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…

Influence of cultivar and its drought tolerance on soil microbiome

Soil microbiome plays a crucial role in plant health and resilience, particularly under abiotic stress conditions such as drought.

The evaluation of tannin activity in south african red wines

Astringency is an important red wine quality attribute, which can be measured both chemically and sensorially. The use of tannin activity shows potential as a valuable chemical measurement in understanding red wine mouthfeel properties such as astringency and bitterness, which is also affected by tannin structural factors, in addition to matrix effects. Tannin activity is defined as the enthalpy of interaction between tannins and a hydrophobic surface. Studies involving tannin activity have been performed since the early 2010’s, but chemosensory studies used to evaluate how structure-activity relationships change across multiple, consecutive vintages are limited. The aim of this study is to investigate how tannin activity may be linked to red wine mouthfeel, and how all these variables may change according to wine age.

Oxygen consumption by diferent oenological tanins in a model wine solution

INTRODUCTION: Oenological tannins are widely used in winemaking to improve some characteristics of wines [1] being the antioxidant properties probably one of the main reasons [2]. However, commercial tannins have different botanical sources and chemical composition [3] which probably determines different antioxidant potential. There are some few references about the antioxidant properties of commercial tannins [4] but none of them have really measured the direct oxygen consumption by them. The aim of this work was to measure the kinetics of oxygen consumption by different commercial tannins in order to determine their real capacities to protect wine against oxygen. MATERIAL AND METHODS: 4 different commercial tannins were used: T1: condensed tannin from grape seeds, T2: gallotannin from chinese gallnuts, T3: ellagitannin from oak and T4: tannin from quebracho containing condensed tannins and ellagitannins.

Impact of type of winemaking vessel on the chemical composition and sensory attributes of Sauvignon blanc 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 the impact of type of winemaking vessel on the chemical composition and sensory attributes of Sauvignon blanc wines. This presentation is based on an original article accessible for free on IVES Technical Reviews.

Moderated consumption of alcoholic beverages and cancer risk

One on three cases of cancer is associated with lifestyle and nutritional patterns, and the excessive intake of alcoholic beverages is a well established risk factor. Moderate drinking has been associated with reduced or increased risk of various types of cancer, but the clinical relevance of the risk rates has not been evaluated in ad hoc prospective investigations.