Vaccine target and carrier molecule nontypeable Haemophilus influenzae protein D dimerizes like the close Escherichia coli GlpQ homolog but unlike other known homolog dimers

Authors

Seth P. Jones, School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York, USA.
Kali H. Cook, School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York, USA.
Melody L. Holmquist, National Technical Institute for the Deaf, Rochester Institute of Technology, Rochester, New York, USA.
Liam J. Almekinder, School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York, USA.
Annie M. Delaney, School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York, USA.
Ryhl Charles, School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York, USA.
Natalie Labbe, School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York, USA.
Janai Perdue, School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York, USA.
Niaya Jackson, School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York, USA.
Michael E. Pichichero, Rochester Regional HealthFollow
Ravinder Kaur, Rochester Regional HealthFollow
Lea V. Michel, School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York, USA.
Michael L. Gleghorn, School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York, USA.

Department

Research

Document Type

Article

Publication Title

Proteins

Abstract

We have determined the 1.8 Å X-ray crystal structure of nonlipidated (i.e., N-terminally truncated) nontypeable Haemophilus influenzae (NTHi; H. influenzae) protein D. Protein D exists on outer membranes of H. influenzae strains and acts as a virulence factor that helps invade human cells. Protein D is a proven successful antigen in animal models to treat obstructive pulmonary disease (COPD) and otitis media (OM), and when conjugated to polysaccharides also has been used as a carrier molecule for human vaccines, for example in GlaxoSmithKline Synflorix™. NTHi protein D shares high sequence and structural identify to the Escherichia coli (E. coli) glpQ gene product (GlpQ). E. coli GlpQ is a glycerophosphodiester phosphodiesterase (GDPD) with a known dimeric structure in the Protein Structural Database, albeit without an associated publication. We show here that both structures exhibit similar homodimer organization despite slightly different crystal lattices. Additionally, we have observed both the presence of weak dimerization and the lack of dimerization in solution during size exclusion chromatography (SEC) experiments yet have distinctly observed dimerization in native mass spectrometry analyses. Comparison of NTHi protein D and E. coli GlpQ with other homologous homodimers and monomers shows that the E. coli and NTHi homodimer interfaces are distinct. Despite this distinction, NTHi protein D and E. coli GlpQ possess a triose-phosphate isomerase (TIM) barrel domain seen in many of the other homologs. The active site of NTHi protein D is located near the center of this TIM barrel. A putative glycerol moiety was modeled in two different conformations (occupancies) in the active site of our NTHi protein D structure and we compared this to ligands modeled in homologous structures. Our structural analysis should aid in future efforts to determine structures of protein D bound to substrates, analog intermediates, and products, to fully appreciate this reaction scheme and aiding in future inhibitor design.

First Page

161

Last Page

170

DOI

10.1002/prot.26418

Volume

91

Issue

2

Publication Date

2-1-2023

PubMed ID

36065600

Recommended Citation

Jones, S. P., Cook, K. H., Holmquist, M. L., Almekinder, L. J., Delaney, A. M., Charles, R., Labbe, N., Perdue, J., Jackson, N., Pichichero, M. E., Kaur, R., Michel, L. V., & Gleghorn, M. L. (2023). Vaccine target and carrier molecule nontypeable Haemophilus influenzae protein D dimerizes like the close Escherichia coli GlpQ homolog but unlike other known homolog dimers. Proteins, 91 (2), 161-170. https://doi.org/10.1002/prot.26418