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…

Berry maturity effects on physic and chemical characteristics of traditional sparkling wines produced from Chardonnay and Sauvignon blanc grapes.

One of the consequences of global warming is the quick berry development giving rise to a disconnection between sugar accumulation and the formation of important quality minor compounds such as phenolics and volatile compounds being a huge challenge for the oenologist [1]. Thus, this phenomenon is forcing the search on strategies for maintaining the quality of wines despite this situation. One possibility is to make an early harvest with a low sugar concentration (18ºbrix) and advanced harvest for sparkling wine (20-21ºbrix) and afterwards to combine base wines properly and carry out the second fermentation trying to compensate the lack of secondary metabolites due to the quick berry development and higher alcohol degree of the second one, not adequate itself for sparkling wine. The aim of this study was to assess the chemical and physical characteristics, mainly volatile profile, and foaming properties of sparkling wines from grapes of Chardonnay and Sauvignon blanc.

Carbon isotope discrimination in berry juice sugars: changes in response to soil water deficits across a range of vitis vinifera cultivars

In wine producing regions around the world, climate change has the potential to decrease the frequency and amount of precipitation and increase average and extreme temperatures. This will lower soil water availability and increase evaporative demand, thereby increasing the frequency and intensity of water deficit experienced in vineyards. Among other things, grapevines manage water deficit by regulating stomatal closure. The dynamics of this regulation, however, have not been well characterized across the range of Vitis vinifera cultivars. Providing a method to understand how different cultivars regulate their stomata, and hence water use in response to changes in soil water deficits will help growers manage vineyards and select plant material to better meet quality and yield objectives in a changing climate.

Viticultural potential assessment and its spatial delineation analysis in Goriška Brda viticultural area

Viticultural potential has a complex conditioning, determined by relief,
soil, climate and lithology. Delineation of viticultural potential from vineyard areas is essential for the purpose to collect the necessary data for viticultural zoning. Using this data, we can achieve greater yield quality, which is the most important criteria in viticulture. The main purpose of this research is
characterizing of viticultural potential and zoning of homogeneous viticultural zones in Goriška Brda region by assessing the suitability of defined ecological factors.

Non Saccharomyces wine yeasts: emerging trends and challenges in winemaking

In the past, the contribution of non-Saccharomyces yeasts in winemaking has always been considered negative for their limited enological attitude if compared with Saccharomyces cerevisiae. In recent decades there has been a reevaluation of the role of non-Saccharomyces wine yeasts especially when used in combination and in support with S. cerevisiae (mixed fermentation). In this regard, selected non-Saccharomyces yeasts could be profitable used to give distinctive features, to enhance flavor and aroma complexity and to reduce the ethanol content of wines. Further emerging trends in the use of these yeasts are related to their role as bioprotectants and producers of health promoters compounds.