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Fundamental of Secondary Structures in Peptide Based Synthetic Nanovaccine Development

Rajagopal Appavu1*, Deepa Mohan1, Ramu Kakumanu2 and Govindaraju Munisamy3
1Molecular Biophysics Unit, Indian Institute of Sciences, Bangalore 560012, India
2Department of Pathology, 301 University Blvd, The University of Texas Medical Branch, Galveston, TX 77550, USA
3Bio-Spatial Technology Research Unit, Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, 620 024 Tamil Nadu, India
*Corresponding Author : Dr. Rajagopal Appavu
Molecular Biophysics Unit
Indian Institute of Sciences, Bangalore 560012, India
Tel: 080 2293 2004
E-mail: [email protected]
Received January 27, 2016; Accepted February 25, 2016; Published March 01,2016
Citation: Appavu R, Mohan D, Kakumanu R, Munisamy G (2016) Fundamental of Secondary Structures in Peptide Based Synthetic Nanovaccine Development.Transcriptomics 4:131. doi:10.4172/2329-8936.1000131
Copyright: © 2016 Appavu R, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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The peptides vaccines are composed of the twenty genetically coded amino acids generally exist as an ensemble of different conformational states in solution. The induction of folded conformations in short peptide vaccine sequences may be achieved by the incorporation of stereochemically constrained non-coded amino acids. The aim of this review briefly provides basic understanding of method of vaccine development.

Peptide; Homologation; Immunotherapy
A large body of work emanating from Appavu et al. and elsewhere has explored the utility of α, α-dialkylated amino acids as inducers of well folded conformations in small peptides [1,2]. α-Aminoisobutyric acid (Aib) has been the most widely used residue, with its helix forming propensity being first suggested on the basis conformational energy calculations [3,4]. Since the appearance of the first crystal structures of Aib containing peptides in the 1970’s, a very large body of experimental work has firmly established the tendency of Aib residues to promote helical conformations [5-7]. The studies have reinforced the view that restricting conformational choices at specific residues in polypeptide chains may be a viable strategy for stabilizing well defined structures, even in short peptides [8]. The incorporation of Aib residues has permitted the crystallization and structure determination of synthetic helical peptides of length between 18-20 residues [5,9,10]. The β-turn, an internally hydrogen bonded structure involving two central residues, is a common structural feature in short peptides and is an important determinant of chain folding in proteins [7,11]. The proline residue, is the only coded amino acid in which rotation about the N-Cα bond (φ) is limited (φ~-60° ± 20° for LPro) by the constraint of side chain backbone cyclization, as a consequences of pyrrolidine ring formation. Pro is often found at the i+1 position in β-turns. The enantiomer DPro provides an opportunity to stabilize “mirror image” β-turn conformations. An early analysis of protein structures by Thornton and co-workers [12], subsequently expanded by other groups [13], has established the tendency of β-hairpins in proteins to contain type-I′ and II′ β-turn structures, both of which are energetically unfavourable for the chiral L-aminoacids. Necessarily, the achiral Gly residue is often found in these turn segments. The design of peptide β-hairpins has been facilitated by the recognition that the use of the DPro residue at the i+1 position, strongly favors formation of prime turns (type-II′ and type-I′). Since, the first demonstration of this design principle in the mid 1990’s [6,7], a large number of studies have appeared employing DPro-Xxx segments as nucleators of β-hairpin conformations [14]. The area of peptide design has been dramatically influenced in recent years, by therecognition that backbone expanded homologated amino acid residues (β, γ residues) can be used to generate unprecedented folded conformations in short peptides [5,6]. Early successes in these area were achieved using chiral β-residues obtained from the α-aminoacids by Arndt-Eistert homologation and by the use of cyclic residues in which torsional freedom about the Cα-Cβ (θ) bond was restricted. The exploding literature on β and γ-peptides has been extensively reviewed [15]. More recent work has explored the possibility of using β, and γ residues containing gem-dialkyl substituents, which should in principle,restrict conformational freedom about the single bonds, flanking the tetra substituted “C” atom. This principle has been most effectively demonstrated in the case of the β, β-disubstituted γ aminoacid residue, gabapentin (1-aminomethylcyclohexaneacetic acid) [1].The brief view of this review pave the way of conformational properties of short peptides containing Aib, DPro-Xxx segments, D peptide and geminally disubstituted β-aminoacids are significant role in vaccine adjuvant development.
Conformation Directing Effects of Aib Residues
The reduction in stereochemically accessible conformational space upon alkylation at the Cα atom was originally demonstrated by Ramachandran and co-workers in their seminal paper, which appeared nearly fifty years ago. A comparison of the Ramachandran maps for Gly and Ala residues reveals the dramatic reduction in the extent of conformational space that is free of unfavorable van der Waals contacts. Clearly, replacement of a hydrogen atom by a methyl group at the Cα position limits the range of conformational possibilities. Addition of a second alkyl group at the Cα atom, as in the case of Aib, must necessarily further diminish the range of sterically allowed conformations. Ramachandran and Chandrasekaran (1972) recognized that the allowed regions of φ, ψ space for the Aib residue, can be readily estimated by considering only the regions of overlap of the Ramachandran maps for LAla and DAla residues. (Figure 1a) illustrates, the regions of overlap, which suggested that Aib residues are largely constrained to adopt conformations lying in the right (αR) and left (αL) handed helical regions of φ, ψ space. Conformational energy calculations confirmed that helical conformations are indeed most favorable for the Aib residue [6]. The first crystal structures of acyclic Aib containing peptides determined in the late 1970’s, firmly established the ability of Aib residues to promote helical folding even in short peptides [16]. Subsequent crystal structure determination of a very large number of Aib containing peptides confirmed, the overwhelming preference for conformations lying in the helical regions of φ, ψ space [17,18]. (Figure 1b) shows a cluster plot of experimentally determined φ, ψ values for Aib residues. Since, the Aib residue is achiral, both right and left handed helical conformations are energetically favourable, with the result that the Aib residues favour φ, ψ values of ± 60° ± 30°, ± 30° ± 30°. Consequently, Aib residues can occupy both i+1 and i+2 positions in the type-I/III β-turns or type-I′/III′ β-turns [11], and the i+2 position in type-II/II′ β-turns (For a definition of the torsion angles at the i+1 and i+2 residues in β-turns (Figure 2). Continuous helical structures are generated by successive type-I/III or I′/III′ β-turns. It may be noted that for the purposes of this discussion a distinction is not made between type-I and III β-turns, since they only differ slightly in φ, ψ value at the i+2 position. When Aib residues are inserted as guests into all L-amino acid sequences, right handed helical structures (φ~60°, ψ~30°) are favored. In principle, insertion of an Aib-DXxx segment into a host all “L” sequence can nucleate type-I′ β-turns, which in turn may facilitate β-hairpin formation, with registered interstrand hydrogen bonds stabilizing the folded conformations [2]. Figure 3 illustrates these situations. The above discussion suggests that insertion of Aib-Xxx segments into the centre of a host, all L-amino acid residue sequence can result in dramatically different situations, depending upon the nature of the Xxx residue. If the Xxx residue, is an “L” residue, the central segment is likely to favour type-I/III β-turn conformations, with the Aib residue adopting φ, ψ values in the right handed helical (αR) region of φ, ψ space. In this case, a centrally nucleated 310 helical turn serves to propogate a right handed helical structure in the peptide. If Xxx, is a D-residue type I′/III′ turns are favoured, which then facilitate hairpin formation. In this case, both the Aib and Xxx residues adopt φ, ψ values, in the left handed helical (αL) region of φ, ψ space. The octapeptides, Boc-Leu-Phe-Val-Aib-DAla-Leu-Phe-Val-OMe, and Boc-Leu-Val-Val-Aib-DPro-Leu-Val-Val-OMeprovide examples, where hairpin formation is successfully stabilized by centrally positioned Aib- Xxx segments [1,4-7]. Figure 3 schematically illustrates the relationship between β-turn type and the nature of the secondary structure that may be facilitated by a centrally positioned turn segment. However, examples of D-residues adopting right handed helical (αR) conformations, when placed in host L-amino acid sequences have also been reported in peptide crystal structures. For example, the peptides Boc-Leu-Aib- Val-Ala-Leu-Aib-Val-DAla-DLeu-Aib-OMe, and Boc-Leu-Aib-Val-Ala- Leu-Aib-Val-DAla-DLeu-Aib-Leu-Aib-Val-OMe adopt continuous right handed helical conformations, with the D-residues adopting torsion angles φ~-50°, ψ~-60°. It should be noted that αL conformations are generally favored for D-residues, but the difference in the energy is relatively small, 1kcalmol- [14]. These observations suggest that Aib- DXxx segments, may provide a means for studying conformational switching between helical and hairpin structures in designed peptides [13].
The current scenario of secondary structure based peptide vaccine development is important for immunotherapy for both infectious and non-infectious diseases. The torsion angle of vaccines design enhances the antibody production to fight against infections. In the future, the described peptide vaccines are highly potential for HPV Vaccine development technology.

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