短杆菌肽通道内离子K~＋，Na~＋，Li~＋与水的相关性

基于右手螺旋短杆菌肽Ａ离子通道模型,利用分子动力学计算机模拟方法研究了通道内离子Ｋ＋,Ｎａ＋,Ｌｉ＋与水分子的相关性．     

铁蛋白的生物工程应用

铁蛋白是一种普遍存在于生物体内的储铁蛋白,具有铁离子代谢、抗氧化胁迫及消除其他过量金属离子毒害作用的功能。随着对铁蛋白结构和生化功能认识的深入,铁蛋白作为一个含有四氧化三铁核心的特殊蛋白复合体,被广泛应用于生物医学、纳米材料、生物分子成像等各种生物工程领域。该综述针对已知的主要铁蛋白分子,论述了铁蛋白的结构及酶活性机理,基于铁蛋白的多功能分子骨架应用,以及基于铁蛋白磁性的生物分子开关等热点研究,最后对铁蛋白生物工程、生物医学领域的应用和发展进行了展望。     

Ion binding properties and structure stability of the NaK channel

Ion distribution in the selectivity filter and ion-water and ion-protein interactions of NaK channel are systematically investigated by all-atom molecular dynamics simulations, with the tetramer channel protein being embedded in a solvated phospholipid bilayer. Analysis of the simulation results indicates that K⁺ ions prefer to bind within the sites formed by two adjacent planes of oxygen atoms from the selectivity filter, while Na⁺ ions are inclined to bind to a single plane of four oxygen atoms. At the same time, both K⁺ and Na⁺ ions can diffuse in the vestibule, accompanying with movements of the water molecules confined in a complex formed by the vestibule together with four small grottos connecting to it. As a result, K⁺ ions show a wide range of coordination numbers (6-8), while Na⁺ ions display a constant coordination number of ∼ 6 in the selectivity filter, which may result in the loss of selectivity of NaK. It is also found that a Ca²⁺ can bind at the extracellular site as reported in the crystal structure in a partially hydrated state, or at a higher site in a full hydration state. Furthermore, the carbonyl group of Asp66 can reorient to point towards the center pore when an ion exists in the vestibule, while that of Gly65 always aligns tangentially to the channel axis, as in the crystallographic structures.     

A comparison between two prokaryotic potassium channels (KirBac1.1 and KcsA) in a molecular dynamics (MD) simulation study

The two potassium ion channels KirBac1.1 and KcsA are compared in a Molecular Dynamics (MD) simulation study. The location and motion of the potassium ions observed in the simulations are compared to those in the X-ray structures and previous simulations. In our simulations several of the crystallography resolved ion sites in KirBac1.1 are occupied by ions. In addition to this, two in KirBac1.1 unresolved sites where occupied by ions at sites that are in close correspondence to sites found in KcsA. There is every reason to believe that the conserved alignment of the selectivity filter in the potassium ion channel family corresponds to a very similar mechanism for ion transport across the filter. The gate residues, Phe146 in KirBac1.1 and Ala111 in KcsA acted in the simulations as effective barriers which never were passed by ions nor water molecules.     

Ion-specific diffusion rates through transmembrane protein channels. A molecular dynamics study

The migration of different alkali metal cations through a transmembrane model channel is simulated by means of the molecular dynamics technique. The parameters of the model are chosen in close relation to the gramicidin A channel. Coulomb- and van der Waals-type potentials between the ions and flexible carbonyl groups of the pore-forming molecule are used to describe the ion channel interaction. The diffusion properties of the ions are obtained from three-dimensional trajectory calculations. The diffusion rates for the different ions Li+, Na+, K+ and Rb+ are affected not only by the mass of the particles but also very strongly by their size. The latter effect is more pronounced for rigid channels, i.e., for binding vibrational frequencies of the CO groups with v greater than 400 cm-1. In this range the selectivity sequence for the diffusion rates is the inverse of that expected from normal rate theory but agrees with that found in experiments for gramicidin A.     

Recent advances in ion channel research

The field of ion channels has entered into a rapid phase of development in the last few years, partly due to the breakthroughs in determination of the crystal structures of membrane proteins and advances in computer simulations of biomolecules. These advances have finally enabled the long-dreamed goal of relating function of a channel to its underlying molecular structure. Here we present simplified accounts of the competing permeation theories and then discuss their application to the potassium, gramicidin A and calcium channels.     

The nicotinic acetylcholine receptor: from molecular model to single-channel conductance

The nicotinic acetylcholine receptor (nAChR) is the archetypal ligand-gated ion channel. A model of the α7 homopentameric nAChR is described in which the pore-lining M2 helix bundle is treated atomistically and the remainder of the molecule is treated as a “low resolution” cylinder. The surface charge on the cylinder is derived from the distribution of charged amino acids in the amino acid sequence (excluding the M2 segments). This model is explored in terms of its predicted single-channel properties. Based on electrostatic potential profiles derived from the model, the one-dimensional Poisson-Nernst-Planck equation is used to calculate single-channel current/voltage curves. The predicted single-channel conductance is three times higher (ca. 150 pS) than that measured experimentally, and the predicted ion selectivity agrees with the observed cation selectivity of nAChR. Molecular dynamics (MD) simulations are used to estimate the self-diffusion coefficients (D) of water molecules within the channel. In the narrowest region of the pore, D is reduced ca. threefold relative to that of bulk water. Assuming that the diffusion of ions scales with that of water, this yields a revised prediction of the single-channel conductance (ca. 50 pS) in good agreement with the experimental value. We conclude that combining atomistic (MD) and continuum electrostatics calculations is a promising approach to bridging the gap between structure and physiology of ion channels. Received: 2 August 1999 / Revised version: 5 November 1999 / Accepted: 9 November 1999     

Models for binding cooperativities of inhibitors with transthyretin

Here, molecular dynamics (MD) simulations are performed to study the differences of binding channel shapes of TTR with two inhibitors, flufenamic acid (FLU) and one kind of N-phenyl phenoxazine (BPD). The asymmetries of global structure including the central binding channel are found to be intrinsic. Moreover, the conformational changes of the binding channel are responsible for negative cooperativity (NC) or independent cooperativity (IC) of ligands. The results suggested a possible binding mechanism addressing NC of FLU and IC of BPD. For FLU, when the first ligand binds with TTR, it leads to expansion of the second binding site which may weaken the interaction of the second FLU with TTR. But for BPD, the first ligand's binding changes the second site's shape slightly, the second ligand has similar binding ability with TTR in the second site like the first binding event.     

Proton channel models: Filling the gap between experimental data and the structural rationale

Voltage-gated proton channels are integral membrane proteins with the capacity to permeate elementary particles in a voltage and pH dependent manner. These proteins have been found in several species and are involved in various physiological processes. Although their primary topology is known, lack of details regarding their structures in the open conformation has limited analyses toward a deeper understanding of the molecular determinants of their function and regulation. Consequently, the function-structure relationships have been inferred based on homology models. In the present work, we review the existing proton channel models, their assumptions, predictions and the experimental facts that support them. Modeling proton channels is not a trivial task due to the lack of a close homolog template. Hence, there are important differences between published models. This work attempts to critically review existing proton channel models toward the aim of contributing to a better understanding of the structural features of these proteins.     

Potential role of caveolin-1-positive domains in the regulation of the acetylcholine receptor's activable pool: Implications in the pathogenesis of a novel congenital myasthenic syndrome

Cholesterol modulates the plasmalemma's biophysical properties and influences the function and trafficking of membrane proteins. A fundamental phenomenon that remains obscure is how the plasmalemma's lipid composition regulates the activatable pool of membrane receptors. An outstanding model to study this phenomenon is the nicotinic acetylcholine receptor (nAChR), since the nAChR activatable pool has been estimated to be but a small fraction of the receptors present in the plasmalemma. Studies on the effect of cholesterol depletion in the function of the Torpedo californica nAChR, using the lipid-exposed nAChR mutation (αC418W) that produces a congenital myasthenic syndrome (CMS), demonstrated that cholesterol depletion causes a remarkable increase in the αC418W nAChR's macroscopic current whereas not in the wild type (WT). A variety of approaches were used to define the mechanism responsible for the cholesterol depletion mediated-increase in the αC418W nAChR's macroscopic current. The present study suggests that a substantial fraction of the αC418W nAChRs is located in caveolin-1-positive domains, "trapped" in a non-activatable state, and that membrane cholesterol depletion results in the relocation of these receptors to the activatable pool. Co-fractionation and co-immunoprecipitation of the αC418W nAChR and the membrane raft protein caveolin-1 (cav1) support the notion that interactions at lipid-exposed domains regulate the partition of the receptor into membrane raft microdomains. These results have potential implications as a novel mechanism to fine-tune cholinergic transmission in the nervous system and in the pathogenesis associated to the αC418W nAChR.     

Mixed modes in opening of KcsA potassium channel from a targeted molecular dynamics simulation

Potassium channels conduct K⁺ flow selectively across the membrane through a central pore. During a process called gating, the potassium channels undergo a conformational change that opens or closes the ion-conducting pore. The potassium channel KcsA has been structurally determined in its closed state. However, the dynamic mechanism of the gating transition of the KcsA channel is still being investigated. Here, a targeted molecular dynamics simulation up to 150 ns is performed to investigate the detailed opening process of the KcsA channel with an open Kv1.2 structure serving as the target. The channel arrived at a self-determined quasi-stable state within 60 ns. The rigid-body and hinge-bending modes are observed mixed together in the remaining 90 ns long quasi-stable state. The mixed-mode movement seems come from the competition between the helix rigidity and the biased-applied gating force.     

Identification of the phospholipid binding regions of the envelope E protein of flaviviruses by molecular dynamics

Abstract

The Flavivirus genus comprise several important human pathogens, including dengue, West Nile, Yellow fever, Japanese encephalitis, Zika, and tick-borne encephalitis viruses. These enveloped viruses affect more than 2 billion people in the world, mainly in less developed countries. Although some vaccines exist for some flaviviruses, these vaccines are not universally available due to many factors and since their infections are a world-wide public health issue, the development of antiviral molecules is fundamental. Flavivirus membranes, through the help of the envelope E glycoprotein, fuse with endosomal compartments in a pH-dependent way to release their genome into the cytoplasm and require specific lipids, such as bis(monoacylglycero)phosphate (BMP), for efficient fusion. The fundamental role the envelope E protein has on viral entry and membrane fusion suggest that it is an essential antiviral target. In this work, we have used atomistic molecular dynamics simulations to study the binding of the head-group of BMP to the tip of the envelope E proteins of ZIKV, DENV, TBEV and JEV viruses whose three-dimensional structures are known. Our results indicate that, apart from the fusion loop, there are different amino acid residues in different regions of the envelope E proteins of flaviviruses capable of binding the head-group of BMP. These regions should work together to accomplish the binding and fusion of the envelope and endosomal membranes and represent a new target to develop and design potent and effective antiviral agents capable of blocking flavivirus-endosome membrane fusion.      

分子动力学模拟与分子生物力学

生物大分子的微观结构动力学决定其生物学功能,其力学-化学耦合规律是分子生物力学的重点关注方向。分子动力学模拟是耦合生物大分子力学-化学性质微观结构动力学基础的有效手段,其结果可用于预测结构-功能关系、指导实验设计和诠释实验结果。本文简要介绍了分子动力学模拟的方法学特点、基本工作原理及其在分子生物力学中的应用,并展望了未来可能的发展方向和应用前景。     

MD simulations of the central pore of ryanodine receptors and sequence comparison with 2B protein from coxsackie virus

The regulation of intracellular Ca^2 + triggers a multitude of vital processes in biological cells. Ca^2 + permeable ryanodine receptors (RyRs) are the biggest known ion channels and play a key role in the regulation of intracellular calcium concentrations, particularly in muscle cells. In this study, we construct a computational model of the pore region of the skeletal RyR and perform molecular dynamics (MD) simulations. The dynamics and distribution of Ca^2 + around the luminal pore entry of the RyR suggest that Ca^2 + ions are channeled to the pore entry due to the arrangement of (acidic) amino acids at the extramembrane surface of the protein. This efficient mechanism of Ca^2 + supply is thought to be part of the mechanism of Ca^2 + conductance of RyRs. Viral myocarditis is predominantly caused by coxsackie viruses that induce the expression of the protein 2B which is known to affect intracellular Ca^2 + homeostasis in infected cells. From our sequence comparison, it is hypothesized, that modulation of RyR could be due to replacement of its transmembrane domains (TMDs) by those domains of the viral channel forming protein 2B of coxsackie virus. This article is part of a Special Issue entitled: Viral Membrane Proteins — Channels for Cellular Networking.     

Computer simulation of the KvAP voltage-gated potassium channel: steered molecular dynamics of the voltage sensor

The recent crystal structures of the voltage-gated potassium channel KvAP and its isolated voltage-sensing 'paddle' (composed of segments S1-S4) challenge existing models of voltage gating and raise a number of questions about the structure of the physiologically relevant state. We investigate a possible gating mechanism based on the crystal structures in a 10 ns steered molecular dynamics simulation of KvAP in a membrane-mimetic octane layer. The structure of the full KvAP protein has been modified by restraining the S2-S4 domain to the conformation of the isolated high-resolution paddle structure. After an initial relaxation, the paddle tips are pulled through the membrane from the intracellular to the extracellular side, corresponding to a putative change from closed to open. We describe the effect of this large-scale motion on the central pore domain, which remains largely unchanged, on the protein hydrogen-bonding network and on solvent. We analyze the motion of the S3b-S4 portion of the protein and propose a possible coupling mechanism between the paddle motion and the opening of the channel. Interactions between the arginine residues in S4, solvent and chloride ions are likely to play a role in the gating charge.     

Computational studies of gramicidin permeation: An entryway sulfonate enhances cation occupancy at entry sites

The impact on the cation-transport free-energy profile of replacing the C-terminal ethanolamine in the gramicidin A channel with a taurine residue is studied using molecular dynamics simulations of gramicidin A (1JNO) embedded in a lipid bilayer (DMPC) with 1 mol/kg NaCl saline solution. The potential of mean force for ion transport is obtained by umbrella sampling. The presence of a negatively charged sulfonate group at the entrance of the gramicidin channel affects the depth and the location of the binding sites, producing a strong attraction for the cations in the bulk. The potential of mean force by the sulfonate acting directly through electrostatics and van der Waals interactions on the test ion is highly modulated by indirect effects (i.e., sulfonate effects on other components of the system that, in turn, affect the ion free-energy profile in the channel). Because the “entry” sites are located symmetrically at both entry and exit of the channel, the deeper free-energy wells should inhibit exit. Given that the channel has increased conductance experimentally, the simulation results suggest that the channel conductance is normally entry limited.     

Force field comparisons of the heat capacity of carbon nanotubes

The force fields Tersoff, CHARMM, COMPASS, CVFF and PCFF are compared using molecular calculations and simulations of SWNT thermal properties. The heat capacity results from the force fields vary significantly in the low (room) temperature range. The COMPASS force field best reproduces the phonon frequencies calculated from density functional theory and is consistent with the Raman scattering results. The temperature dependent behavior of SWNT heat capacity is investigated using harmonic and quasi-harmonic dynamics theories. The impact of quasi-harmonic analysis is not significant in the low and intermediate temperature range (below 500 K). Thus, force field comparisons based on the harmonic approximation are valid in that temperature range. Above 500 K, heat capacity results based on the Tersoff force field using a quasi-harmonic approximation are further investigated.