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…

Grapevine rootstock field evaluation under drought and saline condition in California

Climate change impacts grape production worldwide and in California drought and salinity became increasingly challenging for grape growers to maintain sustainable production and fruit quality.

Read More

Holistic characterization of Sangiovese clones 

Sangiovese is one of Italy’s most cultivated grape varieties, and currently, over 130 different clones are registered in the national register of grape varieties. However, despite the sangiovese genome having been re-sequenced, limited molecular and genomic information is still available for this cultivar. The present study investigates the complexity of genotype-environment interactions of ten different Sangiovese clones, cultivated in the Chianti Rufina DOCG district over five consecutive vintages (2016-2020).

Read More

The chemical composition of disease resistant hybrid grape cultivars and its impact on wine quality: an exploratory enquiry into sustainable wines

Disease resistant hybrid grape cultivars are now allowed in a number of EU wine PDOs, and are also accepted in a number of countries outside the EU. There is increasing interest in diseases resistant hybrid grape cultivars (RHGCs) because they allow for the production of healthy, high quality grapes with limited use of pesticides and the associated environmental and public health

Read More

Testing the pathogen e-learning and field training course on grapevine virus knowledge and management

One of the reasons of the spread of grapevine virus diseases in
vineyards around the world is the lack of knowledge by the main actors of the wine sector. To face this problem, five partners worked together to develop the PAThOGEN project, a training program aimed to improve grapevine virus knowledge and management. The partnership gathers one French technical center (IFV), one Spanish university (USC), one Italian applied research center (CREA), one Spanish foundation
specialized in training and technology transfer (FEUGA) and one Italian SME specialized in the development of informatics tools and in knowledge transfer (HORTA).The objectives of PAThOGEN are: (i) to develop and
maintain a high-quality work-based Vocational and Education Training program, (ii) to improve the skills of professionals of the wine sector.

Read More

Evolution of the crown procyanidins during wine making and aging in bottle

Condensed tannins are widely distributed in plant‐derived foods and beverages like grape, red wine, nuts, tea, apples and chocolate in which they contribute to multiple sensorial properties such as flavor, color, and taste (astringency and bitterness). During the wine making process,

Read More