Periodic Table of the Amino Acids

Aliphatic
Amidic
Acidic
Sulphurated
Hydroxylic
Alanine
asparagiNe
aspartic AciD
Cysteine
Serine
Glycine
"Q"lutamine
gluEtamic Acid
Methionine
Threonine
Valine
 
Basic
Aromatic
 
Leucine
 
aRginine
Fenylalanine
 
Isoleucine
 
"K"lysine
tYryosine
 
 
Proline
 
Histidine
TryptophWan
 

Amino Acids in Alphabetical Order
    The twenty amino acids  are:

Sometimes it is not possible to differentiate two closely related amino acids,
therefore we have the special cases:
                      Asparagine OR
                      Aspartic Acid    Asx     B
                      Glutamine  OR
                      Glutamic Acid    Glx     Z

Computer Assisted Structure Determination
Using the code for HMG-CAR cited above, we can piece together the sequence led by the condensation reactions leading to peptide bonds.  By clicking on the link for each consecutive amino acid in a Chemscape enabled browser we can transfer the amino acid structures to Net-Chemdraw, perform the condensation reaction and produce the dipeptide as a two dimension structure.  During this process we can enforce the transt relationship between consecutive alpha Carbons.  Repeating this procedure produces a polypeptide which may be checked for consistency.  After this the resulting structure may be converted to the SMILES representation and emailed to the CORINA system in Denmark for overnight processing to deduce probable three dimensional structure.  Alternately, it may be more appropriate and less labor intensive to simply produce the equivalent SMILES condensed polypeptide by noting the head-to-tail COOH-H2N relations and producing the appropriate string for CORINA postprocessing.

Other Goals
Besides labeling the biochemical pathways with actual three dimensional structures in motion, it would be desirable to produce a more appropriate electron density model of the constituent molecules.  These electron cloud models could more clearly depict orbital configuration, hybridization, non-realizable configurations and folding patterns.  Multiple models could be combined in a single viewport and shown reacting to produce the constituents.  By creating a more complete visual simulation of the process, it is hoped that the investigator could be provided with more insight, leading to more productive research and development.

L. Van Warren * (c) 1997 Warren Design Vision * All Rights Reserved

 t(more prevalent than cis relations except with Proline)

An Example
Example:
We would like to reconstruct the 3D structure of HMG-CoA Reductase (HMG-CAR).
In the process we discover that the structure of HMG-CAR in Hevea brasiliensis is:

SEQUENCE
              5        10        15        20        25        30
    1 M D E V R R R P P K H I V R K D H D G E V L N S F S H G H H
   31 L P P L K P S D Y S L P L S L Y L A N A L V F S L F F S V A
   61 Y F L L H R W R E K I R K S T P L H I V T F P E I A A L I C
   91 L V A S V I Y L L G F F G I G F V H S F S R A S T D S W D V
  121 E E Y D D D N I I I K E D T R P T G A C A A P S L D C S L S
  151 L P T K I H A P I V S T T T T S T L S D D D E Q I I K S V V
  181 S G S I P S Y S L E S K L G N C K R A A L I R R E T L Q R M
  211 S G R S L E G L P L D G F D Y E S I L G Q C C E M A I G Y V
  241 Q I P V G I A G P L L L D G K E Y T V P M A T T E G C L V A
  271 S A N R G C K A I Y A S G G A T S V L L R D G M T R A P V V
  301 R F P T A K R A A D L K F F M E D P D N F D T I A V V F N K
  331 S S R F A R L Q S V Q C A I A G K N L Y M R F S C S T G D A
  361 M G M N M V S K A V Q N V I D Y L Q N D F P D M D V I G L T
  391 G N F C A D K K A A A V N W I E G R G K S V V C E A I I K E
  421 E V V K K V L K T N V A A L V E L N M I K N L T G S A V A G
  451 S L G G F N A H A S N M V T A V Y I A T G Q D P A Q N V E S
  481 S H C I T M M E A V N D G K D L H I S V S M P S I E L G T V
  511 G G G T Q L A S Q S A C L N L L G V K G A S K D S P G S N S
  541 R L L A T I V A G S V L A G E L S L M S A I A A G Q L V N S
 571 H M K Y N R S A K D V S K I T F

    We note that the suffix -ase implies that HMG-CAR is an enzyme.
    Enzymes are proteins, and proteins are linear heteropolymers of fixed length.
    Heteropolymer means different monomers that are connected in sequence.
    The monomers are amino acids.  Each letter in the sequence is an amino acid code.
    The length of a protein varies from a few tens to approximately a thousand.
    This particular HMG-CAR enzyme protein (there are several) is 586 amino acids units long.

We will solve this problem but first lets start with a simpler example.

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