Related papers: Space Layout of Low-entropy Hydration Shells Guide…
Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and…
Based on recent studies on hydrophobic interactions, it is devoted to investigate the directional nature of hydrophobic interactions. It means that the hydrophobic interactions are dependent on the relative orientations as the solutes tend…
We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
A protein is a linear chain containing a set of amino acids, which folds on itself to create a specific native structure, also called the minimum energy conformation. It is the native structure that determines the functionality of each…
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins.…
Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of…
Motion of protein drops on crystallization media during routine handling is a major factor affecting the reproducibility of crystallization conditions. Drop stability can be enhanced by chemical patterning to more effectively pin the drop's…
A theoretical approach is developed to quantify hydrophobic hydration and interactions on a molecular scale, with the goal of gaining insight into the molecular origins of hydrophobic effects. The model is based on the fundamental relation…
Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…
This paper considers a broadly biologically relevant question of a chain (such as a protein) binding to a sequence of receptors with matching multiple ligands distributed along the chain. This binding is critical in cell adhesion events,…
H-bonds are known to play an important role in the folding of proteins into three-dimensional structures, which in turn determine their diverse functions. The conformations around H-bonds are important, in that they can be non-local along…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
We develop a simple correspondence between hydrophobic surface topology of globular proteins and and an effective protein-protein adhesiveness parameter of the Baxter type. We discuss within this framework analytical interpretation of the…
We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In particular, we suggest considering sulfur atoms contained in…
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…
Studies of liquid water in its supercooled region have led to many insights into the structure and behavior of water. While bulk water freezes at its homogeneous nucleation temperature of approximately 235 K, for protein hydration water,…