酸敏感离子通道与脑梗死

急性脑梗死约占全部脑卒中的70%,病死率和致残率高,且极易复发。但目前针对急性脑梗死在时间窗内溶栓、抗凝等治疗手段不能从根本上切实有效地修复受损脑组织,且伴有出血等风险。寻找脑梗死形成发展的原因并予以治疗迫在眉睫。酸中毒是引起缺血性脑损伤的重要机制。大量实验研究表明,酸中毒能加重神经元的缺血性损伤,且其梗死面积与酸中毒的程度直接相关。但缺血产生的酸中毒如何引起神经元损伤的确切机制尚不明确。最近研究发现酸中毒能激活一种在中枢及周围神经中广泛存在的膜通道,即酸敏感离子通道,它对Ca^2＋通透,能引起细胞内Ca^2＋超载,同时能激活胞内酶引起细胞内蛋白质、脂类及核酸的降解,加重缺血后脑损伤。本文就酸敏感离子通道1a与脑梗死做一综述。     

酸敏感离子通道与脑梗死

急性脑梗死约占全部脑卒中的70%,病死率和致残率高,且极易复发。但目前针对急性脑梗死在时间窗内溶栓、抗凝等治疗手段不能从根本上切实有效地修复受损脑组织,且伴有出血等风险。寻找脑梗死形成发展的原因并予以治疗迫在眉睫。酸中毒是引起缺血性脑损伤的重要机制。大量实验研究表明,酸中毒能加重神经元的缺血性损伤,且其梗死面积与酸中毒的程度直接相关。但缺血产生的酸中毒如何引起神经元损伤的确切机制尚不明确。最近研究发现酸中毒能激活一种在中枢及周围神经中广泛存在的膜通道,即酸敏感离子通道,它对Ca2+通透,能引起细胞内Ca2+超载,同时能激活胞内酶引起细胞内蛋白质、脂类及核酸的降解,加重缺血后脑损伤。本文就酸敏感离子通道1a与脑梗死做一综述。     

The mechanism of proton exclusion in the aquaporin-1 water channel

Aquaporins are efficient, yet strictly selective water channels. Remarkably, proton permeation is fully blocked, in contrast to most other water-filled pores which are known to conduct protons well. Blocking of protons by aquaporins is essential to maintain the electrochemical gradient across cellular and subcellular membranes. We studied the mechanism of proton exclusion in aquaporin-1 by multiple non-equilibrium molecular dynamics simulations that also allow proton transfer reactions. From the simulations, an effective free energy profile for the proton motion along the channel was determined with a maximum-likelihood approach. The results indicate that the main barrier is not, as had previously been speculated, caused by the interruption of the hydrogen-bonded water chain, but rather by an electrostatic field centered around the fingerprint Asn-Pro-Ala (NPA) motif. Hydrogen bond interruption only forms a secondary barrier located at the ar/R constriction region. The calculated main barrier height of 25-30 kJ mol(-1) matches the barrier height for the passage of protons across pure lipid bilayers and, therefore, suffices to prevent major leakage of protons through aquaporins. Conventional molecular dynamics simulations additionally showed that negatively charged hydroxide ions are prevented from being trapped within the NPA region by two adjacent electrostatic barriers of opposite polarity.     

Intracellular ASIC1a regulates mitochondrial permeability transition-dependent neuronal death

Acid-sensing ion channel 1a (ASIC1a) is the key proton receptor in nervous systems, mediating acidosis-induced neuronal injury in many neurological disorders, such as ischemic stroke. Up to now, functional ASIC1a has been found exclusively on the plasma membrane. Here, we show that ASIC1a proteins are also present in mitochondria of mouse cortical neurons where they are physically associated with adenine nucleotide translocase. Moreover, purified mitochondria from ASIC1a^−/− mice exhibit significantly enhanced Ca²⁺ retention capacity and accelerated Ca²⁺ uptake rate. When challenged with hydrogen peroxide (H₂O₂), ASIC1a^−/− neurons are resistant to cytochrome c release and inner mitochondrial membrane depolarization, suggesting an impairment of mitochondrial permeability transition (MPT) due to ASIC1a deletion. Consistently, H₂O₂-induced neuronal death, which is MPT dependent, is reduced in ASIC1a^−/− neurons. Additionally, significant increases in mitochondrial size and oxidative stress levels are detected in ASIC1a^−/− mouse brain, which also displays marked changes (>2-fold) in the expression of mitochondrial proteins closely related to reactive oxygen species signal pathways, as revealed by two-dimensional difference gel electrophoresis followed by mass spectrometry analysis. Our data suggest that mitochondrial ASIC1a may serve as an important regulator of MPT pores, which contributes to oxidative neuronal cell death.     

Molecular dynamics simulations of enhanced green fluorescent proteins: effects of F64L,S65T and T203Y mutations on the ground-state proton equilibria

Molecular dynamics simulations with the Amber force field are carried out to study two mutants of the green fluorescent protein (GFP), namely EGFP (F64L/S65T) and T203Y-EGFP (E(2)GFP). Those variants display an opposite equilibrium between the structural A and B states, associated with neutral and anionic protonation forms of the chromophore. Configurations of those two states are simulated for each variant and the energetics of their equilibrium in the two mutants is studied by evaluating the change in the relative free energy of A and B states (DeltaG(AB)) upon T203Y mutation. The resulting DeltaDeltaG(AB) agrees with the value inferred from absorption measurements. A comparison of the hydrogen bond network around the chromophore rationalizes the different population of state A and B in EGFP and E(2)GFP. On the basis of structural and energetic considerations, a mechanism for destabilization of the neutral chromophore in S65T mutants is proposed. Simulations of the B state of the S65T variant and of WT GFP are also performed for comparison and to test the force field parameters of the chromophore derived for the present calculations. Possible paths of proton transfer leading to nonfluorescent states of the chromophore are discussed in light of the photodynamical behavior of GFP, as revealed by fluorescence correlation spectroscopy and single-molecule experiments.     

Molecular dynamics analysis of potent inhibitors of M2 proton channel against H1N1 swine influenza virus

The recent H1N1 (swine) influenza pandemic highlighted the urgent need of having effective anti‐viral strategies. In addition to neuraminidase inhibitors, there is another class of anti-viral drug known as M2 inhibitors that were, in the past, effective in treating seasonal influenza. However, due to the emergence of M2 inhibitor‐resistant influenza viruses, this class of drugs was not recommended for clinical usage in the latest influenza pandemic. In order to identify novel M2 inhibitors, we have performed molecular docking using a traditional Chinese medicine database (http://tcm.cmu.edu.tw/index.php). Docking and subsequent de novo designs gave 10 derivatives that have much better docking results than the control. Of these 10 derivatives, the top three, methyl isoferulate_1, genipin_1 and genipin_2, were selected for molecular dynamics simulation. During the simulation run, the top three derivatives all had stable interactions with M2 residues, Ser31 and Ala30. Methyl isoferulate_1 also has stable interaction to His37. Therefore, we recommend these three derivatives for further biomolecular experiments and clinical studies.     

Role of acidosis,NMDA receptors,and acid-sensitive ion channel 1a (ASIC1a) in neuronal death induced by ischemia

This review collects data on the influence of intracellular and extracellular acidosis on neuronal viability and the effect of acidosis on neuronal damage progressing under brain ischemia/hypoxia. Particular attention is devoted to the involvement of ionotropic glutamic receptors and acid-sensitive ion channel 1a in these processes. Published in Russian in Biokhimiya, 2008, Vol. 73, No. 11, pp. 1461–1466.     

Dynamics of desensitization and recovery of proton-activated ion channels in pheochromocytoma cells

Proton-activated ion channels of the ASIC 1a subtype in pheochromocytoma PC12 cells were inactivated under the long-lasting influence of an acidic milieu (pH 6.0) because of desensitization developing in a monoexponential mode with τ = 1.7 ± 0.3 sec. The recovery of currents after desensitization was also monoexponential, with τ = 4.9 ± 0.8 sec. Approximation of the dose-effect curve by the Hill equation showed that activation of a channel of this type needs, most probably, binding of three hydrogen ions. Neirofiziologiya/Neurophysiology, Vol. 39, No. 1, pp. 9–14, January–February, 2007.     

Comparative docking studies of CYP1b1 and its PCG-associated mutant forms

Molecular docking has been used to compare and contrast the binding modes of oestradiol with the wild-type and some disease-associated mutant forms of the human CYP1b1 protein. The receptor structures used for docking were derived from molecular dynamics simulations of homology-modelled structures. Earlier studies involving molecular dynamics and principal component analysis indicated that mutations could have a disruptive effect on function, by destabilizing the native properties of the functionally important regions, especially those of the haem-binding and substrate-binding regions, which constitute the site of catalytic activity of the enzyme. In order to gain more insights into the possible differences in substrate-binding and catalysis between the wild-type and mutant proteins, molecular docking studies were carried out. Mutants showed altered protein-ligand interactions compared with the wild-type as a consequence of changes in the geometry of the substrate-binding region and in the position of haem relative to the active site. An important difference in ligand-protein interactions between the wild-type and mutants is the presence of stacking interaction with phenyl residues in the wild-type, which is either completely absent or considerably weaker in mutants. The present study revealed essential differences in the interactions between ligand and protein in wild-type and disease mutants, and helped in understanding the deleterious nature of disease mutations at the level of molecular function.     

Theoretical modeling of the O-intermediate structure of bacteriorhodopsin

Bacteriorhodopsin is a prototype of efficient molecular machinery functioning as a light-activated proton pump. Among the five distinct intermediates (K, L, M, N, and O) of the photocycle, there is less structural information on the later stages compared with the early intermediates. Here, we report the structural modeling of the O-intermediate for which the determination of experimental structure remains difficult. Hypothetical conformational change of the molecule from the light-adapted state to the O-intermediate state was simulated by gradually changing the protonation state of two residues. To achieve accurate molecular modeling, we carefully constructed a realistic system of the native purple membrane. The modeled structure of the O-intermediate has some implications about proton transfer in the later stages of the photocycle and the structural response of bacteriorhodopsin to the inner charge distribution.     

Comparative simulation studies of native and single-site mutant human beta-defensin-1 peptides

Human defensins play important roles in a broad range of biological functions, such as microbial defense and immunity. Yet, little is known about their molecular properties, i.e. secondary structure stability, structural variability, important side chain interactions, surface charge distribution, and resistance to thermal fluctuations, and how these properties are related to their functions. To assess these factors, we studied the native human β-defensin-1 monomer and dimer as well as several single-site mutants using molecular dynamics simulations. The results showed that disulfide bonds are important determinants in maintaining the defensins’ structural integrity, as no structural transitions were observed at 300?K and only minor structural unfolding was detected upon heating to 500?K. The α-helix was less thermally stable than the core β-sheet structure held together by hydrogen bonds and hydrophobic interactions. The monomer α-helix stability was directly correlated, whereas the end-to-end distance was inversely correlated to the experimentally measured β-defensin-1 chemotactic activity, in the order: mutant 2 (Gln24Glu)?>?mutant 3 (Lys31Ala)?=?wild type?>?mutant 1 (Asn4Ala). The structural stability of the β-defensin-1 dimer species exhibited an inverse correlation to their chemotactic activity. In dimers formed by mutants 2 and 3, we observed sliding of one monomer upon the surface of the other in the absence of unbinding. This dynamic sliding feature may enhance the molecular oligomerization of β-defensin-1 peptides contributing to their antibacterial activity. It could also help these peptides orient correctly in the CC chemokine receptor 6 binding site, thereby initiating their chemotactic activity. In agreement with this notion, the remarkable sliding behavior was observed only for the mutants with the highest chemotactic activity.     

Interleukin-1β and tumor necrosis factor-α augment acidosis-induced rat articular chondrocyte apoptosis via nuclear factor-kappaB-dependent upregulation of ASIC1a channel

The acute-phase proinflammatory cytokines interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α) demonstrate high-level expression and pleiotropic biological effects, and contribute to the progression and persistence of rheumatoid arthritis (RA). Acid hydrarthrosis is also an important pathological characteristic of RA, and the acid-sensing ion channel 1a (ASIC1a) plays a critical role in acidosis-induced chondrocyte cytotoxicity. However, the roles of IL-1β and TNF-α in acid-induced apoptosis of chondrocytes remain unclear. Rat adjuvant arthritis and primary articular chondrocytes were used as in vivo and in vitro model systems, respectively. ASIC1a expression in articular cartilage was increased and highly colocalized with nuclear factor (NF)-κB expression in vivo. IL-1β and TNF-α could upregulate ASIC1a expression. These cytokines activated mitogen-activated protein kinase and NF-κB pathways in chondrocytes, while the respective inhibitors of these signaling pathways could partially reverse the ASIC1a upregulation induced by IL-1β and TNF-α. Dual luciferase and gel-shift assays and chromatin immunoprecipitation-polymerase chain reaction demonstrated that IL-1β and TNF-α enhanced ASIC1a promoter activity in chondrocytes by increasing NF-κB DNA-binding activities, which was in turn prevented by the NF-κB inhibitor ammonium pyrrolidinedithiocarbamate. IL-1β and TNF-α also decreased cell viability but enhanced LDH release, intracellular Ca²⁺ concentration elevation, loss of mitochondrial membrane potential, cleaved PARP and cleaved caspase-3/9 expression, and apoptosis in acid-stimulated chondrocytes, which effects could be abrogated by the specific ASIC1a inhibitor psalmotoxin-1 (PcTX-1), ASIC1a-short hairpin RNA or calcium chelating agent BAPTA-AM. These results indicate that IL-1β and TNF-α can augment acidosis-induced cytotoxicity through NF-κB-dependent up-regulation of ASIC1a channel expression in primary articular chondrocytes.     

Analysis of the structure of HIV-1 protease complexed with a hexapeptide inhibitor. Part II: Molecular dynamic studies of the active site region

Six models of the catalytic site of HIV-1 protease complexed with a reduced peptide inhibitor, MVT-101, were investigated. These studies focused on the details of protonation of the active site, its total net charge and hydrogen bonding pattern, which was consistent with both the observed coplanar configuration of the acidic groups of the catalytic aspartates (Asp-25 and Asp-125) and the observed binding mode of the inhibitor. Molecular dynamic simulations using AMBER 4.0 indicated that the active site should be neutral. The planarity of the aspartate dyad may be due to the formation of two hydrogen bonds: one between the inner O_δ1oxygen atoms of the two catalytic aspartates and another between the O_δ2atom of Asp-125 and the nitrogen atom of the reduced peptide bond of the bound inhibitor. This would require two additional protonations, either of both aspartates, or of one Asp and the amido nitrogen atom of Nle-204. Our results favor the Asp-inhibitor protonation but the other one is not excluded. Implications of these findings for the mechanism of enzymatic catalysis are discussed. Dynamic properties of the hydrogen bond network in the active site and an analysis of the interaction energy between the inhibitor and the protease are presented. © 1997 Wiley-Liss, Inc.     

Molecular dynamics directed rational design and fluorescence binding assay of phosphopeptide ligands for PLK polo-box domain

Polo-like kinase 1 (PLK1) plays a critical role during multiple stages of cell cycle progression and is involved in the development and metastasis of malignant tumours. The protein contains a regulatory polo-box domain (PBD) that can recognise and bind to a wide variety of phosphorylated substrates. Here, a systematic amino acid preference profile of phosphopeptide interaction with PLK1 PBD domain was created based on the crystal structures of the domain in complex with its natural phosphopeptide ligands. With the profile we were able to explore the structural basis and energetic landscape of phosphopeptide binding to the domain. Moreover, in addition to domain peptide-binding pocket we also examined the intermolecular interaction between the N-terminal region of phosphopeptide and a newly discovered crystal packing site of the domain. All the harvested information was successfully integrated to guide the structural design and optimisation of phosphopeptide ligands with improved affinity and selectivity for the domain, which were then confirmed in vitro by fluorescence anisotropy assays. Structural analysis and energetic analysis revealed that the phosphopeptide ligand can be divided into three functionally independent sections: a N-terminal flexible tail, a C-terminal unbinding tail and a central binding region. The N-terminal tail possesses a high flexibility that can roll over on the surface of PBD crystal packing site, while the C-terminal tail points out of the peptide-binding pocket of the domain and no substantial interaction can be observed between them. In contrast, the central region binds tightly to the domain pocket and exhibits modest conformational change over different ligands.     

Contribution of residues in second transmembrane domain of ASIC1a protein to ion selectivity

Acid-sensing ion channels (ASICs) are proton-gated cation-selective channels expressed in the peripheral and central nervous systems. The ion permeation pathway of ASIC1a is defined by residues 426–450 in the second transmembrane (TM2) segment. The gate, formed by the intersection of the TM2 segments, localizes near the extracellular boundary of the plasma membrane. We explored the contribution to ion permeation and selectivity of residues in the TM2 segment of ASIC1a. Studies of accessibility with positively charged methanethiosulfonate reagents suggest that the permeation pathway in the open state constricts below the gate, restricting the passage to large ions. Substitution of residues in the intracellular vestibule at positions 437, 438, 443, or 446 significantly increased the permeability to K⁺ versus Na⁺. ASIC1a shows a selectivity sequence for alkali metals of Na⁺>Li⁺>K⁺≫Rb⁺>Cs⁺. Alanine and cysteine substitutions at position 438 increased, to different extents, the relative permeability to Li⁺, K⁺, Rb⁺, and Cs⁺. For these mutants, ion permeation was not a function of the diameter of the nonhydrated ion, suggesting that Gly-438 encompasses an ion coordination site that is essential for ion selectivity. M437C and A443C mutants showed slightly increased permeability to K⁺, Rb⁺, and Cs⁺, suggesting that substitutions at these positions influence ion discrimination by altering molecular sieving. Our results indicate that ion selectivity is accomplished by the contribution of multiple sites in the pore of ASIC1a.