br /> <br /> '''Amino acid trace'''<br /> Here's a much more simplified view that <scene name='70/703491/Basic_representations/3'>traces the chains</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!<br /> <br /> <br /> What we really need to do next is to have a basic introduction to protein structure. The section that follows is based on the [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure Introduction to Protein Structure] Proteopedia page.<br /> <br /> <br /> == Levels of Protein Structure ==<br /> '''Primary structure'''<br /> <br /> Proteins are polymers of amino acids joined together in linear chains. There are four recognised levels of structural organisation for proteins.<br /> The first, referred to as the <scene name='57/575866/Primary_sequence/2'>primary structure</scene>, is simply the amino acid sequence, from the N terminus (start) to the C terminus (end) of the protein.<br /> <br /> <br /> '''Secondary Structure'''<br /> <br /> The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances. This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/1'>hydrogen bonds</scene> along the amino acid backbone. There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta strands, a planar (flat) arrangement of amino acids which often line up together to from so-called beta sheets.<br /> <br /> <br /> '''Tertiary Structure'''<br /> <br /> These secondary structures <scene name='57/575866/Global_secondary_structures/1'>pack together</scene> to form the overall form of the entire peptide chain, called the <scene name='57/575866/Tertiary/1'>tertiary structure</scene>.<br /> <br /> <br /> '''Quaternary Structure'''<br /> <br /> Some proteins, such as the hemoglobin molecule displayed here, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called <scene name='57/575866/Tertiary/2'>quaternary structure</scene>.<br /> <br /> <br /> == Secondary Structure in chymotrypsin ==<br /> Now that we know something about the structural organisation of proteins, let's go back to our chymotrypsin molecule and have another look.<br /> This time, we'll display a <scene name='User:Michael_Roberts/BIOL115_Chymo/2ndry_structure/1'>cartoon representation</scene> indicating the main secondary structural elements. We can see that the main structural form in chymotrypsin is the beta strand, (orange), with only a small amount of α-helix. We can also see that the protein is organised into two structurally-similar domains. Each domain contains a group of beta strands arranged as anti-parallel sheets forming a circular structure known as a beta barrel. You can rotate the molecule so that you can see down through each of the two beta barrels in turn.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2408794 User:Michael Roberts/Open-Day Demo 2015-06-03T12:37:15Z

<p>Michael Roberts: </p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> <br /> <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'><br /> ==Representing protein structures==<br /> '''Spacefill model'''<br /> <br /> The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> <br /> <br /> <br /> '''Ball-and-stick molecular model'''<br /> This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example. <br /> <br /> <br /> <br /> '''Amino acid trace'''<br /> Here's a much more simplified view that <scene name='70/703491/Basic_representations/3'>traces the chains</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!<br /> <br /> <br /> What we really need to do next is to have a basic introduction to protein structure. The section that follows is based on the [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure Introduction to Protein Structure] Proteopedia page.<br /> <br /> <br /> == Levels of Protein Structure ==<br /> '''Primary structure'''<br /> <br /> Proteins are polymers of amino acids joined together in linear chains. There are four recognised levels of structural organisation for proteins.<br /> The first, referred to as the <scene name='57/575866/Primary_sequence/2'>primary structure</scene>, is simply the amino acid sequence, from the N terminus (start) to the C terminus (end) of the protein.<br /> <br /> <br /> '''Secondary Structure'''<br /> <br /> The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances. This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/1'>hydrogen bonds</scene> along the amino acid backbone. There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta strands, a planar (flat) arrangement of amino acids which often line up together to from so-called beta sheets.<br /> <br /> <br /> '''Tertiary Structure'''<br /> <br /> These secondary structures <scene name='57/575866/Global_secondary_structures/1'>pack together</scene> to form the overall form of the entire peptide chain, called the <scene name='57/575866/Tertiary/1'>tertiary structure</scene>.<br /> <br /> <br /> '''Quaternary Structure'''<br /> <br /> Some proteins, such as the hemoglobin molecule displayed here, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called <scene name='57/575866/Tertiary/2'>quaternary structure</scene>.<br /> <br /> <br /> == Secondary Structure in chymotrypsin ==<br /> Now that we know something about the structural organisation of proteins, let's go back to our chymotrypsin molecule and have another look. This time, we'll display a <scene name='User:Michael_Roberts/BIOL115_Chymo/2ndry_structure/1'>cartoon representation</scene> indicating the main secondary structural elements. We can see that the main structural form in chymotrypsin is the beta strand, (orange), arranged as anti-parallel sheets which form a circular structure known as a beta barrel. You can rotate the molecule so that you can see down through each of the two beta barrels in turn.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2408666 User:Michael Roberts/Open-Day Demo 2015-06-03T12:20:20Z

<p>Michael Roberts: </p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> <br /> <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'><br /> ==Representing protein structures==<br /> '''Spacefill model'''<br /> <br /> The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> <br /> <br /> <br /> '''Ball-and-stick molecular model'''<br /> This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example. <br /> <br /> <br /> <br /> '''Amino acid trace'''<br /> Here's a much more simplified view that <scene name='70/703491/Basic_representations/3'>traces the chains</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!<br /> <br /> <br /> What we really need to do next is to have a basic introduction to protein structure. The section that follows is based on the [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure Introduction to Protein Structure] Proteopedia page.<br /> <br /> <br /> == Levels of Protein Structure ==<br /> '''Primary structure'''<br /> <br /> Proteins are polymers of amino acids joined together in linear chains. There are four recognised levels of structural organisation for proteins.<br /> The first, referred to as the <scene name='57/575866/Primary_sequence/2'>primary structure</scene>, is simply the amino acid sequence, from the N terminus (start) to the C terminus (end) of the protein.<br /> <br /> <br /> '''Secondary Structure'''<br /> <br /> The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances. This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/1'>hydrogen bonds</scene> along the amino acid backbone. There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta sheet, a flat, sheet-like arrangement of amino acids.<br /> <br /> <br /> '''Tertiary Structure'''<br /> <br /> These secondary structures <scene name='57/575866/Global_secondary_structures/1'>pack together</scene> to form the overall form of the entire peptide chain, called the <scene name='57/575866/Tertiary/1'>tertiary structure</scene>.<br /> <br /> <br /> '''Quaternary Structure'''<br /> <br /> Some proteins, such as the hemoglobin molecule displayed here, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called <scene name='57/575866/Tertiary/2'>quaternary structure</scene>.<br /> <br /> <br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2408566 User:Michael Roberts/Open-Day Demo 2015-06-03T11:47:57Z

<p>Michael Roberts: </p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> <br /> <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'><br /> == Spacefill view ==<br /> The view on the right shows a model of '''chymotrypsin''', an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> <br /> <br /> <br /> == Ball-and-stick molecular model ==<br /> This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example. <br /> <br /> <br /> <br /> == Amino acid trace ==<br /> Here's a much more simplified view that <scene name='70/703491/Basic_representations/3'>traces the chains</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!<br /> <br /> <br /> What we really need to do next is to have a basic [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure introduction to protein structure]. This link will take you to a page that introduces you to the basic concepts.<br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2408208 User:Michael Roberts/Open-Day Demo 2015-06-03T11:39:40Z

<p>Michael Roberts: </p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'><br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> The view on the right shows a model of '''chymotrypsin''', an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> <br /> This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example. <br /> <br /> Here's a much more simplified view that <scene name='70/703491/Basic_representations/3'>traces the chains</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!<br /> <br /> What we really need to do next is to have a basic [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure introduction to protein structure]. This link will take you to a page that introduces you to the basic concepts.<br /> <br /> </StructureSection><br /> == References ==<br /> <references/></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2408090 User:Michael Roberts/Open-Day Demo 2015-06-03T11:36:40Z

<p>Michael Roberts: </p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'><br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> The view on the right shows a model of '''chymotrypsin''', an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> <br /> This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example. <br /> <br /> Here's a much more simplified view that <scene name='70/703491/Basic_representations/3'>traces the chains</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!<br /> <br /> What we really need to do next is to have a basic [introduction to protein structure]. This link will take you to a page that introduces you to the basic concepts.<br /> <br /> </StructureSection><br /> == References ==<br /> <references/></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2407971 User:Michael Roberts/Open-Day Demo 2015-06-03T11:23:10Z

<p>Michael Roberts: </p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'><br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> The view on the right shows a model of '''chymotrypsin''', an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> </StructureSection><br /> == References ==<br /> <references/></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2407899 User:Michael Roberts/Open-Day Demo 2015-06-03T11:15:07Z

<p>Michael Roberts: </p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'><br /> <br /> Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.<br /> <br /> The view on the right shows a model of '''chymotrypsin''', an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.<br /> <br /> In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.<br /> This view shows chymotrypsin in the familiar 'ball and stick' representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.<br /> <br /> </StructureSection><br /> == References ==<br /> <references/></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2407809 User:Michael Roberts/Open-Day Demo 2015-06-03T10:55:05Z

<p>Michael Roberts: </p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' <scene='70/703491/Basic_representations/1'>scene 1</scene>><br /> This is a default text for your page '''Michael Roberts/Open-Day Demo'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br /> <br /> <br /> <br /> </StructureSection><br /> == References ==<br /> <references/></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Open-Day_Demo&diff=2407801 User:Michael Roberts/Open-Day Demo 2015-06-03T10:45:08Z

<p>Michael Roberts: New page: ==Interactive visualisation of 3D protein structures== <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry 1afq)' scene=''> This ...</p> <hr /> <div>==Interactive visualisation of 3D protein structures==<br /> <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene=''><br /> This is a default text for your page '''Michael Roberts/Open-Day Demo'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br /> <br /> <br /> <br /> </StructureSection><br /> == References ==<br /> <references/></div>

Michael Roberts https://proteopedia.org/index.php?title=Tutorial:How_do_we_get_the_oxygen_we_breathe&diff=2400353 Tutorial:How do we get the oxygen we breathe 2015-04-30T13:53:18Z

<p>Michael Roberts: increased size of structure window</p> <hr /> <div>__NOTOC__<br /> <StructureSection load='1hh0' size='600' side='right' caption='' scene='Hemoglobin/Foursubunits/5' ><br /> <div style='background-color:yellow;padding:10px;margin:10px;'>This tutorial is designed for high school and beginning college students (ages 14-19). A more detailed tutorial is available at [[Hemoglobin]]</div><br /> When we breathe, or respire, oxygen from the air is taken up by blood in our lungs and soon delivered to each of the cells in our body through our circulatory system. Among other uses, our cells use oxygen as the final electron acceptor in a process called aerobic respiration -- a process that converts the energy in food and nutrients into a form of energy that the cell can readily use (molecules of ATP, adenosine triphosphate). The cells of large organisms like humans use aerobic respiration because other forms of energy production are less efficient, and oxygen is plentiful. (''THINK'': Do fish use aerobic respiration?)<br /> <br /> But, although oxygen is transported in our blood to reach each of the cells in our body, oxygen does not dissolve well in blood. So how is oxygen transported in the blood?<br /> <br /> ===Hemoglobin, the oxygen taxi===<br /> A protein called <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_bio_caption/1'>hemoglobin</scene> (Hb), seen on the right, is the answer to the challenge of transporting oxygen in the blood. The many molecules of hemoglobin in our blood serve as “taxis” for oxygen molecules: oxygen molecules bind to hemoglobin molecules in areas where oxygen is plenty, such as in the lungs, and oxygen molecules then dissociate from hemoglobin when they reach oxygen-poor areas, such as near cells far from the lungs. In this way the hemoglobin in our blood traffics oxygen to every cell in our body. Hemoglobin needs to bind to oxygen tightly in the oxygen-rich atmosphere of the lungs and to be able to release oxygen rapidly in the relatively oxygen-poor environment of the tissues. It does this in a most elegant and intricately coordinated way. ''The story of hemoglobin is a prototypical example of the relationship between structure and function in a protein molecule.''<br /> <br /> ===The structure of hemoglobin===<br /> =====Hemoglobin is a tetramer=====<br /> In the three-dimensional structure of hemoglobin to the right, you see two <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_light_blue_chains/2'>light-blue chains</scene> and two <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_light_green_chains/1'>light-green chains</scene>. (''Drag the hemoglobin structure with the mouse to rotate it. To zoom, use your scroll-wheel, or drag while holding shift.'') These are the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_four_monomers/1'>four monomers</scene> of the hemoglobin molecule, and they are shown in a cartoon-style representation where a single curved line connects the α-carbons in the amino acids of each chain and the [[secondary structure]] α-helices are shown as simplified cartoon helices. Because hemoglobin is composed of four monomers, it is called a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_tetramer/2'>tetramer</scene>. The two types of monomers that make up the hemoglobin tetramer are distinguished by their color: the two α<scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_alpha_monomers/1'>-monomers</scene> in light-blue and the two β<scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_beta_monomers/1'>-monomers</scene> in light-green. Each α-monomer is a chain of 141 amino acids and each β-monomer is a chain of 146 amino acids. Be careful not to get confused with the context in which we use the label "α", or "alpha": remember that both the α- and the β-monomers contain α-carbons and α-helices. (''THINK'': How many amino acids does it take to build a molecule of hemoglobin?)<br /> This next view shows the <scene name='Hemoglobin/Alpha2beta2/7'>tetramer</scene> in space-fill representation, with the alpha and beta chains coloured differently.<br /> <br /> =====Each monomer has a heme group=====<br /> Notice that each monomer, whether α or β, has a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Four_hemes/3'>molecule</scene> associated with it that is represented by several multicolored, overlapping, small spheres. These molecules are called <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/One_heome/2'>heme groups</scene>, and they are where oxygen binds to hemoglobin, which we will soon observe. Do the colors of the spheres represent the true colors of the heme group? No, they do not. Remember that we are looking at a representation of the real structure, and in this case we have artificially colored each atom in the heme according to a common color scheme called the [[CPK|Corey-Pauling-Koltun]] scheme ( {{Template:ColorKey_Element_C}}<br /> {{Template:ColorKey_Element_H}}<br /> {{Template:ColorKey_Element_O}}<br /> {{Template:ColorKey_Element_N}}<br /> {{Template:ColorKey_Element_S}}<br /> {{Template:ColorKey_Element_Fe}} ). Remember too that although we cannot change the positions of the atoms in our experimentally determined protein structure, we can freely choose different ways to show, color, and connect these atoms in order to best comprehend and convey the niceties of the complex 3D structure. We have previously represented the atoms of the heme group as individual spheres in what is called a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Spacefill_heme/3'>spacefilling representation</scene>, but we could just as easily represent the atoms as very small spheres with thick lines connecting the bonded atoms in what is called a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Ballandstick_heme/3'>ball and stick representation</scene>. Notice that the positions and identities of the atoms do not change. (''THINK'': Earlier we learned that the α- and β-monomers have so far been shown in cartoon representation. Why can’t we show the heme groups in cartoon representation?)<br /> <br /> =====Capturing oxygen=====<br /> Hemoglobin captures oxygen and transports it through the bloodstream by binding oxygen to each of its <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Four_hemes/3'>four heme groups</scene>. These <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/One_heome/2'>heme groups</scene> are prosthetic groups; they are non-protein chemical compounds that are associated with hemoglobin and are necessary for its function. Each heme is <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme_composition/1'>ring molecule made up of</scene> {{Template:ColorKey_Element_C}}arbon, {{Template:ColorKey_Element_N}}itrogen, {{Template:ColorKey_Element_O}}xygen and hydrogen, with a single <font color="#E06633">'''Fe<sup>2+</sup>'''</font> (iron) ion at its center, coordinated by the four surrounding nitrogens. Each heme is roughly <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Planar_heme/1'>planar</scene>, and is held in place within the monomer by a hydrophobic interactions and a covalent bond between the iron ion and a nitrogen atom in the side chain of what is termed the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Proximal_histidine/1'>proximal histidine</scene>. Another histidine, termed the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Distal_histidine/2'>distal histidine</scene>, helps in oxygen binding by preventing oxidation of the iron atom (which would prevent oxygen from binding) and by preventing other molecules from binding.<br /> <br /> When oxygen is abundant, an <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/1'>oxygen molecule binds to the iron</scene> in the heme group. (''THINK'': Are there other changes besides the oxygen binding to the iron ion? Why might there be other changes?) We can watch oxygen binding in the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/2'>context of an entire monomer</scene> (colored in rainbow colors from the N terminus of the monomer to its C terminus) or in a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/1'>close-up view</scene> of the heme group.<br /> {{Template:Button Toggle Animation2}}<br /> <br /> When oxygen binds the heme, we notice a conformation change in the hemoglobin monomer holding the heme that bound oxygen -- in other words, when oxygen binds, the monomer changes shape. The difference in conformation between the oxygenated and deoxygenated monomer turns out to be crucial for the function of hemoglobin. Remember that hemoglobin does not exist as a monomer, but rather as a tetramer. As a result, when one monomer in a deoxygenated hemoglobin molecule binds oxygen, that monomer’s conformation change forces a similar conformation change in the remaining three monomers, causing them to adopt a conformation more favorable to oxygen binding. Said differently, as soon as one monomer in the tetramer of the hemoglobin molecule binds oxygen, the other three monomers are much more likely to bind oxygen than they were before. This mechanism of accelerated binding through monomer conformation propagation is called cooperative binding. <br /> <br /> =====Carbon monoxide also binds the heme=====<br /> Here is where the laws of chemistry present us with an interesting problem: The heme group has the chemical and structural capabilities to capture an <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/O2/2'>oxygen molecule</scene>, but an oxygen molecule (O<sub>2</sub>) happens to be similar in shape and chemistry to a molecule of <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Co/2'>carbon monoxide</scene> (CO). The result is that carbon monoxide can also bind to the iron in the heme groups of hemoglobin, although the distal histidine helps prevent this. In fact, carbon monoxide binds to the heme with about 230 times the affinity of oxygen, meaning that if both gases are available, carbon monoxide will outcompete oxygen for heme binding sites. (''THINK'': We often install carbon monoxide detectors in our homes to alert us to high concentrations of this gas. Why might carbon monoxide gas pose a danger to human beings?)<br /> <br /> ===Mutated hemoglobin causes sickle-cell disease===<br /> A mutation in the gene coding for hemoglobin causes a disease called sickle-cell anemia. The <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Sickle_one_protein_cartoon/1'>mutated hemoglobin</scene> results in red blood cells with a diseased, sickle shape instead of a healthy, disk shape. These sickle cells can block blood vessels due to their abnormal shape and cause damage to tissue and organs. (''OBSERVE'': Does the mutated hemoglobin look different than normal hemoglobin?)<br /> <br /> <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Sickle_one_protein/5'>Sickle-cell hemoglobin</scene>, shown here in spacefilling representation, differs from normal hemoglobin at a single amino acid. In the mutant, the amino acid valine takes the place of glutamate as the sixth amino acid in the beta monomer chain. Glutamate, a hydrophilic amino acid, is replaced by valine, a hydrophobic amino acid, at a location on the surface of the protein, and this creates a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Hydrophobic_spot_in_mutant/3'>hydrophobic spot</scene>. There is <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Hydrophobic_spot_in_both/3'>another relevant hydrophobic spot</scene> near the heme binding pocket in the beta-monomer that is present in both normal and sickle-cell deoxygenated hemoglobin. (''OBSERVE'': Can you find the two hydrophobic spots on the two beta-monomers in sickle-cell hemoglobin?) This second hydrophobic spot sticks to the first hydrophobic spot, present only in the mutant, causing the hemoglobin molecules to <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Sickle_hemoglobin_chain/2'>aggregate</scene> into long fibers. We show just two hemoglobin molecules stuck together, but this fiber can extend to include a large number of hemoglobin molecules in a long fiber. A <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Sickle_hemoglobin_chain_close/4'>closer look</scene> shows us the valine from the first, mutant, hydrophobic spot in hydrophobic interaction with the alanine and leucine from the second hydrophobic spot. (''THINK'': Why might these hemoglobin fibers cause sickle-cell red blood cell shape?)<br /> </StructureSection><br /> <br /> ==See Also==<br /> *[[Hemoglobin]]<br /> *PDB entry [[1hho]] (oxygenated, 2.1 Å)<br /> *PDB entry [[1hga]] (deoxygenated, 2.1 Å)<br /> *PDB entry [[1hbs]] (deoxygenated, sickle cell mutant, 3.0 Å)<br /> <br /> ==External Resources==<br /> *{{Wikipedia|Hemoglobin}}<br /> *[http://highered.mcgraw-hill.com/olcweb/cgi/pluginpop.cgi?it=swf::640::480::/sites/dl/free/0077290828/811360/Hemoglobin_Causes_Net_Diffusion_of_Oxygen.swf::Hemoglobin%20Causes%20Net%20Diffusion%20of%20Oxygen Hemoglobin Causes Net Diffusion of Oxygen (Interactive Demo)] - Oxygen diffuses freely across oxygen-permeable membranes such as those found where capillaries (small blood vessels) in the lungs make contact with the air we breathe. When oxygen diffuses from the air in our lungs across the walls of these capillaries and into our blood, it is taken up by hemoglobin -- this causes even more oxygen to diffuse into the blood in order to balance the concentration (partial pressure) of free oxygen in our blood with that in the air in our lungs. Explore the interactive demonstration to see this diffusion in action.<br /> <br /> {{Clear}}<br /> <br /> ==Content Contributors==<br /> This page includes scenes, structures and ideas from [[User:Eric_Martz|Eric Martz]], [[User:Frieda S. Reichsman|Frieda S. Reichsman]] and [[User:Angel_Herraez|Angel Herraez]].<br /> [[Category:Featured in BAMBED]]<br /> [[es:Tutorial:How_do_we_get_the_oxygen_we_breathe_%28Spanish%29]]</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/BIOL115_Myo&diff=2398695 User:Michael Roberts/BIOL115 Myo 2015-04-27T12:58:37Z

<p>Michael Roberts: </p> <hr /> <div>[[Image:myo.png|left|200px|thumb|Myoglobin with oxygen bound to heme ([[1a6m]])]]<br /> <br /> <br /> <span style="font-size:150%">'''The heme group and oxygen binding in myoglobin.'''</span><br /> <br /> <br /> Myoglobin is a protein whose function is to store oxygen in muscle tissues. Like heamoglobin, it is red in colour, and it is myoglobin that gives muscle its strong red colour.<br /> <br /> Myoglobin was the first globular protein for which the 3-dimensional structure was solved, back in the late 1950s. It gives its name to the 'globin fold', a common alpha domain motif. An alpha domain is a structural region composed entirley of alpha-helix.<br /> <br /> <br /> Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.<br /> <br /> <StructureSection load='1mbo' size='600' side='right' caption='Structure of Myoglobin (PDB entry [[1mbo]])' scene='User:Michael_Roberts/BIOL115_Myo/Start/1'><br /> == Molecular model: ==<br /> The initial view here is a ball-and-stick representation of the molecular structure of myoglobin.<br /> <br /> <br /> '''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.<br /> 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.<br /> 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.<br /> <br /> <br /> '''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.<br /> <br /> <br /> <br /> '''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.<br /> {{Template:ColorKey_Hydrophobic}}, {{Template:ColorKey_Polar}}<br /> <br /> 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.<br /> 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.<br /> <br /> <br /> == The Heme Group ==<br /> Now let's turn our attention to the main function of myoglobin - oxygen binding.<br /> 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.<br /> <br /> Central to the heme group is an <scene name='User:Michael_Roberts/BIOL115_Myo/Heme/3'>iron (Fe) atom</scene>.<br /> <br /> <br /> '''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>.<br /> 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).<br /> 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.<br /> <br /> <br /> '''OXYGEN''':<br /> 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.<br /> 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>.<br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/BIOL115_Myo&diff=2398694 User:Michael Roberts/BIOL115 Myo 2015-04-27T12:44:09Z

<p>Michael Roberts: </p> <hr /> <div>[[Image:myo.png|left|200px|thumb|Myoglobin with oxygen bound to heme ([[1a6m]])]]<br /> <br /> <br /> <span style="font-size:150%">'''The heme group and oxygen binding in myoglobin.'''</span><br /> <br /> <br /> Myoglobin is a protein whose function is to store oxygen in muscle tissues. Like heamoglobin, it is red in colour, and it is myoglobin that gives muscle its strong red colour.<br /> <br /> Myoglobin was the first globular protein for which the 3-dimensional structure was solved, back in the late 1950s. It gives its name to the 'globin fold', a common alpha domain motif. An alpha domain is a structural region composed entirley of alpha-helix.<br /> <br /> <br /> Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.<br /> <br /> <StructureSection load='1mbo' size='600' side='right' caption='Structure of Myoglobin (PDB entry [[1mbo]])' scene='User:Michael_Roberts/BIOL115_Myo/Start/1'><br /> == Molecular model: ==<br /> The initial view here is a ball-and-stick representation of the molecular structure of myoglobin.<br /> <br /> <br /> '''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.<br /> 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.<br /> 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.<br /> <br /> <br /> '''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.<br /> <br /> <br /> <br /> '''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.<br /> {{Template:ColorKey_Hydrophobic}}, {{Template:ColorKey_Polar}}<br /> <br /> 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.<br /> 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.<br /> <br /> <br /> == The Heme Group ==<br /> Now let's turn our attention to the main function of myoglobin - oxygen binding.<br /> 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.<br /> <br /> Central to the heme group is an <scene name='User:Michael_Roberts/BIOL115_Myo/Heme/3'>iron (Fe) atom</scene>.<br /> <br /> <br /> '''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>.<br /> 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 (7th residue of helix E).<br /> Note how the iron is pulled out slightly to one side of the plane of the heam group as a result of it's co-ordination with the side chain of the proximal histidine.<br /> <br /> <br /> '''OXYGEN''':<br /> 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.<br /> Note the angled orientation of the oxygen relative to the plane of the heam. The natural binding of oxygen to heam in solution would be the O<sub>2</sub> molecule perpendicular to the plane. In myoglobin (and haemoglobin) the presence of the distal His forces to O<sub>2</sub> to one side, reducing the affinity of the heam-O<sub>2</sub> binding, thus allowing release of oxygen when pO<sub>2</sub> is low. The same effect of the distal His also reduces the affinity of heam for carbon monoxide.<br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/BIOL115_Myo&diff=2398693 User:Michael Roberts/BIOL115 Myo 2015-04-27T12:22:52Z

<p>Michael Roberts: </p> <hr /> <div>[[Image:myo.png|left|200px|thumb|Myoglobin with oxygen bound to heme ([[1a6m]])]]<br /> <br /> <br /> <span style="font-size:150%">'''The heme group and oxygen binding in myoglobin.'''</span><br /> <br /> <br /> Myoglobin is a protein whose function is to store oxygen in muscle tissues. Like heamoglobin, it is red in colour, and it is myoglobin that gives muscle its strong red colour.<br /> <br /> Myoglobin was the first globular protein for which the 3-dimensional structure was solved, back in the late 1950s. It gives its name to the 'globin fold', a common alpha domain motif. An alpha domain is a structural region composed entirley of alpha-helix.<br /> <br /> <br /> Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.<br /> <br /> <StructureSection load='1mbo' size='600' side='right' caption='Structure of Myoglobin (PDB entry [[1mbo]])' scene='User:Michael_Roberts/BIOL115_Myo/Start/1'><br /> == Molecular model: ==<br /> The initial view here is a ball-and-stick representation of the molecular structure of myoglobin.<br /> <br /> <br /> '''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.<br /> 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.<br /> 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.<br /> <br /> <br /> '''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.<br /> <br /> <br /> <br /> '''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.<br /> {{Template:ColorKey_Hydrophobic}}, {{Template:ColorKey_Polar}}<br /> <br /> 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.<br /> 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.<br /> <br /> <br /> == The Heme Group ==<br /> Now let's turn our attention to the main function of myoglobin - oxygen binding.<br /> 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.<br /> <br /> Central to the heme group is an <scene name='User:Michael_Roberts/BIOL115_Myo/Heme/3'>iron (Fe) atom</scene>.<br /> <br /> <br /> '''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>.<br /> 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.<br /> Note how the iron is pulled out slightly to one side of the plane of the heam group as a result of it's co-ordination with the side chain of the proximal histidine.<br /> <br /> <br /> '''OXYGEN''':<br /> 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.<br /> Note the angled orientation of the oxygen relative to the plane of the heam. The natural binding of oxygen to heam in solution would be the O<sub>2</sub> molecule perpendicular to the plane. In myoglobin (and haemoglobin) the presence of the distal His forces to O<sub>2</sub> to one side, reducing the affinity of the heam-O<sub>2</sub> binding, thus allowing release of oxygen when pO<sub>2</sub> is low. The same effect of the distal His also reduces the affinity of heam for carbon monoxide.<br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/BIOL115_Myo&diff=2398692 User:Michael Roberts/BIOL115 Myo 2015-04-27T12:20:18Z

<p>Michael Roberts: </p> <hr /> <div>[[Image:myo.png|left|200px|thumb|Myoglobin with oxygen bound to heme ([[1a6m]])]]<br /> <br /> <br /> <span style="font-size:150%">'''The heme group and oxygen binding in myoglobin.'''</span><br /> <br /> <br /> Myoglobin is a protein whose function is to store oxygen in muscle tissues. Like heamoglobin, it is red in colour, and it is myoglobin that gives muscle its strong red colour.<br /> <br /> Myoglobin was the first globular protein for which the 3-dimensional structure was solved, back in the late 1950s. It gives its name to the 'globin fold', a common alpha domain motif. An alpha domain is a structural region composed entirley of alpha-helix.<br /> <br /> <br /> Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.<br /> <br /> <StructureSection load='1mbo' size='600' side='right' caption='Structure of Myoglobin (PDB entry [[1mbo]])' scene='User:Michael_Roberts/BIOL115_Myo/Start/1'><br /> == Molecular model: ==<br /> The initial view here is a ball-and-stick representation of the molecular structure of myoglobin.<br /> <br /> <br /> '''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.<br /> 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.<br /> 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.<br /> <br /> <br /> '''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.<br /> <br /> <br /> <br /> '''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.<br /> {{Template:ColorKey_Hydrophobic}}, {{Template:ColorKey_Polar}}<br /> <br /> 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.<br /> 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.<br /> <br /> <br /> == The Heme Group ==<br /> Now let's turn our attention to the main function of myoglobin - oxygen binding.<br /> 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.<br /> <br /> Central to the heme group is an <scene name='User:Michael_Roberts/BIOL115_Myo/Heme/3'>iron (Fe) atom</scene>.<br /> <br /> <br /> '''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>.<br /> 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.<br /> Note how the iron is pulled out slightly to one side of the plane of the heam group as a result of it's co-ordination with the side chain of the proximal histidine.<br /> <br /> <br /> '''OXYGEN''':<br /> 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.<br /> Note the angled orientation of the oxygen relative to the plane of the heam. The natural binding of oxygen to heam in solution would be the O2 molecule perpendicular to the plane. In myoglobin (and haemoglobin) the presence of the distal His forces to O2 to one side, reducing the affinity of the heam-O2 binding, thus allowing release of oxygen when pO2 is low. The same effect of the distal His also reduces the affinity of heam for carbon monoxide.<br /> <br /> </StructureSection></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/BIOL115_CaM&diff=2394017 User:Michael Roberts/BIOL115 CaM 2015-04-13T15:47:26Z

<p>Michael Roberts: </p> <hr /> <div>[[Image:CaM.png|left|250px|thumb|Crystal Structure of Calmodulin [[1cll]]]]<br /> <br /> <span style="font-size:150%">'''Sequence and structure of EF hands'''</span><br /> <br /> <br /> The EF hand motif is present in a many proteins and it commonly bestows the ability to bind Ca<sup>2+</sup> ions. It was first identified in parvalbumin, a muscle protein. Here we'll have a look at the Ca<sup>2+</sup>-binding protein [[calmodulin]], which possesses four EF hands. Calmodulin and its isoform, troponinC, are important intracellular Ca<sup>2+</sup>-binding proteins.<br /> <br /> The structure below, obtained by X-ray crystallography, represents the Ca<sup>2+</sup>-binding protein calmodulin. It has a dumbell-shaped structure with two identical lobes connected by a central alpha-helix. Each lobe comprises three α-helices joined by loops. A helix-loop-helix motif forms the basis of each EF hand.<br /> <br /> <br /> Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.<br /> <br /> <StructureSection load='1cll' size='600' side='right' caption='Structure of human calmodulin (PDB entry [[1cll]])' scene='User:Michael_Roberts/BIOL115_CaM/Wireframe/3'><br /> == Molecular Model: ==<br /> We'll start with a simple ball-and-stick representation of the protein. This shows all of the atoms that make up the protein and the bonds between them.<br /> <br /> <br /> '''BACKBONE''':<br /> The ball-and-stick view shows us all the atoms, but if we're mainly interested in the overall structure of the protein, this can be too much detail.<br /> This next veiw takes us right down to a minimal representation that simply traces the <scene name='User:Michael_Roberts/BIOL115_CaM/Backbone/1'>"backbone" </scene>of the protein. The backbone includes the peptide linkages between each amino acid, along with the alpha-carbon atoms to which the side chains are attached. Notice that helical regions can now easily be seen.<br /> <br /> <br /> '''SECONDARY STRUCTURE''': This is shown more clearly by a <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/2'>ribbon diagram</scene>. The computer calculates where regions of secondary structure occur and draws them in cartoon-style 'ribbons'. <br /> The α-helical region is now clearly defined, and there are also regions of β-structure.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> The short anti-parallel beta-sheet between the adjacent EF hand loops are observed in calmodulins from various species.<br /> <br /> <br /> == Calcium Binding ==<br /> '''CALCIUM IONS''':<br /> In each EF hand loop, the Ca<sup>2+</sup> ions are bound by amino acid residues in and near the loops.<br /> <br /> The structure shown here has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>calcium ions</scene> bound. In this condition, the protein adopts the extended structure shown. The EF hand-forming helices are bent away from the long linking helix, revealing hydrophobic residues and exposing the linking chain.<br /> <br /> <br /> '''CO-ORDINATING RESIDUES''':<br /> To illustrate how Ca<sup>2+</sup> is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/1'>residues that take part in binding</scene> one of the Ca<sup>2+</sup> ions.<br /> <br /> <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/2'>Zoom in</scene> to see this more clearly. <br /> <br /> <br /> '''CO-ORDINATING ATOMS''':<br /> To highlight the atoms that co-ordinate the Ca<sup>2+</sup> ion, we can now enlarge those that are close (within 2.7 Å). This shows that <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/3'>seven oxygen</scene> atoms form the calcium co-ordination shell. Five are contributed by the side chain carboxyl groups of Asp and Glu and a sixth by the peptide carbonyl of Gln. The seventh oxygen is provided by an associated water molecule. <br /> <br /> <br /> == Binding to target proteins ==<br /> '''ACTIVE & INACTIVE CALMODULIN:'''<br /> At resting levels of cytosolic Ca<sup>2+</sup> (~100 nM), calmodulin exists predominantly in the calcium-free form. This is called <scene name='User:Michael_Roberts/BIOL115_CaM/Inactive_calmodulin/1'>apo-calmodulin</scene> and its structure is more compact than the structure we saw earlier <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>with bound calcium</scene>. Note the extended α-helix linking the two EF-hand-containing domains in the Ca-bound structure, which is interrupted in the <scene name='User:Michael_Roberts/BIOL115_CaM/Inactive_calmodulin/1'>Ca-free form</scene>. Here, the terminal helices are folded down concealing their hydrophobic surfaces and the central chain, which is not now α-helical along its whole length, is not exposed.<br /> <br /> <br /> '''CALMODULIN INTERACTS WITH ITS TARGET:'''<br /> The Ca<sup>2+</sup>-bound form of calmodulin with its exposed hydrophobic surfaces that you have already observed can <scene name='User:Michael_Roberts/BIOL115_CaM/Active_calmodulin/1'>interact with a target protein</scene>. It does this by wrapping around a specific sequence on the target molecule, which is then forced into an α-helical structure. <br /> <br /> The target molecule here (shown in blue) is the calmodulin-regulated enzyme, myosin light chain kinase. Only a short sequence from this protein, the calmodulin binding domain, is shown.<br /> <br /> In this view, <scene name='54/541097/Active_calmodulin/3'>polar and non-polar residues</scene> are coloured in order to highlight the hydrophobic interior of the molecule, which forms the binding site for the myosin light chain kinase calmodulin binding domain.<br /> {{Template:ColorKey_Hydrophobic}}, {{Template:ColorKey_Polar}}<br /> </StructureSection><br /> <br /> '''External Resources.'''<br /> You can view a nice animation of the conformational change undergone by calmodulin upon calcium binding by following this link [http://morph2.molmovdb.org/results.rpy?jobid=8350057535].</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/BIOL115_CaM&diff=2394015 User:Michael Roberts/BIOL115 CaM 2015-04-13T15:21:28Z

<p>Michael Roberts: </p> <hr /> <div>[[Image:CaM.png|left|250px|thumb|Crystal Structure of Calmodulin [[1cll]]]]<br /> <br /> <span style="font-size:150%">'''Sequence and structure of EF hands'''</span><br /> <br /> <br /> The EF hand motif is present in a many proteins and it commonly bestows the ability to bind Ca<sup>2+</sup> ions. It was first identified in parvalbumin, a muscle protein. Here we'll have a look at the Ca<sup>2+</sup>-binding protein [[calmodulin]], which possesses four EF hands. Calmodulin and its isoform, troponinC, are important intracellular Ca<sup>2+</sup>-binding proteins.<br /> <br /> The structure below, obtained by X-ray crystallography, represents the Ca<sup>2+</sup>-binding protein calmodulin. It has a dumbell-shaped structure with two identical lobes connected by a central alpha-helix. Each lobe comprises three α-helices joined by loops. A helix-loop-helix motif forms the basis of each EF hand.<br /> <br /> <br /> Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.<br /> <br /> <StructureSection load='1cll' size='600' side='right' caption='Structure of human calmodulin (PDB entry [[1cll]])' scene='User:Michael_Roberts/BIOL115_CaM/Wireframe/3'><br /> == Molecular Model: ==<br /> We'll start with a simple ball-and-stick representation of the protein. This shows all of the atoms that make up the protein and the bonds between them.<br /> <br /> <br /> '''BACKBONE''':<br /> The ball-and-stick view shows us all the atoms, but if we're mainly interested in the overall structure of the protein, this can be too much detail.<br /> This next veiw takes us right down to a minimal representation that simply traces the <scene name='User:Michael_Roberts/BIOL115_CaM/Backbone/1'>"backbone" </scene>of the protein. The backbone includes the peptide linkages between each amino acid, along with the alpha-carbon atoms to which the side chains are attached. Notice that helical regions can now easily be seen.<br /> <br /> <br /> '''SECONDARY STRUCTURE''': This is shown more clearly by a <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/2'>ribbon diagram</scene>. The computer calculates where regions of secondary structure occur and draws them in cartoon-style 'ribbons'. <br /> The α-helical region is now clearly defined, and there are also regions of β-structure.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> The short anti-parallel beta-sheet between the adjacent EF hand loops are observed in calmodulins from various species.<br /> <br /> <br /> == Calcium Binding ==<br /> '''CALCIUM IONS''':<br /> In each EF hand loop, the Ca<sup>2+</sup> ions are bound by amino acid residues in and near the loops.<br /> <br /> The structure shown here has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>calcium ions</scene> bound. In this condition, the protein adopts the extended structure shown. The EF hand-forming helices are bent away from the long linking helix, revealing hydrophobic residues and exposing the linking chain.<br /> <br /> <br /> '''CO-ORDINATING RESIDUES''':<br /> To illustrate how Ca<sup>2+</sup> is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/1'>residues that take part in binding</scene> one of the Ca<sup>2+</sup> ions.<br /> <br /> <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/2'>Zoom in</scene> to see this more clearly. <br /> <br /> <br /> '''CO-ORDINATING ATOMS''':<br /> To highlight the atoms that co-ordinate the Ca<sup>2+</sup> ion, we can now enlarge those that are close (within 2.7 Å). This shows that <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/3'>seven oxygen</scene> atoms form the calcium co-ordination shell. Five are contributed by the side chain carboxyl groups of Asp and Glu and a sixth by the peptide carbonyl of Gln. The seventh oxygen is provided by an associated water molecule. <br /> <br /> <br /> == Binding to target proteins ==<br /> '''ACTIVE & INACTIVE CALMODULIN:'''<br /> At resting levels of cytosolic Ca<sup>2+</sup> (~100 nM), calmodulin exists predominantly in the calcium-free form. This is called <scene name='User:Michael_Roberts/BIOL115_CaM/Inactive_calmodulin/1'>apo-calmodulin</scene> and its structure is more compact than the structure we saw earlier <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>with bound calcium.</scene>. Note the extended α-helix linking the two EF-hand-containing domains in the Ca-bound structure, which is interrupted in the <scene name='User:Michael_Roberts/BIOL115_CaM/Inactive_calmodulin/1'>Ca-free form</scene>. Here, the terminal helices are folded down concealing their hydrophobic surfaces and the central chain, which is not now α-helical along its whole length, is not exposed.<br /> <br /> <br /> '''CALMODULIN INTERACTS WITH ITS TARGET:'''<br /> The Ca<sup>2+</sup>-bound form of calmodulin with its exposed hydrophobic surfaces that you have already observed can <scene name='User:Michael_Roberts/BIOL115_CaM/Active_calmodulin/1'>interact with a target protein</scene>. It does this by wrapping around a specific sequence on the target molecule, which is then forced into an α-helical structure. <br /> <br /> The target molecule here (shown in blue) is the calmodulin-regulated enzyme, myosin light chain kinase. Only a short sequence from this protein, the calmodulin binding domain, is shown.<br /> <br /> In this view, <scene name='54/541097/Active_calmodulin/3'>polar and non-polar residues</scene> are coloured in order to highlight the hydrophobic interior of the molecule, which forms the binding site for the myosin light chain kinase calmodulin binding domain.<br /> {{Template:ColorKey_Hydrophobic}}, {{Template:ColorKey_Polar}}<br /> </StructureSection><br /> <br /> '''External Resources.'''<br /> You can view a nice animation of the conformational change undergone by calmodulin upon calcium binding by following this link [http://morph2.molmovdb.org/results.rpy?jobid=8350057535].</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/BIOL115_CaM&diff=2394014 User:Michael Roberts/BIOL115 CaM 2015-04-13T14:55:04Z

<p>Michael Roberts: </p> <hr /> <div>[[Image:CaM.png|left|250px|thumb|Crystal Structure of Calmodulin [[1cll]]]]<br /> <br /> <span style="font-size:150%">'''Sequence and structure of EF hands'''</span><br /> <br /> <br /> The EF hand motif is present in a many proteins and it commonly bestows the ability to bind Ca<sup>2+</sup> ions. It was first identified in parvalbumin, a muscle protein. Here we'll have a look at the Ca<sup>2+</sup>-binding protein [[calmodulin]], which possesses four EF hands. Calmodulin and its isoform, troponinC, are important intracellular Ca<sup>2+</sup>-binding proteins.<br /> <br /> The structure below, obtained by X-ray crystallography, represents the Ca<sup>2+</sup>-binding protein calmodulin. It has a dumbell-shaped structure with two identical lobes connected by a central alpha-helix. Each lobe comprises three α-helices joined by loops. A helix-loop-helix motif forms the basis of each EF hand.<br /> <br /> <br /> Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.<br /> <br /> <StructureSection load='1cll' size='600' side='right' caption='Structure of human calmodulin (PDB entry [[1cll]])' scene='User:Michael_Roberts/BIOL115_CaM/Wireframe/3'><br /> == Molecular Model: ==<br /> We'll start with a simple ball-and-stick representation of the protein. This shows all of the atoms that make up the protein and the bonds between them.<br /> <br /> <br /> '''BACKBONE''':<br /> The ball-and-stick view shows us all the atoms, but if we're mainly interested in the overall structure of the protein, this can be too much detail.<br /> This next veiw takes us right down to a minimal representation that simply traces the <scene name='User:Michael_Roberts/BIOL115_CaM/Backbone/1'>"backbone" </scene>of the protein. The backbone includes the peptide linkages between each amino acid, along with the alpha-carbon atoms to which the side chains are attached. Notice that helical regions can now easily be seen.<br /> <br /> <br /> '''SECONDARY STRUCTURE''': This is shown more clearly by a <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/2'>ribbon diagram</scene>. The computer calculates where regions of secondary structure occur and draws them in cartoon-style 'ribbons'. <br /> The α-helical region is now clearly defined, and there are also regions of β-structure.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> The short anti-parallel beta-sheet between the adjacent EF hand loops are observed in calmodulins from various species.<br /> <br /> <br /> == Calcium Binding ==<br /> '''CALCIUM IONS''':<br /> In each EF hand loop, the Ca<sup>2+</sup> ions are bound by amino acid residues in and near the loops.<br /> <br /> The structure shown here has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>calcium ions</scene> bound. In this condition, the protein adopts the extended structure shown. The EF hand-forming helices are bent away from the long linking helix, revealing hydrophobic residues and exposing the linking chain.<br /> <br /> <br /> '''CO-ORDINATING RESIDUES''':<br /> To illustrate how Ca<sup>2+</sup> is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/1'>residues that take part in binding</scene> one of the Ca<sup>2+</sup> ions.<br /> <br /> <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/2'>Zoom in</scene> to see this more clearly. <br /> <br /> <br /> '''CO-ORDINATING ATOMS''':<br /> To highlight the atoms that co-ordinate the Ca<sup>2+</sup> ion, we can now enlarge those that are close (within 2.7 Å). This shows that <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/3'>seven oxygen</scene> atoms form the calcium co-ordination shell. Five are contributed by the side chain carboxyl groups of Asp and Glu and a sixth by the peptide carbonyl of Gln. The seventh oxygen is provided by an associated water molecule. <br /> <br /> <br /> == Binding to target proteins ==<br /> '''ACTIVE & INACTIVE CALMODULIN:'''<br /> At resting levels of cytosolic Ca<sup>2+</sup> (~100 nM), calmodulin exists predominantly in the calcium-free form. This is called <scene name='User:Michael_Roberts/BIOL115_CaM/Inactive_calmodulin/1'>apo-calmodulin</scene> and its structure is more compact than the structure we saw earlier <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>with bound calcium.</scene>. Note the extended α-helix linking the two EF-hand-containing domains in the Ca-bound structure, which is interrupted in the <scene name='User:Michael_Roberts/BIOL115_CaM/Inactive_calmodulin/1'>Ca-free form</scene>. Here, the terminal helices are folded down concealing their hydrophobic surfaces and the central chain, which is not now α-helical along its whole length, is not exposed.<br /> <br /> <br /> '''CALMODULIN INTERACTS WITH ITS TARGET:'''<br /> The Ca<sup>2+</sup>-bound form of calmodulin with its exposed hydrophobic surfaces that you have already observed can <scene name='User:Michael_Roberts/BIOL115_CaM/Active_calmodulin/1'>interact with a target protein</scene>. It does this by wrapping around a specific sequence on the target molecule, which is then forced into an α-helical structure. <br /> <br /> The target molecule here (shown in blue) is the calmodulin-regulated enzyme, myosin light chain kinase. Only a short sequence from this protein, the calmodulin binding domain, is shown.<br /> </StructureSection><br /> <br /> '''External Resources.'''<br /> You can view a nice animation of the conformational change undergone by calmodulin upon calcium binding by following this link [http://morph2.molmovdb.org/results.rpy?jobid=8350057535].</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Haemoglobin&diff=2394013 User:Michael Roberts/Haemoglobin 2015-04-13T14:15:05Z

<p>Michael Roberts: Replacing page with '__'</p> <hr /> <div>__</div>

Michael Roberts https://proteopedia.org/index.php?title=Tutorial:How_do_we_get_the_oxygen_we_breathe&diff=2394012 Tutorial:How do we get the oxygen we breathe 2015-04-13T14:12:27Z

<p>Michael Roberts: </p> <hr /> <div>__NOTOC__<br /> <StructureSection load='1hh0' size='500' side='right' caption='' scene='Hemoglobin/Foursubunits/5' ><br /> <div style='background-color:yellow;padding:10px;margin:10px;'>This tutorial is designed for high school and beginning college students (ages 14-19). A more detailed tutorial is available at [[Hemoglobin]]</div><br /> When we breathe, or respire, oxygen from the air is taken up by blood in our lungs and soon delivered to each of the cells in our body through our circulatory system. Among other uses, our cells use oxygen as the final electron acceptor in a process called aerobic respiration -- a process that converts the energy in food and nutrients into a form of energy that the cell can readily use (molecules of ATP, adenosine triphosphate). The cells of large organisms like humans use aerobic respiration because other forms of energy production are less efficient, and oxygen is plentiful. (''THINK'': Do fish use aerobic respiration?)<br /> <br /> But, although oxygen is transported in our blood to reach each of the cells in our body, oxygen does not dissolve well in blood. So how is oxygen transported in the blood?<br /> <br /> ===Hemoglobin, the oxygen taxi===<br /> A protein called <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_bio_caption/1'>hemoglobin</scene> (Hb), seen on the right, is the answer to the challenge of transporting oxygen in the blood. The many molecules of hemoglobin in our blood serve as “taxis” for oxygen molecules: oxygen molecules bind to hemoglobin molecules in areas where oxygen is plenty, such as in the lungs, and oxygen molecules then dissociate from hemoglobin when they reach oxygen-poor areas, such as near cells far from the lungs. In this way the hemoglobin in our blood traffics oxygen to every cell in our body. Hemoglobin needs to bind to oxygen tightly in the oxygen-rich atmosphere of the lungs and to be able to release oxygen rapidly in the relatively oxygen-poor environment of the tissues. It does this in a most elegant and intricately coordinated way. ''The story of hemoglobin is a prototypical example of the relationship between structure and function in a protein molecule.''<br /> <br /> ===The structure of hemoglobin===<br /> =====Hemoglobin is a tetramer=====<br /> In the three-dimensional structure of hemoglobin to the right, you see two <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_light_blue_chains/2'>light-blue chains</scene> and two <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_light_green_chains/1'>light-green chains</scene>. (''Drag the hemoglobin structure with the mouse to rotate it. To zoom, use your scroll-wheel, or drag while holding shift.'') These are the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_four_monomers/1'>four monomers</scene> of the hemoglobin molecule, and they are shown in a cartoon-style representation where a single curved line connects the α-carbons in the amino acids of each chain and the [[secondary structure]] α-helices are shown as simplified cartoon helices. Because hemoglobin is composed of four monomers, it is called a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_tetramer/2'>tetramer</scene>. The two types of monomers that make up the hemoglobin tetramer are distinguished by their color: the two α<scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_alpha_monomers/1'>-monomers</scene> in light-blue and the two β<scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_beta_monomers/1'>-monomers</scene> in light-green. Each α-monomer is a chain of 141 amino acids and each β-monomer is a chain of 146 amino acids. Be careful not to get confused with the context in which we use the label "α", or "alpha": remember that both the α- and the β-monomers contain α-carbons and α-helices. (''THINK'': How many amino acids does it take to build a molecule of hemoglobin?)<br /> This next view shows the <scene name='Hemoglobin/Alpha2beta2/7'>tetramer</scene> in space-fill representation, with the alpha and beta chains coloured differently.<br /> <br /> =====Each monomer has a heme group=====<br /> Notice that each monomer, whether α or β, has a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Four_hemes/3'>molecule</scene> associated with it that is represented by several multicolored, overlapping, small spheres. These molecules are called <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/One_heome/2'>heme groups</scene>, and they are where oxygen binds to hemoglobin, which we will soon observe. Do the colors of the spheres represent the true colors of the heme group? No, they do not. Remember that we are looking at a representation of the real structure, and in this case we have artificially colored each atom in the heme according to a common color scheme called the [[CPK|Corey-Pauling-Koltun]] scheme ( {{Template:ColorKey_Element_C}}<br /> {{Template:ColorKey_Element_H}}<br /> {{Template:ColorKey_Element_O}}<br /> {{Template:ColorKey_Element_N}}<br /> {{Template:ColorKey_Element_S}}<br /> {{Template:ColorKey_Element_Fe}} ). Remember too that although we cannot change the positions of the atoms in our experimentally determined protein structure, we can freely choose different ways to show, color, and connect these atoms in order to best comprehend and convey the niceties of the complex 3D structure. We have previously represented the atoms of the heme group as individual spheres in what is called a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Spacefill_heme/3'>spacefilling representation</scene>, but we could just as easily represent the atoms as very small spheres with thick lines connecting the bonded atoms in what is called a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Ballandstick_heme/3'>ball and stick representation</scene>. Notice that the positions and identities of the atoms do not change. (''THINK'': Earlier we learned that the α- and β-monomers have so far been shown in cartoon representation. Why can’t we show the heme groups in cartoon representation?)<br /> <br /> =====Capturing oxygen=====<br /> Hemoglobin captures oxygen and transports it through the bloodstream by binding oxygen to each of its <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Four_hemes/3'>four heme groups</scene>. These <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/One_heome/2'>heme groups</scene> are prosthetic groups; they are non-protein chemical compounds that are associated with hemoglobin and are necessary for its function. Each heme is <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme_composition/1'>ring molecule made up of</scene> {{Template:ColorKey_Element_C}}arbon, {{Template:ColorKey_Element_N}}itrogen, {{Template:ColorKey_Element_O}}xygen and hydrogen, with a single <font color="#E06633">'''Fe<sup>2+</sup>'''</font> (iron) ion at its center, coordinated by the four surrounding nitrogens. Each heme is roughly <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Planar_heme/1'>planar</scene>, and is held in place within the monomer by a hydrophobic interactions and a covalent bond between the iron ion and a nitrogen atom in the side chain of what is termed the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Proximal_histidine/1'>proximal histidine</scene>. Another histidine, termed the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Distal_histidine/2'>distal histidine</scene>, helps in oxygen binding by preventing oxidation of the iron atom (which would prevent oxygen from binding) and by preventing other molecules from binding.<br /> <br /> When oxygen is abundant, an <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/1'>oxygen molecule binds to the iron</scene> in the heme group. (''THINK'': Are there other changes besides the oxygen binding to the iron ion? Why might there be other changes?) We can watch oxygen binding in the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/2'>context of an entire monomer</scene> (colored in rainbow colors from the N terminus of the monomer to its C terminus) or in a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/1'>close-up view</scene> of the heme group.<br /> {{Template:Button Toggle Animation2}}<br /> <br /> When oxygen binds the heme, we notice a conformation change in the hemoglobin monomer holding the heme that bound oxygen -- in other words, when oxygen binds, the monomer changes shape. The difference in conformation between the oxygenated and deoxygenated monomer turns out to be crucial for the function of hemoglobin. Remember that hemoglobin does not exist as a monomer, but rather as a tetramer. As a result, when one monomer in a deoxygenated hemoglobin molecule binds oxygen, that monomer’s conformation change forces a similar conformation change in the remaining three monomers, causing them to adopt a conformation more favorable to oxygen binding. Said differently, as soon as one monomer in the tetramer of the hemoglobin molecule binds oxygen, the other three monomers are much more likely to bind oxygen than they were before. This mechanism of accelerated binding through monomer conformation propagation is called cooperative binding. <br /> <br /> =====Carbon monoxide also binds the heme=====<br /> Here is where the laws of chemistry present us with an interesting problem: The heme group has the chemical and structural capabilities to capture an <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/O2/2'>oxygen molecule</scene>, but an oxygen molecule (O<sub>2</sub>) happens to be similar in shape and chemistry to a molecule of <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Co/2'>carbon monoxide</scene> (CO). The result is that carbon monoxide can also bind to the iron in the heme groups of hemoglobin, although the distal histidine helps prevent this. In fact, carbon monoxide binds to the heme with about 230 times the affinity of oxygen, meaning that if both gases are available, carbon monoxide will outcompete oxygen for heme binding sites. (''THINK'': We often install carbon monoxide detectors in our homes to alert us to high concentrations of this gas. Why might carbon monoxide gas pose a danger to human beings?)<br /> <br /> ===Mutated hemoglobin causes sickle-cell disease===<br /> A mutation in the gene coding for hemoglobin causes a disease called sickle-cell anemia. The <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Sickle_one_protein_cartoon/1'>mutated hemoglobin</scene> results in red blood cells with a diseased, sickle shape instead of a healthy, disk shape. These sickle cells can block blood vessels due to their abnormal shape and cause damage to tissue and organs. (''OBSERVE'': Does the mutated hemoglobin look different than normal hemoglobin?)<br /> <br /> <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Sickle_one_protein/5'>Sickle-cell hemoglobin</scene>, shown here in spacefilling representation, differs from normal hemoglobin at a single amino acid. In the mutant, the amino acid valine takes the place of glutamate as the sixth amino acid in the beta monomer chain. Glutamate, a hydrophilic amino acid, is replaced by valine, a hydrophobic amino acid, at a location on the surface of the protein, and this creates a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Hydrophobic_spot_in_mutant/3'>hydrophobic spot</scene>. There is <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Hydrophobic_spot_in_both/3'>another relevant hydrophobic spot</scene> near the heme binding pocket in the beta-monomer that is present in both normal and sickle-cell deoxygenated hemoglobin. (''OBSERVE'': Can you find the two hydrophobic spots on the two beta-monomers in sickle-cell hemoglobin?) This second hydrophobic spot sticks to the first hydrophobic spot, present only in the mutant, causing the hemoglobin molecules to <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Sickle_hemoglobin_chain/2'>aggregate</scene> into long fibers. We show just two hemoglobin molecules stuck together, but this fiber can extend to include a large number of hemoglobin molecules in a long fiber. A <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Sickle_hemoglobin_chain_close/4'>closer look</scene> shows us the valine from the first, mutant, hydrophobic spot in hydrophobic interaction with the alanine and leucine from the second hydrophobic spot. (''THINK'': Why might these hemoglobin fibers cause sickle-cell red blood cell shape?)<br /> </StructureSection><br /> <br /> ==See Also==<br /> *[[Hemoglobin]]<br /> *PDB entry [[1hho]] (oxygenated, 2.1 Å)<br /> *PDB entry [[1hga]] (deoxygenated, 2.1 Å)<br /> *PDB entry [[1hbs]] (deoxygenated, sickle cell mutant, 3.0 Å)<br /> <br /> ==External Resources==<br /> *{{Wikipedia|Hemoglobin}}<br /> *[http://highered.mcgraw-hill.com/olcweb/cgi/pluginpop.cgi?it=swf::640::480::/sites/dl/free/0077290828/811360/Hemoglobin_Causes_Net_Diffusion_of_Oxygen.swf::Hemoglobin%20Causes%20Net%20Diffusion%20of%20Oxygen Hemoglobin Causes Net Diffusion of Oxygen (Interactive Demo)] - Oxygen diffuses freely across oxygen-permeable membranes such as those found where capillaries (small blood vessels) in the lungs make contact with the air we breathe. When oxygen diffuses from the air in our lungs across the walls of these capillaries and into our blood, it is taken up by hemoglobin -- this causes even more oxygen to diffuse into the blood in order to balance the concentration (partial pressure) of free oxygen in our blood with that in the air in our lungs. Explore the interactive demonstration to see this diffusion in action.<br /> <br /> {{Clear}}<br /> <br /> ==Content Contributors==<br /> This page includes scenes, structures and ideas from [[User:Eric_Martz|Eric Martz]], [[User:Frieda S. Reichsman|Frieda S. Reichsman]] and [[User:Angel_Herraez|Angel Herraez]].<br /> [[Category:Featured in BAMBED]]<br /> [[es:Tutorial:How_do_we_get_the_oxygen_we_breathe_%28Spanish%29]]</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Haemoglobin&diff=2394011 User:Michael Roberts/Haemoglobin 2015-04-13T14:01:37Z

<p>Michael Roberts: New page: __NOTOC__ <StructureSection load='1hh0' size='500' side='right' caption='' scene='Hemoglobin/Foursubunits/5' > When we breathe, or respire, oxygen from the air is taken up by blood in our...</p> <hr /> <div>__NOTOC__<br /> <StructureSection load='1hh0' size='500' side='right' caption='' scene='Hemoglobin/Foursubunits/5' ><br /> <br /> When we breathe, or respire, oxygen from the air is taken up by blood in our lungs and soon delivered to each of the cells in our body through our circulatory system. Among other uses, our cells use oxygen as the final electron acceptor in a process called aerobic respiration -- a process that converts the energy in food and nutrients into a form of energy that the cell can readily use (molecules of ATP, adenosine triphosphate). The cells of large organisms like humans use aerobic respiration because other forms of energy production are less efficient, and oxygen is plentiful. (''THINK'': Do fish use aerobic respiration?)<br /> <br /> But, although oxygen is transported in our blood to reach each of the cells in our body, oxygen does not dissolve well in blood. So how is oxygen transported in the blood?<br /> <br /> ===Hemoglobin, the oxygen taxi===<br /> A protein called <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_bio_caption/1'>hemoglobin</scene> (Hb), seen on the right, is the answer to the challenge of transporting oxygen in the blood. The many molecules of hemoglobin in our blood serve as “taxis” for oxygen molecules: oxygen molecules bind to hemoglobin molecules in areas where oxygen is plenty, such as in the lungs, and oxygen molecules then dissociate from hemoglobin when they reach oxygen-poor areas, such as near cells far from the lungs. In this way the hemoglobin in our blood traffics oxygen to every cell in our body. Hemoglobin needs to bind to oxygen tightly in the oxygen-rich atmosphere of the lungs and to be able to release oxygen rapidly in the relatively oxygen-poor environment of the tissues. It does this in a most elegant and intricately coordinated way. ''The story of hemoglobin is a prototypical example of the relationship between structure and function in a protein molecule.''<br /> <br /> ===The structure of hemoglobin===<br /> =====Hemoglobin is a tetramer=====<br /> In the three-dimensional structure of hemoglobin to the right, you see two <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_light_blue_chains/2'>light-blue chains</scene> and two <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_light_green_chains/1'>light-green chains</scene>. (''Drag the hemoglobin structure with the mouse to rotate it. To zoom, use your scroll-wheel, or drag while holding shift.'') These are the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_four_monomers/1'>four monomers</scene> of the hemoglobin molecule, and they are shown in a cartoon-style representation where a single curved line connects the α-carbons in the amino acids of each chain and the [[secondary structure]] α-helices are shown as simplified cartoon helices. Because hemoglobin is composed of four monomers, it is called a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_tetramer/2'>tetramer</scene>. The two types of monomers that make up the hemoglobin tetramer are distinguished by their color: the two α<scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_alpha_monomers/1'>-monomers</scene> in light-blue and the two β<scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_beta_monomers/1'>-monomers</scene> in light-green. Each α-monomer is a chain of 141 amino acids and each β-monomer is a chain of 146 amino acids. Be careful not to get confused with the context in which we use the label "α", or "alpha": remember that both the α- and the β-monomers contain α-carbons and α-helices. (''THINK'': How many amino acids does it take to build a molecule of hemoglobin?)<br /> <br /> =====Each monomer has a heme group=====<br /> Notice that each monomer, whether α or β, has a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Four_hemes/3'>molecule</scene> associated with it that is represented by several multicolored, overlapping, small spheres. These molecules are called <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/One_heome/2'>heme groups</scene>, and they are where oxygen binds to hemoglobin, which we will soon observe. Do the colors of the spheres represent the true colors of the heme group? No, they do not. Remember that we are looking at a representation of the real structure, and in this case we have artificially colored each atom in the heme according to a common color scheme called the [[CPK|Corey-Pauling-Koltun]] scheme ( {{Template:ColorKey_Element_C}}<br /> {{Template:ColorKey_Element_H}}<br /> {{Template:ColorKey_Element_O}}<br /> {{Template:ColorKey_Element_N}}<br /> {{Template:ColorKey_Element_S}}<br /> {{Template:ColorKey_Element_Fe}} ). Remember too that although we cannot change the positions of the atoms in our experimentally determined protein structure, we can freely choose different ways to show, color, and connect these atoms in order to best comprehend and convey the niceties of the complex 3D structure. We have previously represented the atoms of the heme group as individual spheres in what is called a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Spacefill_heme/3'>spacefilling representation</scene>, but we could just as easily represent the atoms as very small spheres with thick lines connecting the bonded atoms in what is called a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Ballandstick_heme/3'>ball and stick representation</scene>. Notice that the positions and identities of the atoms do not change. (''THINK'': Earlier we learned that the α- and β-monomers have so far been shown in cartoon representation. Why can’t we show the heme groups in cartoon representation?)<br /> <br /> =====Capturing oxygen=====<br /> Hemoglobin captures oxygen and transports it through the bloodstream by binding oxygen to each of its <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Four_hemes/3'>four heme groups</scene>. These <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/One_heome/2'>heme groups</scene> are prosthetic groups; they are non-protein chemical compounds that are associated with hemoglobin and are necessary for its function. Each heme is <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme_composition/1'>ring molecule made up of</scene> {{Template:ColorKey_Element_C}}arbon, {{Template:ColorKey_Element_N}}itrogen, {{Template:ColorKey_Element_O}}xygen and hydrogen, with a single <font color="#E06633">'''Fe<sup>2+</sup>'''</font> (iron) ion at its center, coordinated by the four surrounding nitrogens. Each heme is roughly <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Planar_heme/1'>planar</scene>, and is held in place within the monomer by a hydrophobic interactions and a covalent bond between the iron ion and a nitrogen atom in the side chain of what is termed the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Proximal_histidine/1'>proximal histidine</scene>. Another histidine, termed the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Distal_histidine/2'>distal histidine</scene>, helps in oxygen binding by preventing oxidation of the iron atom (which would prevent oxygen from binding) and by preventing other molecules from binding.<br /> <br /> When oxygen is abundant, an <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/1'>oxygen molecule binds to the iron</scene> in the heme group. (''THINK'': Are there other changes besides the oxygen binding to the iron ion? Why might there be other changes?) We can watch oxygen binding in the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/2'>context of an entire monomer</scene> (colored in rainbow colors from the N terminus of the monomer to its C terminus) or in a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/1'>close-up view</scene> of the heme group.<br /> {{Template:Button Toggle Animation2}}<br /> <br /> When oxygen binds the heme, we notice a conformation change in the hemoglobin monomer holding the heme that bound oxygen -- in other words, when oxygen binds, the monomer changes shape. The difference in conformation between the oxygenated and deoxygenated monomer turns out to be crucial for the function of hemoglobin. Remember that hemoglobin does not exist as a monomer, but rather as a tetramer. As a result, when one monomer in a deoxygenated hemoglobin molecule binds oxygen, that monomer’s conformation change forces a similar conformation change in the remaining three monomers, causing them to adopt a conformation more favorable to oxygen binding. Said differently, as soon as one monomer in the tetramer of the hemoglobin molecule binds oxygen, the other three monomers are much more likely to bind oxygen than they were before. This mechanism of accelerated binding through monomer conformation propagation is called cooperative binding. <br /> <br /> =====Carbon monoxide also binds the heme=====<br /> Here is where the laws of chemistry present us with an interesting problem: The heme group has the chemical and structural capabilities to capture an <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/O2/2'>oxygen molecule</scene>, but an oxygen molecule (O<sub>2</sub>) happens to be similar in shape and chemistry to a molecule of <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Co/2'>carbon monoxide</scene> (CO). The result is that carbon monoxide can also bind to the iron in the heme groups of hemoglobin, although the distal histidine helps prevent this. In fact, carbon monoxide binds to the heme with about 230 times the affinity of oxygen, meaning that if both gases are available, carbon monoxide will outcompete oxygen for heme binding sites. (''THINK'': We often install carbon monoxide detectors in our homes to alert us to high concentrations of this gas. Why might carbon monoxide gas pose a danger to human beings?)<br /> <br /> ===Mutated hemoglobin causes sickle-cell disease===<br /> A mutation in the gene coding for hemoglobin causes a disease called sickle-cell anemia. The <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Sickle_one_protein_cartoon/1'>mutated hemoglobin</scene> results in red blood cells with a diseased, sickle shape instead of a healthy, disk shape. These sickle cells can block blood vessels due to their abnormal shape and cause damage to tissue and organs. (''OBSERVE'': Does the mutated hemoglobin look different than normal hemoglobin?)<br /> <br /> <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Sickle_one_protein/5'>Sickle-cell hemoglobin</scene>, shown here in spacefilling representation, differs from normal hemoglobin at a single amino acid. In the mutant, the amino acid valine takes the place of glutamate as the sixth amino acid in the beta monomer chain. Glutamate, a hydrophilic amino acid, is replaced by valine, a hydrophobic amino acid, at a location on the surface of the protein, and this creates a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Hydrophobic_spot_in_mutant/3'>hydrophobic spot</scene>. There is <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Hydrophobic_spot_in_both/3'>another relevant hydrophobic spot</scene> near the heme binding pocket in the beta-monomer that is present in both normal and sickle-cell deoxygenated hemoglobin. (''OBSERVE'': Can you find the two hydrophobic spots on the two beta-monomers in sickle-cell hemoglobin?) This second hydrophobic spot sticks to the first hydrophobic spot, present only in the mutant, causing the hemoglobin molecules to <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Sickle_hemoglobin_chain/2'>aggregate</scene> into long fibers. We show just two hemoglobin molecules stuck together, but this fiber can extend to include a large number of hemoglobin molecules in a long fiber. A <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Sickle_hemoglobin_chain_close/4'>closer look</scene> shows us the valine from the first, mutant, hydrophobic spot in hydrophobic interaction with the alanine and leucine from the second hydrophobic spot. (''THINK'': Why might these hemoglobin fibers cause sickle-cell red blood cell shape?)<br /> </StructureSection><br /> <br /> ==See Also==<br /> *[[Hemoglobin]]<br /> *PDB entry [[1hho]] (oxygenated, 2.1 Å)<br /> *PDB entry [[1hga]] (deoxygenated, 2.1 Å)<br /> *PDB entry [[1hbs]] (deoxygenated, sickle cell mutant, 3.0 Å)<br /> <br /> ==External Resources==<br /> *{{Wikipedia|Hemoglobin}}<br /> *[http://highered.mcgraw-hill.com/olcweb/cgi/pluginpop.cgi?it=swf::640::480::/sites/dl/free/0077290828/811360/Hemoglobin_Causes_Net_Diffusion_of_Oxygen.swf::Hemoglobin%20Causes%20Net%20Diffusion%20of%20Oxygen Hemoglobin Causes Net Diffusion of Oxygen (Interactive Demo)] - Oxygen diffuses freely across oxygen-permeable membranes such as those found where capillaries (small blood vessels) in the lungs make contact with the air we breathe. When oxygen diffuses from the air in our lungs across the walls of these capillaries and into our blood, it is taken up by hemoglobin -- this causes even more oxygen to diffuse into the blood in order to balance the concentration (partial pressure) of free oxygen in our blood with that in the air in our lungs. Explore the interactive demonstration to see this diffusion in action.<br /> <br /> {{Clear}}<br /> <br /> ==Content Contributors==<br /> This page includes scenes, structures and ideas from [[User:Eric_Martz|Eric Martz]], [[User:Frieda S. Reichsman|Frieda S. Reichsman]] and [[User:Angel_Herraez|Angel Herraez]].<br /> [[Category:Featured in BAMBED]]<br /> [[es:Tutorial:How_do_we_get_the_oxygen_we_breathe_%28Spanish%29]]</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts&diff=2394010 User:Michael Roberts 2015-04-13T13:59:07Z

<p>Michael Roberts: </p> <hr /> <div>*[[User:Michael Roberts/Haemoglobin]]<br /> <br /> * Full Real Name: Michael Roberts<br /> <br /> * Position: Senior Lecturer<br /> <br /> * Institution (NO ABBREVIATIONS): Lancaster University<br /> <br /> * City, State/Province, Country: Lancaster, Lancashire, UK<br /> <br /> * Field of Expertise or Study: Plant molecular biology & signalling</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/BIOL115_CaM&diff=2394007 User:Michael Roberts/BIOL115 CaM 2015-04-13T11:36:54Z

<p>Michael Roberts: Undo revision 2394006 by Michael Roberts (Talk)</p> <hr /> <div>[[Image:CaM.png|left|250px|thumb|Crystal Structure of Calmodulin [[1cll]]]]<br /> <br /> <span style="font-size:150%">'''Sequence and structure of EF hands'''</span><br /> <br /> <br /> The EF hand motif is present in a many proteins and it commonly bestows the ability to bind Ca<sup>2+</sup> ions. It was first identified in parvalbumin, a muscle protein. Here we'll have a look at the Ca<sup>2+</sup>-binding protein [[calmodulin]], which possesses four EF hands. Calmodulin and its isoform, troponinC, are important intracellular Ca<sup>2+</sup>-binding proteins.<br /> <br /> The structure below, obtained by X-ray crystallography, represents the Ca<sup>2+</sup>-binding protein calmodulin. It has a dumbell-shaped structure with two identical lobes connected by a central alpha-helix. Each lobe comprises three α-helices joined by loops. A helix-loop-helix motif forms the basis of each EF hand.<br /> <br /> <br /> Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.<br /> <br /> <StructureSection load='1cll' size='600' side='right' caption='Structure of human calmodulin (PDB entry [[1cll]])' scene='User:Michael_Roberts/BIOL115_CaM/Wireframe/3'><br /> == Molecular Model: ==<br /> We'll start with a simple ball-and-stick representation of the protein. This shows all of the atoms that make up the protein and the bonds between them.<br /> <br /> <br /> '''BACKBONE''':<br /> The ball-and-stick view shows us all the atoms, but if we're mainly interested in the overall structure of the protein, this can be too much detail.<br /> This next veiw takes us right down to a minimal representation that simply traces the <scene name='User:Michael_Roberts/BIOL115_CaM/Backbone/1'>"backbone" </scene>of the protein. The backbone includes the peptide linkages between each amino acid, along with the alpha-carbon atoms to which the side chains are attached. Notice that helical regions can now easily be seen.<br /> <br /> <br /> '''SECONDARY STRUCTURE''': This is shown more clearly by a <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/2'>ribbon diagram</scene>. The computer calculates where regions of secondary structure occur and draws them in cartoon-style 'ribbons'. <br /> The α-helical region is now clearly defined, and there are also regions of β-structure.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> The short anti-parallel beta-sheet between the adjacent EF hand loops are observed in calmodulins from various species.<br /> <br /> <br /> == Calcium Binding ==<br /> '''CALCIUM IONS''':<br /> In each EF hand loop, the Ca<sup>2+</sup> ions are bound by amino acid residues in and near the loops.<br /> <br /> The structure shown here has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>calcium ions</scene> bound. In this condition, the protein adopts the extended structure shown. The EF hand-forming helices are bent away from the long linking helix, revealing hydrophobic residues and exposing the linking chain.<br /> <br /> <br /> '''CO-ORDINATING RESIDUES''':<br /> To illustrate how Ca<sup>2+</sup> is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/1'>residues that take part in binding</scene> one of the Ca<sup>2+</sup> ions.<br /> <br /> <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/2'>Zoom in</scene> to see this more clearly. <br /> <br /> <br /> '''CO-ORDINATING ATOMS''':<br /> To highlight the atoms that co-ordinate the Ca<sup>2+</sup> ion, we can now enlarge those that are close (within 2.7 Å). This shows that <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/3'>seven oxygen</scene> atoms form the calcium co-ordination shell. Five are contributed by the side chain carboxyl groups of Asp and Glu and a sixth by the peptide carbonyl of Gln. The seventh oxygen is provided by an associated water molecule. <br /> <br /> <br /> == Binding to target proteins ==<br /> '''INACTIVE CALMODULIN:'''<br /> At resting levels of cytosolic Ca<sup>2+</sup> (~100 nM), calmodulin exists predominantly in the calcium-free form. This is called apo-calmodulin and <scene name='User:Michael_Roberts/BIOL115_CaM/Inactive_calmodulin/1'>its structure </scene>is more compact.<br /> <br /> The terminal helices are folded down concealing their hydrophobic surfaces and the central chain, which is not a helical along its whole length, is not exposed.<br /> <br /> <br /> '''CALMODULIN INTERACTS WITH ITS TARGET:'''<br /> The Ca<sup>2+</sup>-bound form of calmodulin with its exposed hydrophobic surfaces that you have already observed can <scene name='User:Michael_Roberts/BIOL115_CaM/Active_calmodulin/1'>interact with a target protein</scene>. It does this by wrapping around a specific sequence on the target molecule, which is then forced into an α-helical structure. <br /> <br /> The target molecule here (shown in blue) is the calmodulin-regulated enzyme, myosin light chain kinase. Only a short sequence from this protein, the calmodulin binding domain, is shown.<br /> </StructureSection><br /> <br /> '''External Resources.'''<br /> You can view a nice animation of the conformational change undergone by calmodulin upon calcium binding by following this link [http://morph2.molmovdb.org/results.rpy?jobid=8350057535].</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/BIOL115_CaM&diff=2394006 User:Michael Roberts/BIOL115 CaM 2015-04-13T11:33:58Z

<p>Michael Roberts: </p> <hr /> <div>[[Image:CaM.png|left|250px|thumb|Crystal Structure of Calmodulin [[1cll]]]]<br /> <br /> <span style="font-size:150%">'''Sequence and structure of EF hands'''</span><br /> <br /> <br /> The EF hand motif is present in a many proteins and it commonly bestows the ability to bind Ca<sup>2+</sup> ions. It was first identified in parvalbumin, a muscle protein. Here we'll have a look at the Ca<sup>2+</sup>-binding protein [[calmodulin]], which possesses four EF hands. Calmodulin and its isoform, troponinC, are important intracellular Ca<sup>2+</sup>-binding proteins.<br /> <br /> The structure below, obtained by X-ray crystallography, represents the Ca<sup>2+</sup>-binding protein calmodulin. It has a dumbell-shaped structure with two identical lobes connected by a central alpha-helix. Each lobe comprises three α-helices joined by loops. A helix-loop-helix motif forms the basis of each EF hand.<br /> <br /> <br /> Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.<br /> <br /> <StructureSection load='1cll' size='600' side='right' caption='Structure of human calmodulin (PDB entry [[1cll]])' scene='User:Michael_Roberts/BIOL115_CaM/Wireframe/3'><br /> == Molecular Model: ==<br /> We'll start with a simple ball-and-stick representation of the protein. This shows all of the atoms that make up the protein and the bonds between them.<br /> <br /> <br /> '''BACKBONE''':<br /> The ball-and-stick view shows us all the atoms, but if we're mainly interested in the overall structure of the protein, this can be too much detail.<br /> This next veiw takes us right down to a minimal representation that simply traces the <scene name='User:Michael_Roberts/BIOL115_CaM/Backbone/1'>"backbone" </scene>of the protein. The backbone includes the peptide linkages between each amino acid, along with the alpha-carbon atoms to which the side chains are attached. Notice that helical regions can now easily be seen.<br /> <br /> <br /> '''SECONDARY STRUCTURE''': This is shown more clearly by a <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/5'>ribbon diagram</scene>. The computer calculates where regions of secondary structure occur and draws them in cartoon-style 'ribbons'. <br /> The α-helical region is now clearly defined, and there are also regions of β-structure.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> The short anti-parallel beta-sheet between the adjacent EF hand loops are observed in calmodulins from various species.<br /> <br /> <br /> == Calcium Binding ==<br /> '''CALCIUM IONS''':<br /> In each EF hand loop, the Ca<sup>2+</sup> ions are bound by amino acid residues in and near the loops.<br /> <br /> The structure shown here has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/4'>calcium ions</scene> bound. In this condition, the protein adopts the extended structure shown. The EF hand-forming helices are bent away from the long linking helix, revealing hydrophobic residues and exposing the linking chain.<br /> <br /> <br /> '''CO-ORDINATING RESIDUES''':<br /> To illustrate how Ca<sup>2+</sup> is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/5'>residues that take part in binding</scene> one of the Ca<sup>2+</sup> ions.<br /> <br /> <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/6'>Zoom in</scene> to see this more clearly. <br /> <br /> <br /> '''CO-ORDINATING ATOMS''':<br /> To highlight the atoms that co-ordinate the Ca<sup>2+</sup> ion, we can now enlarge those that are close (within 2.7 Å). This shows that <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/4'>seven oxygen</scene> atoms form the calcium co-ordination shell. Five are contributed by the side chain carboxyl groups of Asp and Glu and a sixth by the peptide carbonyl of Gln. The seventh oxygen is provided by an associated water molecule. <br /> <br /> <br /> == Binding to target proteins ==<br /> '''INACTIVE CALMODULIN:'''<br /> At resting levels of cytosolic Ca<sup>2+</sup> (~100 nM), calmodulin exists predominantly in the calcium-free form. This is called apo-calmodulin and <scene name='User:Michael_Roberts/BIOL115_CaM/Inactive_calmodulin/1'>its structure </scene>is more compact.<br /> <br /> The terminal helices are folded down concealing their hydrophobic surfaces and the central chain, which is not a helical along its whole length, is not exposed.<br /> <br /> <br /> '''CALMODULIN INTERACTS WITH ITS TARGET:'''<br /> The Ca<sup>2+</sup>-bound form of calmodulin with its exposed hydrophobic surfaces that you have already observed can <scene name='User:Michael_Roberts/BIOL115_CaM/Active_calmodulin/1'>interact with a target protein</scene>. It does this by wrapping around a specific sequence on the target molecule, which is then forced into an α-helical structure. <br /> <br /> The target molecule here (shown in blue) is the calmodulin-regulated enzyme, myosin light chain kinase. Only a short sequence from this protein, the calmodulin binding domain, is shown.<br /> </StructureSection><br /> <br /> '''External Resources.'''<br /> You can view a nice animation of the conformational change undergone by calmodulin upon calcium binding by following this link [http://morph2.molmovdb.org/results.rpy?jobid=8350057535].</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Sandbox_1&diff=1801547 User:Michael Roberts/Sandbox 1 2013-05-20T17:51:40Z

<p>Michael Roberts: </p> <hr /> <div>== Possible animated exhibition display ==<br /> <Structure load='1qja' size='700' frame='true' align='left' caption='Insert caption here' scene='User:Michael_Roberts/Sandbox_1/Storey/1' /><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> === A comparative representation of ... ===<br /> <br /> {|<br /> |<applet load='2cga' name='A' size='300' frame='true' align='right' caption='A-DNA' align='left' scene=''/><br /> |<applet load='1afq' name='B' size='300' frame='true' align='right' caption='B-DNA' align='left' scene=''/><br /> |}<br /> <br /> {{Clear}}<br /> <center><br /> '''Synchronize the three applets showing chymotrypsinogen and α-chymotrypsin by clicking the checkbox'''<br /> <jmol><br /> <jmolCheckbox><br /> <target>A</target><br /> <br /> <scriptWhenChecked> sync jmolAppletB,jmolAppletZ </scriptWhenChecked><br /> <scriptWhenUnchecked> sync OFF</scriptWhenUnchecked><br /> <text> Synchronize</text><br /> </jmolCheckbox><br /> </jmol><br /> </center><br /> <br /> {{Clear}}</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Sandbox_1&diff=1801546 User:Michael Roberts/Sandbox 1 2013-05-20T17:50:54Z

<p>Michael Roberts: </p> <hr /> <div><br /> == Possible animated exhibition display ==<br /> <Structure load='1qja' size='700' frame='true' align='left' caption='Insert caption here' scene='User:Michael_Roberts/Sandbox_1/Storey/1' /><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> === A comparative representation of ... ===<br /> <br /> {|<br /> |<applet load='2cga' name='A' size='300' frame='true' align='right' caption='A-DNA' align='left' scene=''/><br /> |<applet load='1afq' name='B' size='300' frame='true' align='right' caption='B-DNA' align='left' scene=''/><br /> |}<br /> <br /> {{Clear}}<br /> <center><br /> '''Synchronize the three applets showing chymotrypsinogen and α-chymotrypsin by clicking the checkbox'''<br /> <jmol><br /> <jmolCheckbox><br /> <target>A</target><br /> <br /> <scriptWhenChecked> sync jmolAppletB,jmolAppletZ </scriptWhenChecked><br /> <scriptWhenUnchecked> sync OFF</scriptWhenUnchecked><br /> <text> Synchronize</text><br /> </jmolCheckbox><br /> </jmol><br /> </center><br /> <br /> {{Clear}}</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Sandbox_1&diff=1801545 User:Michael Roberts/Sandbox 1 2013-05-20T17:43:49Z

<p>Michael Roberts: </p> <hr /> <div><Structure load='1qja' size='700' frame='true' align='left' caption='Insert caption here' scene='User:Michael_Roberts/Sandbox_1/Storey/1' /><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> === A comparative representation of ... ===<br /> <br /> {|<br /> |<applet load='2cga' name='A' size='300' frame='true' align='right' caption='A-DNA' align='left' scene=''/><br /> |<applet load='1afq' name='B' size='300' frame='true' align='right' caption='B-DNA' align='left' scene=''/><br /> |}<br /> <br /> {{Clear}}<br /> <center><br /> '''Synchronize the three applets showing chymotrypsinogen and α-chymotrypsin by clicking the checkbox'''<br /> <jmol><br /> <jmolCheckbox><br /> <target>A</target><br /> <br /> <scriptWhenChecked> sync jmolAppletB,jmolAppletZ </scriptWhenChecked><br /> <scriptWhenUnchecked> sync OFF</scriptWhenUnchecked><br /> <text> Synchronize</text><br /> </jmolCheckbox><br /> </jmol><br /> </center><br /> <br /> {{Clear}}</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Sandbox_1&diff=1801542 User:Michael Roberts/Sandbox 1 2013-05-20T17:30:02Z

<p>Michael Roberts: </p> <hr /> <div><Structure load='1qja' size='700' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /><br /> <br /> <br /> <br /> === A comparative representation of ... ===<br /> <br /> {|<br /> |<applet load='2cga' name='A' size='300' frame='true' align='right' caption='A-DNA' align='left' scene=''/><br /> |<applet load='1afq' name='B' size='300' frame='true' align='right' caption='B-DNA' align='left' scene=''/><br /> |}<br /> <br /> {{Clear}}<br /> <center><br /> '''Synchronize the three applets showing chymotrypsinogen and α-chymotrypsin by clicking the checkbox'''<br /> <jmol><br /> <jmolCheckbox><br /> <target>A</target><br /> <br /> <scriptWhenChecked> sync jmolAppletB,jmolAppletZ </scriptWhenChecked><br /> <scriptWhenUnchecked> sync OFF</scriptWhenUnchecked><br /> <text> Synchronize</text><br /> </jmolCheckbox><br /> </jmol><br /> </center><br /> <br /> {{Clear}}</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/BIOL115_CaM&diff=1789505 User:Michael Roberts/BIOL115 CaM 2013-05-03T16:28:03Z

<p>Michael Roberts: </p> <hr /> <div>[[Image:CaM.png|left|250px|thumb|Crystal Structure of Calmodulin [[1cll]]]]<br /> <br /> <span style="font-size:150%">'''Sequence and structure of EF hands'''</span><br /> <br /> <br /> The EF hand motif is present in a many proteins and it commonly bestows the ability to bind Ca<sup>2+</sup> ions. It was first identified in parvalbumin, a muscle protein. Here we'll have a look at the Ca<sup>2+</sup>-binding protein [[calmodulin]], which possesses four EF hands. Calmodulin and its isoform, troponinC, are important intracellular Ca<sup>2+</sup>-binding proteins.<br /> <br /> The structure below, obtained by X-ray crystallography, represents the Ca<sup>2+</sup>-binding protein calmodulin. It has a dumbell-shaped structure with two identical lobes connected by a central alpha-helix. Each lobe comprises three α-helices joined by loops. A helix-loop-helix motif forms the basis of each EF hand.<br /> <br /> <br /> Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.<br /> <br /> <StructureSection load='1cll' size='600' side='right' caption='Structure of human calmodulin (PDB entry [[1cll]])' scene='User:Michael_Roberts/BIOL115_CaM/Wireframe/3'><br /> == Molecular Model: ==<br /> We'll start with a simple ball-and-stick representation of the protein. This shows all of the atoms that make up the protein and the bonds between them.<br /> <br /> <br /> '''BACKBONE''':<br /> The ball-and-stick view shows us all the atoms, but if we're mainly interested in the overall structure of the protein, this can be too much detail.<br /> This next veiw takes us right down to a minimal representation that simply traces the <scene name='User:Michael_Roberts/BIOL115_CaM/Backbone/1'>"backbone" </scene>of the protein. The backbone includes the peptide linkages between each amino acid, along with the alpha-carbon atoms to which the side chains are attached. Notice that helical regions can now easily be seen.<br /> <br /> <br /> '''SECONDARY STRUCTURE''': This is shown more clearly by a <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/2'>ribbon diagram</scene>. The computer calculates where regions of secondary structure occur and draws them in cartoon-style 'ribbons'. <br /> The α-helical region is now clearly defined, and there are also regions of β-structure.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> The short anti-parallel beta-sheet between the adjacent EF hand loops are observed in calmodulins from various species.<br /> <br /> <br /> == Calcium Binding ==<br /> '''CALCIUM IONS''':<br /> In each EF hand loop, the Ca<sup>2+</sup> ions are bound by amino acid residues in and near the loops.<br /> <br /> The structure shown here has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>calcium ions</scene> bound. In this condition, the protein adopts the extended structure shown. The EF hand-forming helices are bent away from the long linking helix, revealing hydrophobic residues and exposing the linking chain.<br /> <br /> <br /> '''CO-ORDINATING RESIDUES''':<br /> To illustrate how Ca<sup>2+</sup> is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/1'>residues that take part in binding</scene> one of the Ca<sup>2+</sup> ions.<br /> <br /> <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/2'>Zoom in</scene> to see this more clearly. <br /> <br /> <br /> '''CO-ORDINATING ATOMS''':<br /> To highlight the atoms that co-ordinate the Ca<sup>2+</sup> ion, we can now enlarge those that are close (within 2.7 Å). This shows that <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/3'>seven oxygen</scene> atoms form the calcium co-ordination shell. Five are contributed by the side chain carboxyl groups of Asp and Glu and a sixth by the peptide carbonyl of Gln. The seventh oxygen is provided by an associated water molecule. <br /> <br /> <br /> == Binding to target proteins ==<br /> '''INACTIVE CALMODULIN:'''<br /> At resting levels of cytosolic Ca<sup>2+</sup> (~100 nM), calmodulin exists predominantly in the calcium-free form. This is called apo-calmodulin and <scene name='User:Michael_Roberts/BIOL115_CaM/Inactive_calmodulin/1'>its structure </scene>is more compact.<br /> <br /> The terminal helices are folded down concealing their hydrophobic surfaces and the central chain, which is not a helical along its whole length, is not exposed.<br /> <br /> <br /> '''CALMODULIN INTERACTS WITH ITS TARGET:'''<br /> The Ca<sup>2+</sup>-bound form of calmodulin with its exposed hydrophobic surfaces that you have already observed can <scene name='User:Michael_Roberts/BIOL115_CaM/Active_calmodulin/1'>interact with a target protein</scene>. It does this by wrapping around a specific sequence on the target molecule, which is then forced into an α-helical structure. <br /> <br /> The target molecule here (shown in blue) is the calmodulin-regulated enzyme, myosin light chain kinase. Only a short sequence from this protein, the calmodulin binding domain, is shown.<br /> </StructureSection><br /> <br /> '''External Resources.'''<br /> You can view a nice animation of the conformational change undergone by calmodulin upon calcium binding by following this link [http://morph2.molmovdb.org/results.rpy?jobid=8350057535].</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/BIOL115_CaM&diff=1789501 User:Michael Roberts/BIOL115 CaM 2013-05-03T16:17:37Z

<p>Michael Roberts: </p> <hr /> <div>[[Image:CaM.png|left|250px|thumb|Crystal Structure of Calmodulin [[1cll]]]]<br /> <br /> <span style="font-size:150%">'''Sequence and structure of EF hands'''</span><br /> <br /> <br /> The EF hand motif is present in a many proteins and it commonly bestows the ability to bind Ca<sup>2+</sup> ions. It was first identified in parvalbumin, a muscle protein. Here we'll have a look at the Ca<sup>2+</sup>-binding protein [[calmodulin]], which possesses four EF hands. Calmodulin and its isoform, troponinC, are important intracellular Ca<sup>2+</sup>-binding proteins.<br /> <br /> The structure below, obtained by X-ray crystallography, represents the Ca<sup>2+</sup>-binding protein calmodulin. It has a dumbell-shaped structure with two identical lobes connected by a central alpha-helix. Each lobe comprises three α-helices joined by loops. A helix-loop-helix motif forms the basis of each EF hand.<br /> <br /> <br /> Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.<br /> <br /> <StructureSection load='1cll' size='600' side='right' caption='Structure of human calmodulin (PDB entry [[1cll]])' scene='User:Michael_Roberts/BIOL115_CaM/Wireframe/3'><br /> == Molecular Model: ==<br /> We'll start with a simple ball-and-stick representation of the protein. This shows all of the atoms that make up the protein and the bonds between them.<br /> <br /> <br /> '''BACKBONE''':<br /> The ball-and-stick view shows us all the atoms, but if we're mainly interested in the overall structure of the protein, this can be too much detail.<br /> This next veiw takes us right down to a minimal representation that simply traces the <scene name='User:Michael_Roberts/BIOL115_CaM/Backbone/1'>"backbone" </scene>of the protein. The backbone includes the peptide linkages between each amino acid, along with the alpha-carbon atoms to which the side chains are attached. Notice that helical regions can now easily be seen.<br /> <br /> <br /> '''SECONDARY STRUCTURE''': This is shown more clearly by a <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/2'>ribbon diagram</scene>. The computer calculates where regions of secondary structure occur and draws them in cartoon-style 'ribbons'. <br /> The α-helical region is now clearly defined, and there are also regions of β-structure.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> The short anti-parallel beta-sheet between the adjacent EF hand loops are observed in calmodulins from various species.<br /> <br /> <br /> == Calcium Binding ==<br /> '''CALCIUM IONS''':<br /> In each EF hand loop, the Ca<sup>2+</sup> ions are bound by amino acid residues in and near the loops.<br /> <br /> The structure shown here has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>calcium ions</scene> bound. In this condition, the protein adopts the extended structure shown. The EF hand-forming helices are bent away from the long linking helix, revealing hydrophobic residues and exposing the linking chain.<br /> <br /> <br /> '''CO-ORDINATING RESIDUES''':<br /> To illustrate how Ca<sup>2+</sup> is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/1'>residues that take part in binding</scene> one of the Ca<sup>2+</sup> ions.<br /> <br /> <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/2'>Zoom in</scene> to see this more clearly. <br /> <br /> <br /> '''CO-ORDINATING ATOMS''':<br /> To highlight the atoms that co-ordinate the Ca<sup>2+</sup> ion, we can now enlarge those that are close (within 2.7 Å). This shows that <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/3'>seven oxygen</scene> atoms form the calcium co-ordination shell. Five are contributed by the side chain carboxyl groups of Asp and Glu and a sixth by the peptide carbonyl of Gln. The seventh oxygen is provided by an associated water molecule. <br /> <br /> <br /> == Binding to target proteins ==<br /> '''INACTIVE CALMODULIN:'''<br /> At resting levels of cytosolic Ca<sup>2+</sup> (~100 nM), calmodulin exists predominantly in the calcium-free form. This is called apo-calmodulin and <scene name='User:Michael_Roberts/BIOL115_CaM/Inactive_calmodulin/1'>its structure </scene>is more compact.<br /> <br /> The terminal helices are folded down concealing their hydrophobic surfaces and the central chain, which is not a helical along its whole length, is not exposed.<br /> <br /> <br /> '''CALMODULIN INTERACTS WITH ITS TARGET:'''<br /> The Ca<sup>2+</sup>-bound form of calmodulin with its exposed hydrophobic surfaces that you have already observed can <scene name='User:Michael_Roberts/BIOL115_CaM/Active_calmodulin/1'>interact with a target protein</scene>. It does this by wrapping around a specific sequence on the target molecule, forcing it to adopt an α-helical structure. <br /> <br /> The target molecule here (shown in blue) is the calmodulin-regulated enzyme, myosin light chain kinase. Only a short sequence from this protein, the calmodulin binding domain, is shown.<br /> </StructureSection><br /> <br /> '''External Resources.'''<br /> You can view a nice animation of the conformational change undergone by calmodulin upon calcium binding by following this link [http://morph2.molmovdb.org/results.rpy?jobid=8350057535].</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Sandbox_1&diff=1789497 User:Michael Roberts/Sandbox 1 2013-05-03T15:31:28Z

<p>Michael Roberts: </p> <hr /> <div>=== A comparative representation of ... ===<br /> <br /> {|<br /> |<applet load='2cga' name='A' size='300' frame='true' align='right' caption='A-DNA' align='left' scene=''/><br /> |<applet load='1afq' name='B' size='300' frame='true' align='right' caption='B-DNA' align='left' scene=''/><br /> |}<br /> <br /> {{Clear}}<br /> <center><br /> '''Synchronize the three applets showing chymotrypsinogen and α-chymotrypsin by clicking the checkbox'''<br /> <jmol><br /> <jmolCheckbox><br /> <target>A</target><br /> <br /> <scriptWhenChecked> sync jmolAppletB,jmolAppletZ </scriptWhenChecked><br /> <scriptWhenUnchecked> sync OFF</scriptWhenUnchecked><br /> <text> Synchronize</text><br /> </jmolCheckbox><br /> </jmol><br /> </center><br /> <br /> {{Clear}}</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/BIOL115_Chymo&diff=1789495 User:Michael Roberts/BIOL115 Chymo 2013-05-03T15:12:51Z

<p>Michael Roberts: </p> <hr /> <div>[[Image:Chymo.png|left|150px|thumb|Chymotrypsin active site [[1aqf]]]]<br /> <br /> <br /> <span style="font-size:150%">'''Chymotrypsin.'''</span><br /> <br /> <br /> Chymotrypsin is a member of a family of enzymes all of which cleave peptide bonds through the action of an active site serine (the ''serine proteases'').<br /> This family includes the pancreatic enzymes chymotrypsin, trypsin and elastase as well as a variety of other proteases (e.g. cocoonase, thrombin, acrosomal protease, ''etc.''). Chymotrypsin, trypsin and elastase show a high degree of similarity in their overall tertiary structure, but have different substrate specificities determined by the different properties of the substrate binding site on each enzyme.<br /> <br /> <br /> Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.<br /> <br /> <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='User:Michael_Roberts/BIOL115_Chymo/Start/1'><br /> == Tertiary structure ==<br /> Chymotrypsin is initially synthesized as a 245 amino acid inactive precursor (a zymogen) termed chymotrypsinogen. Activation of chymotrypsinogen involves proteolytic cleavage at two sites along the chain and removal of two amino acids at each cleavage site. The resultant <scene name='User:Michael_Roberts/BIOL115_Chymo/Chains/1'>three chains</scene> are shown here (chain 1 = 1-13 in green; chain 2 = 16-146 in red; chain 3 = 149-24 in blue). Note, some amino acids at the temini of these chains are not shown in this representation (e.g. 11-13, 149, ). This is because these residues show too much flexibility in the crystal structures to give X-ray diffraction patterns which would locate them in space.<br /> <br /> The three chains are held together by five <scene name='User:Michael_Roberts/BIOL115_Chymo/Chains/2'>disulfide bonds</scene>. Can you identify the specific cys residues linked in each disulfide bond? Why do you think is it very difficult to obtain active chymotrypsin after denaturation and renaturation?<br /> <br /> <br /> <br /> == Beta Barrels, Protein Domains and the Active Center ==<br /> The chymotrypsin molecule is folded into two <scene name='User:Michael_Roberts/BIOL115_Chymo/2ndry_structure/1'>domains</scene>, each containing six beta strands (orange) arranged as anti-parallel sheets which form a circular structure known as a beta barrel. Rotate the molecule so that you can see down through each of the two beta barrels in turn.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> The <scene name='User:Michael_Roberts/BIOL115_Chymo/2ndry_structure/2'>active site residues</scene> (Ser-195, His-57 and Asp-102 shown here in spacefill representation), are far apart in the primary sequence but are brought together in a crevice formed between the two beta barrel protein domains.<br /> <br /> <br /> == The Active Site Triad ==<br /> <br /> The <scene name='User:Michael_Roberts/BIOL115_Chymo/2ndry_structure/3'>active site</scene> of chymotrypsin consists of Asp102 positioned close to His 57 and Ser 195. The precise mechanism of action is still debated, but it appears that a hydrogen on the his imidazole ring is transferred to the Asp 102 carboxylate (either via a "charge relay system" or via a "low barrier H-bond"). This shift results in the histidine ring being able to accept the serine 195 hydroxyl hydrogen, forming a very nucleophilic serine alkoxide ion.<br /> <br /> <br /> '''Binding of the Substrate'''<br /> This structure contains a competitive inhibitor, <scene name='User:Michael_Roberts/BIOL115_Chymo/Substrate/1'>D-leucyl-L-phenylalanyl-p-fluorobenzylamide</scene>. This is a dipeptide of Leu and Phe (orange), plus a fluorobenzylamide group (red), which is aromatic and bound in the specificity pocket (see next button). In an actual substrate, the peptide bond cleaved would be to the carboxyl side of the aromatic amino acid. In this inhibitor, there are two residues to the amide side, but there is no residue to what would be the carboxyl side. Thus, there is no cleavable bond in this structure.<br /> <br /> <br /> '''The Active Site Environment'''<br /> A specific pocket adjacent to the active site triad determines the specificity of the protease (chymotrypsin cleaves adjacent to large aromatic side chains, trypsin adjacent to Lys or Arg residues). In this view, the <scene name='User:Michael_Roberts/BIOL115_Chymo/Substrate/3'>residues making up this pocket</scene> are shown as spacefilling (yellow) and the three residues which are predominant determinants of this specificity are shown in shades of green. These are amino acids 189, 216 and 226 which line a pocket adjacent to the active site triad. The residues in the catalytic triad are blue, whilst the fluorobenzylamide inhibitor is now shown as a stick representation.<br /> <br /> Here, the fluorobenzylamide group (red) of the inhibitor is bound in this pocket. In trypsin and chymotrypsin, residues 216 and 226 are both glycine (lime green), which has a minimal side chain, leaving space so that bulky side chains in the substrate protein can extend into the interior of this pocket. In contrast, in elastase, these residues are Val and Thr, which have side chains that partly fill the pocket so that bulky R groups will not fit into it. In chymotrypsin, residue 189 is a serine (green) and this allows bulky aromatic R groups to interact with the pocket predominantly via van der Waals forces. In trypsin, residue 189 is the negatively-charged Asp, and this allows binding of substrates with positively charged Lys or Arg residues.</div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/BIOL115_CaM&diff=1789141 User:Michael Roberts/BIOL115 CaM 2013-05-02T16:35:57Z

<p>Michael Roberts: </p> <hr /> <div>[[Image:CaM.png|left|250px|thumb|Crystal Structure of Calmodulin [[1cll]]]]<br /> <br /> <span style="font-size:150%">'''Sequence and structure of EF hands'''</span><br /> <br /> <br /> The EF hand motif is present in a many proteins and it commonly bestows the ability to bind Ca<sup>2+</sup> ions. It was first identified in parvalbumin, a muscle protein. Here we'll have a look at the Ca<sup>2+</sup>-binding protein [[calmodulin]], which possesses four EF hands. Calmodulin and its isoform, troponinC, are important intracellular Ca<sup>2+</sup>-binding proteins.<br /> <br /> The structure below, obtained by X-ray crystallography, represents the Ca<sup>2+</sup>-binding protein calmodulin. It has a dumbell-shaped structure with two identical lobes connected by a central alpha-helix. Each lobe comprises three α-helices joined by loops. A helix-loop-helix motif forms the basis of each EF hand.<br /> <br /> <br /> Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.<br /> <br /> <StructureSection load='1cll' size='600' side='right' caption='Structure of human calmodulin (PDB entry [[1cll]])' scene='User:Michael_Roberts/BIOL115_CaM/Wireframe/3'><br /> == Molecular Model: ==<br /> We'll start with a simple ball-and-stick representation of the protein. This shows all of the atoms that make up the protein and the bonds between them.<br /> <br /> <br /> '''BACKBONE''':<br /> The ball-and-stick view shows us all the atoms, but if we're mainly interested in the overall structure of the protein, this can be too much detail.<br /> This next veiw takes us right down to a minimal representation that simply traces the <scene name='User:Michael_Roberts/BIOL115_CaM/Backbone/1'>"backbone" </scene>of the protein. The backbone includes the peptide linkages between each amino acid, along with the alpha-carbon atoms to which the side chains are attached. Notice that helical regions can now easily be seen.<br /> <br /> <br /> '''SECONDARY STRUCTURE''': This is shown more clearly by a <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/2'>ribbon diagram</scene>. The computer calculates where regions of secondary structure occur and draws them in cartoon-style 'ribbons'. <br /> The α-helical region is now clearly defined, and there are also regions of β-structure.<br /> <br /> ''Colour key:''<br /> {{Template:ColorKey_Helix}},<br /> {{Template:ColorKey_Strand}}.<br /> <br /> The short anti-parallel beta-sheet between the adjacent EF hand loops are observed in calmodulins from various species.<br /> <br /> <br /> == Calcium Binding ==<br /> '''CALCIUM IONS''':<br /> In each EF hand loop, the Ca<sup>2+</sup> ions are bound by amino acid residues in and near the loops.<br /> <br /> The structure shown here has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>calcium ions</scene> bound. In this condition, the protein adopts the extended structure shown. The EF hand-forming helices are bent away from the long linking helix, revealing hydrophobic residues and exposing the linking chain.<br /> <br /> <br /> '''CO-ORDINATING RESIDUES''':<br /> To illustrate how Ca<sup>2+</sup> is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/1'>residues that take part in binding</scene> one of the Ca<sup>2+</sup> ions.<br /> <br /> <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/2'>Zoom in</scene> to see this more clearly. <br /> <br /> <br /> '''CO-ORDINATING ATOMS''':<br /> To highlight the atoms that co-ordinate the Ca<sup>2+</sup> ion, we can now enlarge those that are close (within 2.7 Å). This shows that <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/3'>seven oxygen</scene> atoms form the calcium co-ordination shell. Five are contributed by the side chain carboxyl groups of Asp and Glu and a sixth by the peptide carbonyl of Gln. The seventh oxygen is provided by an associated water molecule. <br /> <br /> <br /> == Binding to target proteins ==<br /> '''INACTIVE CALMODULIN:'''<br /> At resting levels of cytosolic Ca<sup>2+</sup> (~100 nM), calmodulin exists predominantly in the calcium-free form. This is called apo-calmodulin and <scene name='User:Michael_Roberts/BIOL115_CaM/Inactive_calmodulin/1'>its structure </scene>is more compact.<br /> <br /> The terminal helices are folded down concealing their hydrophobic surfaces and the central chain, which is not a helical along its whole length, is not exposed.<br /> <br /> <br /> '''CALMODULIN INTERACTS WITH ITS TARGET:'''<br /> The Ca2+-bound form of calmodulin with its exposed hydrophobic surfaces that you have already observed can <scene name='User:Michael_Roberts/BIOL115_CaM/Active_calmodulin/1'>interact with a target protein</scene>. It does this by wrapping around a specific sequence on the target molecule, forcing it to adopt an a-helical structure. <br /> <br /> The target molecule here (shown in blue) is the calmodulin-regulated enzyme, myosin light chain kinase. Only a short sequence from this protein, the calmodulin binding domain, is shown.<br /> </StructureSection><br /> <br /> '''External Resources.'''<br /> You can view a nice animation of the conformational change undergone by calmodulin upon calcium binding by following this link [http://morph2.molmovdb.org/results.rpy?jobid=8350057535].</div>

Michael Roberts https://proteopedia.org/index.php?title=Michael_Roberts/BIOL115/ERK2&diff=1789104 Michael Roberts/BIOL115/ERK2 2013-05-02T13:18:05Z

<p>Michael Roberts: </p> <hr /> <div>[[Image:2erk.png|left|170px|thumb|MAP kinase ERK2 ([[2erk]])]]<br /> <br /> <br /> <span style="font-size:150%" >'''The active site in mitogen-activated protein kinase ERK2.'''</span><br /> <br /> <br /> <Structure load='2erk' size='850' frame='true' align='right' caption='MAPK ERK2' scene='Insert optional scene name here' /><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/6'>Secondary structure</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/5'>Sticks</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/4'>Add ATP-binding</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/2'>Add substrate-binding</scene><br /> <br /> <scene name='Michael_Roberts/BIOL115/ERK2/Active_site-reveal/1'>Add catalytic loop</scene></div>

Michael Roberts https://proteopedia.org/index.php?title=Michael_Roberts/BIOL115/ERK2&diff=1789103 Michael Roberts/BIOL115/ERK2 2013-05-02T13:13:41Z

<p>Michael Roberts: </p> <hr /> <div>[[Image:2erk.png|left|200px|thumb|MAP kinase ERK2 ([[2ek]])]]<br /> <br /> <br /> <span style="font-size:150%">'''The active Site in Mitogen-activated protein kinase ERK2.'''</span><br /> <br /> <br /> <Structure load='2erk' size='850' frame='true' align='right' caption='MAPK ERK2' scene='Insert optional scene name here' /><br /> <br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/6'>Secondary structure</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/5'>Sticks</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/4'>Add ATP-binding</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/2'>Add substrate-binding</scene><br /> <br /> <scene name='Michael_Roberts/BIOL115/ERK2/Active_site-reveal/1'>Add catalytic loop</scene></div>

Michael Roberts https://proteopedia.org/index.php?title=Michael_Roberts/BIOL115/ERK2&diff=1789100 Michael Roberts/BIOL115/ERK2 2013-05-02T13:04:59Z

<p>Michael Roberts: </p> <hr /> <div>== The active Site in Mitogen-activated protein kinase ERK2 ==<br /> <br /> <Structure load='2erk' size='850' frame='true' align='right' caption='MAPK ERK2' scene='Insert optional scene name here' /><br /> <br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/6'>Secondary structure</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/5'>Sticks</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/4'>Add ATP-binding</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/2'>Add substrate-binding</scene><br /> <br /> <scene name='Michael_Roberts/BIOL115/ERK2/Active_site-reveal/1'>Add catalytic loop</scene></div>

Michael Roberts https://proteopedia.org/index.php?title=Michael_Roberts/BIOL115/ERK2&diff=1789099 Michael Roberts/BIOL115/ERK2 2013-05-02T12:58:02Z

<p>Michael Roberts: </p> <hr /> <div>== The active Site in Mitogen-activated protein kinase ERK2 ==<br /> <br /> <Structure load='2erk' size='850' frame='true' align='right' caption='MAPK ERK2' scene='Insert optional scene name here' /><br /> <br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/6'>Secondary structure</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/5'>Sticks</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/4'>Add ATP-binding</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/2'>Add substrate-binding</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/1'>Add catalytic loop</scene></div>

Michael Roberts https://proteopedia.org/index.php?title=Michael_Roberts/BIOL115/ERK2&diff=1789098 Michael Roberts/BIOL115/ERK2 2013-05-02T12:56:51Z

<p>Michael Roberts: New page: == The active Site in Mitogen-activated protein kinase ERK2 == <Structure load='2erk' size='700' frame='true' align='right' caption='MAPK ERK2' scene='Insert optional scene name here' /> ...</p> <hr /> <div>== The active Site in Mitogen-activated protein kinase ERK2 ==<br /> <br /> <Structure load='2erk' size='700' frame='true' align='right' caption='MAPK ERK2' scene='Insert optional scene name here' /><br /> <br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/6'>Secondary structure</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/5'>Sticks</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/4'>Add ATP-binding</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/2'>Add substrate-binding</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/1'>Add catalytic loop</scene></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Sandbox_1&diff=1789097 User:Michael Roberts/Sandbox 1 2013-05-02T12:52:12Z

<p>Michael Roberts: </p> <hr /> <div><Structure load='2erk' size='700' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /><br /> <br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/6'>Secondary structure</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/5'>Sticks</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/4'>Add ATP-binding</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/2'>Add substrate-binding</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site-reveal/1'>Add catalytic loop</scene><br /> <br /> <br /> <br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site/1'>Active site domains</scene><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site/2'>spacefill</scene></div>

Michael Roberts https://proteopedia.org/index.php?title=User:Michael_Roberts/Sandbox_1&diff=1789096 User:Michael Roberts/Sandbox 1 2013-05-02T11:16:28Z

<p>Michael Roberts: </p> <hr /> <div><Structure load='2erk' size='700' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /><br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site/1'>Active site domains</scene><br /> <br /> <br /> <scene name='User:Michael_Roberts/Sandbox_1/Active_site/2'>spacefill</scene></div>

Michael Roberts