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…

Rootstock mediated responses of grapevine (Vitis vinifera L.) metabolism and physiology to combined water deficit and salinity stress in Syrah grafts

Water deficit and salinity are increasingly affecting the viticulture and wine industry. These two stresses are intimately related; understanding the physiological and metabolic responses of grapevines to water deficit, salinity and combined stress is critical for developing strategies to mitigate the nega- tive impacts of these stresses on wine grape production. These strategies can include selecting more tolerant grapevine cultivars and graft combinations, improving irrigation management, and using soil amendments to reduce the effects of salinity. For this purpose, understanding the response of grape- vine metabolism to altered water balance and salinity is of pivotal importance.

Sardinia terroir and Cannonau: a zoning approach to discover an ancient tradition

Cannonau variety is historically grown in a large Sardinia area (Jerzu district) and the vineyards are planted both in the plane and in the sloped hills reaching also 650 m of altitude a.s.l. Thus, in order to discover how climate, soil diversity and growing traditions could account for differences in grape and wine quality, this trial was carried out.

Evoluzione stagionale delle temperature ed andamento della maturazione nel vitigno Aglianico: risultati di un quadriennio di osservazioni in Campania

In viticoltura, la comprensione dell’influenza della temperatura dell’aria sulla dinamica della maturazione assume importante rilievo in relazione all’ ottimizzazione dell’ epoca di raccolta da cui dipende in modo significativo la qualità del prodotto finale.

Integrated approach to grape stalks valorization: sustainable recovery of bioactive compounds and biofuel production

Grape stalks are a byproduct of the winemaking process and represent a valuable and inexpensive source of bioactive compounds. While their direct use in whole bunch fermentation is known, the majority of grape stalks are discarded, posing environmental and economic challenges.

Variability of Tempranillo grape quality within the Ribera del Duero do (Spain) and relationships with climatic characteristics

The aim of this research was to evaluate the variability of ripening characteristics of the Tempranillo variety within the Ribera del Duero Designation of Origin (Spain) and it relationships with soil characteristics