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…

The effect of management practices and landscape context on vineyard biodiversity

Intensification is considered one of the major drivers of biodiversity loss in farmland. The more intensive management practices that have been adopted the last decades, contributed to species declines from all taxonomic groups. Moreover, agricultural intensification has led to an important change of land use. Complex, mixed agro-ecosystems with cultivated and non-cultivated habitats have been converted to simplified, intensive and homogeneous ones with severe effects on biodiversity.

Improving the phenolic composition of cv tempranillo wines by blending grapes of different ripening state

The aim of this work was to reduce the alcohol content of Tempranillo wine. Tempranillo wines were produced by grapes harvested at different ripening dates (August 11 which was 21 oBrix and September 28 with 25 oBrix). At the second date, the Tempranillo wines were elaborated as follows: grapes were destemmed, crushed and collected into 50 L stainless-steel vats. Before preferementative maceration in cold, 50 % (M1) and 70 % (M2) of the must have been replaced by the same percentage of must from the first harvest. In addition, a control wine (C) was performed with only grapes from the second harvest.

Characterization of intact glycoside aroma precursors of recovered minority Spanish red grape varieties by High-Resolution Mass Spectrometry

In Spain, the wide diversity of red grapevine varieties represents an advantage when choosing the most suitable one for cultivation based on different climatic conditions, without implying a loss of their enological potential.

Molecular binding mechanisms between grape seed polypeptides and wine anthocyanins by fluorescence spectroscopy and computational techniques

In recent years, proteins endogenous to grape have become of great interest to the wine industry because they represent a new alternative to other biopolymers subjected to more legal restrictions (i.e. animal origin and synthetics) that can be used in technological applications to modulate sensory attributes such as wine color and have a positive impact on wine quality.

Evaluation of vineyards, fruit and wine affected by wild fire smoke

Wineries may randomly reject fruit from vineyards near wild fires exposed to smoke. It is difficult to determine if fruit has been compromised in quality when exposed to smoke