Peptides – a collection of words, nouns and terms to review – natural peptides, synthetic peptides, peptide mimics, artificial peptides, modified peptides and more.


WHAT ARE PEPTIDES?

Insulin bovine

Peptides are macro molecules that contain amino acid monomers linked together by peptide (amide) bonds. The covalent bonds are formed when the carboxyl group of one amino acid reacts with the amino group of another. Peptides are usually considered to be smaller than proteins. This is based on their size, however, there appears to be no clear boundary at which a peptide becomes a protein. Therefore Insulin, which is a dipeptide linked together by cysteine bonds, is sometimes considered to be a peptide or a protein. The shortest peptides are dipeptides, made up of 2 amino acids joined by a single peptide bond. Larger peptides are tripeptides, tetrapeptides, and so on.  Polypeptides are peptides that contain a longer, continuous, and linear peptide chain.

Peptide Synthesis BSI

Definition Number of amino acids
Dipeptide 2
Tripeptide 3
Tetrapeptide 4
Pentapeptide 5
Oligopeptide 2 to approximately 10
Polypeptide Approximately 10 to approximately 100
Protein More than 50
Macropeptide More than 100
Cyclopeptide 2 and more; No N-terminus and no C-terminus

.

MORE DEFINITIONS OF PEPTIDES

The IUPAC definition: “A peptide is any compound produced by amide formation between a carboxyl group of one amino acid and an amino group of another. The amide bonds in peptides may be called peptide bonds. The word peptide usually applies to compounds whose amide bonds are formed between C-l of one amino acid and N-2 of another (sometimes called eupeptide bonds), but it includes compounds with residues linked by other amide bonds (sometimes called isopeptide bonds). Peptides with fewer than about 10-20 residues may also be called oligopeptides; those with more, polypeptides. Polypeptides of specific sequence of more than about 50 residues are usually known as proteins, but authors differ greatly on where they start using this term.”

(Source:   IUPAC-IUB Joint Commission on Biochemical Nomenclature.)

.

The shortest definition I have found is the following.

.

“Any compound in which two or more amino-acids are linked together in a linear sequence, the carboxyl group of each acid being joined to the amino group of the next.”

(Source Jones, 2006)

.

Configuration and structure of peptides

.

All amino acids found in proteins and most peptides are of the “L” configuration. The Cahn-Ingold-Prelog nomenclature uses an “S” to describe this configuration. These amino acids are also known as 2-, alpha-, or α-amino acids with the generic formula H2NCHRCOOH. In most cases the R is an organic substituent known as a “side-chain“.  Most natural amino acids are found as L-stereoisomers (“left-handedisomers). A few D-amino acids (“right-handed”) have been found to occur in bacterial envelopes and are also present in some antibiotics

The C-terminal carboxy group and the N-terminal amino group are common to all amino acids, therefore it is the side group that defines the different amino acids and also determines their individual characteristics. Furthermore, these characteristics also determine the structure and function of the amino acid within the context of a peptide or protein.  A variety of amino acids with different functional groups as side chains are available including, acidic, basic, hydrophobic, hydrophilic, redox-active, bulky, and compact moieties. 

Examples of the structure for a few peptides

Peptides 1

Hirudin

The three-dimensional structure of the N-terminal 51-residue domain of recombinant hirudin in aqueous solution is illustrated. This structure was determined by 1H nuclear magnetic resonance (NMR) spectroscopy, and the resulting high-quality solution structure was compared with corresponding structures obtained from studies with the intact, 65-residue polypeptide chain of hirudin. This is an example of globular peptides that contain cysteine-bridges.

[Szyperski T, Güntert P, Stone SR, Wüthrich K.; Nuclear magnetic resonance solution structure of hirudin(1-51) and comparison with corresponding three-dimensional structures determined using the complete 65-residue hirudin polypeptide chain. J Mol Biol. 1992 Dec 20;228(4):1193-205.]

The peptide hirudin occurs naturally in the salivary glands of medicinal leeches (such as Hirudo medicinalis) and has a blood anticoagulant properties.

The peptide bond

The linkage between amino acids in proteins and peptides is called the peptide bond. The condensation reaction involving the carboxyl group of one amino acid and the amino group of another resulting in a simultaneous release of a water molecule creates this bond. Due to resonance of the amide C-N bond in the peptide bond the peptide bond has some double bond character which limits the free rotation of this bond. This feature also limits the degree of freedom available to the structure of a polypeptide or protein.

Resonance

Peptide bond formation and resonance structures.

Dehydration of the reacting amino acids links the two amino acids together. The resulting amide linkage is the peptide bond. The resonance structures illustrate the partial double bond character of the C-N bond.  

The word or term “Peptid” or “Peptide” was first coined in 1902 Emil Fischer. The term was derived from protein degradation products “pepton(s)” originating from the Greek word peptos, which means “verdaut” or digested, and the ending of the term polysaccharide, indicating a polymer made up of monomers, in this case sugar units.

.

How many peptide arrangements are possible?

The sequence of amino acids in the polypeptide chain, also called the primary structure of a polypeptide or protein, can be established by selective chemical and/or enzymatic cleavage of the peptide or protein followed by separation the products, amino acid analysis, and sequence determination. Natural peptides or proteins are made up from 20 amino acids. The combination of these 20 amino acid in the sequences of polypeptides allow for a tremendous variety of possible peptides.

In general, the total number of different linear arrangements of n objects taken in groups of r at a time is given by: Eq 1 

where any of the n objects can be used as many r times.

For example if n = 3 and r = 3 for a tripeptide Eq 3

In general, the number of permutations, or ordered arrangements of a set of n objects taken in groups of r at a time, is given by:

nPr = n(n-1)(n-2) ……(n-r+1). If all n objects are used: nPn = n!

For example if three (3) amino acids are taken at a time:  nPn = 3! = 3 x 2 x 1 = 6

  • A peptide containing a sequence of 4 amino acids made with 4 different amino acids will result in a theoretical number of 44 = 256 possible peptides.
  • A peptide containing a sequence of 4 amino acids made with 20 different amino acids gives a theoretical number of 204 =  160,000 possible peptides.
  • A protein that contains 300 amino acids in its sequence and is made with 20 different types of amino acids can have 20300 different linear arrays of amino acids. This is equal to 2.037 x 10390 different proteins.  This results in a tremendous amount of possible peptides or proteins.

Each polypeptide synthesized in a cell is encoded by a single gene. The DNA sequences of chromosomal genes encode the amino acid sequences of all proteins and most peptides. The “codons” of a gene are arranged sequentially in the same order in which the amino acids appear in a polypeptide. See the “genetic code” for more details.

. . .

The following is a list of nouns, terms or words describing different types of peptides

.

Allopeptide

A peptide from a different individual (Greek allos, other) of the same species (Used in immunology).

Apopeptide

Refers to the free peptide component of a bioactive peptide in a cofactor complex, the cofactor having been removed (Greek apo-, away from).

Carbopeptoid

Refers to an oligomer in which carbohydrate units are linked through amide bonds.

Conopeptide

Refers to a peptide toxin from the marine snail genus Conus.

Cropeptide

cropeptide W. This peptide is found in cosmetic and toiletry formulations: a hydrolysis product of wheat used in lotions, shampoos, etc. and which is said to have moisturising properties.

Cyclotide

This is derived from cyclopeptide as the class name for small proteins with cystine knots. It is now frequently used.

Depsipeptide

Refers to a peptide in which a position in the molecule which could have been occupied by an amino acid residue is taken by a hydroxy acid residue. The word is derived from the Greek word depsein, meaning ‘to make supple, to tan’.

Eupeptide

Refers to a peptide in which the amino acid residues are linked only through α-functions, i.e. a ‘normal’ or ‘ordinary’ peptide.

Holopeptide

This is

(1) A complete peptide as opposed to fragments thereof.

(2) A complete peptide cofactor complex as opposed to the apopeptide.  

Homopeptide

Refers to a peptide comprising only identical amino acid residues. Note that when the prefix homo– is applied to amino acids, it indicates carbon chain extension, as in a homologous series.

Isopeptide

Refers to a peptide in which there are inter-residue amide bonds between side chains.

Macropeptide

A term used in dairy science referring to a product of milk coagulation, usually appearing as ‘casein macropeptide’.

Oligopeptide

Refers to a peptide made up of a few amino acid residues.

Peptidaceous

Derived by analogy with proteinaceous which is infrequently used and redundant alternative to peptidic.

Peptidal

An infrequently used and redundant alternative to peptidic.

Peptidergic

Used in neuroscience refereeing to liberating, stimulated by, or involving a peptide or peptides. Derived by analogy with adrenergic, cholinergic etc.

Peptidic

Pertaining to or having the nature or composition of the peptide class. This term can often be encountered in the negative form nonpeptidic.

Peptidoid

Online dictionaries gave two slightly different definitions:

(1) ‘A condensation product of two amino acids involving at least one condensing group other than the α-carboxyl or α-amino group; e.g. glutathione’. (2) ‘A compound formed by the condensation of two amino acids, with the linkage involving at least one group that is not a carboxyl or an amino group’.

Peptidome

Derived by analogy with proteome: all the peptides in a cell or tissue.

Peptidomimetic

Refers to a molecule, usually a synthetic drug candidate, which is designed to resemble a bioactive peptide in functionality, and/or overall shape, so that it can interact at that peptide’s receptors. It has structural features which diverge widely from those of the peptide, such as pseudopeptide bonds or conformational constraints. Peptidomimetics can also be found in natural sources. For example, morphine is one such natural peptidomimetic.

Peptidyl

A term from the chemical nomenclature referring to an acyl group derived from a C-terminal carboxyl group of a peptide. Another definition of this term is ‘a radical. . .’, an unfortunate use of the word radical in its archaic chemical sense, in which it meant a group or substituent.

Peptoid

Refers to a peptide analogue in which one or more of the proteinogenic amino acid residues has been replaced by the isomer in which the side chain has been relocated from to , for example in which leucine (-isobutylglycine) is replaced by -isobutylglycine. Hence the terms dipeptoid, tripeptoid, polypeptoid, peptoidic.

Peptolide

This is an obsolete term; a synonym for depsipeptide.

Polypeptide

Refers to a peptide comprising many amino acid residues. Formerly describing any such peptide, but in most cases either peptide or protein is now used. But the term finds current and appropriate use in sequential polypeptides, i.e. peptides with repeating amino acid sequences, e.g. the collagen model H-(GlyGlyPro)n-OH.

Propeptide

A biosynthetic precursor of a bioactive peptide. The use of the prefix pro– here is potentially confusing, as in ordinary English it means ‘deputising for’ or ‘in favor of’ as well as ‘coming before’. Prepeptide is a less-used synonym; a prepropeptide is a biosynthetic precursor of a biosynthetic precursor.

Pseudopeptide

Refers to a synonym for a peptidomimetic, but this use is becoming obsolete as well, like peptide surrogate. The adjectival use pseudopeptide bond remains current; in symbolic representation ψ, psi, is used to indicate a pseudopeptide, e.g. the analogue obtained by reduction of the peptide bond in GlyGly is represented Glyψ[CH2NH]Gly.

Retropeptide

(1) A peptide analogue in which one or more peptide bonds –CONH– is replaced by –NHCO–. If in addition the configurations of the α-chiral centers are inverted, then the combination term retroinverso peptide is used.

(2) A peptide analogue in which the sequence of the amino acid residues in the parent peptide is reversed. Clearly, these definitions can be confusing, and its use should be carefully considered.

Telopeptide

Refers to a peptide corresponding to a part of a terminal (Greek telos, end) region of a protein. It is an ironic consequence of using Greek for word design that the term for a peptide from within (Greek endon) a sequence, as opposed to from an end, is endopeptide (commonly found as endopeptidase, antonym exopeptidase).

Tetracosapeptide

A peptide of 24 amino acid residues, i.e. a 24-mer. Hence tetracosactide, tetracosactrin, β-corticotropin-(1–24)-peptide.

Xenopeptide

This term is used in immunology and means “a peptide”.

.

 Since peptides are synthesized using amino acids the general properties of the amino acids found in proteins are listed below.

.

General Properties of Amino Acids

.

Name

Symbol

MW

MW

(-H2O)

Structure

Solubility (g/100 mL H2O at 25°C)

UV Abs Log e (lmax)
pH ~ 7.0

Three Letter Code

One Letter Code

Alanine

Ala

A

89.09

71.08

16.65

Arginine

Arg

R

174.20

156.19

15

Asparagine

Asn

N

132.12

114.10

3.53

Aspartic Acid

Asp

D

133.10

115.09

0.778

Cysteine

Cys

C

121.15

103.15

very soluble

2.46
(250 nm)

Glutamic Acid

Glu

E

147.13

129.12

0.864

Glutamine

Gln

Q

146.15

128.13

2.5

Glycine

Gly

G

75.07

57.05

 Gly

24.99

Histidine

His

H

155.16

137.14

4.19

3.77
(211 nm)

Isoleucine

Ile

I

131.17

113.16

4.117

Leucine

Leu

L

131.17

113.16

2.426

Lysine

Lys

K

146.19

128.17

very

soluble

Methionine

Met

M

149.21

131.20

3.381

Phenylalanine

Phe

F

165.19

147.18

2.965

3.97
(206 nm)
2.30
(257 nm)

Proline

Pro

P

115.13

97.12

162.3

Serine

Ser

S

105.09

87.08

5.023

Threonine

Thr

T

119.12

101.11

very

soluble

Tryptophan

Trp

W

204.23

186.21

1.136

4.67
(219 nm)
3.75
(280 nm)

Tyrosine

Tyr

Y

181.19

163.18

0.0453

3.90
(222 nm)
3.15
(274 nm)

Valine

Val

V

117.15

99.13

8.85

Reference

CRC Handbook of Chemistry and Physics, CRC Press, Inc., Cleveland, OH, 58 (1977).

Jones, John H.; Words derived from the noun peptide. J. Peptide Sci. 2006; 12: 79–81.  Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/psc.724

Nomenclature and Symbolism for Amino Acids and Peptides

The Merck Index, Merck & Co., Inc., Whitehouse Station, NJ 12 (1996)

.

BSI can help you with your peptide and protein based research needs. 


A variety of synthetic modified or unmodified peptides are available.

Call us at 1-800-227-0627 or move your mouse to “www.biosyn.com“ !



Categories: Micro peptides, Neuropeptides, Peptide Synthesis, peptides, Polypeptides, Short peptides, Signaling Peptides, Solid Phase Peptide Synthesis, Stapled Peptides, Synthesis, Synthetic peptides

Tags: , , , , , , , , , , ,

2 replies

  1. Thanks to explain deeply about peptides I like your explanation style. Before reading your blog, I have many Questions in my mind about peptides. Now I am happy 🙂 I will post this superb info on my blog http://purchasepeptides.com/,

  2. This is the right web site for everyone who wants to understand this
    topic. You understand a whole lot its almost tough to argue with
    you (not that I really would want to…HaHa). You certainly put a fresh spin on a topic that’s been written about for decades.
    Great stuff, just excellent!

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

%d bloggers like this: