Related papers: How Cations Change Peptide Structure
By using single-DNA observation with fluorescence microscopy, we observed the effects of divalent and trivalent cations on the higher-order structure of giant DNA (T4 DNA with 166 kbp). It was found that divalent cations, such as Mg(2+) and…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
The ion-lipid interface in Langmuir monolayers of Dipalmitoylphosphatidylcholine (DPPC) on pure water and 10 mM solutions of Na+ and K+ at different [K+]/[Na+] (a), atom/atom ratios, were studied initially by Surface Pressure (p) versus…
By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that…
Systems in which particles can self-assemble into mono- or bilayers can form variety of stable and metastable structures on a nanometer length scale. For this reason confinement has a particularly strong effect on such systems. We discuss…
Quantum chemical calculations have been employed to investigate the solvation of lithium cations in ethylene carbonate/propylene carbonate and propylene carbonate/dimethyl carbonate mixed electrolytes. The impact of the presence of the…
Biomolecules are complex systems stabilized by a delicate balance of weak interactions, making it important to assess all energetic contributions in an accurate manner. However, it is a priori unclear which contributions make more of an…
We report dynamic Monte Carlo simulation on conformational transition of H-shaped branched polymers by varying main chain (backbone) and side chain (branch) length. H-shaped polymers in comparison with equivalent linear polymers exhibit a…
The consequences of recent experimental finding that hydrogen bonds of the anti-parallel $\beta $-sheet in nonspecific binding site of serine proteases become significantly shorter and stronger synchronously with the catalytic act are…
In this paper we investigate the effects of varying cation valency and concentration on the rheology of entangled lambda DNA solutions. We show that monovalent cations moderately increase the viscoelasticty of the solutions mainly by…
Many variants of RNA, DNA, and even proteins can be considered semiflexible polymers, where bending stiffness, as a type of energetic penalty, competes with attractive van der Waals forces in structure formation processes. Here, we…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
We provide a simple scheme for predicting the electronic structure of van-der-Waals bound systems, based on the mere knowledge of the electronic structure of the subunits. We demonstrate this with the example of nano-peapods, consisting of…
We present a data set from a first-principles study of amino-methylated and acetylated (capped) dipeptides of the 20 proteinogenic amino acids - including alternative possible side chain protonation states and their interactions with…
The stacking of different 2D materials provides a promising approach to realize new states of quantum matter. In this combined scanning tunneling microscopy (STM) and density functional theory (DFT) study we show that the structure in…
The chemical bonding in the carbide core and the surface chemistry in a new group of transition-metal carbides Tin+1Cn-Tx (n=1,2) called MXenes have been investigated by surface-sensitive valence band X-ray photoelectron spectroscopy.…
The aqueous solvent profoundly influences protein folding, yet its effects are relatively poorly understood. In this study, we investigate the impact of solvation on the folding of lattice proteins by using Monte Carlo simulations. The…
A survey is presented of current investigations of the impact of band structure effects on various aspects of the interaction of charged particles with real solids. The role that interband transitions play in the decay mechanism of bulk…
The effects of monovalent (Na+, K+) and divalent (Mg2+, Ca2+, Mn2+) ions on the interaction between DNA and histone are studied using the molecular combing technique. Lamda-DNA molecules and DNA-histone complexes incubated with metal…
We propose the conformon as a quantum of conformational change for energy transfer in alpha-helical proteins. The underlying mechanism of interaction between the quantum of excitation and the conformational degrees of freedom is nonlinear…