The PentaFOLD 3.0 Algorithm for the Selection of Stable Elements of Secondary Structure to be Included in Vaccine Peptides

Conjugation with the Carrier Helped to Reveal acidification-Induced Structural Shift in the Peptide from Phospholipase Domain of Parvovirus B19

Spectroscopic studies on domains and peptides of large proteins are complicated because of the tendency of short peptides to form oligomers in aquatic buffers, but conjugation of a peptide with a carrier protein may be helpful. In this study we approved that a fragment of SK30 peptide from phospholipase A2 domain of VP1 Parvovirus B19 capsid protein (residues: 144-159; 164; 171-183; sequence: SAVDSAARIHDFRYSQLAKLGINPYTHWTVADEELLKNIK) turns from random coil to alpha helix in the acidic medium only in case if it had been conjugated with BSA (through additional N-terminal Cys residue, turning it into CSK31 peptide, and SMCC linker) according to CD-spectroscopy results. In contrast, unconjugated SK30 peptide does not undergo such shift because it forms stable oligomers connected by intermolecular antiparallel beta sheet, according to IR-spectroscopy, CD-spectroscopy, blue native gel electrophoresis and centrifugal ultrafiltration, as, probably, the whole isolated phospholipase domain of VP1 protein does. However, being a part of the long VP1 capsid protein, phospholipase domain may change its fold during the acidification of the medium in the endolysosome by the way of the formation of contacts between protonated His153 and Asp175, promoting the shift from random coil to alpha helix in its N-terminal part. This study opens up a perspective of vaccine development, since rabbit polyclonal antibodies against the conjugate of CSK31 peptide with BSA, in which the structure of the second alpha helix from the phospholipase A2 domain should be reproduced, can bind epitopes of the complete recombinant unique part of VP1 Parvovirus B19 capsid (residues: 1-227).

Comparative Study of SERS-Spectra of NQ21 Peptide on Silver Particles and in Gold-Coated "Nanovoids"

The NQ21 peptide has relatively recently attracted attention in the biomedical sphere due to its prospects for facilitating the engineering of the HIV1 vaccine and ELISA test. Today, there is still a need for a reliable and fast methodology that reveals the secondary structure of this analyte at the low concentrations conventionally used in vaccines and immunological assays. The present research determined the differences between the surface-enhanced Raman scattering (SERS) spectra of NQ21 peptide molecules adsorbed on solid SERS-active substrates depending on their geometry and composition. The ultimate goal of our research was to propose an algorithm and SERS-active material for structural analysis of peptides. Phosphate buffer solutions of the 30 µg/mL NQ21 peptide at different pH levels were used for the SERS measurements, with silver particles on mesoporous silicon and gold-coated "nanovoids" in macroporous silicon. The SERS analysis of the NQ21 peptide was carried out by collecting the SERS spectra maps. The map assessment with an originally developed algorithm resulted in defining the effect of the substrate on the secondary structure of the analyte molecules. Silver particles are recommended for peptide detection if it is not urgent to precisely reveal all the characteristic bands, because they provide greater enhancement but are accompanied by analyte destruction. If the goal is to carefully study the secondary structure and composition of the peptide, it is better to use SERS-active gold-coated "nanovoids". Objective results can be obtained by collecting at least three 15 × 15 maps of the SERS spectra of a given peptide on substrates from different batches.