Peptide design and solubility

Peptides are complex biomolecules. Depending on the amino acid composition, each peptide is unique with regard to its chemical and physical properties. Most peptides of biological interest are derived from native proteins. The trans-membrane region of a protein is not usually exposed and should be avoided. Similarly, any region that undergoes post-translational modification (e.g. glycosylation), should also be avoided, since antibodies raised against this sequence may not recognize the modified native protein. Frequently, the derived sequences are altered, generally in the ‘non-essential’, or say less-important, amino acid residues, although the important/essential amino acid residues are not always easy to determine.

Bio-Synthesis routinely assists clients to pinpoint potentially problematic amino acids and modify them to improve peptide assembly, solubility, stability, and antigenicity. Our modification methods include:

• Amino Acid Substitution – Improve the peptide solubility and stability
• Chemical Modification – Improve solubility and stability, structure-function studies
• Spacer Insertion - Improve peptide solubility such as O-linker or PEG linker
• Peptide Conjugation - Antisera production ligand attachments - chromophores, affinity ligands
• N- and C-Termini Capping – Avoid introducing extra charge, increase stability
• N-or C-term Adding Single Cys – For linking or conjugation via maleimide approach

Peptide Solubility

The influence of the amino acid sequence on the chemical and physical characteristics of an individual peptide is vast. Thus, we can only give some general guidelines for solubility prediction:

• Peptides shorter than 5 residues are usually soluble in water or aqueous buffer, except if the whole sequence consists of hydrophobic amino acids (like W, L, I, F, M, V, Y).
• Hydrophilic peptides containing >25% charged residues (like D, K, R, H, E) and <25% hydrophobic amino acids are usually soluble in water or aqueous buffer.
• Hydrophobic peptides containing 50% and more hydrophobic residues may be insoluble or only partly soluble in aqueous solutions. In this case we recommend using organic solvents like DMSO, DMF or acetonitrile.
• Peptides containing a very high (>75%) proportion of D, E, H, K, N, Q, R, S, T, Y are capable of building intermolecular hydrogen bonds (cross-linking), thus forming gels in aqueous solutions. These peptides should either be treated according to the instructions for hydrophobic peptides or by changing the pH value if possible.

Depending on the peptide sequence, some amino acids or peptide properties directly influence physical and/or chemical behavior of peptides. Among these one can find peptide solubility, peptide stability and peptide charge. Please refer to the tables below for amino acid classifications:

Click here for free online peptide/antibody designing software.