Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies

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The polyQ expansion in huntingtin protein (HTT) is the prime cause of Huntington's disease (HD). The recent cryoelectron microscopy (cryo-EM) structure of HTT-HAP40 complex provided the structural information on its HEAT-repeat domains. Here, we present an ...

Proteins' biological functions are defined by the geometric and chemical structure of their 3D molecular surfaces. Recent works have shown that geometric deep learning can be used on mesh-based representations of proteins to identify potential functional s ...

The topic of this thesis is the development of new reconstruction methods for cryo-electron microscopy (cryo-EM). Cryo-EM has revolutionized the field of structural biology over the last decade and now permits the regular discovery of biostructures. Yet, t ...

Non-covalent interactions are ubiquitous in nature. The diversity and functionality of these interactions are employed by nature as a universal tool for building the molecular mechanism of life. Although weak, these interactions play a key role in both for ...

The regulation of several processes inside and outside the cell depends on the action of a particular class of enzymes, called allosteric. In allosteric macromolecules, binding a ligand at one site affects the binding activity at a distal functional site, ...

Centrioles are evolutionarily conserved multi-protein organelles essential for forming cilia and centrosomes. Centriole biogenesis begins with self-assembly of SAS-6 proteins into 9-fold symmetrical ring polymers, which then stack into a cartwheel that sca ...

The control of molecular systems by electrical charge or light is a prerequisite for their application in nanoelectronics. Such potential has been uniquely exploited in quinone-based resorcin[4]arene cavitands that can act as molecular grippers, reversibly ...

The work presented in this thesis focused on the synthesis and characterization of new metalloligands based on iron(II) clathrochelate complexes. Clathrochelates can be functionalized peripherally with donor groups capable of coordinating metal ions. The s ...

Understanding the structure of a protein complex is crucial in determining its function. However, retrieving accurate 3D structures from microscopy images is highly challenging, particularly as many imaging modalities are two-dimensional. Recent advances i ...

Immense field enhancement and nanoscale confinement of light are possible within nanoparticle-on-mirror (NPoM) plasmonic resonators, which enable novel optically activated physical and chemical phenomena and render these nanocavities greatly sensitive to m ...

Energy piles are shallow geothermal systems integrated into structures already required for structural functions of civil works that provide both geothermal energy supply and structural support to the built environments. This research work is driven by the ...

Supramolecular assemblies with controlled morphology are of paramount importance for energy transport in organic semiconductors. Despite considerable freedom in molecular design, the preparation of dyes that form one dimensional J-aggregates is challenging ...

Narrow-band photoluminescence (PL) together with high quantum efficiency from organic molecules is essential for high-color-purity emitters. Supramolecular assemblies like J-aggregates are promising materials due to their narrow PL signal with full-width a ...

Predicting interactions between proteins and other biomolecules solely based on structure remains a challenge in biology. A high-level representation of protein structure, the molecular surface, displays patterns of chemical and geometric features that fin ...

Protein structure is tightly intertwined with function according to the laws of evolution. Understanding how structure determines function has been the aim of structural biology for decades. Here, we have wondered instead whether it is possible to exploit ...

BackgroundLarge-scale datasets of protein structures and sequences are becoming ubiquitous in many domains of biological research. Experimental approaches and computational modelling methods are generating biological data at an unprecedented rate. The deta ...

Protein dynamics is undoubtedly a pervasive ingredient in all biological functions. However, structural biology has been strongly driven by a static-centered view of protein architecture. We argue that the recent advances of cryo-electron microscopy (EM) h ...

Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies

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The Polyglutamine Expansion at the N-Terminal of Huntingtin Protein Modulates the Dynamic Configuration and Phosphorylation of the C-Terminal HEAT Domain

Fast end-to-end learning on protein surfaces

Reconstruction Methods for Cryo-Electron Microscopy: From Model-based to Data-driven

Structural and analytical identifications of biomolecules by cold ion spectroscopy of non-covalent complexes

Mechanics and co-evolution of allosteric materials and proteins

Tuning SAS-6 architecture with monobodies impairs distinct steps of centriole assembly

Spectro-electrochemical toolbox for monitoring and controlling quinone-mediated redox-driven molecular gripping

Synthesis and Characterization of Coordination Cages Based on Clathrochelate Metalloligands

3D Structure From 2D Microscopy Images Using Deep Learning

Structural Order of the Molecular Adlayer Impacts the Stability of Nanoparticle-on-Mirror Plasmonic Cavities

Cyclic thermomechanical behaviour of pile-soil interface and design methods for energy pile foundations

Excitonic channels from bio-inspired templated supramolecular assembly of J-aggregate nanowirest

Exciton Dynamics and Effects of Structural Order in Morphology-Controlled J-Aggregate Assemblies

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning

Protein Structural Information and Evolutionary Landscape by In Vitro Evolution

rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics

Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction?