Globular Proteins
From Proteopedia
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=== Circular Layers === | === Circular Layers === | ||
| - | Load the <scene name='Globular_Proteins/Circular_layers/1'>structure</scene>. The circular layers formed by the β-sheet barrel (yellow) and <font color="#ff0000">α-helix barrel</font> are clearly seen in this view, giving what would appear to be two layers. <scene name='Globular_Proteins/Circular_layers_phobic/1'>Next scene</scene> shows that hydrophobic residues occupy the central circular cavity as well as the space between the two circular layers. With this being the case one could say that the isomerase had four layers of backbone. <scene name='Globular_Proteins/Circular_layers_polar/1'>Display polar residues</scene>. As the structure rotates one can see that most of the polar residues are on the surface, but there are few within the central cavity and between the two circular layers. | + | Load the <scene name='Globular_Proteins/Circular_layers/1'>structure</scene>. The circular layers formed by the β-sheet barrel (yellow) and <font color="#ff0000">α-helix barrel</font> are clearly seen in this view, giving what would appear to be two layers. <scene name='Globular_Proteins/Circular_layers_phobic/1'>Next scene</scene> shows that hydrophobic residues occupy the central circular cavity as well as the space between the two circular layers. With this being the case one could say that the isomerase had four layers of backbone. <scene name='Globular_Proteins/Circular_layers_polar/1'>Display polar residues</scene>. As the structure rotates one can see that most of the polar residues are on the surface, but there are few within the central cavity and between the two circular layers. The β-sheet of the barrel is parallel because after forming a strand of the sheet the peptide chain loops out, forms an α-helix and then loops back to form another strand of the sheet running in the same direction as the previous strand and, thereby, making the sheet parallel. |
=== Five Layers === | === Five Layers === | ||
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* <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. | ||
* <scene name='Globular_Proteins/Gluccanase/1'>Endoglucanase A</scene> - an α-helical barrel. Catalytic core of 1,4-beta glucan-glucanohydrolase from ''Clostridium thermocellum''. | * <scene name='Globular_Proteins/Gluccanase/1'>Endoglucanase A</scene> - an α-helical barrel. Catalytic core of 1,4-beta glucan-glucanohydrolase from ''Clostridium thermocellum''. | ||
| - | + | * <scene name='Globular_Proteins/Leu_rich/1'>Leucin-rich repeat variant</scene> - a novel structural motif. It is an iron-sulfur protein from ''Azotobacter vinelandii'' and involved in redox reactions of nitrogen fixation. | |
==== β-Sheets Predominate ==== | ==== β-Sheets Predominate ==== | ||
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==== Mixture of α-helix and β-Sheet ==== | ==== Mixture of α-helix and β-Sheet ==== | ||
* <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/Tp_isomerase/1'>Triose phosphate isomerase</scene> - The β-sheet of the barrel is parallel because after forming a strand of the sheet the peptide chain loops out, forms an α-helix and then loops back to form another strand of the sheet running in the same direction as the previous strand and, thereby, making the sheet parallel. Find the four layers of backbone in this example. | ||
* <scene name='Globular_Proteins/Flavodxin/1'>Flavodoxin</scene> - This type of structure is also called doubly wound parallel β-sheet because of the loops of α-helices on both sides of the sheet. In some cases these doubly wound sheets contain a few antiparallel strands forming a mixed β-sheet. Can you find the three layers of backbone in these doubly wound sheets contain? | * <scene name='Globular_Proteins/Flavodxin/1'>Flavodoxin</scene> - This type of structure is also called doubly wound parallel β-sheet because of the loops of α-helices on both sides of the sheet. In some cases these doubly wound sheets contain a few antiparallel strands forming a mixed β-sheet. Can you find the three layers of backbone in these doubly wound sheets contain? | ||
* <scene name='Globular_Proteins/Pg_mutase/1'>Phosphoglycerate mutase</scene> - There is one antiparallel strand in the sheet, and the double winding is more extensive. | * <scene name='Globular_Proteins/Pg_mutase/1'>Phosphoglycerate mutase</scene> - There is one antiparallel strand in the sheet, and the double winding is more extensive. | ||
Revision as of 16:05, 25 February 2011
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 structures. Three important types of secondary structures are helices, β-sheets and turns. The tertiary structure is the overall 3D structure of a protein molecule and is produced by folding the helices and sheets upon themselves, and in the process of this folding turns and loops are formed. 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.[1] Important characteristics in the absence of backbone layers are the presence of disulfice bonds, the presence of chelated metal ions or that they are intrinsically unstructured[1]. 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 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.
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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.
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