772 research outputs found
Dynamics, energetics, and selectivity of the low-K+ KcsA channel structure.
No full textPotassium channels are a diverse family of integral membrane proteins through which K(+) can pass selectively. There is ongoing debate about the nature of conformational changes associated with the opening/closing and conductive/nonconductive states of potassium channels. The channels partly exert their function by varying their conductance through a mechanism known as C-type inactivation. Shortly after the activation of K(+) channels, their selectivity filter stops conducting ions at a rate that depends on various stimuli. The molecular mechanism of C-type inactivation has not been fully understood yet. However, the X-ray structure of the KcsA channel obtained in the presence of low K(+) concentration is thought to be representative of a K(+) channel in the C-type inactivated state. Here, extensive, fully atomistic molecular dynamics and free-energy simulations of the low-K(+) KcsA structure in an explicit lipid bilayer are performed to evaluate the stability of this structure and the selectivity of its binding sites. We find that the low-K(+) KcsA structure is stable on the timescale of the molecular dynamics simulations performed, and that ions preferably remain in S1 and S4. In the absence of ions, the selectivity filter evolves toward an asymmetric architecture, as already observed in other computations of the high-K(+) structure of KcsA and KirBac. The low-K(+) KcsA structure is not permeable by Na(+), K(+), or Rb(+), and the selectivity of its binding sites is different from that of the high-K(+) structure
Atypical mechanism of conduction in potassium channels.
No full textPotassium channels can conduct passively K+ ions with rates of up to approximately 10(8) ions per second at physiological conditions, and they are selective to these species by a factor of 10(4) over Na+ ions. Ion conduction has been proposed to involve transitions between 2 main states, with 2 or 3 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 2-3 kcal mol(-1). Here, we present an alternative mechanism for conduction of K+ in potassium 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+
Gating at the selectivity filter of ion channels that conduct Na+ and K+ ions.
No full textThe NaK channel is a cation selective channel with similar permeability for K(+) and Na(+). The available crystallographic structure of wild-type (WT) NaK is usually associated with a conductive state of the channel. Here, potential of mean force for complete conduction events of Na(+) and K(+) ions through NaK show that: i), large energy barriers prevent the passage of ions through the WT NaK structure, ii), the barriers are correlated to the presence of a hydrogen bond between Asp-66 and Asn-68, and iii), the structure of NaK mutated to mimic cyclic nucleotide-gated channels conducts Na(+) and K(+). These results support the hypothesis that the filter of cation selective channels can adopt at least two different structures: a conductive one, represented by the x-ray structures of the NaK-CNG chimeras, and a closed one, represented by the x-ray structures of the WT NaK
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 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
DNA-recognition process described by MD simulations of the lactose repressor protein on a specific and a non-specific DNA sequence.
No full textThe lactose repressor protein may bind DNA in two possible configurations: a specific one, if the DNA sequence corresponds to a binding site, and a non-specific one otherwise. To find its target sequences, the lactose repressor first binds non-specifically to DNA, and subsequently, it rapidly searches for a binding site. Atomic structures of non-specific and specific complexes are available from crystallographic and nuclear magnetic resonance experiments. However, what remains unknown is a detailed description of the steps that transform the non-specific complex into the specific one. Here, how the protein first recognizes its binding site has been studied using molecular dynamics simulations. The picture that emerges is that of a protein that is as mobile when interacting with non-specific DNA sequences as when free in solution. This high degree of mobility allows the protein to rapidly sample different DNA sequences. In contrast, when the protein encounters a binding site, the configuration ensemble collapses, and the protein sliding movements along the DNA sequence become scarce. The binding energies in the specific and non-specific complexes were analysed using the Molecular Mechanics Poisson Boltzmann Surface Area approach. These results represent a first step towards a throughout characterization of the DNA-recognition process
Fijación de paños de yeserías en el período nazarí en la Alhambra, Granada
No full textEste trabajo parte de la observación y estudio de obras en el
campo de las yeserías hispanomusulmanas, y más concretamente en
decoraciones de la Alhambra. Trata de establ ecer el sistema de
sujeción y colocación de las placas de yesería sobre paramentos
verticales. Son muy escasos los trabajos específicos acerca de
decoraciones en yeso (Kawiak, 1991; de Luxán et al., 1995; Rubio
Domene, 1995) y en ellos en raras ocasiones s e analizan los
morteros de sujeción (de la Torre et al., en prensa). Por tanto, el
planteamiento del estudio de este sistema de fijación ha comenzado
por la observación de los distintos materiales y características que
presentaban en diferentes lugares.This work presents various studies carried out on paraments
decorated with hispano -muslim gypsum-plaster ornamentation
(yeserías) in the Alhambra, specifically on the Nazarí period (XIII -
XV C.). To do so, we have examined decorations that have
survived to the present day either as fragments or as complete
panels. The most representative decorations were chosen, as well as
those offering the best conditions for observation and sampling.
In addition to field observations, XRD analyses have been
made to determine the mineralogical composition of the panels and
of the fixtures.
We have thus been able to fix upon the system of placement
and fastening of the gypsum plaster panels on the vertical paraments
in the Alhambra during the Nazarí period, results which may be
extrapolable to other periods and to other hispano -muslim
constructions
Critical Assessment of Common Force Fields for Molecular Dynamics Simulations of Potassium Channels
No full textFor the last two decades, the KcsA K+ channel has served as a case study to understand how potassium channels operate at the atomic scale, and molecular dynamics simulations have contributed significantly to the current knowledge of the atomic mechanisms of conduction, inactivation, and gating in this family of membrane proteins. Currently, microsecond trajectories are becoming the new standard in the field, and consequently, it is critical to assess and compare the performance of the classical force fields ordinarily used in simulations of biological systems as well as to quantitatively assess the agreement with experimental data for trajectories of this order of magnitude. To that extent, we performed classical molecular dynamics simulations with CHARMM36 and AMBER-ff14sb force fields using atomic models based on the experimental structure of the KcsA channel in the open/conductive state, at conditions of ionic concentrations and membrane potentials resembling the ones adopted in experiments. In simulations using the CHARMM force field, the experimental open/conductive structure of the channel exhibited high conformational plasticity and fast collapse toward an occluded state. In contrast, in an identical set of simulations using the AMBER force field, no major deviations from the experimental structure were recorded. Force field development is a complex process in which many approximations are typically required and adopted. The results presented here provide additional motivation to further improve the existing models and, crucially, alert practitioners about limitations
Examining ion channel properties using free-energy methods.
No full textRecent advances in structural biology have revealed the architecture of a number of transmembrane channels, allowing for these complex biological systems to be understood in atomistic detail. Computational simulations are a powerful tool by which the dynamic and energetic properties, and thereby the function of these protein architectures, can be investigated. The experimentally observable properties of a system are often determined more by energetic than dynamics, and therefore understanding the underlying free energy (FE) of biophysical processes is of crucial importance. Critical to the accurate evaluation of FE values are the problems of obtaining accurate sampling of complex biological energy landscapes, and of obtaining accurate representations of the potential energy of a system, this latter problem having been addressed through the development of molecular force fields. While these challenges are common to all FE methods, depending on the system under study, and the questions being asked of it, one technique for FE calculation may be preferable to another, the choice of method and simulation protocol being crucial to achieve efficiency. Applied in a correct manner, FE calculations represent a predictive and affordable computational tool with which to make relevant contact with experiments. This chapter, therefore, aims to give an overview of the most widely implemented computational methods used to calculate the FE associated with particular biochemical or biophysical events, and to highlight their recent applications to ion channels
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
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