The cystine‐stabilized α‐helix: A common structural motif of ion‐channel blocking neurotoxic peptides

Kobayashi, Yuji; Takashima, Hiroyuki; Tamaoki, Haruhiko; Kyōgoku, Yoshimasa; Lambert, Paul F.; Kuroda, Hisaya; Chino, Naoyoshi; Watanabe, Takushi X.; Kimura, Terutoshi; Sakakibara, Shumpei; Moröder, Luis

doi:10.1002/bip.360311009

Cited by 106 publications

(74 citation statements)

References 27 publications

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“…Two intramolecular disulfide bonds ( 3 Cys- 17 Cys and 5 Cys-13 Cys) stabilize the CSH motif. 41,42 The X-ray structure 44 shows that the homod- imer complex of KR-CSH-ET1 is stabilized by intermolecular interactions of three types: two salt bridges, phenylalanine stacking (i.e., hydrophobic core) at the interface, and a β-sheet including the strands in the CSH motif.…”

Section: A Setting the Systemmentioning

confidence: 99%

“…This strand and helix are tightly linked by the disulfide bonds, constituting a cystine-stabilized helical (CSH) motif. 41,42 ET1 aggregates at a concentration between 1 and 4 mM, which interferes with NMR structural determination. Therefore, to increase the solubility, the N-terminal of ET1 was extended by two charged amino-acid residues (Lys and Arg), which exist in its precursor protein.…”

Section: Introductionmentioning

confidence: 99%

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A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent

Higo

Umezawa²,

Nakamura³

2013

The Journal of Chemical Physics

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We propose a novel generalized ensemble method, a virtual-system coupled multicanonical molecular dynamics (V-McMD), to enhance conformational sampling of biomolecules expressed by an all-atom model in an explicit solvent. In this method, a virtual system, of which physical quantities can be set arbitrarily, is coupled with the biomolecular system, which is the target to be studied. This method was applied to a system of an Endothelin-1 derivative, KR-CSH-ET1, known to form an antisymmetric homodimer at room temperature. V-McMD was performed starting from a configuration in which two KR-CSH-ET1 molecules were mutually distant in an explicit solvent. The lowest freeenergy state (the most thermally stable state) at room temperature coincides with the experimentally determined native complex structure. This state was separated to other non-native minor clusters by a free-energy barrier, although the barrier disappeared with elevated temperature.

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Section: A Setting the Systemmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent

Higo

Umezawa²,

Nakamura³

2013

The Journal of Chemical Physics

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“…This structure is in many ways reminiscent of a subclass of cystine knot structures classified as cystine-stabilized ␣-helices (CSH motifs (40,41)), although there are differences in the sequence positions of individual cysteines in the SMB domain relative to the helix compared with prototypical CSH motifs. Such structures are known to function in binding extracellular ligands (41).…”

Section: Figmentioning

confidence: 99%

The Solution Structure of the N-terminal Domain of Human Vitronectin

Mayasundari¹,

Whittemore²,

Serpersu

et al. 2004

Journal of Biological Chemistry

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The three-dimensional structure of an N-terminal fragment comprising the first 51 amino acids from human plasma vitronectin, the somatomedin B (SMB) domain, has been determined by two-dimensional NMR approaches. An average structure was calculated, representing the overall fold from a set of 20 minimized structures. The core residues (18 -41) overlay with a root mean square deviation of 2.29 ؎ 0.62 Å. The N-and Cterminal segments exhibit higher root mean square deviations, reflecting more flexibility in solution and/or fewer long-range NOEs for these regions. Residues 26 -30 form a unique single-turn ␣-helix, the locus where plasminogen activator inhibitor type-1 (PAI-1) is bound. This structure of this helix is highly homologous with that of a recombinant SMB domain solved in a co-crystal with PAI-1 (Zhou, A., Huntington, J. A., Pannu, N. S., Carrell, R. W., and Read, R. J. (2003) Nat. Struct. Biol. 10, 541-544), although the remainder of the structure differs. Significantly, the pattern of disulfide cross-links observed in this material isolated from human plasma is altogether different from the disulfides proposed for recombinant forms. The NMR structure reveals the relative orientation of binding sites for cell surface receptors, including an integrin-binding site at residues 45-47, which was disordered and did not diffract in the co-crystal, and a site for the urokinase receptor, which overlaps with the PAI-1-binding site.Human vitronectin is a glycoprotein found in the circulation, where it contributes to hemostasis by regulating blood coagulation and fibrinolysis (1, 2). Vitronectin is also found in the ECM, 1 where it plays important roles in cell adhesion, pericellular proteolysis, tissue invasion, angiogenesis, and metastasis (3-7). The variety of functions of vitronectin in the two microenvironments is a manifestation of its ability to interact with numerous humoral and cellular proteins. An important binding partner for vitronectin is the serine protease inhibitor PAI-1, which also is found both in circulation and the ECM. Furthermore, it has different activities depending upon this localization; the anti-protease activity of PAI-1 that regulates thrombolysis in the circulation is targeted instead toward pericellular proteolysis when localized to the ECM or cell/matrix boundary. Vitronectin binds to PAI-1 with high affinity and stabilizes the inhibitor in its active conformation (8, 9). Vitronectin can also associate with PAI-1 and assemble to form higher order complexes (10) that exhibit altered adhesive functions (11). Key to the adhesive functions of vitronectin are its interactions with cell-surface receptors including integrins and uPAR.A widely accepted model suggests that vitronectin is organized into functional domains that provide the broad repertoire necessary for binding to target ligands (12)(13)(14). We recently used computational methods to predict the structure of the three domains comprising vitronectin (15). A threading algorithm gave high confidence predictions for the central domai...

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“…They have a threedimensional structure with some conserved motifs [27] but their affinity and specificity towards different targets may vary. Those targets include ion channels, present in different tissues.…”

Section: Discussionmentioning

confidence: 99%

Purification, characterization and biosynthesis of parabutoxin 3, a component of Parabuthus transvaalicus venom

et al. 2002

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A novel peptidyl inhibitor of voltage-gated K + channels, named parabutoxin 3 (PBTx3), has been purified to homogeneity from the venom of Parabuthus transvaalicus. This scorpion toxin contains 37 residues, has a mass of 4274 Da and displays 41% identity with charybdotoxin (ChTx, also called Ôa-KTx1.1Õ). PBTx3 is the tenth member (called Ôa-KTx1.10Õ) of subfamily 1 of K + channel-blocking peptides known thus far. Electrophysiological experiments using Xenopus laevis oocytes indicate that PBTx3 is an inhibitor of Kv1 channels (Kv1.1, Kv1.2, Kv1.3), but has no detectable effects on Kir-type and ERG-type channels. The dissociation constants (K d ) for Kv1.1, Kv1.2 and Kv1.3 channels are, respectively, 79 lM, 547 nM and 492 nM. A synthetic gene encoding a PBTx3 homologue was designed and expressed as a fusion protein with the maltose-binding protein (MBP) in Escherichia coli. The recombinant protein was purified from the bacterial periplasm compartment using an amylose affinity resin column, followed by a gel filtration purification step and cleavage by factor X a (fX a ) to release the recombinant toxin peptide (rPBTx3). After final purification and refolding, rPBTx3 was shown to be identical to the native PBTx3 with respect to HPLC retention time, mass spectrometric analysis and functional properties. The threedimensional structure of PBTx3 is proposed by homology modelling to contain a double-stranded antiparallel b sheet and a single a-helix, connected by three disulfide bridges. The scaffold of PBTx3 is homologous to most other a-KTx scorpion toxins.

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The cystine‐stabilized α‐helix: A common structural motif of ion‐channel blocking neurotoxic peptides

Cited by 106 publications

References 27 publications

A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent

A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent

The Solution Structure of the N-terminal Domain of Human Vitronectin

Purification, characterization and biosynthesis of parabutoxin 3, a component of Parabuthus transvaalicus venom

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