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…

The impacts of simulated heatwaves on the induction and maintenance of bud cold tolerance in cultivated and wild-type Vitis species

Low temperatures are required for the acquisition and maintenance of bud cold tolerance, which are necessary for grapevines to survive freezing temperatures in winter.

Read More

Overhead spray water treatment as a mitigation strategy for reducing vine stress and preserving grape quality during heatwaves

Changes in climate have been influencing the quality of wine grapes worldwide. The impact of extreme climate events over short periods is increasingly recognized as a serious risk to grape quality and yield quantity. In this study the mitigation effects of a pulsed water spray on vine canopy during heatwave events has been evaluated for maintaining vine condition during the growing season and grape quality. Vines of three varieties (Malbec, Bonarda, and Syrah) under drip irrigation in the UNCuyo experimental vineyard were treated with an overhead pulsed water spray.

Read More

Prosensorial potential of new fungi-resistant varieties in modern oenology

The introduction into the Italian wine supply chain of the latest generation of fungi-resistant grapevine varieties, endowed with a greater or lesser strong resistance to downy and powdery mildews, represents a valid tool of making viticulture more sustainable, particularly in northern regions of the peninsula, where climatic conditions accentuate the pressure of fungal diseases. However, the affirmation of resistant varieties is a function of their agronomic value, as well as of their oenological and sensorial value. The purpose of this study was to evaluate in detail the sensory potential of the new resistant varieties, in order to understand their real possibility of inclusion in the modern global enological context.

Read More

The role of terroir in tourism led amenity migration: contrasting effects in Tuscany and the Okanagan valley of British Columbia

Definitions of terroir elude consistent agreement. As defined geographical space the common denominators of its conceptualization include natural and cultural elements of life

Read More

Which microorganisms contribute to mousy off-flavour in our wines?

In this video recording of the IVES science meeting 2024, Mariona H Gil i Cortiella (Universidad Autónoma de Chile, Santiago de Chile, Chile) speaks about Which microorganisms contribute to mousy off-flavour in owines. This presentation is based on articles accessible for free on OENO One and IVES Technical Reviews.

Read More