Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel

Structure and dynamics of voltage-gated ion channels, in particular the motion of the S4 helix, is a highly interesting and hotly debated topic in current membrane protein research. It has critical implications for insertion and stabilization of membrane proteins as well as for finding how transitions occur in membrane proteins—not to mention numerous applications in drug design. Here, we present a full 1 µs atomic-detail molecular dynamics simulation of an integral Kv1.2 ion channel, comprising 120,000 atoms. By applying 0.052 V/nm of hyperpolarization, we observe structural rearrangements, including up to 120° rotation of the S4 segment, changes in hydrogen-bonding patterns, but only low amounts of translation. A smaller rotation (∼35°) of the extracellular end of all S4 segments is present also in a reference 0.5 µs simulation without applied field, which indicates that the crystal structure might be slightly different from the natural state of the voltage sensor. The conformation change upon hyperpolarization is closely coupled to an increase in 310 helix contents in S4, starting from the intracellular side. This could support a model for transition from the crystal structure where the hyperpolarization destabilizes S4–lipid hydrogen bonds, which leads to the helix rotating to keep the arginine side chains away from the hydrophobic phase, and the driving force for final relaxation by downward translation is partly entropic, which would explain the slow process. The coordinates of the transmembrane part of the simulated channel actually stay closer to the recently determined higher-resolution Kv1.2 chimera channel than the starting structure for the entire second half of the simulation (0.5–1 µs). Together with lipids binding in matching positions and significant thinning of the membrane also observed in experiments, this provides additional support for the predictive power of microsecond-scale membrane protein simulations

Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules

The rugged energy landscape of biomolecules together with shortcomings of traditional molecular dynamics (MD) simulations require specialized methods for capturing large-scale, long-time configurational changes along with chemical dynamics behavior. In this report, MD-based methods for biomolecules are surveyed, involving modification of the potential, simulation protocol, or algorithm as well as global reformulations. While many of these methods are successful at probing the thermally accessible configuration space at the expense of altered kinetics, more sophisticated approaches like transition path sampling or Markov chain models are required to obtain mechanistic information, reaction pathways, and/or reaction rates. Divide-and-conquer methods for sampling and for piecing together reaction rate information are especially suitable for readily available computer cluster networks. Successful applications to biomolecules remain a challenge

310-Helix Conformation Facilitates the Transition of a Voltage Sensor S4 Segment toward the Down State

AbstractThe activation of voltage-gated ion channels is controlled by the S4 helix, with arginines every third residue. The x-ray structures are believed to reflect an open-inactivated state, and models propose combinations of translation, rotation, and tilt to reach the resting state. Recently, experiments and simulations have independently observed occurrence of 310-helix in S4. This suggests S4 might make a transition from α- to 310-helix in the gating process. Here, we show 310-helix structure between Q1 and R3 in the S4 segment of a voltage sensor appears to facilitate the early stage of the motion toward a down state. We use multiple microsecond-steered molecular simulations to calculate the work required for translating S4 both as α-helix and transformed to 310-helix. The barrier appears to be caused by salt-bridge reformation simultaneous to R4 passing the F233 hydrophobic lock, and it is almost a factor-two lower with 310-helix. The latter facilitates translation because R2/R3 line up to face E183/E226, which reduces the requirement to rotate S4. This is also reflected in a lower root mean-square deviation distortion of the rest of the voltage sensor. This supports the 310 hypothesis, and could explain some of the differences between the open-inactivated- versus activated-states

Voltage-Controlled Enzymes: The New Janus Bifrons

The Ciona intestinalis voltage-sensitive phosphatase, Ci-VSP, was the first Voltage-controlled Enzyme (VEnz) proven to be under direct command of the membrane potential. The discovery of Ci-VSP conjugated voltage sensitivity and enzymatic activity in a single protein. These two facets of Ci-VSP activity have provided a unique model for studying how membrane potential is sensed by proteins and a novel mechanism for control of enzymatic activity. These facets make Ci-VSP a fascinating and versatile enzyme. Ci-VSP has a voltage sensing domain (VSD) that resembles those found in voltage-gated channels (VGC). The VSD resides in the N-terminus and is formed by four putative transmembrane segments. The fourth segment contains charged residues which are likely involved in voltage sensing. Ci-VSP produces sensing currents in response to changes in potential, within a defined range of voltages. Sensing currents are analogous to gating currents in VGC. As known, these latter proteins contain four VSDs which are entangled in a complex interaction with the pore domain - the effector domain in VGC. This complexity makes studying the basis of voltage sensing in VGC a difficult enterprise. In contrast, Ci-VSP is thought to be monomeric and its catalytic domain - the VSP\u27s effector domain - can be cleaved off without disrupting the basic electrical functioning of the VSD. For these reasons, VSPs are considered a great model for studying the activity of a VSD in isolation. Finally, VSPs are also phosphoinositide phosphatases. Phosphoinositides are signaling lipids found in eukaryotes and are involved in many processes, including modulation of VGC activity and regulation of cell proliferation. Understanding VSPs as enzymes has been the center of attention in recent years and several reviews has been dedicated to this area. Thus, this review will be focused instead on the other face of this true JanusBifrons and recapitulate what is known about VSPs as electrically active proteins

Bioinformatics for Membrane Lipid Simulations: Models, Computational Methods, and Web Server Tools

Biological membranes are complex environments consisting of different types of lipids and membrane proteins. The structure of a lipid bilayer is typically difficult to study because the membrane liquid crystalline state is made up of multiple disordered lipid molecules. This complicates the description of the lipid membrane properties by the conformation of any single lipid molecule. Molecular dynamics (MD) simulations have been used extensively to investigate properties of membrane lipids, lipid vesicles, and membrane protein systems. All-atom membrane models can elucidate detailed contacts between membrane proteins and its surrounding lipids, while united-atom and coarse-grained description have allowed larger models and longer timescales up to microsecond mark to be probed. Additionally, membrane models with mixed phospholipids and lipopolysaccharide content have made it possible to model improved views of biological membranes. Here, we present an overview of commonly used lipid force fields by the biosimulation community, useful tools for membrane MD simulations, and recent advances in membrane simulations

PIP2-Binding Site in Kir Channels: Definition by Multiscale Biomolecular Simulations†

Phosphatidylinositol bisphosphate (PIP(2)) is an activator of mammalian inwardly rectifying potassium (Kir) channels. Multiscale simulations, via a sequential combination of coarse-grained and atomistic molecular dynamics, enabled exploration of the interactions of PIP(2) molecules within the inner leaflet of a lipid bilayer membrane with possible binding sites on Kir channels. Three Kir channel structures were investigated: X-ray structures of KirBac1.1 and of a Kir3.1-KirBac1.3 chimera and a homology model of Kir6.2. Coarse-grained simulations of the Kir channels in PIP(2)-containing lipid bilayers identified the PIP(2)-binding site on each channel. These models of the PIP(2)-channel complexes were refined by conversion to an atomistic representation followed by molecular dynamics simulation in a lipid bilayer. All three channels were revealed to contain a conserved binding site at the N-terminal end of the slide (M0) helix, at the interface between adjacent subunits of the channel. This binding site agrees with mutagenesis data and is in the proximity of the site occupied by a detergent molecule in the Kir chimera channel crystal. Polar contacts in the coarse-grained simulations corresponded to long-lived electrostatic and H-bonding interactions between the channel and PIP(2) in the atomistic simulations, enabling identification of key side chains

The Molecular Mechanism by which PIP2 Opens the Intracellular G-Loop Gate of a Kir3.1 Channel

Abstract Inwardly rectifying potassium (Kir) channels are characterized by a long pore comprised of continuous transmembrane and cytosolic portions. A high-resolution structure of a Kir3.1 chimera revealed the presence of the cytosolic (G-loop) gate captured in the closed or open conformations. Here, we conducted molecular-dynamics simulations of these two channel states in the presence and absence of phosphatidylinositol bisphosphate (PIP2), a phospholipid that is known to gate Kir channels. Simulations of the closed state with PIP2 revealed an intermediate state between the closed and open conformations involving direct transient interactions with PIP2, as well as a network of transitional inter- and intrasubunit interactions. Key elements in the G-loop gating transition involved a PIP2-driven movement of the N-terminus and C-linker that removed constraining intermolecular interactions and led to CD-loop stabilization of the G-loop gate in the open state. To our knowledge, this is the first dynamic molecular view of PIP2-induced channel gating that is consistent with existing experimental data

Mecanismos de condução iônica em canais de sódio

Dissertação (mestrado)—Universidade de Brasília, Instituto de Ciências Biológicas, Departamento de Biologia Celular, 2013.Canais iônicos (CIs) são proteínas transmembrânicas capazes de regular o fluxo de íons, para dentro e para fora das células, abrindo e fechando seus poros. Tal regulação se da em resposta a diferentes estímulos, como ligação de moléculas, diferenças de potencial eletrostático, estímulos mecânicos, etc. Além disso, em geral, CIs são altamente seletivos a um íon. Assim, em função do íon transportado pelo canal, estes podem ser denominados canais de Na+, K+, Ca++ ou Cl-. O funcionamento de CIs está relacionado a uma variedade de funções biológicas essenciais como: contração muscular, sinapses, geração e transmissão de impulsos nervosos, controle da pressão osmótica, secreção hormonal, percepção do ambiente e consciência, entre outros. Portanto, essas proteínas tem sido alvo de intensas investigações ao longo das ultimas décadas. Diversas estruturas cristalográficas de canais iônicos foram resolvidas nos últimos anos. Conjuntamente com avanços no poder computacional, tais estruturas possibilitam a investigação de CIs com alta resolução, via simulações de dinâmica molecular (DM). Em 2011 foi publicada a primeira estrutura cristalográfica de canal de Na+: um CI bacteriano denominado NavAb (Payandeh et al., 2011). Observa-se que o poro de CIs apresenta uma estrutura geral comum. Em contrapartida, a região responsável pela discriminação dos íons, o chamado filtro de seletividade (FS), naturalmente mostra diferenças consideráveis. Segundo pode ser observado na estrutura cristalográfica, o FS de canais de Na+ e relativamente curto e amplo, sendo portanto capaz de acomodar íons hidratados no seu interior. Além disso, e sugerido que íons dispõem de certa mobilidade no interior desse FS. Tal descrição difere significativamente do ambiente constrito e pouco hidratado observado no FS de canais de K+. Frente a isso, espera-se que os mecanismos de condução em canais de Na+ e K+ sejam diferentes. Neste trabalho, cálculos de energia livre (via metadinâmica) e simulações de DM com aplicação de potenciais eletrostáticos transmembrânicos foram empregados na investigação do mecanismo de condução de canais de Na+, através do CI NavAb. Conjuntamente, ambas metodologias mostram que os íons ligam-se essencialmente a três sítios no interior do FS, chamados HFS, CEN e IN. Mostrou-se também que o movimento de íons e água no interior do filtro e pouco restrito. Em decorrência disso, e permitida a ocupação concomitante de um único sitio do FS por mais de um íon, o que implica em um mecanismo fundamentalmente distinto daquele observado em canais de K+. Outro resultado interessante aponta para uma assimetria nos mecanismos de condução de Na+ em condições de hiperpolarização ou equilíbrio (ΔV≤0) e de despolarização (ΔV>0). O mecanismo de condução predominante a ΔV ≤ 0 envolve essencialmente a participação de dois Na+. Em contrapartida, a ΔV > 0, o mecanismo conta com três íons, sendo que a chegada do terceiro estimula a liberação de um dos íons anteriormente presentes no canal. Perspectivas desse estudo impactam algumas das questões mais desafiantes da biofísica molecular atual, tais como: identificar os fatores determinantes da seletividade iônica; compreender melhor a relação estrutura-função de canais iônicos eucariotos, particularmente canais de Na+ e Ca++; mecanismo de ação de anestésicos e aplicações nanobiotecnológicas. _______________________________________________________________________________________________________ ABSTRACTIon channels (ICs) are transmembrane (TM) protein pores, capable of regulating the flow of ions in and out of the cells by opening and closing the hydrated pathway they form. This can be done in response to various stimuli, such as binding of ligands, voltage, mechanical stimuli, etc. Moreover, most ICs are highly selective. Hence, according to the ion they selectively transport, ICs can be denominated either Na+, K+, Ca++ or Cl- channels. ICs functioning is essential to a variety of biological functions, e.g.: muscular contraction, electric signaling in neurons, control of the osmotic pressure, hormone secretion, consciousness, etc. Therefore have been the subject of intense research over the last 50 years. Several IC crystal structures have been resolved over the last few years. Along with improvements in computer processing power, such structures enable the investigation of ICs with atomic resolution, by means of molecular dynamics (MD) simulations. In 2011 the first crystal structure of a sodium channel (a bacterial channel named NavAb) was published (Payandeh et al., 2011). While ICs display a pore with overall conserved structure, significant differences can be seen in the so-called selectivity filter (SF): the pore region responsible for discriminating between different ionic species. As of its crystal structure, the Na+ channel SF is relatively short and wide, and thence can fit hydrated cations. Besides, ions and water molecules are expected to have a certain degree of mobility inside the SF. Such SF characteristics greatly differ from the narrow dehydrated environment described for the K+ channel SF. In this context, conduction mechanisms are also expected to be significantly different in these channels. Here, free energy calculations and MD simulations with an applied TM voltage were harnessed to investigate the conduction mechanisms of Na+ channels. Altogether, these methodologies indicate that Na+ ions can bind to three main sites within the SF, named HFS, CEN and IN. Because the movement of ions and water is less restricted, a side-by-side configuration of ions is permitted. This implies in a conduction mechanism fundamentally different from what is known for K+ channels. What is more, this study describes an asymmetry in the conduction mechanisms taking place under hyperpolarizing/neutral (ΔV≤0) and depolarizing (ΔV>0) conditions. Under ΔV≤0, conduction involves two Na+ ions bound to the filter. Contrastingly, under ΔV>0, 3 ions participate and the approach of the third ion triggers the conduction. Perspectives of this study can impart some of the most interesting questions in the molecular biophysics field, such as: identify the determinants of ion selectivity; better understand the structure-function interplay in eukaryotic ICs, specially Na+ and Ca++; the molecular mechanism of anesthetics action and nanobiotechnological applications