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Protein Crystallography in Vaccine Research and Development.

Malito E, Carfi A, Bottomley MJ - Int J Mol Sci (2015)

Bottom Line: The use of protein X-ray crystallography for structure-based design of small-molecule drugs is well-documented and includes several notable success stories.However, it is less well-known that structural biology has emerged as a major tool for the design of novel vaccine antigens.We discuss several examples of the crystallographic characterization of vaccine antigen structures, alone or in complexes with ligands or receptors.

View Article: PubMed Central - PubMed

Affiliation: Protein Biochemistry Department, Novartis Vaccines & Diagnostics s.r.l. (a GSK Company), Via Fiorentina 1, 53100 Siena, Italy. enrico.x.malito@gsk.com.

ABSTRACT
The use of protein X-ray crystallography for structure-based design of small-molecule drugs is well-documented and includes several notable success stories. However, it is less well-known that structural biology has emerged as a major tool for the design of novel vaccine antigens. Here, we review the important contributions that protein crystallography has made so far to vaccine research and development. We discuss several examples of the crystallographic characterization of vaccine antigen structures, alone or in complexes with ligands or receptors. We cover the critical role of high-resolution epitope mapping by reviewing structures of complexes between antigens and their cognate neutralizing, or protective, antibody fragments. Most importantly, we provide recent examples where structural insights obtained via protein crystallography have been used to design novel optimized vaccine antigens. This review aims to illustrate the value of protein crystallography in the emerging discipline of structural vaccinology and its impact on the rational design of vaccines.

No MeSH data available.


(A) The crystal structure of the complex fHbp-Fab 12C1 (pdb 2YPV) is depicted with green/blue surface for N and C termini of fHbp, and light/dark gray for light and heavy chains of Fab 12C1. The epitope and paratope surfaces are colored in red and yellow, respectively; (B) Surface representations of fHbp (colored as in panel A), allowing comparison of the Fab 12C1 epitope (red patch) as revealed by HDX-MS (top) and X-ray crystallography (bottom). For clarity, the surface of fHbp only is shown, after re-orientation (~90° about the Y-axis) of the view in A; (C) Surface locations of fHbp residues (red patches, labeled) which when mutated to Alanine inhibit human fH binding. The entire interface of the interaction with fH on the surface of fHbp is outlined with a black line, as revealed previously [41].
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ijms-16-13106-f002: (A) The crystal structure of the complex fHbp-Fab 12C1 (pdb 2YPV) is depicted with green/blue surface for N and C termini of fHbp, and light/dark gray for light and heavy chains of Fab 12C1. The epitope and paratope surfaces are colored in red and yellow, respectively; (B) Surface representations of fHbp (colored as in panel A), allowing comparison of the Fab 12C1 epitope (red patch) as revealed by HDX-MS (top) and X-ray crystallography (bottom). For clarity, the surface of fHbp only is shown, after re-orientation (~90° about the Y-axis) of the view in A; (C) Surface locations of fHbp residues (red patches, labeled) which when mutated to Alanine inhibit human fH binding. The entire interface of the interaction with fH on the surface of fHbp is outlined with a black line, as revealed previously [41].

Mentions: Indeed, both EM and HDX-MS have emerged as increasingly powerful tools for mapping conformational epitopes under native conditions, i.e., using full-length folded proteins, not linear peptides or fragments [39]. For example, HDX-MS was used to map the protective epitope of a mAb targeting the meningococcal factor H binding protein (fHbp), a Bexsero® antigen, and the results were in close agreement with the crystal structure of the same complex [40] (Figure 2A,B). Analysis of the Fab 12C1/fHbp complex structure in silico and subsequent sequence and structure-guided site-directed mutagenesis studies revealed that the variant 1-specific conformational epitope targeted by 12C1 is not dependent on just one or two key residues, but rather is determined by a large discontinuous conformational epitope, which was optimally identified only by protein crystallography. Interestingly, the Fab binding site on the surface of fHbp overlapped significantly with the binding site of human factor H revealed by a previous co-crystal structure [41], and this competition for overlapping surfaces may well contribute to the strong bactericidal efficiency of this mAb [42].


Protein Crystallography in Vaccine Research and Development.

Malito E, Carfi A, Bottomley MJ - Int J Mol Sci (2015)

(A) The crystal structure of the complex fHbp-Fab 12C1 (pdb 2YPV) is depicted with green/blue surface for N and C termini of fHbp, and light/dark gray for light and heavy chains of Fab 12C1. The epitope and paratope surfaces are colored in red and yellow, respectively; (B) Surface representations of fHbp (colored as in panel A), allowing comparison of the Fab 12C1 epitope (red patch) as revealed by HDX-MS (top) and X-ray crystallography (bottom). For clarity, the surface of fHbp only is shown, after re-orientation (~90° about the Y-axis) of the view in A; (C) Surface locations of fHbp residues (red patches, labeled) which when mutated to Alanine inhibit human fH binding. The entire interface of the interaction with fH on the surface of fHbp is outlined with a black line, as revealed previously [41].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4490488&req=5

ijms-16-13106-f002: (A) The crystal structure of the complex fHbp-Fab 12C1 (pdb 2YPV) is depicted with green/blue surface for N and C termini of fHbp, and light/dark gray for light and heavy chains of Fab 12C1. The epitope and paratope surfaces are colored in red and yellow, respectively; (B) Surface representations of fHbp (colored as in panel A), allowing comparison of the Fab 12C1 epitope (red patch) as revealed by HDX-MS (top) and X-ray crystallography (bottom). For clarity, the surface of fHbp only is shown, after re-orientation (~90° about the Y-axis) of the view in A; (C) Surface locations of fHbp residues (red patches, labeled) which when mutated to Alanine inhibit human fH binding. The entire interface of the interaction with fH on the surface of fHbp is outlined with a black line, as revealed previously [41].
Mentions: Indeed, both EM and HDX-MS have emerged as increasingly powerful tools for mapping conformational epitopes under native conditions, i.e., using full-length folded proteins, not linear peptides or fragments [39]. For example, HDX-MS was used to map the protective epitope of a mAb targeting the meningococcal factor H binding protein (fHbp), a Bexsero® antigen, and the results were in close agreement with the crystal structure of the same complex [40] (Figure 2A,B). Analysis of the Fab 12C1/fHbp complex structure in silico and subsequent sequence and structure-guided site-directed mutagenesis studies revealed that the variant 1-specific conformational epitope targeted by 12C1 is not dependent on just one or two key residues, but rather is determined by a large discontinuous conformational epitope, which was optimally identified only by protein crystallography. Interestingly, the Fab binding site on the surface of fHbp overlapped significantly with the binding site of human factor H revealed by a previous co-crystal structure [41], and this competition for overlapping surfaces may well contribute to the strong bactericidal efficiency of this mAb [42].

Bottom Line: The use of protein X-ray crystallography for structure-based design of small-molecule drugs is well-documented and includes several notable success stories.However, it is less well-known that structural biology has emerged as a major tool for the design of novel vaccine antigens.We discuss several examples of the crystallographic characterization of vaccine antigen structures, alone or in complexes with ligands or receptors.

View Article: PubMed Central - PubMed

Affiliation: Protein Biochemistry Department, Novartis Vaccines & Diagnostics s.r.l. (a GSK Company), Via Fiorentina 1, 53100 Siena, Italy. enrico.x.malito@gsk.com.

ABSTRACT
The use of protein X-ray crystallography for structure-based design of small-molecule drugs is well-documented and includes several notable success stories. However, it is less well-known that structural biology has emerged as a major tool for the design of novel vaccine antigens. Here, we review the important contributions that protein crystallography has made so far to vaccine research and development. We discuss several examples of the crystallographic characterization of vaccine antigen structures, alone or in complexes with ligands or receptors. We cover the critical role of high-resolution epitope mapping by reviewing structures of complexes between antigens and their cognate neutralizing, or protective, antibody fragments. Most importantly, we provide recent examples where structural insights obtained via protein crystallography have been used to design novel optimized vaccine antigens. This review aims to illustrate the value of protein crystallography in the emerging discipline of structural vaccinology and its impact on the rational design of vaccines.

No MeSH data available.