Biology subjects

Voet, A. R.

Publications and source records attributed to Voet, A. R..

7 recordsLinked to original sources

bioRxiv2026

DESPOT: Direction-Enhanced Scoring POTentials

Knowledge-based potentials (KBPs) remain among the most reliable and interpretable scoring functions for protein-ligand interactions, yet most share two structural limitations. They assume that the space around each protein atom is isotropic, and their interaction-conditioned reference state cannot represent regions of space that are preferentially left empty. We introduce DESPOT (Direction-Enhanced Scoring POTentials), an all-atom anisotropic KBP that overcomes both. DESPOT classifies atoms into isotropic, axially symmetric, and fully anisotropic symmetry classes from their hybridization and bonding environment, and discretizes the surrounding interaction space using the according symmetry. By adopting a positionally averaged reference state and using a void ligand atom type, it learns, for every point around a protein atom, the probability that the point is occupied by a given ligand atom type or preferentially left empty - a ligand-independent description that naturally encodes steric exclusion. This occupancy-conditioned potential captures the precise, atom-level placement of ligand atoms; we pair it with a complementary geometry-conditioned, residue-level formulation (DESPOT-screen, in the spirit of KORP-PL) and combine the two inverse-Boltzmann scores into a consensus score, DESPOT-combo. Derived from 110,943 curated, energy-minimized complexes drawn from the CROWN database and evaluated on the CASF-2016 benchmark, DESPOT achieves competitive scoring power (Pearson r = 0.61), while DESPOT-combo attains best-in-class docking power (89.5% top-1 success); all anisotropic DESPOT variants significantly outperform isotropic KBPs and established empirical scoring functions in virtual screening. Anisotropy is decisive for rejecting geometrically implausible poses, and uniting the atom-level precision of DESPOT with the implicit flexibility tolerance of the residue-level score yields the most consistent performance across tasks. Because the same occupancy-conditioned potentials can be evaluated over an empty grid, DESPOT generates molecular interaction fields as well, unifying pose scoring with direction-aware binding-site characterization within a single interpretable model.

bioinformatics↗

bioRxiv2026

CROWN: Curated Repository Of Well-resolved Noncovalent interactions

The development of machine-learning models for protein-ligand interactions is constrained by the quality and diversity of the available structural data. Existing resources force researchers into a trade-off: carefully curated collections such as PDBBind and HiQBind offer high structural reliability but cover only a narrow slice of the Protein Data Bank (PDB), whereas large-scale resources such as PLINDER provide broad coverage with minimal quality control. We present CROWN (Curated Repository Of Well-resolved Non-covalent interactions), a machine-learning-ready dataset that reconciles scale and rigor through a fully automated preprocessing pipeline. Starting from the PDB database, CROWN applies a series of interleaved quality filters and processing stages that address crystallographic resolution, ligand identity, pocket completeness, structural repair, interaction quality, and protonation at physiological pH. The pipeline finishes with a constrained energy-minimization step built on custom flat-bottomed restraints - a step absent from all existing protein-ligand datasets - that balances crystallographic evidence against the relaxation of intramolecular strain. By reconciling the heterogeneous refinement practices of different depositions without distorting the experimentally observed binding geometry, this step yields a structurally uniform collection of 178,263 complexes, representing a roughly four-fold increase in protein diversity over PDBBind and HiQBind. Rather than organizing the data around sparsely available, bias-prone binding affinities, CROWN adopts a geometry-centric design philosophy that treats the three-dimensional arrangement of atoms at the binding interface as a self-consistent source of information. To demonstrate its value as a training resource, we trained two knowledge-based scoring functions on CROWN and benchmarked them on CASF-2016: relative to HiQBind-trained counterparts, CROWN-trained models showed markedly improved ranking power (mean Spearman correlation rising from 0.509 to 0.637) and docking power (top-1 near-native pose recovery of 0.785 versus 0.724). Because CROWN imposes no requirement for affinity labels, it can in principle support any model that learns from or is evaluated against protein-ligand complex structures. We anticipate that it will serve as a broadly useful resource for tasks such as the training of binder generation, protein design or protein folding models conditioned on bound ligands, the development of scoring functions or benchmarking of interaction-prediction methods.

bioinformatics↗

bioRxiv2026

Design and characterization of SAKe, a new building block for protein self-assembly

The nanofabrication of functional protein-based surfaces is challenging due to the chemical complexity of proteins and their unpredictable behavior at the solid-liquid interface. Many proteins of interest -such as antibodies or large enzymatic complexes - lack strong and dynamic protein-protein and protein-surface interactions necessary to drive self-assembly of stable arrays with high surface coverage. Additionally, adsorption-induced conformational changes at the solid-liquid interface could lead to a loss of activity and increase the risk of undesirable interfacial processes. Here we introduce SAKe, a kelch-like designer protein, as a versatile platform to address these challenges. Ancestral sequence reconstruction led to high thermal stability, and the high symmetry allowed modularity of the proteins core. Rational engineering of the bottom side allowed SAKe to form large (up to 5 micrometers in length), well-defined and pH-dependent two-dimensional assemblies while maintaining structural integrity, which is key for further development of functional materials. SAKe self-assembly was investigated through in-liquid atomic force microscopy on muscovite mica. High resolution imaging confirmed the integrity of the SAKe protein upon adsorption on the solid-liquid interface. These results showcase the SAKe protein as a platform for the further engineering of functional protein-based two-dimensional materials.

bioengineering↗

bioRxiv2024

1-Aminocyclopropane-1-carboxylic acid oxidase determines the fate of ethylene biosynthesis in a tissue-specific way to fine-tune development and stress resilience

Ethylene is involved in several developmental processes and responses towards (a)biotic stress. In seed plants, ethylene is produced from its precursor 1-aminocyclopropane-1-carboxylic acid (ACC) by the enzyme ACC-oxidase (ACO). Despite its key role in ethylene synthesis, the ACO gene family has not yet been fully characterized. We investigated the five ACO members of Arabidopsis thaliana and revealed a tissue-and developmentally specific expression pattern. Furthermore, the five ACO enzymes each have a different capacity to produce ethylene. Combined, this allows for a precise spatial and temporal regulation of ethylene synthesis. At the sub-cellular level, we uncovered that ACOs reside in the cytosol, where ethylene is likely synthesized, but surprisingly also in the nucleus. Using reverse genetics of single and higher order aco mutants we revealed a high degree of gene redundancy and minimal phenotypes. A lack of ethylene synthesis by knocking out all five ACOs did not impair normal vegetative and generative development but did influence processes associated with high rates of ethylene production such as petal abscission. This suggests that ethylene is not a prime regulator of development, but more a moderator. We also showed that the inability to synthesize ethylene impairs some abiotic (nutrient deficiency and metal toxicity) and biotic (Botrytis cinerea) stress responses, similar as plants insensitive towards ethylene, corroborating the role of ethylene in mediating stress responses. In conclusion, the ACO gene family enables plants to fine-tune their ethylene synthesis rates, but a lack their off is not crucial for normal development and stress survival.

plant biology↗

bioRxiv2022

Intracellular BAPTA directly inhibits PFKFB3, thereby impeding mTORC1-driven Mcl-1 translation and killing Mcl-1-addicted cancer cells

Intracellular Ca2+ signals control several physiological and pathophysiological processes. The main tool to chelate intracellular Ca2+ is intracellular BAPTA (BAPTAi), usually introduced into cells as a membrane-permeant acetoxymethyl ester (BAPTA-AM). We previously demonstrated that BAPTAi enhanced apoptosis induced by venetoclax, a Bcl-2 antagonist, in diffuse large B-cell lymphoma (DLBCL). These findings implied a novel interplay between intracellular Ca2+ signaling and anti-apoptotic Bcl-2 function. Hence, we set out to identify the underlying mechanisms by which BAPTAi enhances cell death in B-cell cancers. In this study, we observed that BAPTAi alone induced apoptosis in lymphoma cell models that were highly sensitive to S63845, an Mcl-1 antagonist. BAPTAi provoked a rapid decline in Mcl-1 protein levels by inhibiting mTORC1-driven MCL-1 translation. Overexpression of nondegradable Mcl-1 rescued BAPTAi-induced cell death. We further examined how BAPTAi diminished mTORC1 activity and found that BAPTAi impaired glycolysis by directly inhibiting 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3) activity, an up to now unkown effect of BAPTAi. All aforementioned effects of BAPTAi were also elicited by a BAPTAi analog with low affinity for Ca2+. Thus, our work reveals PFKFB3 inhibition as an unappreciated Ca2+-independent mechanism by which BAPTAi impairs cellular metabolism and ultimately the survival of Mcl-1-dependent cancer cells. Our work has two important implications. First, direct inhibition of PFKFB3 emerged as a key regulator of mTORC1 activity and a promising target in the treatment of Mcl-1-dependent cancers. Second, cellular effects caused by BAPTAi are not necessarily related to Ca2+ signaling. Our data support the need for a reassessment of the role of Ca2+ in cellular processes when findings were based on the use of BAPTAi.

cell biology↗

bioRxiv2022

A widely applicable and cost-effective method for general and specific RNA-protein complex isolation

Despite important methodological advances made in the past few years, a widely applicable, cost-effective and easily scalable procedure that can be routinely used to isolate ribonucleoprotein complexes (RNPs) remains elusive. We describe a versatile method that connects aspects of existing methods in a workflow optimized to reach the above goals and called it "Silica-based Acidic Phase Separation (SAPS)-capture". To validate the method, the 18S rRNP of S. cerevisiae was captured. To illustrate its applicability, we isolated a repertoire of RNPs in A. thaliana. This procedure can provide the community with a powerful tool to advance the study of ribonomes and RNPs in any organism or tissue type.

molecular biology↗

bioRxiv2021

Structure and Stability of the designer protein WRAP-T and its permutants

{beta}-Propeller proteins are common natural disc-like pseudo-symmetric proteins that contain multiple repeats ( blades) each consisting of a 4-stranded anti-parallel {beta}-sheet. So far, 4- to 12-bladed {beta}-propellers have been discovered in nature showing large functional and sequential variation. Using computational design approaches, we created perfectly symmetric {beta}-propellers out of natural pseudo-symmetric templates. These proteins are useful tools to study protein evolution of this very diverse fold. While the 7-bladed architecture is the most common, no symmetric 7-bladed monomer has been created and characterized so far. Here we describe such a engineered protein, based on a highly symmetric natural template, and test the effects of circular permutation on its stability. Geometrical analysis of this protein and other artificial symmetrical proteins reveals no systematic constraint that could be used to help in engineering of this fold, and suggests sequence constraints unique to each {beta}-propeller sub-family.

biophysics↗