The promotion of secondary structures in single-stranded DNA by drugs that bind to duplex DNA: an atomic force microscopy study

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Aerolysin‐like proteins are a family of pore‐forming toxins with potential biotechnological applications as nanopore sensors for biomolecular detection and sequencing. Despite their conserved structural fold, the low sequence identity complicates sequence ...

Low-dimensional materials exhibiting stable magnetic ordering are interesting from a fundamental point of view as well as for future application in information technologies. Metalorganic magnets, created by linking metal atoms with specific organic molecul ...

We demonstrate the reversible control of interactions between a local molecular spin, hosted within an iron phthalocyanine (FePc) molecule, and the conduction electrons of a supporting Au(111) surface. Using the tip of a scanning tunneling microscope, we d ...

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

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 ...

Recently, single-particle cryo-electron microscopy emerged as a technique capable of determining protein structures at near-atomic resolution and resolving protein dynamics with a temporal resolution ranging from second to milliseconds. This thesis describ ...

The invention of 3D atomic force microscopy (3D-AFM) has enabled visualizing subnanoscale 3D hydration structures. Meanwhile, its applications to imaging flexible molecular chains have started to be experimentally explored. However, the validity and princi ...

Transmembrane protein 16 F (TMEM16F) is a Ca2+-activated homodimer which functions as an ion channel and a phospholipid scramblase. Despite the availability of several TMEM16F cryogenic electron microscopy (cryo-EM) structures, the mechanism of activation ...

The alloying of two-dimensional (2D) transition metal dichalcogenides (TMDs) is an established route to produce robust semiconductors with continuously tunable optoelectronic properties. However, typically reported methods for fabricating alloyed 2D TMD na ...

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 ...

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

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 ...

BackgroundAging in postmitotic tissues is associated with clonal expansion of somatic mitochondrial deletions, the origin of which is not well understood. Such deletions are often flanked by direct nucleotide repeats, but this alone does not fully explain ...

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

All coronaviruses are characterized by spike glycoproteins whose S1 subunits contain the receptor binding domain (RBD). The RBD anchors the virus to the host cellular membrane to regulate the virus transmissibility and infectious process. Although the prot ...

We study the plasmon modes of gold nanorods (as short as similar to 100 nm) on a nonmetallic conductive substrate using scanning tunneling microscope-induced light emission (STM-LE) with a nonplasmonic tungsten tip at room temperature in high vacuum (10-7 ...

Engineering protein biosensors that sensitively respond to specific biomolecules by triggering precise cellular responses is a major goal of diagnostics and synthetic cell biology. Previous biosensor designs have largely relied on binding structurally well ...

The local physical properties - such as shape and flexibility - of the DNA double-helix is today widely believed to be influenced by nucleic acid sequence in a non-trivial way. Furthermore, there is strong evidence that these properties play a role in many ...

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 ...

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 ...

The promotion of secondary structures in single-stranded DNA by drugs that bind to duplex DNA: an atomic force microscopy study

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Exploring New Nanopore Sensors from the Aerolysin Family

2D Metalorganic Ferromagnets

Engineering Spin Interaction Channels of FePc on Au(111)

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

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

Microsecond Time-Resolved Cryo-Electron Microscopy

Revealing the Mechanism Underlying 3D-AFM Imaging of Suspended Structures by Experiments and Simulations

Structural heterogeneity of the ion and lipid channel TMEM16F

Composition-tunable transition metal dichalcogenide nanosheets via a scalable, solution-processable method

Predicting protein interactions using geometric deep learning on protein surfaces

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

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

Secondary structure of the human mitochondrial genome affects formation of deletions

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Secondary Structures of MERS-CoV, SARS-CoV, and SARS-CoV-2 Spike Proteins Revealed by Infrared Vibrational Spectroscopy

Selectively Exciting and Probing Radiative Plasmon Modes on Short Gold Nanorods by Scanning Tunneling Microscope-Induced Light Emission

Computational design of dynamic receptor—peptide signaling complexes applied to chemotaxis

Landscapes of DNA Mechanics and Genomes

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

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