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4.5: Alpha, Alpha-Beta and Beta Structure Proteins, and Little Secondary Structure

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    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 basis 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 classifcation 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 \(\PageIndex{1}\) below.

    Alpha protein_Orthogonal bundle_Zbeta_DomainRNA-editing Enzyme ADAR1(1xmk) .png

    NIH_NCBI_iCn3D_Banner.svg 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 \(\PageIndex{2}\) below.

    Alpha protein_Updown bundles_Phospholipase A2 from Agkistrodon acutus venom (1mc2).png

    NIH_NCBI_iCn3D_Banner.svg 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 \(\PageIndex{3}\) below.

    Beta protein Roll_Second SH3 domain from ponsin (2O9S).png

    NIH_NCBI_iCn3D_Banner.svg Figure \(\PageIndex{3}\):  Beta protein Roll:  Second SH3 domain from ponsin (2O9S), (Copyright; author via source). 
    Click the image for a popup or use this external link:  https://structure.ncbi.nlm.nih.gov/i...xYZBXHWpt3njf7

     

    b.  Sandwich.  Example:  Mcg immunoglobulin light chain variable domain (4unu), shown in the interactive iCn3D model in Figure \(\PageIndex{4}\) below.

    Beta protein Sandwich - Mcg immunoglobulin light chain variable domain (4unu).png

    NIH_NCBI_iCn3D_Banner.svg Figure \(\PageIndex{4}\):  Beta protein Sandwich - Mcg immunoglobulin light chain variable domain (4unu) (Copyright; author via source). 
    Click the image for a popup or use this external link:  https://structure.ncbi.nlm.nih.gov/i...4vcY5svrBveJp7

     

    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 \(\PageIndex{5}\) below.

    Alpha-Beta protein Two layer sandwich - HIV-1 Nef-SF2 Core Domain (4U5W).png

      NIH_NCBI_iCn3D_Banner.svg 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 \(\PageIndex{6}\) below.

    Alpha-Beta Three layer sandwich (aba) -  Human biliverdin IX beta reductase (1hdo).png

    NIH_NCBI_iCn3D_Banner.svg 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 

     

    Few Secondary Structures

    The proteins most likely can adopt different conformation on binding to target molecules.

    a.  HIV-1 TAT (Transactivating) Protein (1JFW), shown in the interactive iCn3D model in Figure \(\PageIndex{7}\) below.

    Few Secondary Structures - HIV-1 TAT (Transactivating) Protein (1JFW).png

    NIH_NCBI_iCn3D_Banner.svg 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 \(\PageIndex{8}\) below.

    .Few Secondary Structures - Rat rat metallothionein-2 (4MT2).png

    NIH_NCBI_iCn3D_Banner.svg 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