Genomic and Structural Characterization of Kunitz-Type Peptide LmKTT-1a Highlights Diversity and Evolution of Scorpion Potassium Channel Toxins

Background

Recently, a new subfamily of long-chain toxins with a Kunitz-type fold was found in scorpion venom glands. Functionally, these toxins inhibit protease activity and block potassium channels. However, the genomic organization and three-dimensional (3-D) structure of this kind of scorpion toxin has not been reported.

Principal Findings

Here, we characterized the genomic organization and 3-D nuclear magnetic resonance structure of the scorpion Kunitz-type toxin, LmKTT-1a, which has a unique cysteine pattern. The LmKTT-1a gene contained three exons, which were interrupted by two introns located in the mature peptide region. Despite little similarity to other Kunitz-type toxins and a unique pattern of disulfide bridges, LmKTT-1a possessed a conserved Kunitz-type structural fold with one α-helix and two β-sheets. Comparison of the genomic organization, 3-D structure, and functional data of known toxins from the α-KTx, β-KTx, γ-KTx, and κ-KTx subfamily suggested that scorpion Kunitz-type potassium channel toxins might have evolved from a new ancestor that is completely different from the common ancestor of scorpion toxins with a CSα/β fold. Thus, these analyses provide evidence of a new scorpion potassium channel toxin subfamily, which we have named δ-KTx.

Conclusions/Significance

Our results highlight the genomic, structural, and evolutionary diversity of scorpion potassium channel toxins. These findings may accelerate the design and development of diagnostic and therapeutic peptide agents for human potassium channelopathies.     

Adaptive Evolution of Scorpion Sodium Channel Toxins

Gene duplication followed by positive Darwinian selection is an important evolutionary event at the molecular level, by which a gene can gain new functions. Such an event might have occurred in the evolution of scorpion sodium channel toxin genes (- and -groups). To test this hypothesis, a robust statistical method from Yang and co-workers based on the estimation of the nonsynonymous-to-synonymous rate ratio ( = d_N/d_S) was performed. The results provide clear statistical evidence for adaptive molecular evolution of scorpion - and -toxin genes. A good match between the positively selected sites (evolutionary epitopes) and the putative bioactive surface (functional epitopes) indicates that these sites are most likely involved in functional recognition of sodium channels. Our results also shed light on the importance of the B-loop in the functional diversification of scorpion - and -toxins.     

蝎氯毒素结构、功能与应用研究

蝎氯毒素是一类能特异阻断神经胶质瘤氯电流的短链蝎毒素。它们具有高度的同源性、保守的基因序列与相似的3-D结构。根据其结构与功能的关系,推测它们可能有相似的药理功能。其中,Chlorotoxin(Cltx)能与神经胶质瘤细胞特异相互作用,并抑制其侵袭与转移。     

Characterization of Kbot21 Reveals Novel Side Chain Interactions of Scorpion Toxins Inhibiting Voltage-Gated Potassium Channels

Scorpion toxins are important pharmacological tools for probing the physiological roles of ion channels which are involved in many physiological processes and as such have significant therapeutic potential. The discovery of new scorpion toxins with different specificities and affinities is needed to further characterize the physiology of ion channels. In this regard, a new short polypeptide called Kbot21 has been purified to homogeneity from the venom of Buthus occitanus tunetanus scorpion. Kbot21 is structurally related to BmBKTx1 from the venom of the Asian scorpion Buthus martensii Karsch. These two toxins differ by only two residues at position 13 (R /V) and 24 (D/N).Despite their very similar sequences, Kbot21 and BmBKTx1 differ in their electrophysiological activities. Kbot21 targets K_V channel subtypes whereas BmBKTx1 is active on both big conductance (BK) and small conductance (SK) Ca²⁺-activated K⁺ channel subtypes, but has no effects on Kv channel subtypes. The docking model of Kbot21 with the Kv1.2 channel shows that the D24 and R13 side-chain of Kbot21 are critical for its interaction with K_V channels.     

Antagonism by Local Anesthetics of Sodium Channel Activators in the Presence of Scorpion Toxins: Two Mechanisms for Competitive Inhibition

1. The interaction of veratridine (VTD), a Na+ channel activator, scorpion alpha-toxin (LQ), an open state Na+ channel stabilizer, and the local anesthetic, lidocaine (LID), a channel inhibitor, at the neuronal sodium channel was assessed by measuring VTD-dependent slow depolarizations of frog sciatic nerve using the sucrose-gap method. 2. The slow depolarizing action of veratridine was potentiated more than 10-fold by the peptide LQ toxin, whereas its competitive inhibition by lidocaine was unchanged by LQ. 3. We conclude that the antagonism between VTD and a LID molecule during slow depolarization is allosteric, involving a trapping of the Na+ channel by LID in the inactivated state that has a very low affinity for VTD. 4. The binding of VTD to the open state of the channel, which is stabilized by LQ, may be inhibited by orthosteric competition at overlapping sites since both LID and VTD bind avidly and rapidly to open channels.     

Dynamic Diversification from a Putative Common Ancestor of Scorpion Toxins Affecting Sodium, Potassium, and Chloride Channels

Scorpions have survived successfully over millions of years without detectable changes in their morphology. Instead, they have developed an efficient alomonal machinery and a stinging device supporting their needs for prey and defense. They produce a large variety of polypeptidic toxins that bind and modulate ion channel conductance in excitable tissues. The binding site, mode of action, and chemical properties of many toxins have been studied extensively, but little is known about their genomic organization and diversity. Genes representing each of the major classes of Buthidae scorpion toxins, namely, ``long' toxins, affecting sodium channels (alpha, depressant, and excitatory), and ``short' toxins, affecting potassium and chloride channels, were isolated from a single scorpion segment and analyzed. Each toxin type was found to be encoded by a gene family. Regardless of toxin length, 3-D structure, and site of action, all genes contain A+T-rich introns that split, at a conserved location, an amino acid codon of the signal sequence. The introns vary in length and sequence but display identical boundaries, agree with the GT/AG splice junctions, and contain T-runs downstream of a putative branch point, 5′-TAAT-3′. Despite little sequence similarity among all toxin classes, the conserved gene organization, intron features, and common cysteine-stabilized α-helical (CSH) core connecting an α-helix to a three-stranded β-sheet suggest, that they all evolved from an ancestral common progenitor. Furthermore, the vast diversity found among genomic copies, cDNAs, and their protein products for each toxin suggests an extensive evolutionary process of the scorpion ``pharmaceutical factory,' whose success is due, most likely, to the inherent permissiveness of the toxin exterior to structural alterations. Received: 16 March 1998 / Accepted: 30 July 1998     

Molecular Dynamics Simulations of Scorpion Toxin Recognition by the Ca-Activated Potassium Channel KCa3.1

The Ca²⁺-activated channel of intermediate-conductance (K_Ca3.1) is a target for antisickling and immunosuppressant agents. Many small peptides isolated from animal venoms inhibit K_Ca3.1 with nanomolar affinities and are promising drug scaffolds. Although the inhibitory effect of peptide toxins on K_Ca3.1 has been examined extensively, the structural basis of toxin-channel recognition has not been understood in detail. Here, the binding modes of two selected scorpion toxins, charybdotoxin (ChTx) and OSK1, to human K_Ca3.1 are examined in atomic detail using molecular dynamics (MD) simulations. Employing a homology model of K_Ca3.1, we first determine conduction properties of the channel using Brownian dynamics and ascertain that the simulated results are in accord with experiment. The model structures of ChTx-K_Ca3.1 and OSK1-K_Ca3.1 complexes are then constructed using MD simulations biased with distance restraints. The ChTx-K_Ca3.1 complex predicted from biased MD is consistent with the crystal structure of ChTx bound to a voltage-gated K⁺ channel. The dissociation constants (K_d) for the binding of both ChTx and OSK1 to K_Ca3.1 determined experimentally are reproduced within fivefold using potential of mean force calculations. Making use of the knowledge we gained by studying the ChTx-K_Ca3.1 complex, we attempt to enhance the binding affinity of the toxin by carrying out a theoretical mutagenesis. A mutant toxin, in which the positions of two amino acid residues are interchanged, exhibits a 35-fold lower K_d value for K_Ca3.1 than that of the wild-type. This study provides insight into the key molecular determinants for the high-affinity binding of peptide toxins to K_Ca3.1, and demonstrates the power of computational methods in the design of novel toxins.     

Molecular Dynamics Simulations of Scorpion Toxin Recognition by the Ca2+-Activated Potassium Channel KCa3.1

The Ca²⁺-activated channel of intermediate-conductance (K_Ca3.1) is a target for antisickling and immunosuppressant agents. Many small peptides isolated from animal venoms inhibit K_Ca3.1 with nanomolar affinities and are promising drug scaffolds. Although the inhibitory effect of peptide toxins on K_Ca3.1 has been examined extensively, the structural basis of toxin-channel recognition has not been understood in detail. Here, the binding modes of two selected scorpion toxins, charybdotoxin (ChTx) and OSK1, to human K_Ca3.1 are examined in atomic detail using molecular dynamics (MD) simulations. Employing a homology model of K_Ca3.1, we first determine conduction properties of the channel using Brownian dynamics and ascertain that the simulated results are in accord with experiment. The model structures of ChTx-K_Ca3.1 and OSK1-K_Ca3.1 complexes are then constructed using MD simulations biased with distance restraints. The ChTx-K_Ca3.1 complex predicted from biased MD is consistent with the crystal structure of ChTx bound to a voltage-gated K⁺ channel. The dissociation constants (K_d) for the binding of both ChTx and OSK1 to K_Ca3.1 determined experimentally are reproduced within fivefold using potential of mean force calculations. Making use of the knowledge we gained by studying the ChTx-K_Ca3.1 complex, we attempt to enhance the binding affinity of the toxin by carrying out a theoretical mutagenesis. A mutant toxin, in which the positions of two amino acid residues are interchanged, exhibits a 35-fold lower K_d value for K_Ca3.1 than that of the wild-type. This study provides insight into the key molecular determinants for the high-affinity binding of peptide toxins to K_Ca3.1, and demonstrates the power of computational methods in the design of novel toxins.     

Unique Mechanism of the Interaction between Honey Bee Toxin TPNQ and rKir1.1 Potassium Channel Explored by Computational Simulations: Insights into the Relative Insensitivity of Channel towards Animal Toxins

Background

The 21-residue compact tertiapin-Q (TPN_Q) toxin, a derivative of honey bee toxin tertiapin (TPN), is a potent blocker of inward-rectifier K⁺ channel subtype, rat Kir1.1 (rKir1.1) channel, and their interaction mechanism remains unclear.

Principal Findings

Based on the flexible feature of potassium channel turrets, a good starting rKir1.1 channel structure was modeled for the accessibility of rKir1.1 channel turrets to TPN_Q toxin. In combination with experimental alanine scanning mutagenesis data, computational approaches were further used to obtain a reasonable TPN_Q toxin-rKir1.1 channel complex structure, which was completely different from the known binding modes between animal toxins and potassium channels. TPN_Q toxin mainly adopted its helical domain as the channel-interacting surface together with His12 as the pore-blocking residue. The important Gln13 residue mainly contacted channel residues near the selectivity filter, and Lys20 residue was surrounded by a polar “groove” formed by Arg118, Thr119, Glu123, and Asn124 in the channel turret. On the other hand, four turrets of rKir1.1 channel gathered to form a narrow pore entryway for TPN_Q toxin recognition. The Phe146 and Phe148 residues in the channel pore region formed strong hydrophobic protrusions, and produced dominant nonpolar interactions with toxin residues. These specific structure features of rKir1.1 channel vestibule well matched the binding of potent TPN_Q toxin, and likely restricted the binding of the classical animal toxins.

Conclusions/Significance

The TPN_Q toxin-rKir1.1 channel complex structure not only revealed their unique interaction mechanism, but also would highlight the diverse animal toxin-potassium channel interactions, and elucidate the relative insensitivity of rKir1.1 channel towards animal toxins.     

肽类毒素(蜘蛛、蝎、芋螺)的三维结构

多肽类毒素研究是目前毒素研究的一个重点,对多肽类毒素的三维结构的研究是了解其结构与功能关系的重要基础.对蜘蛛、蝎以及芋螺这3类代表性的有毒动物的多肽类毒素在结构研究方面的进展及其三维结构的特点进行了介绍.其中,蜘蛛毒素多肽分子的结构主要发现有ICK模体(Inhibitor Cystine Knot motif)和D DH模体(disulfided-irectedh-airpin)两类,蝎毒素中长链肽类毒素分子和短链肽类毒素分子的结构明显不同,前者以CSα/β结构模体(Cyss-tabilizedα/βfold m otif)为主,后者则以α/β脚手架结构模体(α/βscaffoldm otif)为主.相对于蜘蛛和蝎而言,芋螺肽类毒素分子的三维结构则表现得更为复杂多样.     

蝎β型昆虫毒素的结构及其与钠通道作用机制

蝎毒素是蝎为防卫的需要而产生的一系列活性短肽.其中蝎昆虫特异性毒素可特异性结合并调控昆虫可兴奋细胞膜上的钠离子通道,是研究离子通道结构与功能的首选探针,并在转基因抗虫植物及生物杀虫剂研究方面具有潜在的应用价值.本文对蝎β型昆虫毒素的结构与功能及其对钠离子通道的作用方式和β毒素的电压传感器捕获(voltage sensor-trapping)模型做一综述,为进一步揭示蝎β毒素的结构与功能的关系和在农作物抗虫领域的应用提供依据.     

Structure of a Pancreatic ATP-Sensitive Potassium Channel

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马氏蝎毒毒素的分离纯化及其对红细胞膜作用的初步研究

本文用山东产马氏蝎(Buthus martensii kashi)粗毒为材料,经SephadexG-50和Sp-Sephadex C-25二次柱层析,分离纯化获得三个毒峰部分,毒性比粗毒分别提高40—100倍。 纯度鉴定表明三个毒峰的聚丙烯酰胺凝胶电泳和等电聚焦电泳均为一条带,等电点分别为8.7,9.1,9.1,分子量用SDS-不连续聚丙烯酰胺凝胶电泳测定分别为6,600,5,000和8,500。对纯化蝎毒毒素的氨基酸组分也作了分析。 蝎毒毒素对人红细胞膜作用的初步探索结果表明:它使人红细胞膜的Na.K-ATP酶活性和膜脂流动性有所降低。     

Single Cell Genomics of the Brain: Focus on Neuronal Diversity and Neuropsychiatric Diseases

Single cell genomics has made increasingly significant contributions to our understanding of the role that somatic genome variations play in human neuronal diversity and brain diseases. Studying intercellular genome and epigenome variations has provided new clues to the delineation of molecular mechanisms that regulate development, function and plasticity of the human central nervous system (CNS). It has been shown that changes of genomic content and epigenetic profiling at single cell level are involved in the pathogenesis of neuropsychiatric diseases (schizophrenia, mental retardation (intellectual/leaning disability), autism, Alzheimer’s disease etc.). Additionally, several brain diseases were found to be associated with genome and chromosome instability (copy number variations, aneuploidy) variably affecting cell populations of the human CNS. The present review focuses on the latest advances of single cell genomics, which have led to a better understanding of molecular mechanisms of neuronal diversity and neuropsychiatric diseases, in the light of dynamically developing fields of systems biology and “omics”.     

The Persistent Question of Potassium Channel Permeation Mechanisms

Potassium channels play critical roles in many physiological processes, providing a selective permeation route for K⁺ ions in and out of a cell, by employing a carefully designed selectivity filter, evolutionarily conserved from viruses to mammals. The structure of the selectivity filter was determined at atomic resolution by x-ray crystallography, showing a tight coordination of desolvated K⁺ ions by the channel. However, the molecular mechanism of K⁺ ions permeation through potassium channels remains unclear, with structural, functional and computational studies often providing conflicting data and interpretations. In this review, we will present the proposed mechanisms, discuss their origins, and will critically assess them against all available data. General properties shared by all potassium channels are introduced first, followed by the introduction of two main mechanisms of ion permeation: soft and direct knock-on. Then, we will discuss critical computational and experimental studies that shaped the field. We will especially focus on molecular dynamics (MD) simulations, that provided mechanistic and energetic aspects of K⁺ permeation, but at the same time created long-standing controversies. Further challenges and possible solutions are presented as well.     

东亚钳蝎毒素BmKT四个同源基因的克隆及基因组织分析

BmKT是从本室构建的cDNA文库中筛选到的1个α钠通道毒素,根据其全长cDNA序列设计引物,采用PCR法以蝎总基因组DNA为模板,获得4个BmKT的同源基因,分别命名为BmKT′和BmKTa、BmKTb、BmKTb′.序列分析表明：BmKT′和BmKTa基因含有大小分别为509 bp和506 bp的内含子,位于信号肽编码区内,插入信号肽-4位残基Gly密码子的第一个碱基G之后;而BmKTb和BmKTb′ 的内含子大小均为418 bp．这4个BmKT的同源基因内含子符合GT/AG拼接规律,其中BmKT′和BmKTa的内含子A+T含量分别为61.7%和61.9%,低于目前已报导的大多数蝎毒素基因A+T含量,大大低于它们第一外显子A+T含量（71.7%）,略高于第二外显子A+T含量（55.5%）;而BmKTb,BmKTb′的内含子A+T含量分别为75.8%和76.1%,与目前已报导的大多数蝎毒素基因A+T含量相似．BmKT′基因的外显子与BmKT基因cDNA所对应氨基酸序列仅在信号肽中-7位有一个氨基残基的差异（BmKT: Leu→BmKTa: Val）;而BmKTa基因外显子所推断的氨基酸序列与BmKT前体比较,则在成熟肽的+54位发生了突变（BmKT: Lys→BmKTa: Asn）,是与BmKT同源的一个新基因．BmKTb基因和BmKTb′基因所编码的前体肽与BmKT基因对应的前体肽同源性约为65%,显然BmKTb和BmKTb′是不同于BmKT的2个新基因（GenBank登录号: BmKT′, AY786186; BmKTa, AY676142; BmKTb, AY676140; BmKTb′, AY676141）     

Functional Consequences of a Decreased Potassium Affinity in a Potassium Channel Pore : Ion Interactions and C-Type Inactivation

Ions bound near the external mouth of the potassium channel pore impede the C-type inactivation conformational change (Lopez-Barneo, J., T. Hoshi, S. Heinemann, and R. Aldrich. 1993. Receptors Channels. 1:61– 71; Baukrowitz, T., and G. Yellen. 1995. Neuron. 15:951–960). In this study, we present evidence that the occupancy of the C-type inactivation modulatory site by permeant ions is not solely dependent on its intrinsic affinity, but is also a function of the relative affinities of the neighboring sites in the potassium channel pore. The A463C mutation in the S6 region of Shaker decreases the affinity of an internal ion binding site in the pore (Ogielska, E.M., and R.W. Aldrich, 1998). However, we have found that this mutation also decreases the C-type inactivation rate of the channel. Our studies indicate that the C-type inactivation effects observed with substitutions at position A463 most likely result from changes in the pore occupancy of the channel, rather than a change in the C-type inactivation conformational change. We have found that a decrease in the potassium affinity of the internal ion binding site in the pore results in lowered (electrostatic) interactions among ions in the pore and as a result prolongs the time an ion remains bound at the external C-type inactivation site. We also present evidence that the C-type inactivation constriction is quite local and does not involve a general collapse of the selectivity filter. Our data indicate that in A463C potassium can bind within the selectivity filter without interfering with the process of C-type inactivation.     

Pentameric Assembly of Potassium Channel Tetramerization Domain-Containing Protein 5

We report the X-ray crystal structure of human potassium channel tetramerization domain-containing protein 5 (KCTD5), the first member of the family to be so characterized. Four findings were unexpected. First, the structure reveals assemblies of five subunits while tetramers were anticipated; pentameric stoichiometry is observed also in solution by scanning transmission electron microscopy mass analysis and analytical ultracentrifugation. Second, the same BTB (bric-a-brac, tramtrack, broad complex) domain surface mediates the assembly of five KCTD5 and four voltage-gated K ⁺ (Kv) channel subunits; four amino acid differences appear crucial. Third, KCTD5 complexes have well-defined N- and C-terminal modules separated by a flexible linker that swivels by ∼ 30^o; the C-module shows a new fold and is required to bind Golgi reassembly stacking protein 55 with ∼ 1 μM affinity, as judged by surface plasmon resonance and ultracentrifugation. Fourth, despite the homology reflected in its name, KCTD5 does not impact the operation of Kv4.2, Kv3.4, Kv2.1, or Kv1.2 channels.