Related papers: Watching Single Unmodified Enzymes at Work
The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein…
Many fundamental biological processes are regulated by protein-DNA complexes called {\it synaptosomes}, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation remain not…
Concentrated aqueous solutions of the protein lysozyme undergo a liquid solid transition upon a temperature quench into the unstable spinodal region below a characteristic arrest temperature of Tf=15C. We use video microscopy and…
Actin is one of the most studied cytoskeleton proteins showing a very rich span of structures. It can self-assemble actively into dynamical structures that govern the mechanical properties of the cell, its motility and its division.…
We consider self-assembly of proteins into a virus capsid by the methods of molecular dynamics. The capsid corresponds either to SPMV or CCMV and is studied with and without the RNA molecule inside. The proteins are flexible and described…
Biocatalysis is an emerging field that provides an environmentally friendly alternative to conventional catalysis, but still it faces some challenges. One of the major difficulties for biocatalysts that require reactive species like H2O2 as…
Normal mode analysis is a widely used technique for reconstructing conformational changes of proteins from the knowledge of native structures. In this Letter, we investigate to what extent normal modes capture the salient features of the…
We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
Controlling polymorphism in molecular crystals is crucial in the pharmaceutical, dye, and pesticide industries. However, its theoretical description is extremely challenging, due to the associated long timescales ($ > 1 \, \mu s$). We…
The determination of a 'folding core' can help to provide insight into the structure, flexibility, mobility and dynamics, and hence, ultimately, function of a protein - a central concern of structural biology. Changes in the folding core…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
The new equimolar mixture comprises liquid crystalline compounds MHPOBC and partially fluorinated 3F2HPhF6. The phase sequence of the mixture is determined by differential scanning calorimetry, polarizing optical microscopy, X-ray…
Protein functions in cells may be activated or modified by the attachment of several kinds of chemical groups. While protein phosphorylation, i.e. the attachment of a phosphoryl (PO$_3^-$) group, is the most studied form of protein…
Phase-separated biomolecular condensates exhibit a wide range of dynamical properties, which depend on the sequences of the constituent proteins and RNAs. However, it is unclear to what extent condensate dynamics can be tuned without also…
Understanding the fundamental mechanisms of single-atom catalysis (SAC) is important to design systems with improved performance and stability. This is problematic, however, because single-atom active sites are extremely difficult to…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
Crystallization of proteins, specifically proteins of medical relevance, is performed for various reasons such as to understand the protein structure and to design therapies. Obtaining kinetic constants in rate laws for nucleation and…
Proteins must bind to specific other proteins in vivo in order to function. The proteins must bind only to one or a few other proteins of the of order a thousand proteins typically present in vivo. Using a simple model of a protein,…
Quantum mechanical phenomena, such as electronic coherence and entanglement, play a key role in achieving the unrivalled efficiencies of light-energy conversion in natural photosynthetic light-harvesting complexes, and triggered the growing…
The $\beta$-relaxation associated with the sub-glass transition temperature ($T_{\text{g},\beta}$) is attributed to fast, localised molecular motions which can occur below the primary glass transition temperature ($T_{g\alpha}$). Despite…