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.

Download the abstract

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…

Effects of regulated deficit irrigation (RDI) on grape composition in Monastrell grapevines under semiarid conditions

The influence of two pre-veraison and post-veraison regulated deficit irrigation (RDI) strategies on yield and grape quality was analyzed during a two year period for mature grapevines (cv. Monastrell) in Southeastern of Spain

Read More

Viti-Tunnel, an automatically removable protection against diseases, frost and hail, a way to drastically reduce the use of pesticides

Viti-tunnel®, une innovation imaginée pour répondre à deux des objectifs majeurs des viticulteurs : 1.la sécurisation de la vendange : viti-tunnel® permet de protéger les vignobles des pertes de récolte dues aux maladies, au gel et à la grêle. 2.la réduction des pesticides : viti-tunnel® permet de réduire de plus de 90 %, le recours aux produits phytosanitaires et aux passages de pulvérisateurs, et ce, en toute sécurité pour la vendange. Un dispositif automatisé pour protéger les vignes viti-tunnel® est un dispositif de mise à l’abri automatique des rangs de vigne pendant les pluies et les évènements climatiques extrêmes.

Read More

Defining the mechanisms and impact of winemaking treatments on tannin and polysaccharides in red wine: recent progress in creating diverse styles

Tannin and polysaccharide concentration and composition is important in defining the texture of red wines, but can vary due to factors such as cultivar, region, grape ripeness, viticultural practices and winemaking techniques. However, the concentration and composition of these macromolecules is dependent not only on grape tannin and polysaccharide concentration and composition, but also their extractability and, in the case of polysaccharides, their formation by yeast. Through studies into the influence of grape maturity, winemaking and sensory impacts of red grape polysaccharides, seed and skin tannins, recent research in our laboratory has shown that the processes involved in the extraction of these macromolecules from grapes and their retention in wine are very complex.

Read More

Trace-level analysis of phosphonate in wine and must by ion chromatography with inductively coupled plasma mass spectrometry (IC-ICP-MS).

Phosphonic acid and especially potassium dihydrogen phosphonate are widely used to restrain the ubiquitous pressure of grapevine downy mildew in viticulture. Nevertheless, phosphonic acid and its derivatives have been banned in organic viticulture in October 2013, because they have been classified as plant protection products since then.

Read More

The challenge of improving oenological quality in favorable conditions for productivity

Marselan (Cabernet-Sauvignon x Grenache), has been planted for more than 20 years now in Uruguay. Due to its good agronomic and oenological aptitudes under uruguayan conditions, it is currently the red variety with highest plantation rate. The objective of the study was to identify management practices, aimed at improving quality in highly productive vineyards, different fruit/leaf regulation methods were tested in southern Uruguay.

Read More