Amino Acids

Overview

Animation of some Arginine side chain positions

Alpha-amino acids are the building blocks of proteins. They combine in a condensation reaction that releases water and the new "amino acid residue" that is held together by a Peptide Bond. Proteins are defined by their unique sequence of amino acid residues; this sequence is the Primary Structure of the protein. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a vast variety of proteins.

Twenty standard amino acids are used by cells in protein biosynthesis, and these are specified by the general genetic code. These 20 amino acids are biosynthesized from other molecules, but organisms differ in which ones they can synthesize and which ones must be provided in their diet. The ones that cannot be synthesized by an organism are called essential amino acids.

Amino acids are also the basic units of FoldIt. In the structure of a protein, each amino acid contributes one link in the protein Backbone and (usually) one Sidechain. The backbone establishes the basic structural aspects of the protein, and the sidechains determine the details of its biological function.

Here is a list of the amino acids that are known to be found in FoldIt. It is possible that a few others have been or may eventually be used as well, but these are by far the most common.

Amino Acid	3-Letter	1-Letter	Side chain polarity	Side chain acidity or basicity of neutral species	Hydropathy index
Alanine	Ala	A	nonpolar	neutral	1.8
Arginine	Arg	R	polar	basic (strongly)	-4.5
Asparagine	Asn	N	polar	neutral	-3.5
Aspartic acid	Asp	D	polar	acidic	-3.5
Cysteine	Cys	C	polar	neutral	2.5
Glutamic acid	Glu	E	polar	acidic	-3.5
Glutamine	Gln	Q	polar	neutral	-3.5
Glycine	Gly	G	nonpolar	neutral	-0.4
Histidine	His	H	polar	basic (weakly)	-3.2
Isoleucine	Ile	I	nonpolar	neutral	4.5
Leucine	Leu	L	nonpolar	neutral	3.8
Lysine	Lys	K	polar	basic	-3.9
Methionine	Met	M	nonpolar	neutral	1.9
Phenylalanine	Phe	F	nonpolar	neutral	2.8
Proline	Pro	P	nonpolar	neutral	-1.6
Serine	Ser	S	polar	neutral	-0.8
Threonine	Thr	T	polar	neutral	-0.7
Tryptophan	Trp	W	nonpolar	neutral	-0.9
Tyrosine	Tyr	Y	polar	neutral	-1.3
Valine	Val	V	nonpolar	neutral	4.2

This may also be of use foldit-aas

Chemistry

In chemistry, an amino acid is a molecule containing both amine and carboxyl functional groups. In the alpha amino acids, the amino and carboxylate groups are attached to the same carbon, which is called the α–carbon. The various alpha amino acids differ in which side chain (R group) is attached to their alpha carbon. They can vary in size from just a hydrogen atom in glycine through a methyl group in alanine to a large heterocyclic group in tryptophan.

Beyond the amino acids that are found in all forms of life, many non-natural amino acids have vital roles in technology and industry. For example, the chelating agents EDTA and nitrilotriacetic acid are alpha amino acids that are important in the chemical industry.

The only difference between the various amino acids is their different side chains (labeled R) that attach at the middle carbon of each amino acid.

Thus the basic structure of an amino acid can be represented as H2N-CHR-COOH where 2 atoms of Hydrogen are bound to a Nitrogen which is bound to the middle Carbon with a Hydrogen and the R group then the final COOH Carboxylic Acid group.

Amino Acids bind together in their primary sequence using peptide bonds where one H from the NH2 reacts with the OH (hydroxyl) group of the next acid releasing an H2O an forming a strong bond that forms the backbone of the protein in the sequence specified by the DNA -> RNA transcription process.

Sidechain interactions define the 3-dimensional conformation of each protein. Some proteins have more than one different stable conformation; these alternate conformations are called Prions and appear to have a role both in memory and some diseases.

The (20) amino acids shown above are classified according to the chemical properties of the R group: Acidic[2], Basic[3], Uncharged Polar[5], and Non-Polar[10]. Thus we can rewrite the above table as follows.

Class, amino acid(Abbrev, Name), R group

Acidic

D Asp Aspartic acid -CH2-COOH where both the O and the OH are bonded to the C

E Glu Glutamic acid -CH2-CH2-COOH

Basic

K Lys Lysine -CH2-CH2-CH2-CH2-NH3+

R Arg Arginine -CH2-CH2-CH2-NH-C-(NH2)2  :where 2 NH2 groups are attached to the final C

H His Histidine -CH2-<C-HN-HC=NH+-HC=>  :where < chain > actually forms a pentagonal ring bonded at the C

Uncharged Polar

S Ser Serine -CH2-OH

T Thr Threonine -CH-CH3OH  :where both the CH3 and the OH attach at the initial CH

Y Tyr Tyrosine -CH2-<CH=CH-CH=COH-CH=CH->  :where < ... > forms a hexagonal ring with the OH at the far end

N Asn Asparagine -CH2-CONH2  :where both the =O and the -NH2 attach to the C

O Gln Glutamine -CH2-CH2-CONH2  :same as Asparagine but with an extra CH2

C Cys Cysteine -CH2-S-H

Non-Polar

G Gly Glycine -H

A Ala Alanine -CH3

V Val Valine -CH-(CH3)2

L Leu Leucine -CH2-CH-(CH3)2

I Ile Isoleucine -CH-(CH3, CH2-CH3)

P Pro Proline -<CH2-CH2-CH2>  :where the other end of the ring attaches at the N by replacing an H

F Phe Phenylalanine -CH2-<CH=CH-CH=CH-CH=CH->  :like tyrosine without the OH at the far end of the ring.

M Met Methionine -CH2-CH2-S-CH3

W Trp Tryptophan -CH2-<pentagonal ring with NH><Hexagonal Phenyl ring>

A better sense of the actual amino acid structures can be found here.

Notes

• A strong Disulfide Bridge (S-S) sometimes can be created between the sulfur in the side chains in two Cysteine amino acids. This plays a strong role in forming the 3 dimensional protein structure.

• Additional bonds occur between acidic and basic end groups of the side chains.

• Polar side groups like to remain in a polar environment such as the water surrounding the protein. See Hydrophobicity.

• A protein is most stable when in its lowest energy configuration, somewhat like a valley. Interestingly there can be a lower valley over the next rise that is not detected unless a higher energy configuration is achieved. These local minima have to be determined using previous experience and intuition, and also by developing a good sense of Aesthetics.