Related papers: Protein structure, activity and thermal stability …
The molecular mechanism of the solvent motion that is required to instigate the protein structural relaxation above a critical hydration level or transition temperature has yet to be determined. In this work we use quasi-elastic neutron…
We present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the…
We argue that protein native state structures reside in a novel "phase" of matter which confers on proteins their many amazing characteristics. This phase arises from the common features of all globular proteins and is characterized by a…
Protein crystal production is a major bottleneck for the structural characterisation of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy…
Because final properties of nanoscale polymeric structures are largely determined by the solid-state microstructure of the confined polymer, it is imperative not only to understand how the microstructure of polymers develops under nanoscale…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…
In this paper we present a review on our recent experimental investigations into the phase behavior of the deeply cooled water confined in a nanoporous silica material, MCM-41, with elastic neutron scattering technique. Under such strong…
We examine changes in the picosecond structural dynamics with irreversible photobleaching of red fluorescent proteins mCherry, mOrange2 and TagRFP-T. Measurements of the protein dynamical transition using terahertz time-domain spectroscopy…
Water is essential for almost every aspect of life on our planet and, unsurprisingly, its properties have been studied in great detail. However, disproportionately little remains known about the electrical properties of interfacial and…
Proteins have evolved through mutations, amino acid substitutions, since life appeared on Earth, some 109 years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function,…
In this work we employ various methods of analysis (unfolding simulations and comparative analysis of structures and sequences of proteomes of thermophilic organisms) to show that organisms can follow two major strategies of thermophilic…
In this Communication we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein…
The time evolution of temperatures of anisotropic nanoparticles in two and three-body systems are simulated for various relative orientations. Nanoparticles are immersed in a thermal bath at constant temperature. It is shown that in…
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…
We present a versatile setup for investigating the nanofluidic behavior of nanoparticles as a function of the gap distance between two confining surfaces. The setup is designed as an open system which operates with small amounts of…
Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been…
In view of the notorious complexity of protein--protein interactions, simplified models of proteins treated as patchy particles offer a promising strategy to obtain insight into the mechanism of crystallization. Here we report…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
Numerical simulations of hydrated proteins show that protein hydration shells are polarized into a ferroelectric cluster with a large magnitude of its average dipole moment. The emergence of this new mesophase dramatically alters the…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…