Related papers: How Cations Change Peptide Structure
Potassium and sodium ions are crucial for many physiological processes in living systems and play different roles when interacting with proteins and enzymes. Intracellular concentration of potassium is always maintained higher than that of…
We derive structural and binding energy trends for twenty amino acids, their dipeptides, and their interactions with the divalent cations Ca$^{2+}$, Ba$^{2+}$, Sr$^{2+}$, Cd$^{2+}$, Pb$^{2+}$, and Hg$^{2+}$. The underlying data set consists…
Nuclear quantum effects (NQEs) arising from the light mass of hydrogen can influence the structure and stability of hydrogen-bonded biomolecules, yet their role in determining peptide and protein folding remains unclear. Experiments show…
In living organisms, proteins and peptides are often under the influence of mechanical forces, especially in confined spaces such as membrane channels, ribosome exit tunnel, or proteasome gate. Due to the directional nature of proteins as…
Intensive concerns about the biosafety of nanomaterials demand the systematic study of the mechanisms about their biological effects. Many biological effects can be attributed to the interaction of nanomaterials with protein and their…
Electrostatic interactions involving proteins depend not just on the ionic charges involved but also on their chemical identities. Here we examine the origins of incompletely understood differences in the strength of association of…
Post-Translational Modifications (PTMs) are known to play a critical role in the regulation of the protein functions. Their impact on protein structures, and their link to disorder regions have already been spotted on the past decade.…
Peptides play a pivotal role in a wide range of biological activities through participating in up to 40% protein-protein interactions in cellular processes. They also demonstrate remarkable specificity and efficacy, making them promising…
We calculated the effects of structural distortions on the electronic structure of carbon nanotubes. The key modification of the electronic structure brought about by bending a nanotube involves an increased mixing of $\sigma$ and…
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…
Physical properties of colloidal materials can be modified by addition of nanoparticles. Within a model of like-charged mixtures of particles governed by effective electrostatic interactions, we explore the influence of charged…
Cotranslational folding depends on the folding speed and stability of the nascent protein. It remains difficult, however, to predict which proteins cotranslationally fold. Here, we simulate evolution of model proteins to investigate how…
Electronic many-body correlation effects in one-dimensional (1D) systems such as carbon nanotubes have been predicted to modify strongly the nature of photoexcited states. Here we directly probe this effect using broadband elastic light…
If constraints are imposed on a macromolecule, two inequivalent classical models may be used: the stiff and the rigid one. This work studies the effects of such constraints on the Conformational Equilibrium Distribution (CED) of the model…
The thermodynamics of a homopolymeric chain with both Van der Waals and highly-directional hydrogen bond interaction is studied. The effect of hydrogen bonds is to reduce dramatically the entropy of low-lying states and to give raise to…
The effects of cooperativity are studied within Go-Lennard-Jones models of proteins by making the contact interactions dependent on the proximity to the native conformation. The kinetic universality classes are found to remain the same as…
Binding of a ligand on a protein changes the flexibility of certain parts of the protein, which directly affects its function. These changes are not the same at each point, some parts become more flexible and some others become stiffer.…
Weak interactions form the core basis of a vast number of biological processes, in particular, those involving intrinsically disordered proteins. Here, we establish a new technique capable of probing these weak interactions between…
Quantum dot (QD) assemblies are nanostructured networks made from aggregates of QDs and feature improved charge and energy transfer efficiencies compared to discrete QDs. Using first-principles many-body perturbation theory, we…
We study the effect of membrane proteins on the shape, composition and thermodynamic stability of the surrounding membrane. When the coupling between membrane composition and curvature is strong enough the nearby composition and shape both…