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Thursday, March 13, 2008

Examples of Protein Structure

Here's a slideshow of figures from Horton et al. (2006) showing cartoons of various proteins. At first it seems as though every protein is completely different but after a while you begin to notice that there are recurring motifs—especially β sheets in the hydrophobic core of a domain.

Click here to see a full-screen version of the slideshow. More adventuresome readers might want to visit the actual structures on the Protein Data Base (PDB). Here are the links to each PDB record. References to the people who solved the structure can be found in the PDB record.
  • Human (Homo sapiens) serum albumin [PDB 1BJ5] (class: all-α). This protein has several domains consisting of layered α helices and helix bundles.
  • Escherichia coli cytochrome b562 [PDB 1QPU] (class: all-α). This is a heme-binding protein consisting of a single four-helix bundle domain.
  • Escherichia coli UDP N-acetylglucosamine acyl transferase [PDB 1LXA] (class: all-β). The structure of this enzyme shows a classic example of a β-helix domain.
  • Jack bean (Canavalia ensiformis) concanavalin A [PDB 1CON] (class: all-β). This carbohydrate-binding protein (lectin) is a single-domain protein made up of a large β-sandwich fold.
  • Human (Homo sapiens)peptidylprolyl cis/trans isomerase [PDB 1VBS] (class: all-β). The dominant feature of the structure is a β-sandwich fold.
  • Cow (Bos taurus) γ crystallin [PDB 1A45] (class: all-β) This protein contains β-barrel two domains.
  • Jellyfish (Aequorea victoria) green fluorescent protein [PDB
    ] (class: all-β). This is a β-barrel structure with a central α helix. The strands of the sheet are antiparallel.
  • Pig (Sus scrofa) retinol-binding
    protein [PDB 1AQB] (class: all-β). Retinol binds in the interior of a β-barrel fold.
  • Brewer’s yeast (Saccharomyces carlsburgensis) old yellow enzyme
    (FMN oxidoreductase) [PDB 1OYA] (class: α/β). The central fold is an α/β barrel with parallel β strands connected by α helices. Two of the connecting regions are highlighted in yellow.
  • Escherichia coli enzyme required for tryptophan biosynthesis [PDB 1PII] (class: α/β). This is a bifunctional enzyme containing two distinct domains. Each domain is an example of an α/β barrel. The left-hand domain contains the indolglycerol phosphate synthetase activity, and the right-hand domain contains the phosphoribosylanthranilate isomerase activity.
  • Pig (Sus scrofa) adenylyl kinase [PDB 3ADK] (class: α/β). This single-domain protein consists of a five-stranded parallel β sheet with layers of α helices above and below the sheet. The substrate binds in the prominent groove between helices.
  • Escherichia coli flavodoxin [PDB 1AHN] (class: α). The fold
    is a five-stranded parallel twisted sheet surrounded by α helices.
  • Human (Homo sapiens) thioredoxin [PDB 1ERU] (class: ). The structure of this protein is very similar to that of E. coli flavodoxin except that the five-stranded twisted sheet in the thioredoxin fold contains a single antiparallel strand.
  • Escherichia coli L-arabinose-binding protein [PDB 1ABE] (class: α/β). This is a two-domain protein where each domain is similar to
    that in E. coli flavodoxin. The sugar L-arabinose binds in the cavity between the two domains.
  • Escherichia coli DsbA (thiol-disulfide oxidoreductase/disulfide isomerase) [PDB 1A23] (class: α/β). The predominant feature of this structure is a (mostly) antiparallel β sheet sandwiched between α helices. Cysteine side chains at the end of one of the α helices are shown (sulfur atoms are yellow).
  • Neisseria gonorrhea pilin [PDB 2PIL] (class: α + β). This polypeptide is one of the subunits of the pili on the surface of the bacteria responsible for gonorrhea. There are two distinct regions of the structure: a β sheet and a long α helix.
  • Chicken (Gallus gallus) triose phosphate isomerase [PDB 1TIM]. This protein has two identical subunits with α/β barrel folds.
  • HIV-1 aspartic protease [PDB 1DIF]. This protein has two identical all-β subunits that bind symmetrically. HIV protease is the target of many new drugs designed to treat AIDS patients.
  • Streptomyces lividans potassium channel protein [PDB 1BL8]. This membrane-bound protein has four identical subunits, each of which contributes to a membrane-spanning eight-helix bundle.
  • Bacteriophage MS2 capsid protein [PDB 2MS2]. The basic unit of the MS2 capsid is a trimer of identical subunits with a large β sheet.
  • Human (Homo sapiens) hypoxanthine-guanine phosphoribosyl transferase (HGPRT) [PDB 1BZY]. HGPRT is a tetrameric protein containing two different types of subunit.
  • Rhodopseudomonas viridis photosystem [PDB 1PRC]. This complex, membrane-bound protein has two identical subunits (orange, blue) and two other subunits (purple, green) bound to several molecules of photosynthetic pigments.

Horton, H.R., Moran, L.A., Scrimgeour, K.G., perry, M.D. and Rawn, J.D. (2006) Principles of Biochemisty. Pearson/Prentice Hall, Upper Saddle River N.J. (USA)

1 comment :

paul01 said...


From an earlier post of yours

I'm happy to oblige and I've booked a room for either Tuesday April 22nd or Tuesday April 28th. I invite Kirk Durston to come and present his evidence that protein folding studies indicate the presence of an intelligent designer.

Is this still on?