Six Easier Pieces*:
Discovering the 3D structure of Substance P,
using only free internet tools.

Introduction:

Living systems favor the use of small molecules as tokens of exchange in a complex self-sustaining biochemical economy. Examples are oxygen, and carbon dioxide in respiration, the alkali metals in serum electrolytes, glucose in energy storage and a host of others. There are several neurotransmitters that are essential for nerve signal transmission in biological organisms. Most of these are also relatively small molecules. Among them are histamine, dopamine, and serotonin. Others, such as bradykinin and Substance P are molecular bills of slightly larger denomination , the later consisting of 11 amino acids linked by 10 peptide bonds. The structure of the common neurotransmitters have been published on the world wide web, the exception being the subject of this short note, the tachykinin called Substance P.

Neurotransmitters Of Pain
don't see molecule? get Chime plug-in	Structure Table ©1999 L. Van Warren
Histamine Sites	Histamine Properties
Dopamine Sites	Dopamine Properties
Serotonin Sites	Serotonin Properties
Bradykinin Sites	Bradykinin Properties
? Substance P Sites	? Substance P Properties

 

The official definition of tachykinins from the NCBI database is:

TACHYKININS ARE ACTIVE PEPTIDES WHICH EXCITE NEURONS, EVOKE BEHAVIORAL RESPONSES, ARE POTENT VASODILATORS AND SECREATAGOGUES, AND CONTRACT (DIRECTLY OR INDIRECTLY) MANY SMOOTH MUSCLES.

Further investigation reveals that the term Substance P is an alias for several analogs, whose amino acid sequence varies with species. Some of these are given in the following table:

Table 1: Substance P analogs by species

At this writing a thorough search of the web does not yield the three dimensional configuration of Substance P. The "P" in substance P actually stands for powder. When isolated for the first time from horse intestine in the 1930s, it was in powder form.

The point of this technical note is twofold, first the completion of an errand to determine the 3D structure of substance P for a cancer research project, and secondly, to show how it is relatively easy to apply this procedure to other molecules of interest.

Six Easy Steps: Deducing 3D biochemical structures via the web:

Step 1: the amino acid sequence is obtained via NCBI Entrez, it is: KPRPGQFFGL M as seen in the table above.

Step 2: using an/ or the simpler quick aa table one can find that this 11 symbol string translates to:
lysine-proline-arginine-proline-glycine-glutamine-phenylalanine-phenylalanine-glycine-leucine-methionine

Step 3: the L-forms of all the amino acids are pasted into the freely distributed ChemDraw Net product left to right, top to bottom as shown in the figure below:

Step 4: the peptide bonds are formed by condensing out a water using a hydrogen from the primary amine groups and a hydroxyl group from the carboxyl groups:

These peptide bonds are formed by when the line is connected. A hydrogen disappears automatically, but the hydoxyl groups, such as the one seen remaining on the proline in the first row, are erased manually after assembly.

Step 5: In the freeChemDraw Net 4.5 tool there is an option called clean-up structure. Clicking on it produces a more aesthetic 2-D drawing of the structure:

This feature is not in the ChemDraw Standard ($299 academic version), but it is in the ChemDraw Pro version (also $299 at this writing Cambridge software runs specials from time to time, but they can do their own advertising!). If you install ChemDraw Standard, it will ask you if you to delete your ChemDraw Net 4.5, which causes structure clean-up to stop working.

Step 6: In the final step, we select the entire structure in ChemDraw using either the square or round marquee lasso tools. We then choose the option Copy As from the Edit menu and which results in a text representation of the structure being transferred to the system clipboard in SMILES format. Pasting the clipboard contents into another application results in this SMILES text string, representing the structure of Substance P, being transferred. This SMILES text string looks like:

N[C@H](C([C@H]1[C@@H](CCC1)C(NC(NCCC[C@H](N)C([C@H]2[C@@H]
(CCC2)C(NCC(NC(CC[C@H](N)C(N[C@H](C(N[C@H](C(NCC(N[C@@H]
(CC(C)C)C(N[C@@H](CCSC)C(O)=O)=O)=O)=O)CC4=CC=CC=C4)=O)
CC3=CC=CC=C3)=O)=O)=O)=O)=O)=N)=O)=O)CCCCN

When this text string is emailed to the Corina Web Service in Germany, the result is the three dimensional structure below:

The SMILES string for substance P turns out to be 12 characters too long for the interactive 3D service, otherwise we could have obtained the structure in almost real time. The overnight service via email instructions is utilized instead.

Althought the resulting conformation is useful for appreciating three dimensional molecular structure, it is non-unique and often unrealisitic. It is necessary to perform energy minimization to predict plausible configurations of the molecule. This was done using the CS Chem3D Pro software, which was also available free of charge through a special CS web promotion:

Conclusion

This simple six step process can be applied to a large variety of biochemistry applications. The author intends to continue refining this approach for the illustration of biochemical pathways. The enthusiastic reader is urged to repeat these steps for the other analogs listed in table 1.

Acknowledgments