Related papers: Molecular glues stabilize water-mediated hydrogen …
The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus…
Protein nanoparticles have been proven to be highly effective stabilizers of water-in-water emulsions obtained from a number of different types of aqueous two-phase systems (ATPS). The stabilizing efficiency of such particles is attributed…
Medical devices with matrix metalloproteinase (MMP) modulating functionality are highly desirable to restore tissue homeostasis in critical inflammation states, such as chronic wounds, rotator cuff tears and cancer. The introduction of…
Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays require computational methods for efficient PPI prediction.…
To understand the mechanism of trimethylamine N-oxide (TMAO) induced stabilization of folded protein states, we systematically investigated the action of TMAO on several model dipeptides (Leucine, L2, Serine, S2, Glutamine, Q2, Lysine, K2,…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
A large number of water models exists for molecular simulations. They differ in the ability to reproduce specific features of real water instead of others, like the correct temperature for the density maximum or the diffusion coefficient.…
The adhesion of cell membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. In this article, we review recent results from simulations and theory that lead to novel insights on how the binding equilibrium…
The interface between hemoglobin (Hb) and its environment, in particular water, is of great physiological relevance. Here, results from {\it in vitro}, {\it in vivo}, and computational experiments (molecular dynamics simulations) are…
Colloidal microgel particles such as poly(N-isopropylacrylamide) (PNIPAM) shrink reversibly in an aqueous medium due to the expulsion of water at a volume phase transition temperature, VPTT $\sim$33$^\circ$C. Romeo et al. [Adv. Mater. 2010,…
Many proteins and peptides have an intrinsic capacity to sense and induce membrane curvature, and play crucial roles for organizing and remodelling cell membranes. However, the molecular driving forces behind these processes are not well…
Arginine has been a mainstay in biological formulation development for decades. To date, the way arginine modulates protein stability has been widely studied and debated. Here, we employed a hydrophobic polymer to decouple hydrophobic…
The function of membrane-embedded proteins such as ion channels depends crucially on their conformation. We demonstrate how conformational changes in asymmetric membrane proteins may be inferred from measurements of their diffusion. Such…
Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this…
In this work we investigate the Fe$_3$O$_4$(001) surface/water interface by combining several theoretical approaches, ranging from a hybrid functional method (HSE06) to density-functional tight-binding (DFTB) to molecular mechanics (MM).…
Locally (re)structuring colloidal gels $\unicode{x2013}$ micron-sized particles forming a connected network with arrested dynamics $\unicode{x2013}$ enables precise tuning of the micromechanical and -rheological properties of the system. A…
Accurately simulating the properties of liquid water remains a central challenge in molecular simulations. In this work, we use machine learning potentials to investigate how the convergence settings of electronic structure calculations…
Thin liquid films with floating active protein machines are considered. Cyclic mechanical motions within the machines, representing microscopic swimmers, lead to molecular propulsion forces applied to the air-liquid interface. We show that,…