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…

Influenza delle componenti climatiche e pedologiche sulla variabilità dei contenuti polifenolici in alcuni ambienti vitati della DOCG Sagrantino di Montefalco

Obiettivo del progetto è la valutazione dell’influenza climatica e pedologica dell’areale di Montefalco sul vitigno Sagrantino, ponendo particolare attenzione alla componente polifenolica e antocianica. Sono stati quindi messi a confronto, a partire dal 2001 fino al 2008, sei differenti zone tutte situate all’interno dell’areale DOCG Sagrantino di Montefalco; per ciascun vigneto alla vendemmia sono state effettuate analisi sui parametri analitici e sul contenuto polifenolico e antocianico delle uve. Ognuna delle sei zone è inoltre stata caratterizzata dal punto di vista pedoclimatico, valutando l’influenza del clima e della tipologia di suolo sui parametri analitici presi in considerazione.

Read More

A applied viticultural zoning, based on the “secteurs de la reference” methodology, in the Cognac vineyard (France)

Dans les Charentes, en réponse à une crise de production du vignoble destiné à la production de Cognac, un plan de diversification viticole pour des vins de pays de qualité est mis en place. Il nécessite une connaissance des sols et de leurs caractéristiques viticoles pour orienter le choix des types de vins et adapter l’itinéraire technique de production.

Read More

Effects of mulching with municipal solid waste (MSW)-compost on the soil microbiota and decomposition activity in a productive vineyard in Apulia (Italy)

Application of municipal solid waste (MSW)-compost as a mulching material in vineyards supports sustainable practices and aligns with both circular economy and zero-waste principles.

Read More

Dissecting the polysaccharide‐rich grape cell wall matrix during the red winemaking process, using high‐throughput and fractionation methods

Limited information is available on grape wall-derived polymeric structure/composition and how this changes during fermentation. Commercial winemaking operations use enzymes that target the polysaccharide-rich polymers of the cell walls of grape tissues to clarify musts and extract pigments during the fermentations. In this study we have assessed changes in polysaccharide composition/ turnover throughout the winemaking process by applying recently developed cell wall profiling approaches to both wine and pomace polysaccharides. The methods included gas chromatography for monosaccharide composition (GC-MS), infra-red (IR) spectroscopy and comprehensive microarray polymer profiling
(CoMPP) using cell wall probes.

Read More

Stability of 3-mercaptohexanol during white wine storage in relationship to must pre-fermentative fining

3-Mercaptohexanol (3MH) is a volatile thiol occurring in several white and red wines, where it can contribute to fruity attributes. Its content is typically high in wines from certain grape varieties, in particular Sauvignon blanc, where it is considered a varietal marker. The strong nucleophilic character of thiols makes 3MH rather unstable during wine storage, due to the presence of several strong electrophilic species. Among these electrophilics, those arising from the oxidation of flavan3-ols such as catechin and epi-catechin have been indicated as critical for 3MH stability. Accordingly, there is a generalized interest towards the ability of vinification practices to reduce 3MH loss during aging through the management of wine flavan-3-ols content.

Read More