Related papers: Functionality and Protein-Water Interactions
Inherent structure theory is used to discover strong connections between simple characteristics of protein structure and the energy landscape of a Go model. The potential energies and vibrational free energies of inherent structures are…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
Despite recent breakthroughs in understanding how protein sequence relates to structure and function, considerably less attention has been paid to the general features of protein surfaces beyond those regions involved in binding and…
The coffee-ring effect is a universal feature of evaporating sessile droplets with pinned contact line, wherein solutes or particles are advected to the droplet's edge due to evaporation-driven flows. While existing models have successfully…
We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…
Water ice's remarkable properties make it an important material across a range of disciplines. The combination of covalent and hydrogen bonds form a long-range lattice of oxygens, which hosts a disordered yet correlated hydrogen network. We…
A fascinating and open question challenging biochemistry, physics and even geometry is the presence of highly regular motifs such as alpha-helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from…
Biological membranes mainly consist of lipids and proteins. While the proteins have many functions as single molecules, the membrane as a whole displays physical properties that cannot be explained on the single molecule level. For example,…
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…
The mobility of water molecules confined in a silica pore is studied by computer simulation in the low hydration regime, where most of the molecules reside close to the hydrophilic substrate. A layer analysis of the single particle dynamics…
Interfaces are a most common motif in complex systems. To understand how the presence of interfaces affect hydrophobic phenomena, we use molecular simulations and theory to study hydration of solutes at interfaces. The solutes range in size…
A variety of neurodegenerative diseases are associated with the formation of amyloid plaques. Our incomplete understanding of this process underscores the need to decipher the principles governing protein aggregation. Most experimental and…
The main chain dihedral angles play an important role to decide the protein conformation. The native states of a protein can be regard as an ensemble of a lot of similar conformations, in different conformations the main chain dihedral…
The hydrophobic effect (HE) is commonly associated with the demixing of oil and water at ambient conditions and plays the leading role in determining the structure and stability of biomolecular assembly in aqueous solutions. On the…
Liquid water is reluctant to lose hydrogen-bond coordination. Here we reveal that it also demands contraction and reorientation of the second molecular shell to compensate for coordination defects. Such molecular principle will be shown to…
The water dynamics, as characterized by the local hydrophobicity (LH), is investigated for tetrameric hemoglobin and dimeric melittin. For the T0 to R0 transition in Hb it is found that LH provides additional molecular-level insight into…
The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal…
The role of the rigidity of a peptide chain in its equilibrium dynamics is investigated within a realistic model with stringent microscopically derived coupling interaction potential and effective on-site potential. The coupling interaction…
The water hydration shell has decisive impact on the structural and functional properties of RNA. Changes of RNA structure upon melting and in biochemical processes are accompanied by a change of hydration patterns, a process which is…
Confinement can modify the dynamics, the thermodynamics and the structural properties of liquid water, the prototypical anomalous liquid. By considering a general anomalous liquid, suitable for globular proteins, colloids or liquid metals,…