The following page provides information on the amino acid building blocks typically used in solid-phase peptide synthesis (SPPS). Table 1 provides the amino acids and the side-chain functional groups that are often protected during SPPS. This table also provides a variety of different protecting groups that are used for that residue, including the deprotection conditions. The recommended protecting group, which is used by the PPMC, is bolded. Table 2 then provides the structures and molecular weight of both the Fmoc protected and Fmoc deprotected amino acids that are recommended in Table 1. The protected and deprotected molecular weights are often useful for calculating the molecular weight of the peptide if mass spectrometry is performed on synthesis intermediates. Finally, Table 3 provides information on the natural amino acids and their associated molecular weights, as well as their properties and one and three letter codes. A version of these tables can also be downloaded below:
Table 1 – The amino acids and their associated side-chain functional groups that must be protected during solid-phase peptide synthesis. The protecting groups for these sidechains are provided, as well as the method of deprotection and associated comments. Protecting groups in bold are the recommended protecting groups for protocols used within the PPMC.
| Amino Acid (Functionality Protected) | Protecting Groups | Deprotection | Comments |
| Arg (Guanidino N) | Mtr | TFA at 35 °C | Best in small peptides with only one Arg residue. |
| Pmc | TFA | Standard | |
| Pbf1 | TFA | Standard, less likely to react with Trp residues during cleavage than Pmc. Best for peptides with multiple Arg residues.2 | |
| Asp/Glu (Carboxyl) | OtBu3 | TFA | Standard |
| OBzl | H2/Pd, HF | Seldom used | |
| OcHx | HF | Seldom used | |
| Asn/Gln (Amide) | Trt4 | TFA | Standard, suppresses dehydration and increases solubility of the protected amino acid. Prevents side reaction of amide and carbodiimide to form nitriles. |
| Cys (Sulfhydryl) | Acm | Hg(II), I2 | Iodine forms S-S bond during deprotection. Stable to cleavage conditions, useful for preparing protected peptides. |
| tBu | TFSMA, Hg(II), TFA/DMSO/Anisole | Useful in selective formation of multiple disulfide bridges.5 | |
| pMeOBzl | TFMSA | Useful in selective formation of multiple disulfide bridges.5 | |
| Mmt | 1% TFA | On resin modification | |
| Trt4 | TFA, I2 | Standard | |
| His (Imidazole) | Fmoc | Piperidine | Temporary |
| Trt4 | 90% TFA/DCM | Standard6 | |
| Mtt | 15% TFA/DCM | Standard | |
| Lys/Orn (Amino) | Boc7 | TFA | Standard |
| tfa | TFA | Does not form side products during cleavage. | |
| Trt | TFA | Fewer side reactions during cleavage. | |
| Mtt | 1% TFA/DCM | On resin modification | |
| Dde, ivDde | Hydrazine | N-terminal Fmoc protecting group must be replaced with Boc before hydrazine treatment. | |
| Fmoc | Piperidine | Temporary | |
| Ser/Thr (Hydroxyl) | tBu3 | TFA | Standard |
| Trt | 1% TFA/DCM | On resin modification | |
| Bzl | H2/Pd, HF | Seldom used | |
| Trp (Indole) | Boc7 | TFA | Greatly reduces byproducts formed during cleavage. |
| Tyr (Phenol) | tBu3 | TFA | Standard |
| Bzl | H2/Pd, HF | Seldom used |
Table 2 – The PPMC recommended protected amino acids for solid-phase peptide synthesis. Both the Fmoc protected and Fmoc deprotected forms are shown, as well as their associated molecular weight. Groups highlighted in blue are base labile protecting groups, which is the Fmoc group. Groups highlighted in red are acid labile protecting groups. The group highlighted in green needs special procedures to be removed. This is a protecting group whose removal is orthogonal to both acidic and basic deprotection conditions. See the Alloc removal protocol for this residue.
| Amino Acid | Protected Structure | Protected Molecular Weight (g/mol) | Fmoc Deprotected Structure | Fmoc Deprotected Molecular Weight (g/mol) |
| Fmoc-Ala-OH |  | 311.34 |  | 89.09 |
| Fmoc-Arg(Pbf)-OH |  | 648.78 |  | 426.53 |
| Fmoc-Asn(Trt)-OH |  | 596.68 |  | 374.44 |
| Fmoc-Asp(OtBu)-OH |  | 411.45 |  | 189.21 |
| Fmoc-Cys(Trt)-OH |  | 585.72 |  | 363.48 |
| Fmoc-Gln(Trt)-OH |  | 610.71 |  | 388.47 |
| Fmoc-Glu(OtBu)-OH |  | 425.48 |  | 203.24 |
| Fmoc-Gly-OH |  | 297.31 |  | 75.07 |
| Fmoc-His(Trt)-OH |  | 619.72 |  | 397.48 |
| Fmoc-Ile-OH |  | 353.42 |  | 131.18 |
| Fmoc-Leu-OH |  | 353.42 |  | 131.18 |
| Fmoc-Lys(Boc)-OH |  | 468.55 |  | 246.31 |
| Fmoc-Lys(Alloc)-OH |  | 452.51 |  | 230.26 |
| Fmoc-Met-OH |  | 371.45 |  | 149.21 |
| Fmoc-Phe-OH |  | 387.44 |  | 165.19 |
| Fmoc-Pro-OH |  | 337.38 |  | 115.13 |
| Fmoc-Ser(tBu)-OH |  | 383.44 |  | 161.20 |
| Fmoc-Thr(tBu)-OH |  | 397.47 |  | 175.23 |
| Fmoc-Trp(Boc)-OH |  | 526.59 |  | 304.35 |
| Fmoc-Tyr(tBu)-OH |  | 459.54 |  | 237.30 |
| Fmoc-Val-OH |  | 339.39 |  | 117.15 |
Table 3 – The structures, properties, names, and one and three letter codes for the 20 natural amino acids. The amino acid structures are as shown at pH 7.4.
| Amino Acid | Three Letter Code | One Letter Code | Structure | Properties |
| Alanine | Ala | A |  | Hydrophobic |
| Arginine | Arg | R |  | Positively Charged |
| Asparagine | Asn | N |  | Polar Uncharged |
| Aspartic Acid | Asp | D |  | Negatively Charged |
| Cysteine | Cys | C |  | Special Case |
| Glutamine | Gln | Q |  | Polar Uncharged |
| Glutamic Acid | Glu | E |  | Negatively Charged |
| Glycine | Gly | G |  | Special Case |
| Histidine | His | H |  | Positively Charged |
| Isoleucine | Ile | I |  | Hydrophobic |
| Leucine | Leu | L |  | Hydrophobic |
| Lysine | Lys | K |  | Positively Charged |
| Methionine | Met | M |  | Hydrophobic |
| Phenylalanine | Phe | F |  | Hydrophobic Absorbs @ 280 nm |
| Proline | Pro | P |  | Special Case |
| Serine | Ser | S |  | Polar Uncharged |
| Threonine | Thr | T |  | Polar Uncharged |
| Tryptophan | Trp | W |  | Hydrophobic Absorbs @ 280 nm |
| Tyrosine | Tyr | Y |  | Hydrophobic Absorbs @ 280 nm |
| Valine | Val | V |  | Hydrophobic |
References
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- McKay, F. C.; Albertson, N. F. New Amine-Masking Groups for Peptide Synthesis. J. Am. Chem. Soc. 1957, 79 (17), 4686–4690. https://doi.org/10.1021/ja01574a029.