Chemical Forums
Specialty Chemistry Forums => Biochemistry and Chemical Biology Forum => Topic started by: AhmedEzatAlzawalaty on January 12, 2008, 08:35:16 AM
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WHAT is the difference between pepsinogen and pepsin in their structure?
[edit: title changed to be more informative - Yggdrasil]
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A quick search tells me that pepsinogen has 44 more amino acid residues than pepsin -- the extras are cleaved off to make active pepsin.
The actual 3-dimensional structure of proteins is not a trivial thing to know, discovering it requires lots of work, both theoretical based on the shapes (alpha-coil, beta-sheet, and others) and experiments using, for example, x-ray crystallography. You might find it on google, but more likely, you'll want to read a number of journal articles, and build up a personal knowledge of what protein structure means.
In the old days, that only slightly pre-date my time in college, they used to say that there were exactly 4 positional changes in the hemoglobin molecule, when it was bound to an O2 vs a CO2. We know know that is false, there are many more changes.
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The following article may be helpful to you:
A. R. Sielecki, M. Fujinaga, R. J. Read and M. N. G. James, Refined structure of porcine pepsinogen at 1.8 A resolution, (1991) J. Mol. Bio. 219(4): 671-692.
Abstract
The molecular structure of porcine pepsinogen at 1.8 Å resolution has been determined by a combination of molecular replacement and multiple isomorphous phasing techniques. The resulting structure was refined by restrained-parameter least-squares methods. The final R factor (=Σ||Fo|-|Fc||/Σ|Fo|) is 0.164 for 32,264 reflections with I ≥ σ(I) in the resolution range of 8.0 to 1.8 Å. The model consists of 2785 protein atoms in 370 residues, a phosphoryl group on Ser68 and 238 ordered water molecules. The resulting molecular stereochemistry is consistent with a well-refined crystal structure with co-ordinate accuracy in the range of 0.10 to 0.15 Å for the well-ordered regions of the molecule (B < 15 Å2).
For the enzyme portion of the zymogen, the root-mean-square difference in Cα atom co-ordinates with the refined porcine pepsin structure is 0.90 Å (284 common atoms) and with the Cα atoms of penicillopepsin it is 1.63 Å (275 common atoms). The additional 44 N-terminal amino acids of the prosegment (Leu1p to Leu44p, using the letter p after the residue number to distinguish the residues of the prosegment) adopt a relatively compact structure consisting of a long β-strand followed by two approximately orthogonal α-helices and a short 310-helix. Intimate contacts, both electrostatic and hydrophobic interactions, are made with residues in the pepsin active site. The N-terminal β-strand, Leu1p to Leu6p, forms part of the six-stranded β-sheet common to the aspartic proteinases. In the zymogen the first 13 residues of pepsin, Ile1 to Glu13, adopt a completely different conformation from that of the mature enzyme. The Cα atom of Ile1 must move ˜44 Å in going from its position in the inactive zymogen to its observed position in active pepsin. Electrostatic interactions of Lys36pN and hydrogen-bonding interactions of Tyr37pOH and Tyr90H with the two catalytic aspartate groups, Asp32 and Asp215, prevent substrate access to the active site of the zymogen. We have made a detailed comparison of the mammalian pepsinogen fold with the fungal aspartic proteinase fold of penicillopepsin, used for the molecular replacement solution. A structurally derived alignment of the two sequences is presented.
http://dx.doi.org/10.1016/0022-2836(91)90664-R
I found the article by searching the Protein Databank (http://www.rcsb.org/pdb/), a repository for structures of biological macromolecules, for pepsinogen.