Molecules and Diving

by

Larry "Harris" Taylor, Ph.D.

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As a biochemist, I am interested in the three-dimensional structure of biologically active molecules and how ligands (drugs) interact with their receptors (site of initiation of biological response). About a decade ago, I was just learning molecular modeling software. (I use a package called SYBYL on an SGI workstation that renders images in true three dimensions). My approach to learning any new-to-me software package is to “play” with it. So, one rainy Saturday afternoon, as I was beginning to build a library of drug structural coordinate files, I captured the images below. (This was before the days of good image annotation and screen capture, so the technique used was photographing the screen image, which gives text a bit less than crisp.)

The first image (a steroid within the MR receptor  … involved in stress response) is typical of the stuff I do today: This is part of a project I did for an internet course from Birkbeck College for an Advanced Certificate in Protein Structure (Modeling Receptors). 

The rest is now decade-old play, learning various aspects of the software package with a diving motif.  

 

 

   

DIVERS ARE SPECIAL

In the realm of biochemistry, each of the amino acids is assigned a letter of the alphabet. This makes it easier for scientists to communicate information about long strings of amino acids (peptides and proteins). One of the things a molecular modeler does is to color amino acids by function and search for "patterns" that might suggest or explain biological activity. The peptide below is hypothetical. It is a theoretical construct, labeled with the proper single letter amino acid code. It is "chemically correct" (for "chemistry geeks" the structure was energy minimized with the SYBYL rendition of the Kollman All Atom Force Field with consideration of Kollman charges.) in that it represents a reasonable geometry for the chosen amino acid sequence.

While the molecule  is a software construct, I most definitely believe the sentiment expressed in its sequence!

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 About The Author:

Larry "Harris" Taylor, Ph.D. is a biochemist and Diving Safety Coordinator at the University of Michigan. He has authored more than 100 scuba related articles. His personal dive library (See Alert Diver, Mar/Apr, 1997, p. 54) is considered one of the best recreational sources of information In North America.

  Copyright 2001-2004 by Larry "Harris" Taylor

All rights reserved.

Use of these articles for personal or organizational profit is specifically denied.

These articles may be used for not-for-profit diving education