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…

Enological evaluation of the attitude of the grapevine fumin to give varietal wines

Initiatives have been ongoing in recent years to safeguard biodiversity in the oenological sector via a process of enhancement of ancient varieties, under a pressure of a market strongly oriented towards production deriving from native vines of specific geographical zones. In that sense, Aosta Valley
(Italy) has raised the need to preserve and characterize its minority vine varieties which have the potentiality to give varietal wines. Fumin represents the 7% of the production of the region with 16 hectares of vineyards and 753 hectolitres of derived wine. Due to its large phenolic potential, strong astringency and deep colour, it has long been, and is still today, assembled or blended with other varieties as occurs, for example, for the Torrette.

USDA national grapevine germplasm resources: new curators, new directions

The National Plant Germplasm System (NPGS) in the United States Department of Agriculture safeguards numerous species. Grapevines are split in two locations: Davis, CA and Geneva, NY. The two germplasms maintain 43 Vitis species with over 4500 genetically unique accessions.

MONITOR SOME KEY PARAMETERS THROUGH THE IMPLEMENTATION OFCONTINUOUS CONTROL SYSTEMS OF THE MUST-WINE DURING MACERATION-FERMENTATION IN RED WINEMAKING TO MANAGE OPERATIONS IN “AUTOMATION”

This study is aimed to develop a complete tool for the winemaker with, complete and targeted “winemaking recipes” that can be adapted to criteria set by the winemaker, such as: grape variety, grape health status, degree of ripening, desired wine, redox status throughout the alcoholic fermentation.
To get such aim, specific sets of experiments using red grape juices from different varieties (Nebbiolo, Barbera, Pinot noir, etc.) collected at different technological and phenolic maturity points, will be held with “automatized 4.0 tanks” equipped with sensors for measuring: redox potential, dissolved oxygen, relative density, temperature, and color in order to collect a sufficient amount of data preparatory to the creation of operating models in the most widely winemaking situations in which the automatized 4.0 tanks “will be able to independently respond” with the right corrective actions (opening/closing aeration valve, execution/block pumping overs , etc.) if the key parameters exceed the limits of the recommended ranges set in the selected recipe.

Adapting wine production to climate change through the exploration of the diversity of Vitis vinifera cultivars

Major factors involved in wine quality and typicity are soil type, climatic conditions, plant material (rootstock and cultivar), vineyard management practices and winemaking conditions.

Control of grapevine virus diseases in collections and at the stages of propagation in Ukraine

The principles of virological control on different types of grapevine collections and plantations are summarized.