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…

Ten grapevine rootstocks: effects on vegetative development, production and grape quality of cv. Mencia in the d.o. Bierzo (Spain)

Grapevine rootstock is basic to achieve good adaptation of the vine to ground and environment.

The affinity of white wine proteins for bentonite is dependent on wine composition and is directly related to their thermal stability / sensitivity

Bentonite fining is commonly used in oenology to remove all or parts of white wine proteins, which are known to be involved in haze formation. This fining is effective, but has disadvantages: it is not selective, thus molecules responsible for aroma are also removed, it causes substantial volume losses, and finally it generates wastes. Over the last decades, the knowledge of wine proteins has increased: they have been identified, their structures are known, some of them have been crystallized.

Viticulture between adaptation and resilience: the role of the Italian long-term observatories for vineyard energy, water and carbon budgets

Viticulture is exposed to a range of new stressors, that are challenging its sustainability and disrupting famous and well-established production regions. Steady increase of average temperature, recurring heat waves, altered rainfall seasonal distribution, drought spells, increased pathogens pressure, they all mix up with increased frequency, making every growing season a special challenge and calling for new approaches to cope with worrying scenarios.

NOVEL BENZENETHIOLS WITH PHENOLS CAUSE ASHY, SMOKE FLAVOR PERCEPTION IN RED WINES

Smoke impacts on wines are becoming a worldwide problem; the size and severity of wildfires increasing due to influences from changing climates.¹ For over a century, wines have been known to have a unique issue of absorbing chemical compounds derived from wildfire smoke wherein the flavor of the subsequent wine becomes ashy, rubbery, campfire-like, and smoky.² The economic impacts of a smoke-impacted wine can last for years depending on the grape varietal, costing Oregon and Washington states in the United States over a billion dollars from the 2020 wildfires, as an example.³ While years of research have indicated elevated concentrations of smoke-related compounds, such as guaiacol and syringol, in wines after smoke events, unfortunately, replicating the sensory experience using smoke-associated phenols has not had much success.⁴

WINE RACKING IN THE WINERY AND THE USE OF INERT GASES: CONTROL AND OPTIMIZATION OF THE PROCESS

Atmospheric oxygen (O₂) generates oxidation in wines that affect their physicochemical and sensory evolution. The O₂ uptake in the different winemaking processes is generally considered to be negative for the sensory characteristics of white and rosé wines. Wine racking is a critical point of O₂ uptake, as the large surface area of the wine exposed during this operation and the inability to maintain an effective inert gas blanket over it.
The aim was to study the uptake of O₂ during the racking of a model wine as a reference and to compare with purging the destination tank with different inert gases.