Structural Basis of pH Dependence of Neoculin, a Sweet Taste-Modifying Protein

Ohkubo, Takayuki; Tamiya, Minoru; Abe, Keiko; Ishiguro, Masaji

doi:10.1371/journal.pone.0126921

Cited by 7 publications

(4 citation statements)

References 15 publications

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“…Additionally, users obtain information regarding so-called patches, groups of pH-sensitive residues found in a customizable physical distance on the protein structure, which may play a more profound role than individual amino acids in the regulation of protein function upon pH change. To demonstrate the workflow and the power of patcHwork, we carried out sequence-based pH sensitivity analysis of Escherichia coli cell envelope proteins, and structure-based analysis of the taste-modifying protein neoculin ( 26 , 27 ) and the pH-regulated mouse anion exchanger 2 (mAE2) protein ( 28–32 ).…”

Section: Introductionmentioning

confidence: 99%

patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures

Schmitz

Schultze

Vanags

et al. 2022

Nucleic Acids Research

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pH regulates protein function and interactions by altering the charge of individual residues causing loss or gain of intramolecular noncovalent bonds, which may lead to structural rearrangements. While tools to analyze residue-specific charge distribution of proteins at a given pH exist, currently no tool is available to investigate noncovalent bond changes at two different pH values. To make protein pH sensitivity analysis more accessible, we developed patcHwork, a web server that combines the identification of amino acids undergoing a charge shift with the determination of affected noncovalent bonds at two user-defined pH values. At the sequence-only level, patcHwork applies the Henderson–Hasselbalch equation to determine pH-sensitive residues. When the 3D protein structure is available, patcHwork can be employed to gain mechanistic understanding of the effect of pH. This is achieved using the PDB2PQR and PROPKA tools and noncovalent bond determination algorithms. A user-friendly interface allows visualizing pH-sensitive residues, affected salt bridges, hydrogen bonds and aromatic (pi–pi and cation–pi) interactions. patcHwork can be used to identify patches, a new concept we propose of pH-sensitive residues in close proximity on the protein, which may have a major impact on function. We demonstrate the attractiveness of patcHwork studying experimentally investigated pH-sensitive proteins (https://patchwork.biologie.uni-freiburg.de/).

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Section: Introductionmentioning

confidence: 99%

patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures

Schmitz

Schultze

Vanags

et al. 2022

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Additionally, users obtain information regarding so-called patches, groups of pH-sensitive residues found in a customizable physical distance on the protein structure, which may play a more profound role than individual amino acids in the regulation of protein function upon pH change. To demonstrate the workflow and the power of patcHwork, we carried out the sequence-based pH sensitivity analysis of E. coli cell envelope proteins, structures of the taste-modifying protein neoculin (25,26) and the pH-regulated mouse anion exchanger 2 (AE2) protein (27)(28)(29)(30)(31).…”

Section: Introductionmentioning

confidence: 99%

patcHwork: A user-friendly pH sensitivity analysis web server for protein sequences and structures

Schmitz

Schultze

Vanags

et al. 2022

Preprint

View full text Add to dashboard Cite

pH regulates protein function and interactions by altering the charge of individual residues causing the loss or gain of intra-molecular non-covalent bonds, which may additionally lead to structural rearrangements. While tools to analyze residue-specific charge distribution of protein sequences and structures at a given pH exist, currently no tool is available to investigate non-covalent bond changes at two different pH values. In an effort to make protein pH sensitivity analysis more accessible to researchers without computational structural biology background, we developed patcHwork, a web server that combines the identification of amino acids undergoing a charge shift with the determination of affected non-covalent bonds at two user-defined pH values. At the sequence-only level, patcHwork applies the Henderson-Hasselbalch equation to determine pH-sensitive residues. When the 3D protein structure is available, patcHwork can be employed to gain a deeper mechanistic understanding of the effect of pH on a protein of interest. This is achieved using the PDB2PQR and PROPKA tools and non-covalent bond determination algorithms. A user-friendly interface allows visualizing pH-sensitive residues as well as affected salt bridges, hydrogen bonds and aromatic (pi-pi and cation-pi) interactions. Importantly, patcHwork can be used to identify patches, a new concept we propose of pH-sensitive residues in close proximity on the protein structure, which may have a major impact on function. We demonstrate the attractiveness of patcHwork studying experimentally investigated pH-sensitive proteins. (Access:https://patchwork.biologie.uni-freiburg.de/)

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“…Several essential amino acids that are responsible for the taste-modifying properties of neoculin have been identi ed: His-11 in NBS is responsible for the pH-dependent taste-modifying activity of neoculin [25], and Arg-48, Tyr-65, Val-72, and Phe-94 function in the binding and activation of human sweet taste receptors [26]. Changes in the tertiary structure of the subunits at these residues are thought to contribute to the taste-modifying properties of neoculin [27,28].…”

Section: Introductionmentioning

confidence: 99%

De novo transcriptome analysis and comparative expression profiling of genes associated with the taste-modifying protein neoculin in Curculigo latifolia and Curculigo capitulata fruits

Okubo

Terauchi

Okada

et al. 2021

Preprint

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Background Curculigo latifolia is a perennial plant endogenous to Southeast Asia whose fruits contain the taste-modifying protein neoculin, which binds to sweet receptors and makes sour fruits taste sweet. Although similar to snowdrop (Galanthus nivalis) agglutinin (GNA), which contains mannose-binding sites in its sequence and 3D structure, neoculin lacks such sites and has no lectin activity. Whether the fruits of C. latifolia and other Curculigo plants contain neoculin and/or GNA family members was unclear. Results Through de novo RNA-seq assembly of the fruits of C. latifolia and the related C. capitulata and detailed analysis of the expression patterns of neoculin and neoculin-like genes in both species, we assembled 85,697 transcripts from C. latifolia and 76,775 from C. capitulata using Trinity and annotated them using public databases. We identified 70,371 unigenes in C. latifolia and 63,704 in C. capitulata. In total, 38.6% of unigenes from C. latifolia and 42.6% from C. capitulata shared high similarity between the two species. We identified ten neoculin-related transcripts in C. latifolia and 15 in C. capitulata, encoding both the basic and acidic subunits of neoculin in both plants. We aligned these 25 transcripts and generated a phylogenetic tree. Many orthologs in the two species shared high similarity, despite the low number of common genes, suggesting that these genes likely existed before the two species diverged. The relative expression levels of these genes differed considerably between the two species: the transcripts per million (TPM) values of neoculin genes were 60 times higher in C. latifolia than in C. capitulata, whereas those of GNA family members were 15,000 times lower in C. latifolia than in C. capitulata. Conclusions The genetic diversity of neoculin-related genes strongly suggests that neoculin genes underwent duplication during evolution. The marked differences in their expression profiles between C. latifolia and C. capitulata may be due to mutations in regions involved in transcriptional regulation. Comprehensive analysis of the genes expressed in the fruits of these two Curculigo species helped elucidate the origin of neoculin at the molecular level.

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Structural Basis of pH Dependence of Neoculin, a Sweet Taste-Modifying Protein

Cited by 7 publications

References 15 publications

patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures

patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures

patcHwork: A user-friendly pH sensitivity analysis web server for protein sequences and structures

De novo transcriptome analysis and comparative expression profiling of genes associated with the taste-modifying protein neoculin in Curculigo latifolia and Curculigo capitulata fruits

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