Wim Vranken

Wim Vranken
Vrije Universiteit Brussel | VUB · Department of Applied Biological Sciences

Ph.D.

About

147
Publications
24,365
Reads
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9,593
Citations
Citations since 2016
60 Research Items
6010 Citations
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201620172018201920202021202202004006008001,000
201620172018201920202021202202004006008001,000
Additional affiliations
February 2018 - present
Vrije Universiteit Brussel
Position
  • General chemistry, 2nd semester
Description
  • General chemistry for biology and geography, 2nd semester of first year course.
February 2015 - present
Université Libre de Bruxelles
Position
  • Bioinformatician
Description
  • NMR structure calculation and protein disorder prediction
March 2014 - present
Vrije Universiteit Brussel
Position
  • Managing Director
Education
September 1992 - December 1996
Ghent University
Field of study
  • Chemistry

Publications

Publications (147)
Article
Full-text available
Protein function and dynamics are closely related; however, accurate dynamics information is difficult to obtain. Here based on a carefully assembled data set derived from experimental data for proteins in solution, we quantify backbone dynamics properties on the amino-acid level and develop DynaMine-a fast, high-quality predictor of protein backbo...
Article
Full-text available
As methods for analysis of biomolecular structure and dynamics using nuclear magnetic resonance spectroscopy (NMR) continue to advance, the resulting 3D structures, chemical shifts, and other NMR data are broadly impacting biology, chemistry, and medicine. Structure model assessment is a critical area of NMR methods development, and is an essential...
Article
Secretory preproteins of the Sec pathway are targeted post-translationally and cross cellular membranes through translocases. During cytoplasmic transit, mature domains remain non-folded for translocase recognition/translocation. After translocation and signal peptide cleavage, mature domains fold to native states in the bacterial periplasm or traf...
Article
Full-text available
Traditionally, our understanding of how proteins operate and how evolution shapes them is based on two main data sources: the overall protein fold and the protein amino acid sequence. However, a significant part of the proteome shows highly dynamic and/or structurally ambiguous behavior, which cannot be correctly represented by the traditional fixe...
Preprint
Full-text available
An unambiguous description of an experimental setup and analysis, and the subsequent biological observation is vital for accurate data interpretation and reproducible results. Consequently, experimental analyses should be described in a concise, unequivocal and digestible manner. The aim of minimum information guidelines is to define the fundamenta...
Article
Protein phosphorylation is the most common reversible post-translational modification of proteins and is key in the regulation of many cellular processes. Due to this importance, phosphorylation is extensively studied, resulting in the availability of a large amount of mass spectrometry-based phospho-proteomics data. Here, we leverage the informati...
Preprint
Full-text available
Deep mutational scanning is a powerful approach to investigate a wide variety of research questions including protein function and stability. We performed deep mutational scanning on three essential E. coli proteins (FabZ, LpxC and MurA) involved in cell envelope synthesis using high-throughput CRISPR genome editing. This allowed us to study the ef...
Preprint
Full-text available
Secretory preproteins of the Sec pathway bear signal peptides and are targeted post-translationally to cross the plasma membrane or ER through translocases. After translocation and signal peptide cleavage, mature domains fold to native states in the bacterial periplasm or after further trafficking. During cytoplasmic transit, mature domains must re...
Article
Full-text available
The role of intrinsically disordered protein regions (IDRs) in cellular processes has become increas- ingly evident over the last years. These IDRs continue to challenge structural biology experiments be- cause they lack a well-defined conformation, and bioinformatics approaches that accurately delineate dis- ordered protein regions remain essentia...
Preprint
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas9 protein is an effector that plays a major role in a prokaryotic adaptive immune system, by which invading DNA can be targeted and cut for inactivation. The Cas9 endonuclease is directed to target sites by a guide RNA (gRNA) where Cas9 can recognize specific sequences...
Preprint
Full-text available
Protein phosphorylation is the most common post-translational reversible modification of proteins and is key in the regulation of many cellular processes. Due to this importance, phosphorylation is extensively studied, resulting in the availability of a large amount of mass spectrometry based phospho-proteomics data. Here, we leverage the informati...
Preprint
Full-text available
Many examples are known of regions of intrinsically disordered proteins (IDPs) that fold into α-helices upon binding their globular protein targets. In their unbound state these regions possess a small amount of residual helicity, referred to as pre-folded structure, which has been studied on case by case basis. In order to investigate what determi...
Article
Full-text available
The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological contex...
Article
Full-text available
While transcriptome- and proteome-wide technologies to assess processes in protein biogenesis are now widely available, we still lack global approaches to assay post-ribosomal biogenesis events, in particular those occurring in the eukaryotic secretory system. We here develop a method, SECRiFY, to simultaneously assess the secretability of >105 pro...
Conference Paper
Full-text available
This document is an extended abstract of the paper "Interpreting a black-box predictor to gain insights into early folding mechanisms" published in the Computational and Structural Biotechnology Journal [2]. 1 Motivation Proteins perform a multitude of essential functions in nature. The protein sequence encodes its behavior and, by extension, the e...
Article
Full-text available
Protein folding and function are closely connected, but the exact mechanisms by which proteins fold remain elusive. Early folding residues (EFRs) are amino acids within a particular protein that induce the very first stages of the folding process. High-resolution EFR data are only available for few proteins, which has previously enabled the trainin...
Article
Full-text available
Motivation High-throughput experiments are generating ever increasing amounts of various -omics data, so shedding new light on the link between human disorders, their genetic causes, and the related impact on protein behavior and structure. While numerous bioinformatics tools now exist that predict which variants in the human exome cause diseases,...
Preprint
Full-text available
Motivation High-throughput experiments are generating ever increasing amounts of various -omics data, so shedding new light on the link between human disorders, their genetic causes, and the related impact on protein behavior and structure. While numerous bioinformatics tools now exist that predict which variants in the human exome cause diseases,...
Article
Full-text available
We provide integrated protein sequence-based predictions via https://bio2byte.be/b2btools/. The aim of our predictions is to identify the biophysical behaviour or features of proteins that are not readily captured by structural biology and/or molecular dynamics approaches. Upload of a FASTA file or text input of a sequence provides integrated predi...
Article
Full-text available
Intrinsically disordered proteins, defying the traditional protein structure–function paradigm, are a challenge to study experimentally. Because a large part of our knowledge rests on computational predictions, it is crucial that their accuracy is high. The Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment was establish...
Article
Full-text available
Background The SARS-CoV-2 virus, the causative agent of COVID-19, consists of an assembly of proteins that determine its infectious and immunological behavior, as well as its response to therapeutics. Major structural biology efforts on these proteins have already provided essential insights into the mode of action of the virus, as well as avenues...
Article
Full-text available
One of the most intriguing fields emerging in current molecular biology is the study of membraneless organelles formed via liquid–liquid phase separation (LLPS). These organelles perform crucial functions in cell regulation and signalling, and recent years have also brought about the understanding of the molecular mechanism of their formation. The...
Article
Full-text available
Nanobodies are popular and versatile tools for structural biology. They have a compact single immunoglobulin domain organization, bind target proteins with high affinities while reducing their conformational heterogeneity and stabilize multi-protein complexes. Here we demonstrate that engineered nanobodies can also help overcome two major obstacles...
Preprint
Full-text available
The SARS-CoV-2 virus, the causative agent of COVID-19, consists of an assembly of proteins that determine its infectious and immunological behavior, as well as its response to therapeutics. Major structural biology efforts on these proteins have already provided essential insights into the mode of action of the virus, as well as avenues for structu...
Article
Protein phosphorylation is a key post-translational modification (PTM) in many biological processes and is associated to human diseases such as cancer and metabolic disorders. The accurate identification, annotation and functional analysis of phosphosites is therefore crucial to understand their various roles. Phosphosites (P-sites) are mainly anal...
Preprint
The role of intrinsically disordered protein regions (IDRs) in cellular processes has become increasingly evident over the last years. These IDRs continue to challenge structural biology experiments because they lack a well-defined conformation, and bioinformatics approaches that accurately delineate disordered protein regions remain essential for...
Article
Nuclear magnetic resonance (NMR) spectroscopy data provides valuable information on the behaviour of proteins in solution. The primary data to determine when studying proteins are the per-atom NMR chemical shifts, which reflect the local environment of atoms and provide insights into amino acid residue dynamics and conformation. Within an amino aci...
Article
Intrinsically disordered proteins (IDPs) are proteins whose native functional states represent ensembles of highly diverse conformations. Such ensembles are a challenge for quantitative structure comparisons as their conformational diversity precludes optimal superimposition of the atomic coordinates, necessary for deriving common similarity measur...
Preprint
Full-text available
Intrinsically disordered proteins (IDPs) are proteins whose native functional states represent ensembles of highly diverse conformations. Such ensembles are a challenge for quantitative structure comparisons as their conformational diversity precludes optimal superimposition of the atomic coordinates, necessary for deriving common similarity measur...
Article
Motivation: Protein beta-aggregation is an important but poorly understood phenomena involved in diseases as well as in beneficial physiological processes. However, while this task has been investigated for over 50 years, very little is known about its mechanisms of action. Moreover, the identification of regions involved in aggregation is still a...
Article
Full-text available
Machine learning (ML) is ubiquitous in bioinformatics, due to its versatility. One of the most crucial aspects to consider while training a ML model is to carefully select the optimal feature encoding for the problem at hand. Biophysical propensity scales are widely adopted in structural bioinformatics because they describe amino acids properties t...
Article
Full-text available
The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely n...
Article
Motivation: Eukaryotic cells contain different membrane-delimited compartments, which are crucial for the biochemical reactions necessary to sustain cell life. Recent studies showed that cells can also trigger the formation of membraneless organelles composed by phase-separated proteins to respond to various stimuli. These condensates provide new...
Preprint
Nanobodies (Nbs) are popular and versatile tools for structural biology because they have a compact single immunoglobulin domain organization. Nbs bind their target proteins with high affinities while reducing their conformational heterogeneity, and they stabilize multi-protein complexes. Here we demonstrate that engineered Nbs can also help overco...
Article
Full-text available
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-q...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Preprint
Full-text available
Protein phosphorylation is a key post-translational modification (PTM) in many biological processes, and is associated to human diseases such as cancer and metabolic disorders. The accurate identification, annotation and functional analysis of phosphosites is therefore crucial to understand their various roles. Phosphosites (P-sites) are mainly ana...
Article
Full-text available
Chemical shifts (CS) are determined from NMR experiments and represent the resonance frequency of the spin of atoms in a magnetic field. They contain a mixture of information, encompassing the in-solution conformations a protein adopts, as well as the movements it performs. Due to their intrinsically multi-faceted nature, CS are difficult to interp...
Poster
Full-text available
Scop3P integrates sequences (UniProtKB), structures (PDB), and uniformly reprocessed phosphoproteomics data (PRIDE) to annotate all known human phosphosites. Furthermore, these sites are put into biophysical context by annotating each phosphoprotein with per-residue structural propensity, solvent accessibility, disordered probability, and early fol...
Article
Full-text available
Next generation sequencing technologies are providing increasing amounts of sequencing data, paving the way for improvements in clinical genetics and precision medicine. The interpretation of the observed genomic variants in the light of their phenotypic effects is thus emerging as a crucial task to solve in order to advance our understanding of ho...
Article
Motivation: Evolutionary information is crucial for the annotation of proteins in bioinformatics. The amount of retrieved homologs often correlates with the quality of predicted protein annotations related to structure or function. With a growing amount of sequences available, fast and reliable methods for homology detection are essential, as they...
Article
It’s becoming increasingly challenging to efficiently visualize and extract useful insight from complex and big data sets. JavaScript stands out as a suitable programming choice that offers mature libraries, easy implementation, and extensive customization, all of which stay in the shadow of new and rapid developments in the language. To illustrate...
Preprint
Full-text available
While transcriptome- and proteome-wide technologies to assess processes in protein biogenesis up to the ribosome-associated stages are now widely available, we still lack global approaches to assay post-ribosomal processes, in particular those occurring in the eukaryotic secretory system. We developed SECRiFY to simultaneously assess the secretabil...
Article
Full-text available
Protein folding is a complex process that can lead to disease when it fails. Especially poorly understood are the very early stages of protein folding, which are likely defined by intrinsic local interactions between amino acids close to each other in the protein sequence. We here present EFoldMine, a method that predicts, from the primary amino ac...
Article
Full-text available
The MobiDB (URL: mobidb.bio.unipd.it) database of protein disorder and mobility annotations has been significantly updated and upgraded since its last major renewal in 2014. Several curated datasets for intrinsic disorder and folding upon binding have been integrated from specialized databases. The indirect evidence has also been expanded to better...
Article
Full-text available
Soluble functional proteins may transform into insoluble amyloid fibrils that deposit in a variety of tissues. Amyloid formation is a hallmark of age-related degenerative disorders. Perhaps surprisingly, amyloid fibrils can also be beneficial and are frequently exploited for diverse functional roles in organisms. Here we introduce AmyPro, an open-a...
Article
Full-text available
Motivation: Protein function is directly related to amino acid residue composition and the dynamics of these residues. Centrality analyses based on residue interaction networks permit to identify key residues in a protein that are important for its fold or function. Such central residues and their environment constitute suitable targets for mutage...
Article
Motivation: Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for...
Article
Full-text available
High-throughput sequencing methods are generating enormous amounts of genomic data, giving unprecedented insights into human genetic variation and its relation to disease. An individual human genome contains millions of Single Nucleotide Variants: to discriminate the deleterious from the benign ones, a variety of methods have been developed that pr...
Article
Full-text available
Motivation: Genome sequencing is producing an ever-increasing amount of associated protein sequences. Few of these sequences have experimentally validated annotations, however, and computational predictions are becoming increasingly successful in producing such annotations. One key challenge remains the prediction of the amino acids in a given pro...
Article
Full-text available
The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered pro- teins or regions that exist and function without a well-defined three-dimensional structure...
Article
Full-text available
Next Generation Sequencing is dramatically increasing the number of known protein sequences, with related experimentally determined protein structures lagging behind. Structural bioinformatics is attempting to close this gap by developing approaches that predict structure-level characteristics for uncharacterized protein sequences, with most of the...