7 research outputs found
Local Ordering at Mobile Sites in Proteins: Combining Perspectives from NMR Relaxation and Molecular Dynamics
We report on progress
toward improving NMR relaxation analysis
in proteins in terms of the slowly relaxing local structure (SRLS)
approach by developing a method that combines SRLS with molecular
dynamics (MD) simulations. 15NâH bonds from the
Rho GTPase binding domain of plexin-B1 are used as test case. We focus
on the locally restricting/ordering potential of mean force (POMF), u(θ,Ď), at the NâH site (θ and
Ď specify the orientation of the NâH bond in the protein).
In SRLS, u(θ,Ď) is expanded in the basis
set of the real linear combinations of the Wigner rotation matrix
elements with M = 0, DL,|K|(θ,Ď). Because of
limited data sensitivity, only the lowest (L = 2)
terms are preserved; this potential function is denoted by u(SRLS). In MD, the force-field-parametrized
POMF is the potential, u(MD), defined
in terms of the probability distribution, Peq(MD) â expÂ(âu(MD)). Peq(MD), and subsequently u(MD), can be derived from the MD trajectory
as histograms. One might contemplate utilizing u(MD) instead of u(SRLS); however,
histograms cannot be used in SRLS analyses. Here, we approximate u(θ,Ď) in terms of linear combinations of the DL,|K| functions
with L = 1â4 and appropriate symmetry, denoted
by u(DLK), and optimize the latter (via Peq) against u(MD). This yields for every NâH bond an analytical ordering potential, u(DLKâBEST), which exceeds u(SRLS) considerably in accuracy. u(DLKâBEST) can be used fixed in SRLS data fitting, thereby
enabling the determination of additional parameters. This yields a
substantially improved picture of structural dynamics, which is a
significant benefit. The primary achievement of this work is to have
employed for the first time MD data to derive a suitable (in terms
of composition and symmetry) approximation to the SRLS POMF
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Tethered peptide neurotoxins display two blocking mechanisms in the K+ channel pore as do their untethered analogs.
We show here that membrane-tethered toxins facilitate the biophysical study of the roles of toxin residues in K+ channel blockade to reveal two blocking mechanisms in the K+ channel pore. The structure of the sea anemone type I (SAK1) toxin HmK is determined by NMR. T-HmK residues are scanned by point mutation to map the toxin surface, and seven residues are identified to be critical to occlusion of the KcsA channel pore. T-HmK-Lys22 is shown to interact with K+ ions traversing the KcsA pore from the cytoplasm conferring voltage dependence on the toxin off rate, a classic mechanism that we observe as well with HmK in solution and for Kv1.3 channels. In contrast, two related SAK1 toxins, Hui1 and ShK, block KcsA and Kv1.3, respectively, via an arginine rather than the canonical lysine, when tethered and as free peptides
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Designer and natural peptide toxin blockers of the KcsA potassium channel identified by phage display.
Peptide neurotoxins are powerful tools for research, diagnosis, and treatment of disease. Limiting broader use, most receptors lack an identified toxin that binds with high affinity and specificity. This paper describes isolation of toxins for one such orphan target, KcsA, a potassium channel that has been fundamental to delineating the structural basis for ion channel function. A phage-display strategy is presented whereby âź1.5 million novel and natural peptides are fabricated on the scaffold present in ShK, a sea anemone type I (SAK1) toxin stabilized by three disulfide bonds. We describe two toxins selected by sorting on purified KcsA, one novel (Hui1, 34 residues) and one natural (HmK, 35 residues). Hui1 is potent, blocking single KcsA channels in planar lipid bilayers half-maximally (Ki) at 1 nM. Hui1 is also specific, inhibiting KcsA-Shaker channels in Xenopus oocytes with a Ki of 0.5 nM whereas Shaker, Kv1.2, and Kv1.3 channels are blocked over 200-fold less well. HmK is potent but promiscuous, blocking KcsA-Shaker, Shaker, Kv1.2, and Kv1.3 channels with Ki of 1-4 nM. As anticipated, one Hui1 blocks the KcsA pore and two conserved toxin residues, Lys21 and Tyr22, are essential for high-affinity binding. Unexpectedly, potassium ions traversing the channel from the inside confer voltage sensitivity to the Hui1 off-rate via Arg23, indicating that Lys21 is not in the pore. The 3D structure of Hui1 reveals a SAK1 fold, rationalizes KcsA inhibition, and validates the scaffold-based approach for isolation of high-affinity toxins for orphan receptors
Designer and natural peptide toxin blockers of the KcsA potassium channel identified by phage display.
Peptide neurotoxins are powerful tools for research, diagnosis, and treatment of disease. Limiting broader use, most receptors lack an identified toxin that binds with high affinity and specificity. This paper describes isolation of toxins for one such orphan target, KcsA, a potassium channel that has been fundamental to delineating the structural basis for ion channel function. A phage-display strategy is presented whereby âź1.5 million novel and natural peptides are fabricated on the scaffold present in ShK, a sea anemone type I (SAK1) toxin stabilized by three disulfide bonds. We describe two toxins selected by sorting on purified KcsA, one novel (Hui1, 34 residues) and one natural (HmK, 35 residues). Hui1 is potent, blocking single KcsA channels in planar lipid bilayers half-maximally (Ki) at 1 nM. Hui1 is also specific, inhibiting KcsA-Shaker channels in Xenopus oocytes with a Ki of 0.5 nM whereas Shaker, Kv1.2, and Kv1.3 channels are blocked over 200-fold less well. HmK is potent but promiscuous, blocking KcsA-Shaker, Shaker, Kv1.2, and Kv1.3 channels with Ki of 1-4 nM. As anticipated, one Hui1 blocks the KcsA pore and two conserved toxin residues, Lys21 and Tyr22, are essential for high-affinity binding. Unexpectedly, potassium ions traversing the channel from the inside confer voltage sensitivity to the Hui1 off-rate via Arg23, indicating that Lys21 is not in the pore. The 3D structure of Hui1 reveals a SAK1 fold, rationalizes KcsA inhibition, and validates the scaffold-based approach for isolation of high-affinity toxins for orphan receptors
Ctr1 Intracellular Loop Is Involved in the Copper Transfer Mechanism to the Atox1 Metallochaperone
Understanding
the human copper cycle is essential to understand
the role of metals in promoting neurological diseases and disorders.
One of the cycles controlling the cellular concentration and distribution
of copper involves the copper transporter, Ctr1; the metallochaperone,
Atox1; and the ATP7B transporter. It has been shown that the C-terminus
of Ctr1, specifically the last three amino acids, HCH, is involved
in both copper coordination and the transfer mechanism to Atox1. In
contrast, the role of the intracellular loop of Ctr1, which is an
additional intracellular segment of Ctr1, in facilitating the copper
transfer mechanism has not been investigated yet. Here, we combine
various biophysical methods to explore the interaction between this
Ctr1 segment and metallochaperone Atox1 and clearly demonstrate that
the Ctr1 intracellular loop (1) can coordinate CuÂ(I) via interactions
with the side chains of one histidine and two methionine residues
and (2) closely interacts with the Atox1 metallochaperone. Our findings
are another important step in elucidating the mechanistic details
of the eukaryotic copper cycle
Designer and natural peptide toxin blockers of the KcsA potassium channel identified by phage display
Peptide neurotoxins are powerful tools for research, diagnosis, and treatment of disease. Limiting broader use, most receptors lack an identified toxin that binds with high affinity and specificity. This paper describes isolation of toxins for one such orphan target, KcsA, a potassium channel that has been fundamental to delineating the structural basis for ion channel function. A phage-display strategy is presented whereby âź1.5 million novel and natural peptides are fabricated on the scaffold present in ShK, a sea anemone type I (SAK1) toxin stabilized by three disulfide bonds. We describe two toxins selected by sorting on purified KcsA, one novel (Hui1, 34 residues) and one natural (HmK, 35 residues). Hui1 is potent, blocking single KcsA channels in planar lipid bilayers half-maximally (K(i)) at 1 nM. Hui1 is also specific, inhibiting KcsA-Shaker channels in Xenopus oocytes with a K(i) of 0.5 nM whereas Shaker, Kv1.2, and Kv1.3 channels are blocked over 200-fold less well. HmK is potent but promiscuous, blocking KcsA-Shaker, Shaker, Kv1.2, and Kv1.3 channels with K(i) of 1â4 nM. As anticipated, one Hui1 blocks the KcsA pore and two conserved toxin residues, Lys(21) and Tyr(22), are essential for high-affinity binding. Unexpectedly, potassium ions traversing the channel from the inside confer voltage sensitivity to the Hui1 off-rate via Arg(23), indicating that Lys(21) is not in the pore. The 3D structure of Hui1 reveals a SAK1 fold, rationalizes KcsA inhibition, and validates the scaffold-based approach for isolation of high-affinity toxins for orphan receptors
Correction to Thiolate Spin Population of Type I Copper in Azurin Derived from <sup>33</sup>S Hyperfine Coupling
Correction to Thiolate Spin Population of Type I Copper
in Azurin Derived from <sup>33</sup>S Hyperfine Couplin