Publication
The N-Terminal Region of Yeast Protein Phosphatase Ppz1 Is a Determinant for Its Toxicity
Publications associées (36)
Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions
Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...
EPFL2024Protein target highlights in CASP15: Analysis of models by structure providers
Bruno Lemaitre, Luciano Andres Abriata, Samuel Rommelaere, Kuan-Lin Wu, Han Xiao
We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the su ...
WILEY2023A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer
Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...
EPFL2023Systems and methods for de novo design of protein interactions with learned surface fingerprints
Michael Bronstein, Pablo Gainza Cirauqui, Zander Harteveld, Andreas Scheck, Anthony Marchand, Sarah Wehrle, Freyr Sverrisson, Alexandra Krina Van Hall-Beauvais
The present application relates to a computer-implemented systems and methods for protein interaction design using surface fingerprints. The method comprises predicting at least one target interface site with high binding propensity, wherein, optionally, t ...
2023Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions
The sheer size of the protein sequence space is massive: a protein of 100 residues can have 20^100 possible sequence combinations; and knowing that this exceeds the number of atoms in the universe, the chance of randomly discovering a stable new sequence w ...
EPFL2022Chromatin Proteomics to Study Epigenetics - Challenges and Opportunities
Regulation of gene expression is essential for the functioning of all eukaryotic organisms. Understanding gene expression regulation requires determining which proteins interact with regulatory elements in chromatin. MS-based analysis of chromatin has emer ...
AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC2021Alternative dimerization is required for activity and inhibition of the HEPN ribonuclease RnlA
The rnlAB toxin-antitoxin operon from Escherichia co/ifunctions as an anti-phage defense system. RnlA was identified as a member of the HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding domain) superfamily of ribonucleases. The activity of the tox ...
OXFORD UNIV PRESS2021Computational design of highly signaling active membrane receptors through de novo solvent-mediated allosteric networks
Jian Wang, Patrick Daniel Barth
Protein catalysis and allostery require the atomic-level orchestration and motion of residues, ligand, solvent and protein effector molecules, but the ability to design protein activity through precise protein-solvent cooperative interactions has not been ...
2021Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization
Matteo Dal Peraro, Luciano Andres Abriata
Continuous assessment of transferable forcefields for molecular simulations is essential to identify their weaknesses and direct improvement efforts. The latest efforts focused on better describing disordered proteins while retaining proper description of ...
2021Porous silicon-A versatile platform for mass-production of ultrasensitive SERS-active substrates
Surface-enhanced Raman scattering (SERS) spectroscopy is one of the most prospective methods combining state-of-the-art nanomaterials and optical techniques for highly sensitive express-analysis and detection of organic and bioorganic objects in liquids an ...
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