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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 structure of the meningococcal antigen Neisseria adhesin A (NadA) variant 5 (pdb 4CJD) is shown on the left, with the region experimentally determined by X-ray crystallography labeled in red. The two main domains of NadA (head + wings and stalk) are labeled with green and blue arrows/boxes, respectively. All other regions were defined by homology modelling, as described previously [20]. A homology model of NadA variant 3 is also shown, with sequence conservation among variants 1–5 depicted as a gradient from light blue (low sequence identity) to dark blue (high sequence identity). The modeled transmembrane anchor is shown in orange. Red dots indicate regions that were not modeled due to lack of predicted coiled-coil periodicity or homology; (B) A surface representation of the co-crystal structure of the staphylococcal antigen MntC (semi-transparent light yellow surface and dark yellow cartoon) bound to Fab C1 (light and dark grey surfaces depicting light and heavy chains, respectively) (pdb 4NNP). The binding site of C1 on the surface of MntC (red patch) provides insights into the mechanisms of interaction between MntC and its natural receptor MntB. The Mn2+-binding site and the occluded MntB receptor binding sites on MntC are labelled. All figures were prepared using the Pymol software (http://www.pymol.org).
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ijms-16-13106-f001: (A) The structure of the meningococcal antigen Neisseria adhesin A (NadA) variant 5 (pdb 4CJD) is shown on the left, with the region experimentally determined by X-ray crystallography labeled in red. The two main domains of NadA (head + wings and stalk) are labeled with green and blue arrows/boxes, respectively. All other regions were defined by homology modelling, as described previously [20]. A homology model of NadA variant 3 is also shown, with sequence conservation among variants 1–5 depicted as a gradient from light blue (low sequence identity) to dark blue (high sequence identity). The modeled transmembrane anchor is shown in orange. Red dots indicate regions that were not modeled due to lack of predicted coiled-coil periodicity or homology; (B) A surface representation of the co-crystal structure of the staphylococcal antigen MntC (semi-transparent light yellow surface and dark yellow cartoon) bound to Fab C1 (light and dark grey surfaces depicting light and heavy chains, respectively) (pdb 4NNP). The binding site of C1 on the surface of MntC (red patch) provides insights into the mechanisms of interaction between MntC and its natural receptor MntB. The Mn2+-binding site and the occluded MntB receptor binding sites on MntC are labelled. All figures were prepared using the Pymol software (http://www.pymol.org).

Mentions: The NadA variant 5 protein exhibits an elongated structure approximately 220 Å-long, and almost exclusively coiled-coil, which runs from the N terminus to the C terminus. The insertion along the coiled-coil of small β-strand structures (residues N49–G84), contribute to make a broader N-terminal region that forms the head domain (Figure 1A) and splits the coiled-coil in two regions. It is remarkable how this sequence interruption apparently does not result in a structural perturbation of the coiled-coil, but forms wing-like structures that protrude from the stalk and pack against the N-terminal coiled-coil helices. Regions of flexibility or disorder were observed along the stalk, with partial electron densities suggesting unwinding of the coiled-coil towards the C terminus, and thus supporting the notion of flexibility as an intrinsic property of this protein.


Protein Crystallography in Vaccine Research and Development.

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

(A) The structure of the meningococcal antigen Neisseria adhesin A (NadA) variant 5 (pdb 4CJD) is shown on the left, with the region experimentally determined by X-ray crystallography labeled in red. The two main domains of NadA (head + wings and stalk) are labeled with green and blue arrows/boxes, respectively. All other regions were defined by homology modelling, as described previously [20]. A homology model of NadA variant 3 is also shown, with sequence conservation among variants 1–5 depicted as a gradient from light blue (low sequence identity) to dark blue (high sequence identity). The modeled transmembrane anchor is shown in orange. Red dots indicate regions that were not modeled due to lack of predicted coiled-coil periodicity or homology; (B) A surface representation of the co-crystal structure of the staphylococcal antigen MntC (semi-transparent light yellow surface and dark yellow cartoon) bound to Fab C1 (light and dark grey surfaces depicting light and heavy chains, respectively) (pdb 4NNP). The binding site of C1 on the surface of MntC (red patch) provides insights into the mechanisms of interaction between MntC and its natural receptor MntB. The Mn2+-binding site and the occluded MntB receptor binding sites on MntC are labelled. All figures were prepared using the Pymol software (http://www.pymol.org).
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-13106-f001: (A) The structure of the meningococcal antigen Neisseria adhesin A (NadA) variant 5 (pdb 4CJD) is shown on the left, with the region experimentally determined by X-ray crystallography labeled in red. The two main domains of NadA (head + wings and stalk) are labeled with green and blue arrows/boxes, respectively. All other regions were defined by homology modelling, as described previously [20]. A homology model of NadA variant 3 is also shown, with sequence conservation among variants 1–5 depicted as a gradient from light blue (low sequence identity) to dark blue (high sequence identity). The modeled transmembrane anchor is shown in orange. Red dots indicate regions that were not modeled due to lack of predicted coiled-coil periodicity or homology; (B) A surface representation of the co-crystal structure of the staphylococcal antigen MntC (semi-transparent light yellow surface and dark yellow cartoon) bound to Fab C1 (light and dark grey surfaces depicting light and heavy chains, respectively) (pdb 4NNP). The binding site of C1 on the surface of MntC (red patch) provides insights into the mechanisms of interaction between MntC and its natural receptor MntB. The Mn2+-binding site and the occluded MntB receptor binding sites on MntC are labelled. All figures were prepared using the Pymol software (http://www.pymol.org).
Mentions: The NadA variant 5 protein exhibits an elongated structure approximately 220 Å-long, and almost exclusively coiled-coil, which runs from the N terminus to the C terminus. The insertion along the coiled-coil of small β-strand structures (residues N49–G84), contribute to make a broader N-terminal region that forms the head domain (Figure 1A) and splits the coiled-coil in two regions. It is remarkable how this sequence interruption apparently does not result in a structural perturbation of the coiled-coil, but forms wing-like structures that protrude from the stalk and pack against the N-terminal coiled-coil helices. Regions of flexibility or disorder were observed along the stalk, with partial electron densities suggesting unwinding of the coiled-coil towards the C terminus, and thus supporting the notion of flexibility as an intrinsic property of this protein.

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.