terclim by ICS banner
IVES 9 IVES Conference Series 9 Artificial intelligence (AI)-based protein modeling for the interpretation of grapevine genetic variants

Artificial intelligence (AI)-based protein modeling for the interpretation of grapevine genetic variants

Abstract

Genetic variants known to produce single residue missense mutations have been associated with phenotypic traits of commercial interest in grapevine. This is the case of the K284N substitution in VviDXS1 associated with muscat aroma, or the R197L in VviAGL11 causing stenospermocarpic seedless grapes. The impact of such mutations on protein structure, stability, dynamics, interactions, or functional mechanism can be studied by computational methods, including our pyDock scoring, previously developed. For this, knowledge on the 3D structure of the protein and its complexes with other proteins and biomolecules is required, but such knowledge is not available for virtually none of the proteins and complexes in grapevine. Fortunately, the possibility of modeling proteins and complex structures with Artificial Intelligence (AI)-based methods like AlphaFold2 and AlphaFold2-Multimer will facilitate the application of this approach to proteins and complexes without available structure. Moreover, we are developing new methods based on AI to combine AlphaFold models, molecular dynamics (MD), pyDock energy scoring, and CCharPPI descriptors to predict the impact of protein mutations at the molecular level. As a case study, we have modelled the impact of the R197L seedlessness-associated substitution in VviAGL11. This protein is a homo-dimeric transcription factor that interacts with VviMADS4 dimeric protein to form a functional hetero-tetramer. Structural modeling of this complex provides insights into the functional mechanism of this protein and the role of the mentioned mutation. This protein modeling approach could be extended for grapevine mutation analysis at the genomic level.

DOI:

Publication date: June 14, 2024

Issue: Open GPB 2024

Type: Poster

Authors

Luis Ángel Rodríguez-Lumbreras1, Víctor Monteagudo1, Pablo Carbonell-Bejerano1, Fabian Glaser2, Juan Fernández-Recio1*

1 Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-UR-Gobierno de La Rioja, Spain
2 Technion Institute of Technology, Israel

Contact the author*

Keywords

AI-based modeling, Seedless grapes, Protein-protein interactions, Mutation impact analysis, Protein structure

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

Related articles…

Comprehensive analytical workflow for fermented and non-fermented grape-based beverages volatile profiling: higher resolution and reliability for a wide range of molecular structures

The increasing demand for no/low-alcohol beverages (<5% v/v) has intensified the need for technological innovation in grape-based products within this category.

What 2,900 wild grapevines reveal about the genetic diversity of Vitis vinifera L. subsp. sylvestris

Vitis vinifera L. subsp. sylvestris is the wild ancestor of the European cultivated grapevine (V. vinifera L. subsp. sativa).

Monferace a new “old style” for Grignolino wine, an autochthonous Italian variety: unity in diversity

Monferace project is born from an idea of 12 winegrowers willing to create a new “old style” Grignolino wine and inspired byancient winemaking techniques of this variety (1). Monferace wine is produced with 100% Grignolino grapes after 40 months of ageing, of which 24 in wooden barrels of different volumes. Grignolino is an autochthonous Italian variety cultivated in Piedmont (north-west Italy), recently indicated as a “nephew” of the famous Nebbiolo (2) and is used to produce three different DOC wines. The Monferace Grignolino is cultivated in the geographical area identified in the Aleramic Monferrato, defined by the Po and Tanaro rivers, in the heart of Piedmont and the produced wine is characterized by a high content of tannins, marked when young, that evolve over the years. Its color is generally slight ruby red and garnet red with orange highlights with ageing.

Impact of yeast strains on wine profiles of nine PIWIs: focus on volatile thiols

Disease resistant grapevine varieties (PIWI) are increasingly important for sustainable wine production, yet the impact of different yeasts on their wine profiles remains poorly studied. In this study, nine white interspecies varieties (i.e., caladris blanc, fleurtai, hibernal, johanniter, muscaris, sauvignon kretos, soreli, souvignier gris, and voltis) grown at the faculty of agriculture, university of Zagreb (Croatia) were vinified with three different saccharomyces cerevisiae yeasts (control strain, zymaflore x5, and zymaflore xarom).

Perception of Rose Oxide Enantiomers, Linalool and α-Terpineol to Gewürztraminer Wine Aroma

Monoterpenes are important aroma compounds in white wines. Many monoterpenes are chiral and the chiral forms have different aroma qualities.