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…

Research summary on the use of Terroir as a wine purchasing cue

Due to the current challenging nature of the global wine market, and recent growth in number and strength of competitors from non-traditional wine producing countries, European wine producers are focussing on the potential to develop a competitive advantage through the concept of terroir.

Read More

Effect of terroir and winemaking protocol on the chemical and sensory profiles of Pinot Blanc wine

Wine research in the past years has mainly been focused on laboratory scale due to the possibility of controlling winemaking variables. Conversely, studies on wine quality in relation to the winemaking variables at the winery scale may be able to better account for the actual challenges encountered during wine production. Winemaking problems are recently arising from progressive changes in environmental conditions in relation to the terroir. It is important to realize that each wine region may have specific winemaking protocols and that winemakers often base their decisions on subjective, emotional, and empirical opinions. Due to all the above-mentioned issues, taking the correct decision in winemaking to achieve the desired goals may become even more challenging.

Read More

Genetic and developmental regulation of leaf senescence in grapevine rootstocks and grafted scions

Leaf senescence in grapevines is a key developmental process influencing photosynthesis and carbon allocation from source tissues to sinks, with important implications for vineyard productivity.

Read More

Aromatic profile of Savatiano Greek Grape Variety as affected by various terroirs in the PGI zone of Attica.

Regionality, frequently called terroir, is often used to market wines from different locations. Savatiano (Vitis Vinifera L.), is the dominant indigenous variety of the Mesogeia – Attiki region, reaching a percentage of 70% of the total vine cultivation, and being the most widely planted variety in Greece. In this context, this research focuses on the evaluation of the impact of different terroirs within the PGI Attiki zone on the aromatic profile of Savatiano.

Read More

Significance of factors making Riesling an iconic grape variety

Riesling is the iconic grape variety of Germany and accounts for 23% of the German viticulture acreage, which comprises 45% of the worldwide Riesling plantings. Riesling wines offer a wide array of styles from crisp sparkling wines to highly concentrated and sweet Trockenbeerenauslese or Icewines. However, its thin berry skin makes Riesling more vulnerable to detrimental environmental threats than other white wine varieties.  

Read More