4.5: Protein with Alpha, Alpha-Beta, Beta and Little Secondary Structure
- Page ID
- 62322
Proteins can also be classified as to the type and extent of secondary structure found in the protein. A detailed description of protein classes can be found at CATH. Here we will describe the basiv types with a few examples offered for each.
Alpha proteins
In these proteins, the core of the protein is composed of alpha helices. The CATH classification shows two major types
a. Orthogonal bundles. Example: the Z[beta] Domain of the RNA-editing Enzyme ADAR1 (1xmk), shown in the interactive iCn3D model in Figure \(\PageIndex{1}\).
Figure \(\PageIndex{1}\): Alpha protein, Orthogonal bundles: Z[beta] Domain of the RNA-editing Enzyme ADAR1 (1xmk) (Copyright; author via source).
Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...fxHFM9ErUptjY7
b. Updown bundles. Example: Phospholipase A2 from Agkistrodon acutus venom (1mc2), shown in the interactive iCn3D model in Figure \(\PageIndex{2}\).
Figure \(\PageIndex{2}\): Alpha protein, Updown bundles: Phospholipase A2 from Agkistrodon acutus venom (1mc2) (Copyright; author via source).
Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...NGSeK9JAMe3Qh9
Beta proteins
In these proteins, the core is typically antiparallel beta sheets. There are many types of these, including single sheets, rolls, beta barrels, clams, sandwich, propellers, etc (some of which we have already discussed). Here are a few interesting examples.
a. Roll. Example: The second SH3 domain from ponsin (2O9S), shown in the interactive iCn3D model in Figure \(\PageIndex{3}\).
Figure \(\PageIndex{3}\): Beta protein Roll: Second SH3 domain from ponsin (2O9S), (Copyright; author via source).
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b. Sandwich. Example: Mcg immunoglobulin light chain variable domain (4unu), shown in the interactive iCn3D model in Figure \(\PageIndex{4}\).
Figure \(\PageIndex{4}\): Beta protein Sandwich - Mcg immunoglobulin light chain variable domain (4unu) (Copyright; author via source).
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Alpha/Beta proteins
These are the most common class and contain both many beta-alpha-beta motifs with mostly parallel beta strands surrounded by alpha helices. Again, there are many variants for these proteins, including the alpha-beta barrel. We will show two other common ones.
a. Two layer sandwich. Example: HIV-1 Nef-SF2 Core Domain (4U5W), shown in the interactive iCn3D model in Figure \(\PageIndex{5}\).
Figure \(\PageIndex{5}\): Alpha-Beta Two layer sandwich - HIV-1 Nef-SF2 Core Domain (4U5W) (Copyright; author via source).
Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...6Fx6J3ecPJbF3A
b. Three layer sandwich (aba). Example: Human biliverdin IX beta reductase (1hdo), shown in the interactive iCn3D model in Figure \(\PageIndex{6}\).
Figure \(\PageIndex{6}\): Alpha-Beta Three layer sandwich (aba) - Human biliverdin IX beta reductase (1hdo) (Copyright; author via source).
Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...s8GrdasiecmZC8
Little Secondary Structures
These proteins most likely can adopt different conformationdon binding to target molecules. Here are two examples
a. HIV-1 TAT (Transactivating) Protein (1JFW), shown in the interactive iCn3D model in Figure \(\PageIndex{7}\).
Figure \(\PageIndex{7}\): Few Secondary Structures - HIV-1 TAT (Transactivating) Protein (1JFW) (Copyright; author via source).
Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...zVYofj3HFasWBA
b. Rat rat metallothionein-2 (4MT2), shown in the interactive iCn3D model in Figure \(\PageIndex{8}\).
Figure \(\PageIndex{8}\): Few Secondary Structures - Rat rat metallothionein-2 (4MT2) (Copyright; author via source).
Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...fYY4xF2RWd7pD7