290 research outputs found
Selectivity and permeation of alkali metal ions in K +-channels
No full textIon conduction in K +-channels is usually described in terms of concerted movements of K + progressing in a single file through a narrow pore. Permeation is driven by an incoming ion knocking on those ions already inside the protein. A fine-tuned balance between high-affinity binding and electrostatic repulsive forces between permeant ions is needed to achieve efficient conduction. While K +-channels are known to be highly selective for K + over Na +, some K + channels conduct Na + in the absence of K +. Other ions are known to permeate K +-channels with a more moderate preference and unusual conduction features. We describe an extensive computational study on ion conduction in K +-channels rendering free energy profiles for the translocation of three different alkali ions and some of their mixtures. The free energy maps for Rb + translocation show at atomic level why experimental Rb + conductance is slightly lower than that of K +. In contrast to K + or Rb +, external Na + block K + currents, and the sites where Na + transport is hindered are characterized. Translocation of K +/Na + mixtures is energetically unfavorable owing to the absence of equally spaced ion-binding sites for Na +, excluding Na + from a channel already loaded with K +. © 2011 Elsevier Ltd. All rights reserved
On Conduction and Gating in K+-Channels
No full textPotassium channels can conduct passively K+ ions with rates of up to ∼ 108 ions per second at physiological conditions, and they are selective to these species by a factor of 104 over Na+ ions. Ion conduction has been proposed to involve transitions between two main states, with two or three K+ ions occupying the selectivity filter separated by an intervening water molecule. The largest free energy barrier of such a process was reported to be of the order of 2-3kcal mol−1. Here, we present an alternative mechanism for conduction of K+ in K+ channels where site vacancies are involved, and we propose that coexistence of several ion permeation mechanisms is energetically possible. Conduction can be described as a more anarchic phenomenon than previously characterized by the concerted translocations of K+-water-K+. Experiments also suggest that local structural changes in the selectivity filter may act as the a gate referred to as C-type inactivation. An extensive computational study on KirBac, is presented which supports the existence of a physical gate or constriction in the selectivity filter of K+ channels. Our computations identify a new selectivity filter structure, which is likely associated with C-type inactivation
DNA recognition process of the lactose repressor protein studied via metadynamics and umbrella sampling simulations.
No full textThe lactose repressor, LacI, finds its DNA target sites via a process that is faster than what it is expected from a diffusion-driven mechanism. This is possible thanks to nonspecific binding of LacI to DNA, followed by diffusion along the DNA molecule. The diffusion of the protein along DNA might lead to a fast-searching mechanism only if LacI binds with comparable strength to different nonspecific sequences and if, in addition, the value of the binding energy remarkably decreases in the presence of a binding site. The first condition would be favored by loose interactions with the base edges, while the second would take advantage from the opposite situation. In order to understand how the protein satisfies these two opposing requirements, the DNA recognition process was studied by a combination of umbrella sampling and metadynamics simulations. The simulations revealed that when aligned with a specific sequence, LacI establishes polar interactions with the base edges that require ∼4 kcal/mol to be disrupted. In contrast, these interactions are not stable when the protein is aligned with nonspecific sequences. These results confirm that LacI is able to efficiently recognize a specific sequence while sliding along DNA before any structural change of the protein-DNA complex occurs
Method for analyzing web space data
No full textA method for analyzing data from the web that determine the importance that a chosen subject has in society, e.g., subject matter relating a concert, a scientific discovery, a football match, a person, a corporation, a brand, or a car, and analyze such data that can represent the entire society better than the known techniques. The method according to the invention can avoid malicious alterations and is able to measure and detect the temporal relations among all the web resources that talk about a particular topic or subject matter
Expression and Role of Heparan Sulfated Proteoglycans in Pancreatic Cancer
No full textPancreatic cancer is a lethal condition with poor outcomes and an increasing incidence. The unfavourable prognosis is due to the lack of early symptoms and consequent late diagnosis. An effective method for the early diagnosis of pancreatic cancer is therefore sought by many researchers in the field. Heparan sulfated proteoglycan-related genes are often expressed differently in tumors than in normal tissues. Alteration of the tumor microenvironment is correlated with the ability of heparan sulfated proteoglycans to bind cytokines and growth factors and eventually to influence tumor progression. Here we discuss the importance of glypicans, syndecans, perlecan and extracellular matrix modifying enzymes, such as heparanases and sulfatases, as potential diagnostics in pancreatic cancer. We also ran an analysis on a multidimensional cancer genomics database for heparan sulfated proteoglycan-related genes, and report altered expression of some of them
Ion-triggered selectivity in bacterial sodium channels
No full textSince the availability of the first crystal structure of a bacterial Na+ channel in 2011, understanding selectivity across this family of membrane proteins has been the subject of intense research efforts. Initially, free energy calculations based on molecular dynamics simulations revealed that although sodium ions can easily permeate the channel with their first hydration shell almost intact, the selectivity filter is too narrow for efficient conduction of hydrated potassium ions. This steric view of selectivity was subsequently questioned by microsecond atomic trajectories, which proved that the selectivity filter appears to the permeating ions as a highly degenerate, liquid-like environment. Although this liquid-like environment looks optimal for rapid conduction of Na+, it seems incompatible with efficient discrimination between similar ion species, such as Na+ and K+, through steric effects. Here extensive molecular dynamics simulations, combined with Markov state model analyses, reveal that at positive membrane potentials, potassium ions trigger a conformational change of the selectivity toward a nonconductive metastable state. It is this transition of the selectivity filter, and not steric effects, that prevents the outward flux of K+ at positive membrane potentials. This description of selectivity, triggered by the nature of the permeating ions, might have implications on the current understanding of how ion channels, and in particular bacterial Na+ channels, operate at the atomic scale.</p
Molecular dynamics simulations of the TrkH membrane protein.
No full textTrkH is a transmembrane protein that mediates uptake of K(+) through the cell membrane. Despite the recent determination of its crystallographic structure, the nature of the permeation mechanism is still unknown, that is, whether K(+) ions move across TrkH by active transport or passive diffusion. Here, molecular dynamics simulations and the umbrella sampling technique have been employed to shed light on this question. The existence of binding site S3 and two alternative binding sites have been characterized. Analysis of the coordination number renders values that are almost constant, with a full contribution from the carbonyls of the protein only at S3. This observation contrasts with observations of K(+) channels, where the contribution of the protein to the coordination number is roughly constant in all four binding sites. An intramembrane loop is found immediately after the selectivity filter at the intracellular side of the protein, which obstructs the permeation pathway, and this is reflected in the magnitude of the energy barriers
On ionic conduction in potassium channels.
No full textIn ref. 1, we presented an alternative mechanism for conduc- tion of K+ in K+ channels where site vacancies are involved, and we proposed that coexistence of several ion permeation mechanisms is energetically possible. Specifically, we found that conduction can be described as a more anarchic phe- nomenon than previously habitually characterized by the con- certed translocations of K+-water-K+. This alternative pathway entails the possible presence of vacancies, with neither K+ nor water molecules in certain sites; sometimes, ions can even be found at adjacent binding sites. Moreover, we sug- gested that this mechanism is likely to be just one example among a plethora of alternative configurations and conduction pathways that ions and water may adopt during permeation, and that it can be viewed as a perturbation to the long- standing accepted mechanism involving neat, organized ion–water fluxe
K(+) and Na(+) conduction in selective and nonselective ion channels via molecular dynamics simulations.
No full textGenerations of scientists have been captivated by ion channels and how they control the workings of the cell by admitting ions from one side of the cell membrane to the other. Elucidating the molecular determinants of ion conduction and selectivity are two of the most fundamental issues in the field of biophysics. Combined with ongoing progress in structural studies, modeling and simulation have been an integral part of the development of the field. As of this writing, the relentless growth in computational power, the development of new algorithms to tackle the so-called rare events, improved force-field parameters, and the concomitant increasing availability of membrane protein structures, allow simulations to contribute even further, providing more-complete models of ion conduction and selectivity in ion channels. In this report, we give an overview of the recent progress made by simulation studies on the understanding of ion permeation in selective and nonselective ion channels
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