Globular Proteins: Difference between revisions
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Globular proteins have a 3D molecular structure that has a shape that is anywhere from a sphere to a cigar. Usually the structure of a globular protein is divided into three or four levels. The primary structure is simply the sequence of amino acids forming the peptide chain. The peptide chain can be folded in an ordered and repetitive fashion, and the structures with repetitive conformations are called [[Secondary_structure|secondary structures]]. | <StructureSection load='1a7v' size='450' frame='true' side='right' scene ='Globular_Proteins/Two_layers/3' caption='' >__NOTOC__ | ||
Globular proteins have a 3D molecular structure that has a shape that is anywhere from a sphere to a cigar. Usually the structure of a globular protein is divided into three or four levels. The primary structure is simply the sequence of amino acids forming the peptide chain. The peptide chain can be folded in an ordered and repetitive fashion, and the structures with ordered and repetitive conformations are called [[Secondary_structure|secondary structures]]. [[Helices_in_Proteins|Helices]], [[Sheets in Proteins|β-sheets]] and [[Turns in Proteins|turns]] are three important types of secondary structures. Turns are classified as a secondary structure even though their structures are ordered but not repetitive. The tertiary structure is the overall 3D structure of a globular protein and is produced by folding the helices and sheets upon themselves with turns and [[Loops in Proteins|loops]] forming the folds. Non-covalent molecular attractions are important forces in maintaining the folded conformation of a globular protein. For the most part, these attractions are between the atoms of the side chains but can be between the side chains and a bound ligand. Hydrogen bonds between back bone atoms are important in maintaining secondary structures, and those between side chains are involved in maintaining the tertiary structure. Examples of finding and visualizing both types in globular proteins are at [[Hydrogen bonds |hydrogen bonds]]. The attractive forces of [[Salt_bridges |salt bridges]] are important in maintaining some tertiary structures, but they also can be involved in the binding of ligands. The Disulfide bond is the one type of covalent bond that can play an important role in maintaining the tertiary structure as well as connecting two or more peptide chains together. Links to sites having structures that illustrate disulfide bonds are at [[Cystine]]. Some globular proteins have a quaternary structure, and it is formed when two or more globular protein molecules (monomer) join together and form a multimeric unit. [[Hemoglobin]] is a good example of a protein that has a quarternary structure. | |||
The tertiary structure of many globular proteins can be characterized by the number of layers of peptide backbone which are present and the attractive forces which are generated by these layers.<ref name='Garret'>Biochemistry, 4th ed., R. H. Garrett & C. M. Grisham, Thomson/Brooks/Cole, pages 167-170.</ref> Other important characteristics in the absence of backbone layers are the presence of disulfice bonds, of chelated metal ions or of intrinsically unstructured segments <ref name='Garret'/>. The objective of this page is to introduce the tertiary structures of globular proteins by illustrating these characteristics of globular proteins. | |||
== Layers of Backbone Present in the Structure == | == Layers of Backbone Present in the Structure == | ||
Layers of backbone in the core of the structure is a feature that many, but not all, globular proteins have. The number of layers and their location vary for different proteins, but in all of these proteins the hydrophobic forces between the layers play a major role in maintaining the tertiary structure. | Layers of backbone in the core of the structure is a feature that many, but not all, globular proteins have. The number of layers and their location vary for different proteins, but in all of these proteins the hydrophobic forces between the layers play a major role in maintaining the tertiary structure. | ||
=== Two Layers === | === Two Layers === | ||
The ribbons representing the backbones show the two layers of α-helices. The <scene name='Globular_Proteins/Two_layers_phobic/1'>hydrophobic side chains</scene> are shown in ball and stick with one layer colored green and the other cyan. Notice that these side chains are mostly located between the layers and that few are on the exterior of the molecule. The <scene name='Globular_Proteins/Two_layers_polar/1'>polar residues</scene> are now ball & stick, and they tend to be on the surface of the molecule where they can associate with <scene name='Globular_Proteins/Two_layers_water/1'>water</scene>. More clearly see polar groups on the surface by <scene name='Globular_Proteins/Two_layers_polar_rot/1'>rotating structure</scene> so that axis of helix aligns with z-axis. | The ribbons representing the backbones show the two layers of α-helices. The <scene name='Globular_Proteins/Two_layers_phobic/1'>hydrophobic side chains</scene> are shown in ball and stick with one layer colored green and the other cyan. Notice that these side chains are mostly located between the layers and that few are on the exterior of the molecule. View the <scene name='Globular_Proteins/Two_layers_vdw_contact/1'>points of hydrophobic attraction</scene> between the two layers. The <scene name='Globular_Proteins/Two_layers_hbond_contact/2'>hydrogen bonds</scene> between the layers are only on the edges. The <scene name='Globular_Proteins/Two_layers_polar/1'>polar residues</scene> are now ball & stick, and they tend to be on the surface of the molecule where they can associate with <scene name='Globular_Proteins/Two_layers_water/1'>water</scene>. More clearly see polar groups on the surface by <scene name='Globular_Proteins/Two_layers_polar_rot/1'>rotating structure</scene> so that axis of helix aligns with z-axis, compare this scene with a similarly aligned display of the hydrophobic side chains. | ||
=== Three Layers === | === Three Layers === | ||
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=== Five Layers === | === Five Layers === | ||
Load <scene name='Globular_Proteins/Five_layers/ | Load <scene name='Globular_Proteins/Five_layers/3'>structure</scene>. Rotate the structure and attempt to identify the five layers. | ||
The five layers are <scene name='Globular_Proteins/Five_layers_identified/2'>identified</scene> in colors <font color="brown"><b>Brown</b></font> through <font color="#ff0000"><b>Red</b></font>. Display<scene name='Globular_Proteins/Five_layers_phobic/1'> hydrophobic residues</scene>; it is not as obvious as with the previous proteins, but as the structure rotates one can see that most of the spheres are in the interior between the layers. Looking at the <scene name='Globular_Proteins/Five_layers_polar/1'>polar residues</scene>, as it rotates one can observe more spheres on the edges of the structure than were seen in the previous scene. | The five layers are <scene name='Globular_Proteins/Five_layers_identified/2'>identified</scene> in colors <font color="brown"><b>Brown</b></font> through <font color="#ff0000"><b>Red</b></font>. Display<scene name='Globular_Proteins/Five_layers_phobic/1'> hydrophobic residues</scene>; it is not as obvious as with the previous proteins, but as the structure rotates one can see that most of the spheres are in the interior between the layers. Looking at the <scene name='Globular_Proteins/Five_layers_polar/1'>polar residues</scene>, as it rotates one can observe more spheres on the edges of the structure than were seen in the previous scene. | ||
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Other examples of protein having the characteristic of layered backbones will be divided into three categories - predominately α-helix, predominately β-sheets and mixed α-helix and β-sheets. | Other examples of protein having the characteristic of layered backbones will be divided into three categories - predominately α-helix, predominately β-sheets and mixed α-helix and β-sheets. | ||
==== Predominately | ==== Predominately Helices ==== | ||
The peptides in this class have a high contain of α-helix and because of the loops and turns which are present the α-helical strands will be antiparallel with respect to their adjacent strands. | The peptides in this class have a high contain of α-helix and because of the loops and turns which are present the α-helical strands will be antiparallel with respect to their adjacent strands. | ||
* <scene name='Globular_Proteins/Anti_helix_erythrin2/1'>Myohemerythrin</scene> - transports oxygen in some lower animals. Notice that the change in direction produced by the loops creates the antiparallel conformation. | * <scene name='Globular_Proteins/Anti_helix_erythrin2/1'>Myohemerythrin</scene> - transports oxygen in some lower animals. Notice that the change in direction produced by the turns and loops creates the antiparallel conformation. | ||
* <scene name='Globular_Proteins/Human_gh/1'>Human growth human</scene> - small peptide in humans that stimulates cell division and growth in select tissues. | * <scene name='Globular_Proteins/Human_gh/1'>Human growth human</scene> - small peptide in humans that stimulates cell division and growth in select tissues. | ||
* <scene name='Globular_Proteins/Myoglobin2/1'>Myoglobin</scene> - stores molecular oxygen in muscle tissue. Structure of [[myoglobin]] is more complex, but again the striking feature is the antiparallel α-helices. | * <scene name='Globular_Proteins/Myoglobin2/1'>Myoglobin</scene> - stores molecular oxygen in muscle tissue. Structure of [[myoglobin]] is more complex, but again the striking feature is the antiparallel α-helices. | ||
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==== Predominately β-Sheets ==== | ==== Predominately β-Sheets ==== | ||
* <scene name='Globular_Proteins/St_inhibitor/1'>Soybean trypsin inhibitor</scene> - As its name implies this protein inhibits the enzyme trypsin, and this inhibitory effect must be deactivated in the process of preparing soybeans for use in animal feed, so that the proteins in soybeans are hydrolyzed by trypsin. This protein is an example of the antiparallel β-barrel because the circular antiparallel sheet is barrel shaped. It is not as clearly defined as the parallel β-barrel, described above, but it is more common. You can look through the barrel whenever one of the open ends rotates to face the screen. An outer layer of α-helices is not present like it is in the parallel β-barrel, so the side chains projecting from the outer surface of the sheet are polar and make contact with water. | * <scene name='Globular_Proteins/St_inhibitor/1'>Soybean trypsin inhibitor</scene> - As its name implies this protein inhibits the enzyme trypsin, and this inhibitory effect must be deactivated in the process of preparing soybeans for use in animal feed, so that the proteins in soybeans are hydrolyzed by trypsin. This protein is an example of the antiparallel β-barrel because the circular antiparallel sheet is barrel shaped. It is not as clearly defined as the parallel β-barrel, described above, but it is more common. You can look through the barrel whenever one of the open ends rotates to face the screen. An outer layer of α-helices is not present like it is in the parallel β-barrel, so the side chains projecting from the outer surface of the sheet are polar and make contact with water. | ||
* <scene name='Globular_Proteins/Agguluttinin/1'>Aggluttinin</scene> - a mannose specific lectin from the bulb of snowdrop. A lectin is a protein that | * <scene name='Globular_Proteins/Agguluttinin/1'>Aggluttinin</scene> - a mannose specific lectin from the bulb of snowdrop. A lectin is a protein that binds oligsaccharides and glycoproteins and is involved in cell-cell recognition. Notice the prism like shape that is formed by the β-sheets. | ||
* <scene name='Globular_Proteins/Rieske/1'>Rieske protein</scene> - water soluble fragment (head) of the iron-sulfur protein from bovine heart. It is a component of Complex III of the mitochondrial respiratory chain. | * <scene name='Globular_Proteins/Rieske/1'>Rieske protein</scene> - water soluble fragment (head) of the iron-sulfur protein from bovine heart. It is a component of Complex III of the mitochondrial respiratory chain. | ||
* <scene name='Globular_Proteins/Lectin_r_s/1'>Lectin</scene> - from ''R. solanacearum''. It is an example of a protein having a quaternary structure, in this case it is trimeric - <scene name='Globular_Proteins/Lectin_r_s2/1'>three subunits</scene>. This type of structure is called a six-bladed propellor or β-propellor. Each subunit contributes two propellors. | * <scene name='Globular_Proteins/Lectin_r_s/1'>Lectin</scene> - from ''R. solanacearum''. It is an example of a protein having a quaternary structure, in this case it is trimeric - <scene name='Globular_Proteins/Lectin_r_s2/1'>three subunits</scene>. This type of structure is called a six-bladed propellor or β-propellor. Each subunit contributes two propellors. | ||
==== Mixed | ==== Mixed helices and β-Sheets ==== | ||
* <scene name='Globular_Proteins/Tmvp2/1'>Tobacco mosaic virus protein</scene> - forms the capsid of the virus. Again the α-helices, loops and turns are prominent features, and the α-helices are antiparallel. | * <scene name='Globular_Proteins/Tmvp2/1'>Tobacco mosaic virus protein</scene> - forms the capsid of the virus. Again the α-helices, loops and turns are prominent features, and the α-helices are antiparallel. | ||
* <scene name='Globular_Proteins/Porin/1'>Matrix porin</scene> - integral protein from the outer membrane of ''E. coli''. | * <scene name='Globular_Proteins/Porin/1'>Matrix porin</scene> - integral protein from the outer membrane of ''E. coli''. Since the barrel structure is inserted into the interior of the membrane, the outer surface that contacts the membrane must be largely <scene name='Globular_Proteins/Porin_phobic/1'>hydrophobic</scene>, but the ends, which contact water, and much of the interior is <scene name='Globular_Proteins/Porin_polar/1'>polar</scene>. <scene name='Globular_Proteins/Porin_polar_phobic/1'>Both</scene> shown together. | ||
* <scene name='Globular_Proteins/Concan/1'>Concanavalin</scene> - Example of another lectin. Notice that the tertiary structures of the three lectins are different revealing that the structures can be different but yet have the same general function. There are two antiparallel β-sheets with the hydrophobic sides of the sheets facing each other. They are interlocking β-Sheets or have Greek Key Topology, ''i.e.'' after laying down a strand in a sheet, often the peptide chain loops over to the other sheet and lays down a strand in that sheet. | * <scene name='Globular_Proteins/Concan/1'>Concanavalin</scene> - Example of another lectin. Notice that the tertiary structures of the three lectins are different revealing that the structures can be different but yet have the same general function. There are two antiparallel β-sheets with the hydrophobic sides of the sheets facing each other. They are interlocking β-Sheets or have Greek Key Topology, ''i.e.'' after laying down a strand in a sheet, often the peptide chain loops over to the other sheet and lays down a strand in that sheet. | ||
* <scene name='Globular_Proteins/Crystallin/1'>Gamma-Crystallin</scene> - A protein that is a component of the eye lense. This protein is another example of interlocking β-sheet, two of the Greek key bilayers are connected by a looping peptide segment. | * <scene name='Globular_Proteins/Crystallin/1'>Gamma-Crystallin</scene> - A protein that is a component of the eye lense. This protein is another example of interlocking β-sheet, two of the Greek key bilayers are connected by a looping peptide segment. | ||
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* <scene name='Globular_Proteins/Horseshoe/1'>Porcine ribonuclease inhibitor</scene> - contains leucine-rich repeats. | * <scene name='Globular_Proteins/Horseshoe/1'>Porcine ribonuclease inhibitor</scene> - contains leucine-rich repeats. | ||
<table width='500' align='right' cellpadding='10'><tr><td bgcolor='#eeeeee'><center>'''Tertiary Structures of Examples'''<scene name='Globular_Proteins/Two_layers/2'> (Initial scene)</scene></center></td></tr></table> | <table width='500' align='right' cellpadding='10'><tr><td bgcolor='#eeeeee'><center>'''Tertiary Structures of Examples'''<scene name='Globular_Proteins/Two_layers/2'> (Initial scene)</scene></center></td></tr></table> | ||
{{Clear}} | {{Clear}} | ||
== Other Characteristics == | == Other Characteristics == | ||
Disulfide bonds and metal ion chelates can stabilize the tertiary structure in the absence of well organized layers which generate hydrophobic attractions. Some proteins are small in size and therefore do not have large amounts of backbone that can be organized into layers. Others have significant backbone, but the layers are not well organized and therefore are non-stabilizing. The attractions formed by metal ions chelates or disulfide bonds in these proteins are as important or more so than the hydrophobic interactions of the organized layers. | Disulfide bonds and metal ion chelates can stabilize the tertiary structure in the absence of well organized layers which generate hydrophobic attractions. Some proteins are small in size and therefore do not have large amounts of backbone that can be organized into layers. Others have significant backbone, but the layers are not well organized and therefore are non-stabilizing. The attractions formed by metal ions chelates or disulfide bonds in these proteins are as important or more so than the hydrophobic interactions of the organized layers. Examples of both types of bonds will be given. | ||
Some proteins or peptide segments are [[Intrinsically_Disordered_Protein |intrinsically disordered]] (unstructured). Whether a complete protein or a protein segment since they are disordered, they can not be crystallized for x-ray crystallographic study. However, when these peptides or peptide segments bind to other proteins they become ordered segments, and can be crystallized along with the binding protein for x-ray crystallographic study. When these peptides bind to other proteins, since their conformations are extended and not compact, the binding occurs over relatively large surface areas of the binding proteins. Examples given below illustrate the extended conformations of the peptide segments as well as the large binding surface. When viewing the unstructured peptides as unbound segments, realize that the conformation which is being displayed is not a disordered conformation but is the conformation of the bound segments with the structure of the binding protein being hidden. If the peptides or peptide fragments were actually free and unbound, since they are unordered, the individual molecules would have a range of conformations and not just one. | |||
=== Disulfide-Rich Proteins === | === Disulfide-Rich Proteins === | ||
* <scene name='Globular_Proteins/Insulin1/1'>Insulin</scene> - Among its functions is the regulation of glucose uptake by cells. The small peptide contains A and B chains that are connected by disulfide bonds, and the tertiary structure of the A chain is also held in place by a disulfide bond. | * <scene name='Globular_Proteins/Insulin1/1'>Insulin</scene> - Among its functions is the regulation of glucose uptake by cells. The small peptide contains A and B chains that are connected by disulfide bonds, and the tertiary structure of the A chain is also held in place by a disulfide bond. | ||
* <scene name='Globular_Proteins/Crambin/1'>Crambin</scene> - Plant seed peptide. Small single chain peptide with no significant backbone layers but has disulfide bonds to stabilize the tertiary structure. Disulfide bonds, also, have an important role of keeping the relatively high proportion of loops in place. | * <scene name='Globular_Proteins/Crambin/1'>Crambin</scene> - Plant seed peptide. Small single chain peptide with no significant backbone layers but has disulfide bonds to stabilize the tertiary structure. Disulfide bonds, also, have an important role of keeping the relatively high proportion of loops in place. | ||
* <scene name='Globular_Proteins/Pholipase2/1'>Phospholipase A2</scene> - Part of a class of hydrolases that degrade glycerophospholipids. This one specifically hydrolyzes the second acyl group on the glycero group. This example is larger than the other two, but it still does not have well organized backbone layers in part due to the extensive loops. | * <scene name='Globular_Proteins/Pholipase2/1'>Phospholipase A2</scene> - Part of a class of hydrolases that degrade glycerophospholipids. This one specifically hydrolyzes the second acyl group on the glycero group. This example is larger than the other two, but it still does not have well organized backbone layers in part due to the extensive turns and loops. | ||
=== Metal-Rich Proteins === | === Metal-Rich Proteins === | ||
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=== Intrinsically Unstructured Proteins === | === Intrinsically Unstructured Proteins === | ||
<scene name='Globular_Proteins/ | * <scene name='Globular_Proteins/Lef-1/1'>LEF-1</scene>, lymphoid enhancer-binding factor 1. LEF-1 is missing residues 26-47, and these residues are most likely missing because they form an unordered segment. Fill in this gap in your mind's eye, and you will see the large <scene name='Globular_Proteins/Lef-1_2/1'>surface area</scene> with which LEF-1 (yellow) binds to β-catenin. Apparently the binding strength of the missing segment is such that it is not converted to an ordered segment. You may notice that residues 550-561 of β-catenin are also missing, again an unordered segment. | ||
* <scene name='Globular_Proteins/Snap2/2'>SNAP-25</scene> - Domain N2 of synaptosomal-associated protein 25 (blue) from human bound to botulinum neurotoxin type A light chain (botox) from ''C. botulinum''. <scene name='Globular_Proteins/Snap/2'>Domain N2</scene> shown unbound but having the same conformation as the bound peptide. | |||
* <scene name='Globular_Proteins/Sara_sbd2/1'>SARA SBD</scene> - SMAD Anchor for Receptor Activation SMAD-Binding Domain bound to SMAD2 MH2 domain. SARA SBD is the domain of the receptor that binds SMAD, and thereby activates the transforming growth factor-beta signaling pathway. <scene name='Globular_Proteins/Sara_sbd/2'>SMAD-binding domain</scene> shown unbound and displayed as cartoon but having the same conformation as the bound peptide. | |||
* <scene name='Globular_Proteins/Hif-1alpha2/2'>HIF-1alpha</scene> - Hypoxia-inducing factor 1α (C-terminal activation domain) bound to transcription activation zinc finger domain of CREB-binding protein. <scene name='Globular_Proteins/Hif-1alpha/2'>HIF</scene> shown unbound and displayed as cartoon but having the same conformation as the bound peptide. The data of this model was generated by NMR analysis of an aqueous solution of the peptides, and the analysis is rapid enough to distinguish the vibrations of the peptides so that more than one model is produced. It is possible to animate these multiple model and simulate the vibrations of the peptides. Notice that the vibrations are the greatest in the molecules where the attractive forces are the weakest. Animate peptides: Unbound <scene name='Globular_Proteins/Hif-1alpha/1'>HIF</scene>; Bound <scene name='Globular_Proteins/Hif-1alpha2/1'>HIF</scene> | |||
* <scene name='Globular_Proteins/P27-cdk2/1'>p27-Cdk2-Cyclin A</scene> - Cyclin-dependent kinase 2 bound to its activator cyclin A and both bound with a fragment (blue) of p27 which is a kinase inhibitor. Cyclin-dependent kinases have an important role in moving the cell from one phase of the cell cycle to another. <scene name='Globular_Proteins/P27-cdk2-2/2'>p27</scene> shown unbound but having the same conformation as the bound peptide. | |||
* <scene name='Globular_Proteins/P27_30-35/1'>p27 (30-35)-Cdk2-Cyclin A</scene> - different data file than the one above containing a smaller fragment of p27 bound to complex. <scene name='Globular_Proteins/P27_30-35-2/1'>p27</scene> shown unbound but having the same conformation as the bound peptide. Compare the conformation of this small fragment to that of the yellow colored fragment shown unbound above. Since the binding site is the same in both models when the peptides bind, regardless of the length, the peptides generate the same conformation. | |||
</StructureSection> | </StructureSection> | ||
==References== | ==References== | ||
{{Reflist}} | {{Reflist}} | ||