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.

Download the abstract

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…

The influence of terroir on the quality of wine of the Cahors A.O.C

Dans le but d’améliorer la qualité et la typicité des vins de l’Appellation d’0rigine Contrôlée CAHORS, une étude a été réalisée afin de mettre en évidence l’adéquation Cépage-Terroir- Qualité du vin.
Selon la méthodologie proposée par MORLAT et ASSELIN (1992), neuf unités terroirs ont été déterminées. Sur chacune, des parcelles de référence homogènes quant au matériel végétal Cot ou Malbec ( cépage principal de cette appellation greffé sur S04, et aux méthodes culturales, ont été suivies au niveau agronomique et œnologique (GARCIA et al., 1996).

Read More

Revisión de estudios sobre suelos vitícolas de las tierras del Jerez

Dada la importancia de los suelos y de los substratos geológicos en la zonificación vitivinícola, los autores realizan una revisión de estudios sobre las formaciones más importantes en la D.O. Jerez-Xérès-Sherry y Manzanilla-Sanlúcar de Barrameda.

Read More

Aptitude du cépage Chenin à l’élaboration de vins liquoreux en relation avec certaines unités terroirs de base de A.O.C. Coteaux du Layon

Massif and the first sedimentary formations of the western aureole of the Paris Basin. If it is found all over the world (California, Israel, South Africa), it is in this region that it best asserts its identity. It is one of the most interesting grape varieties due to the variety and complexity of the wines it can produce. It can give very dry or very sweet, still or sparkling wines, fresh when young and sublime when ageing, expressing the characteristics of each vintage as much as those of the terroir. The Chenin is a faithful witness of its geographical, geological, pedological and climatic environment; he is the foil of the land. It has strong aptitudes for the production of sweet wines conditioned by overripe grapes often botrytised in the AOC Coteaux du Layon.Massif and the first sedimentary formations of the western aureole of the Paris Basin. If it is found all over the world (California, Israel, South Africa), it is in this region that it best asserts its identity. It is one of the most interesting grape varieties due to the variety and complexity of the wines it can produce. It can give very dry or very sweet, still or sparkling wines, fresh when young and sublime when ageing, expressing the characteristics of each vintage as much as those of the terroir. The Chenin is a faithful witness of its geographical, geological, pedological and climatic environment; he is the foil of the land. It has strong aptitudes for the production of sweet wines conditioned by overripe grapes often botrytised in the AOC Coteaux du Layon.

Read More

La zonazione della valle d’Illasi (Verona)

In the bottom of Val d’Illasi (Verona province), one of the major valleys which passes through the Lessini mountains, viticulture is widely extended. In the territory belonging to Illasi and Tregnago villages, which includes ca. 1100 ha of vineyards, devoted to produce Soave and Valpolicella DOC wines, an experimental survey was conducted on a network of twenty five reference vineyards.

Read More

Aroma characterization of aged cognac spirits: contribution of volatile terpenoid compounds

Cognac spirit aromas result from the presence of a wide variety of volatile odorous compounds associated with the modalities of distilled spirit elaboration and during aging. Indeed, these odorous compounds play an essential role in the finesse and complexity of the aged Cognac.

Read More