Related papers: Correlation between sequence hydrophobicity and su…
What makes a material a good ice nucleating agent? Despite the importance of heterogeneous ice nucleation to a variety of fields, from cloud science to microbiology, major gaps in our understanding of this ubiquitous process still prevent…
We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal…
We investigate the folding behavior of protein sequences by numerically studying all sequences with maximally compact lattice model through exhaustive enumeration. We get the prion-like behavior of protein folding. Individual proteins…
Amide resonance is found to be sensitive to electrostatic field with component parallel or antiparallel to the amide C-N bond, an effect we refer to here as EVPR-CN. EVPR-CN is linear and without threshold in the biologically plausible…
The hydrophobic-polar (HP) model represents proteins as binary strings embedded in lattices, with fold quality measured by an energy score. We prove that the optimal fold energy is not monotonic under concatenation for several standard…
While individual water molecules adsorb strongly on a talc surface (hydrophilic behavior), a droplet of water beads up on the same surface (hydrophobic behavior). To rationalize this dichotomy, we investigate the influence of the…
The local hydration around tetrameric Hb in its T$_0$ and R$_4$ conformational substates is analyzed based on molecular dynamics simulations. Analysis of the local hydrophobicity (LH) for all residues at the $\alpha_1 \beta_2$ and $\alpha_2…
The mechanisms of cold- and pressure-denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here we study several cases of proteins, with or without a unique native state, with or…
Preliminary epidemiologic, phylogenetic and clinical findings suggest that several novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have increased transmissibility and decreased efficacy of several existing…
Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short…
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…
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…
Fundamental studies of the effect of specific ions on hydrophobic interactions are driven by the need to understand phenomena such as hydrophobically driven self-assembly or protein folding. Using beta-peptide-inspired nano-rods, we…
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…
We calculate the ion distributions around an interface in fluid mixtures of highly polar and less polar fluids (water and oil) for two and three ion species. We take into account the solvation and image interactions between ions and…
Drops deposited on rough and hydrophobic surfaces can stay suspended with gas pockets underneath the liquid, then showing very low hydrodynamic resistance. When this superhydrophobic state breaks down, the subsequent wetting process can…
We study a single statistical amphiphilic copolymer chain AB in a selective solvent (e.g.water). Two situations are considered. In the annealed case, hydrophilic (A) and hydrophobic (B) monomers are at local chemical equilibrium and both…
Predicting the three-dimensional (3D) functional structures of proteins remains an important computational milestone in molecular biology to be achieved. This feat is hinged on a clear understanding of the mechanism which proteins use to…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
We model protein folding as a physical stochastic process as follows. The unfolded protein chain is treated as a random coil described by SAW (self-avoiding walk). Folding is induced by hydrophobic forces and other interactions, such as…