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Structural functionality, catalytic mechanism modeling and molecular allergenicity of phenylcoumaran benzylic ether reductase, an olive pollen (Ole e 12) allergen

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Abstract

Isoflavone reductase-like proteins (IRLs) are enzymes with key roles in the metabolism of diverse flavonoids. Last identified olive pollen allergen (Ole e 12) is an IRL relevant for allergy amelioration, since it exhibits high prevalence among atopic patients. The goals of this study are the characterization of (A) the structural-functionality of Ole e 12 with a focus in its catalytic mechanism, and (B) its molecular allergenicity by extensive analysis using different molecular computer-aided approaches covering (1) physicochemical properties and functional-regulatory motifs, (2) sequence analysis, 2-D and 3D structural homology modeling comparative study and molecular docking, (3) conservational and evolutionary analysis, (4) catalytic mechanism modeling, and (5) sequence, structure-docking based B-cell epitopes prediction, while T-cell epitopes were predicted by inhibitory concentration and binding score methods. Structural-based detailed features, phylogenetic and sequences analysis have identified Ole e 12 as phenylcoumaran benzylic ether reductase. A catalytic mechanism has been proposed for Ole e 12 which display Lys133 as one of the conserved residues of the IRLs catalytic tetrad (Asn-Ser-Tyr-Lys). Structure characterization revealed a conserved protein folding among plants IRLs. However, sequence polymorphism significantly affected residues involved in the catalytic pocket structure and environment (cofactor and substrate interaction-recognition). It might also be responsible for IRLs isoforms functionality and regulation, since micro-heterogeneities affected physicochemical and posttranslational motifs. This polymorphism might have large implications for molecular differences in B- and T-cells epitopes of Ole e 12, and its identification may help designing strategies to improve the component-resolving diagnosis and immunotherapy of pollen and food allergy through development of molecular tools.

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Acknowledgments

This study was supported by the following European Regional Development Fund co-financed Grants: MCINN BFU 2004-00601/BFI, BFU 2008-00629, BFU2011-22779, CICE (Junta de Andalucía) P2010-CVI15767, P2010-AGR6274 and P2011-CVI-7487, and by the coordinated project Spain/Germany MEC HA2004-0094. JCJ-L thanks Spanish CSIC and the European Marie Curie research program (FP7-PEOPLE-2011-IOF) for his I3P-BPD-CSIC and PIOF-GA-2011-301550 Grants, respectively.

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Authors and Affiliations

  1. Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Profesor Albareda 1, 18008, Granada, Spain

    Jose C. Jimenez-Lopez & Juan D. Alché

  2. The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia

    Jose C. Jimenez-Lopez

  3. Department of Biology, Rutgers University, 315 Penn Street, Camden, NJ, 08102, USA

    Simeon O. Kotchoni & Emma W. Gachomo

  4. Center for Computational and Integrative Biology (CCIB), Rutgers University, 315 Penn Street, Camden, NJ, 08102, USA

    Simeon O. Kotchoni & Emma W. Gachomo

  5. School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, St Lucia, QLD, 4072, Australia

    Maria C. Hernandez-Soriano

  6. Department of Earth and Environmental Sciences, Katholieke Universiteit Leuven (KULeuven), Kasteelpark Arenberg 20, Box 2459, 3001, Heverlee, Belgium

    Maria C. Hernandez-Soriano

Authors
  1. Jose C. Jimenez-Lopez
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  2. Simeon O. Kotchoni
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  3. Maria C. Hernandez-Soriano
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  4. Emma W. Gachomo
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  5. Juan D. Alché
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Correspondence to Jose C. Jimenez-Lopez.

Electronic supplementary material

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10822_2013_9686_MOESM1_ESM.pdf

Figure S1. Ole e 12 modeling assessment. (a) Ramachandran plot of the modeled Ole e 12 protein. (b) ‘Z-plot’ and (c) ‘e-plot’ of Ole e 12 protein model. (d) Energy level distribution representation in the Ole e 12 protein model. The amino acid colors are clamped at red (highest energy) or blue (lowest energy). Supplementary material 1 (PDF 117 kb)

10822_2013_9686_MOESM2_ESM.pdf

Figure S2. Chemical structures of flavonoids. a) Diagram of the natural polyphenol classification. b) Examples of pollen polyphenols (flavonoids) with significant antioxidant activity by substitution of radicals R1, R2, R3, R4 and R5. c) Basic structures of flavonoid subclasses. Supplementary material 2 (PDF 73 kb)

10822_2013_9686_MOESM3_ESM.pdf

Figure S3. Diagram representation of highly antigenicity regions in olive Ole e 12 protein. Eight areas of high antigenicity are highlighted with gray color shadows, as a result of the combination of paramenters such as hydrophobicity (or hydrophilicity), Kyte-Doolitte scale and Hopp-Woods scale; antigenicity, Welling method and Parker method. Surface accessibility of amino acids, 30% and 50% (discontinue blue and red line, respectively). Supplementary material 3 (PDF 156 kb)

Supplementary material 4 (PDF 90 kb)

Supplementary material 5 (PDF 14 kb)

Supplementary material 7 (PDF 11 kb)

Supplementary material 8 (PDF 54 kb)

Supplementary material 9 (PDF 56 kb)

Glossary

Å

Armstrong

ANOLEA

Atomic non-local environment assessment

ASA

Absolute surface area

Cα

Carbon alpha

CATH

Protein structure classification

CDART

Conserved domain architecture retrieval tool

CDD

Conserved domain database

ExPASy

Expert protein analysis system

FASTA

Fast alignment

FFT

Fast fourier transform

G-factor

Goodness factor

GETAREA

Solvent accessible surface area or solvation energy

GO terms

The gene ontology project

GRAVY

Grand average of hydropathicity

GROMOS96

Force field for molecular dynamics simulation

HLA

Human leukocyte antigen

IC50

Inhibitory concentration

IFR

Isoflavone reductase

IRLs

Isoflavone reductase-like proteins

Jscore

Jury score

MHC

Major histocompatibility complex

NCBI

National center for biotechnology information

NJ

Neighbor-joining

NMR

Nuclear magnetic resonance

PB

Electrostatic Poisson-Boltzmann

PCBER

Phenylcoumaran benzylic ether reductase

PDB

Protein data bank

PIP-Family

PCBER, IFR and PRL family

PIRSF

Family classification system at the protein information resource

PLR

Pinoresinol-lariciresinol reductase

ProSa

Protein structure analysis

PROSITE

Database of protein domains, families and functional sites

PROCHECK

Protein structure validation server

QMEAN

Protein model quality estimation server

SASA

Solvent accessible surface areas

SDR

Short-chain dehydrogenase/reductase

SDAP

Structural database of allergenic proteins

SMART

Simple modular architecture research tool

RMSD

Root mean square deviation

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Jimenez-Lopez, J.C., Kotchoni, S.O., Hernandez-Soriano, M.C. et al. Structural functionality, catalytic mechanism modeling and molecular allergenicity of phenylcoumaran benzylic ether reductase, an olive pollen (Ole e 12) allergen. J Comput Aided Mol Des 27, 873–895 (2013). https://doi.org/10.1007/s10822-013-9686-y

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