Related papers: Nanopores -- a Versatile Tool to Study Protein Dyn…
Intensive concerns about the biosafety of nanomaterials demand the systematic study of the mechanisms about their biological effects. Many biological effects can be attributed to the interaction of nanomaterials with protein and their…
Despite significant progress in static protein structure collection and prediction, the dynamic behavior of proteins, one of their most vital characteristics, has been largely overlooked in prior research. This oversight can be attributed…
Cell-based biosensors constitute a fundamental tool in biotechnology, and their relevance has greatly increased in recent years as a result of a surging demand for reduced animal testing and for high-throughput and cost-effective in vitro…
What can cells gain by using disordered, rather than folded, proteins in the architecture of their skeleton? Disordered proteins take multiple co-existing conformations, and often contain segments which act as random-walk-shaped polymers.…
Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the last few years fold-change detecting mechanisms, based on transcriptional networks, have been…
Solid-state nanopores, nm-sized holes in thin, freestanding membranes, are powerful single-molecule sensors capable of interrogating a wide range of target analytes, from small molecules to large polymers. Interestingly, due to their high…
Advanced photonic tools may enable researchers and clinicians to visualize, track, control and manipulate biological processes at the single-cell level in space and time. Biological systems are complex and highly organized on both spatial…
Solid-state nanopores are emerging platforms for single-molecule protein sequencing due to their tolerance to hash physiology environment and compatibility with different electrical and optical detection methods. However, they suffer from…
The interaction of proteins with small molecules is fundamental to their function in living organisms and it is widely studied in drug development. Here we compare optical trapping dynamics of streptavidin and biotinylated streptavidin…
Neural probes are in vivo invasive devices that combine electrophysiology and optogenetics to gain insight into how the brain operates, down to the single neuron and its network activity. Their integration of stimulation sites and sensors…
Intracellular access with high spatiotemporal resolution can enhance our understanding of how neurons or cardiomyocytes regulate and orchestrate network activity, and how this activity can be affected with pharmacology or other…
Learning from nature's amazing molecular machines, globular proteins, we present a framework for the predictive design of nano-machines. We show that the crucial ingredients for a chain molecule to behave as a machine are its inherent…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Analyzing the physical and chemical properties of single DNA based molecular machines such as polymerases and helicases often necessitates to track stepping motion on the length scale of base pairs. Although high resolution instruments have…
Nitrogen-vacancy (NV) based quantum sensors hold great potential for real-time single-cell sensing with far-reaching applications in fundamental biology and medical diagnostics. Although highly sensitive, the mapping of quantum measurements…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
Based on our formulation of the DNA electrophoresis near a pore [P. Rowghanian and A. Y. Grosberg, Phys. Rev. E 87, 042723 (2013)], we address the electrophoretic DNA capture into a nanopore as a steady-state process of particle absorption…
The capability of accurate prediction of protein functions and properties is essential in the biotechnology industry, e.g. drug development and artificial protein synthesis, etc. The main challenges of protein function prediction are the…