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…

“Terroir” and climate change in Franconia / Germany

Franconia which is a “cool climate” winegrowing region is well known for its fruity white wines. The most common grape cultivars are Silvaner and Mueller-Thurgau.

AN AUTOMATIC CANOPY COOLING SYSTEM TO COPE WITH THE THERMAL-RADIATIVE STRESSES IN THE PIGNOLETTO WHITE GRAPE

In recent years characterized by hot dry summers, the implementation of innovative irrigation tools in the vineyard represents a crucial challenge to ensure optimal production and to avoid excess of water consumption. It is known that the grapevine reacts to multiple stresses – i.e., high temperatures and wa- ter shortage – through adaptive mechanisms that are detrimental to the yield. Furthermore, this condi- tion is usually aggravated by high solar radiation, which could negatively affect the phenolic composi- tion of the grapes. Therefore, a cooling system has been developed aiming to reduce bunches’ sunburn damage.

Smoke tainted wine – what now?

The frequency of bushfires close to wine regions around the world has increased in the last two decades. The economic losses incurred when grapes and wines are discarded due to ‘smoke taint’ are substantial (i.e., hundreds of millions of dollars). Efforts to mitigate and ameliorate smoke taint are therefore crucial. Chardonnay, rosé and cabernet sauvignon wines made from grapes exposed to smoke during the 2020 wildfires in eastern Australia were subjected to various amelioration techniques: the addition of activated carbons, molecularly imprinted polymers (mips), and a proprietary resin (either directly, or following membrane filtration); spinning cone column (scc) distillation; and finally, transformation into vinegar.

Evolution of the appellation of origin concept in the vineyards of Australia

Australia is the seventh largest producer of wine and crushed 1.42 million tonnes of wine grapes in the 2001 vintage.

AOC Saint-Romain, Hautes-Côtes-de-Beaune, Burgundy: analysis of a “terroir”

The aim of this study is to provide an overview of the terroir of Saint-Romain, Burgundy, based on three main information sources: official data relating to vines (CVI), soil cartography and a survey of winegrowers’ practices.