Related papers: The atomic-level mechanism underlying the function…
The molecular mechanism of the solvent motion that is required to instigate the protein structural relaxation above a critical hydration level or transition temperature has yet to be determined. In this work we use quasi-elastic neutron…
Predicting the asymmetric structure and dynamics of solvated hydroxide and hydronium in water has been a challenging task from ab initio molecular dynamics (AIMD). The difficulty mainly comes from a lack of accurate and efficient…
Pore-forming toxins (PFT) are cytolytic proteins belonging to the molecular warfare apparatus of living organisms. The assembly of the functional transmembrane pore requires several intermediate steps ranging from a water-soluble monomeric…
Water plays a major role in bio-systems, greatly contributing to determine their structure, stability and even function. It is well know, for instance, that proteins require a minimum amount of water to be functionally active. Since the…
The rotary sequential hydrolysis of metabolic machine F1-ATPase is a prominent feature to reveal high coordination among multiple chemical sites on the stator F1 ring, which also contributes to tight coupling between the chemical reaction…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic paper Kyte and Doolittle (KD)…
Macroscopic strain experiments revealed that Si crystals traversed by parallel, channel-like nanopores functionalized with the muscle polymer polypyrrole exhibit large and reversible electrochemo-mechanical actuation in aqueous…
A physical model for a structured tetrameric pore is studied. The pore is modeled as a device composed of four subunits, each one exhibiting two possible states (open and closed). The pore is located within a membrane that separates two…
When water molecules are confined to nanoscale spacings, such as in the nanometer size pores of activated carbon fiber (ACF), their freezing point gets suppressed down to very low temperatures ($\sim$ 150 K), leading to a metastable liquid…
In addition to the biologically active monomer of the protein Insulin circulating in human blood, the molecule also exists in dimeric and hexameric forms that are used as storage. The Insulin monomer contains two distinct surfaces, namely…
The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
Two headed motor proteins, such as kinesin and dynein, hidrolyze environmental ATP in order to propel unidirectionally along cytoskeletal filaments such as microtubules. In the case of kinesin, protein heads bind primarily on the alpha…
Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported…
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is…
Cells use homeostatic mechanisms to maintain an optimal composition of distinct types of phospholipids in cellular membranes. The hydrophilic dipolar layer at the membrane interface, composed of phospholipid headgroups, regulates the…
Protein-protein binding enables orderly and lawful biological self-organization, and is therefore considered a miracle of nature. Protein-protein binding is steered by electrostatic forces, hydrogen bonding, van der Waals force, and…
The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…
Large scale molecular dynamics simulations are used to investigate the structural and dynamical modifications of supercooled water when confined inside an hydrophilic nanopore. We then investigate the evolution of the auto-organization of…