To D or not to D: An amino acid mystery unveiled

Amino acids are found in all life forms. Individual amino acids can be joined together to form short polymer chains called peptides or long polymer chains called proteins. Thus, amino acids are known as the building blocks of peptides and proteins. Proteins are needed by our body for metabolic activities such as growth. Lysine, an amino acid, is a component of children’s nutritional supplements.

Peptides and proteins have a unique sequence of constituent amino acids. As an analogy, we can consider the letters in the alphabet as the amino acids. Like those letters which can be combined to form an almost infinite variety of words, amino acids can be joined in different sequences to form an enormous variety of peptides and proteins. The sequence of a peptide or protein is unique so that changing a single amino acid in the chain will change the characteristics of the peptide or protein, as changing the second letter c to g in the word “chance” will change the meaning of the word.

In nature, there exist two types of amino acids: L-amino acid and D-amino acid. L-amino acid and D-amino acid are identical in chemical composition and mass, except that they are mirror images of each other. Does the L or D type of a specific amino acid find its place in a peptide or protein by chance (any type can fit in as long as it is the needed amino acid regardless of whether it is L or D) or by choice?

Peptides and proteins are made up almost exclusively of L-amino acids. The origin and evolution of L-amino acids from a prebiotic environment have long been a mystery. The process by which L-amino acids have originated in life forms has not been fully elucidated, but one notion could be that it was a chance event, such that organisms could have similarly assimilated D-amino acids.

Presumably derived from racemic mixtures (50 percent L-amino acids and 50 percent D-amino acids) of organic molecules produced by abiotic synthetic pathways, L-amino acids were introduced into the first life forms more than 3.5 billion years ago. The L-amino acid is the form which is directly encoded by genes. The D-amino acid has also been found in existence, earlier in bacterial peptides and then in peptides from a wide variety of higher organisms.

Although D-amino acids are much less common than L-amino acids, they are widely distributed in nature. D-amino acids, either as constituents of peptides and proteins or in the form of free amino acids, have been identified in various organisms — from bacteria to mammals, as well as in plants.

Here are some examples of D-amino acid-containing peptides. Dermorphin from skin secretion of frog is a peptide with D-alanine at position 2 in its peptide chain. Achatin-I and fulicin from a land snail have D-phenylalanine and D-asparagine, respectively, at position 2. Both Mytilus-FFRF amide from mussel and a peptide from platypus have D-leucine at position 2. Note this specific position of the D-amino acids and observe a pattern.

The D-amino acids seem to occupy a specific position in the peptide chains. Take the case of contryphans, short chain peptides from venoms of cone snails, containing about 10 constituent amino acids. Several contryphans were initially purified, characterized and synthesized at the University of Utah and later also in other foreign laboratories. In contryphan purified from venom of a cone snail species (Conus radiatus), the D-amino acid (D-tryptophan) occupies position 4 in the peptide chain. In the laboratory synthesis, D-tryptophan was introduced at position 7 (occupied by L-tryptophan in the natural peptide), but the peptide did not show any biological activity, unlike the peptide where the D-tryptophan is at position 4, as found in the natural peptide. Note that either L-tryptophan or D-tryptophan can be potentially present in the peptide chain but only D-tryptophan is found at position 4 and L-tryptophan at position 7, in the natural peptide. All other known contryphans later discovered from other species of cone snails were found to have D-amino acids (D-tryptophan or D-leucine) at similarly homologous positions.

The conversion of L-amino acid to D-amino acid plays a key role in conferring biological activity to an otherwise inert peptide. For example, the cone snail peptide RXIA with a D-phenylalanine is extremely potent, whereas the peptide synthesized with L-phenylalanine at the same position has no significant biological activity.

Racemase, the enzyme that converts L-amino acid to D-amino acid, exists in various organisms. The glutamate racemase in bacteria catalyzes the formation of D-glutamate, which is needed for the synthesis of cell wall peptidoglycan (substance with peptide and carbohydrate components). The serine racemase from rat brain or spider venom can convert L-serine to D-serine. The alanine racemase from muscle of black tiger prawn or seedlings of alfalfa catalyzes the conversion of L-alanine to D-alanine.

During peptide or protein synthesis, messenger ribonucleic acid (mRNA) is decoded in accordance with the rule dictated by the genetic code. Only L-amino acids are incorporated during this process which is also known as translation. Translation is the construction of a peptide or protein with a sequence of amino acids coded by the mRNA. The mRNA is the design used for the construction; its sequence of nucleotides (building blocks of RNA) is used to guide the synthesis of a chain of amino acids that form the peptide or protein. The ribosome is the site where the peptide or protein is made. Transfer RNA (tRNA) delivers the appropriate amino acid to that site. It is always L-amino acids that bind to the corresponding tRNAs, rather than D-amino acids. Thus, the tRNA is said to have a stereospecific requirement. The tRNA, therefore, chooses the type of amino acid (i.e., only L-amino acid) that it delivers to the ribosome. At the end of translation, D-amino acid is introduced in the chosen position within the peptide chain, by the action of a racemase.

It was previously considered that D-amino acids were excluded from life forms, except the D-amino acids found in bacterial antibiotic peptides which are not synthesized through the usual ribosomal route, and without the participation of messenger RNAs. Now, peptides synthesized in the ribosome using L-amino acids, into which D-amino acids have been introduced at chosen positions after translation, have been discovered in higher life forms. In the process of the occurrence of L- or D-amino acids in peptides and proteins, choice seems to edge out chance.

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Elsie C. Jimenez is a professor of chemistry of the University of the Philippines Baguio and currently UP Scientist I. She has undertaken research on contryphans and other D-amino acid-containing peptides from cone snails at the University of Utah in Salt Lake City, Utah, USA. The research was covered by a Commercial Research Agreement signed by the University of the Philippines, Department of Agriculture (Philippines) and the University of Utah. She and her collaborators have acquired US patents on contryphans. The synthetic version of contryphan, which she initially purified from the venom of Conus radiatus, is now available in the market as a research biochemical. She can be reached at [email protected]. Melba C. Patacsil is an instructor in chemistry of UP Baguio. She can be reached at [email protected].