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…

INTENSE PULSED LIGHT FOR VINEYARD WASTEWATER: A PROMISING NEW PROCESS OF DEGRADATION FOR PESTICIDES

The use of pesticides for vine growing is responsible for generating an important volume of wastewater. In 2009, 13 processes were authorized for wastewater treatment but they are expensive and the toxicological impact of the secondary metabolites that are formed is not clearly established. Recently photodecomposition processes have been studied and proved an effectiveness to degrade pesticides and to modify their structures (Maheswari et al., 2010, Lassale et al., 2014). In this field, Pulsed Light (PL) seems to be an interesting and efficient process (Baranda et al., 2017). Therefore, the aim of this work was to investigate the PL technology as a new process for the degradation of pesticides.

Use of ultrasounds to accelerate aging on lees of red wines

Aging on lees (AOL) is a powerful technique to protect varietal aroma and color. Simultaneously, helps to soften tannins and increase and improve wine body and structure. AOL is complementary to barrel aging modulating the wood impact and protecting wine from oxidative conditions.

Adaptation to climate change by determining grapevine cultivar differences using temperature-based phenology models

Grapevine phenology is advancing with increased temperatures associated with climate change. This may result in higher fruit sugar concentrations at harvest and/or earlier compressed harvests and changes in the synchrony of sugar with other fruit metabolites. One adaptation strategy that growers may use to maintain typicity of wine style is to change cultivars. This approach may enable fruit

Screening of phenolic compounds and antioxidant potential of grapes, wine and grape by-products

Polyphenols, bioactive secondary metabolites abundantly found in various grapevine components such as stalks, skins, and seeds, have attracted considerable attention in recent decades due to their potential health benefits. These compounds, including flavan-3-ols, flavanols, flavones, and stilbenes, are known for their antioxidant and anti-inflammatory properties.

Bees, climate changes, and “environmental sustainability 4.1c” in viticulture and the territory for a new global multiproductive “biometaethical district 4.1c”

The use of bees as pollinators in vine varieties with physiologically female flowers (Picolit, Bicane, Ceresa, Moscato rosa, etc.) (Cargnello, 1983) and as bio-indicators for biodiversity and environmental sustainability is well-known. Furthermore, there are interests in: 1-a. Making the viticulture of Belluno (Province of Veneto in North-eastern Italy, which is also famous for the Dolomites -a UNESCO World Heritage-) regain the socioeconomic role which it is entitled to and which it had got in its past by aiming at the enhancement of local grape variety in harmony with others, for example with the neighboring area of the Conegliano and Valdobbiadene Prosecco Superiore DOCG; 2-a. Maintaining and further improving the important natural and healthy environment of Belluno, and making its territory and the “lookout” means of the environmental sustainability, including its vineyards, even more naturally original and sustainable 4.1C.