Stabilization strategies in biomass depolymerization using chemical functionalization

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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 ...

In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

Organic solvents are ubiquitous in industrial and domestic applications from the production of pharmaceuticals to household consumer products. The negative impact of most traditional solvents, especially aprotic types, on the environment, health, and safet ...

Polymers play a central role in shaping our world across various fields, but their heavy reliance on petrochemicals poses climate change, environmental and health risks. To address and alleviate these issues, transitioning to sustainable polymers, sourced ...

As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...

The synthesis of complex sugars is a key aspect of microbial biology. Cyclic beta-1,2-glucan (C beta G) is a circular polysaccharide critical for host interactions of many bacteria, including major pathogens of humans (Brucella) and plants (Agrobacterium). ...

Solving native structures of such large molecules, like biomolecules, is often challenging, particularly due to the potentially infinite number of non-covalent interactions with water. In this thesis, we report the use of cold ion gas-phase action spectros ...

The rapid progress in the field of deep learning has had a significant impact on protein design. Deep learning methods have recently produced a breakthrough in protein structure prediction, leading to the availability of high-quality models for millions of ...

The current reliance on limited petrochemical resources and the resulting ecological outcomes have made the exploration of alternative chemical and energy feedstocks invaluable. As such, the development of sustainable processes with a less harmful total en ...

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

In my thesis, I present an investigation of the dissociation reactions of gas phase molecules on single crystal metal surfaces studied by a molecular beam in combination with Reflection Absorption Infrared Spectroscopy (RAIRS). Two gas/surface systems were ...

Platform chemicals, also known as chemical building blocks, are substances that serve as starting materials for the synthesis of various value-added products, which find a wide range of applications. These chemicals are the key ingredients for many fine an ...

The geometry of biomolecules isolated in the gas phaseusuallydiffers substantially from their native structures in aqueous solution,which are the only ones truly relevant to life science. To connectthe high resolution of cold ion spectroscopy that can be a ...

Carbohydrates are the most abundant organic material on Earth and the structural "material of choice" in many living systems. Nevertheless, design and engineering of synthetic carbohydrate materials presently lag behind that for protein and nucleic acids. ...

Atomic force microscopy (AFM) is capable of nanoscale imaging but has so far only been used on cell surfaces when applied to a living cell. Here, we describe a step-by-step protocol for nanoendoscopy-AFM, which enables the imaging of nanoscale structures i ...

Alkynes are found in a multitude of natural or synthetic bioactive compounds. In addition to the capacity of these chemical motifs to impact the physicochemical properties of a molecule of interest, the well-established reactivity of alkynes makes them ide ...

Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. This k ...

Protein-protein interactions (PPIs) are responsible for regulating many biological processes in human bodies. PPIs often have a large binding site and often interact through an alpha helical segment. Therefore, the inhibition of PPIs can be difficult using ...

Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native conformation of glob ...

Following the hugely successful application of deep learning methods to protein structure prediction, an increasing number of design methods seek to leverage generative models to design proteins with improved functionality over native proteins or novel str ...

Stabilization strategies in biomass depolymerization using chemical functionalization

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Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Predicting protein interactions using geometric deep learning on protein surfaces

Development of Sustainable Carbohydrate-Based Solvents by Acetal Functionalisation of Biomass

New Polymers from Biomass-Derived Hydroxycinnamic Acid Derivatives

Development of tools and methods for protein identification: From single molecules to in vivo applications

Structure-function analysis of the cyclic β-1,2-glucan synthase from Agrobacterium tumefaciens

Bridging Native and Intrinsic Structures of Microhydrated Biomolecules by Cold Ion Spectroscopy

A new age in protein design empowered by deep learning

Separable Brønsted acidic imidazolium salts for polysaccharide hydrolysis in water

De novo designed proteins: a study in engineering novel folds and functions

Gas/Surface reactions probed by reflection absorption infrared spectroscopy

An Overview of Heterogeneous Catalysts Based on Hypercrosslinked Polystyrene for the Synthesis and Transformation of Platform Chemicals Derived from Biomass

Revealing the Structure of Tryptophan in Microhydrated Complexes by Cold Ion Spectroscopy

Visualizing Chiral Interactions in Carbohydrates Adsorbed on Au(111) by High-Resolution STM Imaging

Protocol for live imaging of intracellular nanoscale structures using atomic force microscopy with nanoneedle probes

Hypervalent Iodine: New Reagents and Functionalization of Peptides

De novo design of protein interactions with learned surface fingerprints

Synthesis and application of bifunctional hypervalent iodine reagents for peptide modification

Molten globule-like transition state of protein barnase measured with calorimetric force spectroscopy

Deep learning approaches for conformational flexibility and switching properties in protein design