High-speed AFM reveals accelerated binding of agitoxin-2 to a K+ channel by induced fit

Quantitative Analysis of Therapeutic Antibody Interactions with Fcγ Receptors Using High-Speed Atomic Force Microscopy

This study employed high-speed atomic force microscopy to quantitatively analyze the interactions between therapeutic antibodies and Fcγ receptors (FcγRs). Antibodies are essential components of the immune system and are integral to biopharmaceuticals. The focus of this study was on immunoglobulin G molecules, which are crucial for antigen binding via the Fab segments and cytotoxic functions through their Fc portions. We conducted real-time, label-free observations of the interactions of rituximab and mogamulizumab with the recombinant FcγRIIIa and FcγRIIa. The dwell times of FcγR binding were measured at the single-molecule level, which revealed an extended interaction duration of mogamulizumab with FcγRIIIa compared with that of rituximab. This is linked to enhanced antibody-dependent cellular cytotoxicity that is attributed to the absence of the core fucosylation of Fc-linked N-glycan. This study also emphasizes the crucial role of the Fab segments in the interaction with FcγRIIa as well as that with FcγRIIIa. This approach provided quantitative insight into therapeutic antibody interactions and exemplified kinetic proofreading, where cellular discrimination relies on ligand residence times. Observing the dwell times of antibodies on the effector molecules has emerged as a robust indicator of therapeutic antibody efficacy. Ultimately, these findings pave the way for the development of refined therapeutic antibodies with tailored interactions with specific FcγRs. This research contributes to the advancement of biopharmaceutical antibody design and optimizing antibody-based treatments for enhanced efficacy and precision.

Voltage sensors of a Na+ channel dissociate from the pore domain and form inter-channel dimers in the resting state

Understanding voltage-gated sodium (Nav) channels is significant since they generate action potential. Nav channels consist of a pore domain (PD) and a voltage sensor domain (VSD). All resolved Nav structures in different gating states have VSDs that tightly interact with PDs; however, it is unclear whether VSDs attach to PDs during gating under physiological conditions. Here, we reconstituted three different voltage-dependent NavAb, which is cloned from Arcobacter butzleri, into a lipid membrane and observed their structural dynamics by high-speed atomic force microscopy on a sub-second timescale in the steady state. Surprisingly, VSDs dissociated from PDs in the mutant in the resting state and further dimerized to form cross-links between channels. This dimerization would occur at a realistic channel density, offering a potential explanation for the facilitation of positive cooperativity of channel activity in the rising phase of the action potential.

The insights into calcium ion selectivity provided by ancestral prokaryotic ion channels

Prokaryotic channels play an important role in the structural biology of ion channels. At the end of the 20^th century, the first structure of a prokaryotic ion channel was revealed. Subsequently, the reporting of structures of various prokaryotic ion channels have provided fundamental insights into the structure of ion channels of higher organisms. Voltage-dependent Ca²⁺ channels (Cavs) are indispensable for coupling action potentials with Ca²⁺ signaling. Similar to other proteins, Cavs were predicted to have a prokaryotic counterpart; however, it has taken more than 20 years for one to be identified. The homotetrameric channel obtained from Meiothermus ruber generates the calcium ion specific current, so it is named as CavMr. Its selectivity filter contains a smaller number of negatively charged residues than mutant Cavs generated from other prokaryotic channels. CavMr belonged to a different cluster of phylogenetic trees than canonical prokaryotic cation channels. The glycine residue of the CavMr selectivity filter is a determinant for calcium selectivity. This glycine residue is conserved among eukaryotic Cavs, suggesting that there is a universal mechanism for calcium selectivity. A family of homotetrameric channels has also been identified from eukaryotic unicellular algae, and the investigation of these channels can help to understand the mechanism for ion selection that is conserved from prokaryotes to eukaryotes.

iCDI-W2vCom: Identifying the Ion Channel-Drug Interaction in Cellular Networking Based on word2vec and node2vec

Ion channels are the second largest drug target family. Ion channel dysfunction may lead to a number of diseases such as Alzheimer's disease, epilepsy, cephalagra, and type II diabetes. In the research work for predicting ion channel-drug, computational approaches are effective and efficient compared with the costly, labor-intensive, and time-consuming experimental methods. Most of the existing methods can only be used to deal with the ion channels of knowing 3D structures; however, the 3D structures of most ion channels are still unknown. Many predictors based on protein sequence were developed to address the challenge, while most of their results need to be improved, or predicting web servers are missing. In this paper, a sequence-based classifier, called "iCDI-W2vCom," was developed to identify the interactions between ion channels and drugs. In the predictor, the drug compound was formulated by SMILES-word2vec, FP2-word2vec, SMILES-node2vec, and ECFPs via a 1184D vector, ion channel was represented by the word2vec via a 64D vector, and the prediction engine was operated by the LightGBM classifier. The accuracy and AUC achieved by iCDI-W2vCom via the fivefold cross validation were 91.95% and 0.9703, which outperformed other existing predictors in this area. A user-friendly web server for iCDI-W2vCom was established at http://www.jci-bioinfo.cn/icdiw2v. The proposed method may also be a potential method for predicting target-drug interaction.

Peptide Toxins Targeting KV Channels

A number of peptide toxins isolated from animals target potassium ion (K⁺) channels. Many of them are particularly known to inhibit voltage-gated K⁺ (K_V) channels and are mainly classified into pore-blocking toxins or gating-modifier toxins. Pore-blocking toxins directly bind to the ion permeation pores of K_V channels, thereby physically occluding them. In contrast, gating-modifier toxins bind to the voltage-sensor domains of K_V channels, modulating their voltage-dependent conformational changes. These peptide toxins are useful molecular tools in revealing the structure-function relationship of K_V channels and have potential for novel treatments for diseases related to K_V channels. This review focuses on the inhibition mechanism of pore-blocking and gating-modifier toxins that target K_V channels.

Tethered peptide toxins for ion channels

In this method paper, we describe protocols for using membrane-tethered peptide toxins (T-toxins) to study the structure/function and biophysics of toxin-channel interactions with two-electrode voltage clamp (TEVC). Here, we show how T-toxins can be used to determine toxin equilibrium affinity, to quantify toxin surface level by enzyme-linked immunosorbent assay (ELISA) and/or single-molecule total internal reflection fluorescence (smTIRF) microscopy, to assess toxin association and dissociations rate, to identify toxin residues critical to binding via scanning mutagenesis, and to study of toxin blocking mechanism. The sea anemone type I (SAK1) toxin HmK and a potassium channel are used to demonstrate the strategies. T-toxins offer experimental flexibility that facilitates studies of toxin variants by mutation of the expression plasmid, avoiding the need to synthesize and purify individual peptides, speeding and reducing the cost of studies. T-toxins can be applied to peptide toxins that target pores or regulatory domains, that inhibit or activate, that are derived from different species, and that bind to different types of ion channels.

Direct visualization of the conformational change of FUS/TLS upon binding to promoter-associated non-coding RNA

High-speed AFM revealed the conformational change of fused in sarcoma (FUS) from a compact to an extended structure upon binding of non-coding RNA, which is supposed to allow FUS to bind to CBP/p300 for transcriptional interference. Thus, a mechanistic insight into transcription regulation by FUS and non-coding RNA is provided.

A Molecular Lid Mechanism of K+ Channel Blocker Action Revealed by a Cone Peptide

Many venomous organisms carry in their arsenal short polypeptides that block K⁺ channels in a highly selective manner. These toxins may compete with the permeating ions directly via a "plug" mechanism or indirectly via a "pore-collapse" mechanism. An alternative "lid" mechanism was proposed but remained poorly defined. Here we study the Drosophila Shaker channel block by Conkunitzin-S1 and Conkunitzin-C3, two highly similar toxins derived from cone venom. Despite their similarity, the two peptides exhibited differences in their binding poses and biophysical assays, implying discrete action modes. We show that while Conkunitzin-S1 binds tightly to the channel turret and acts via a "pore-collapse" mechanism, Conkunitzin-C3 does not contact this region. Instead, Conk-C3 uses a non-conserved Arg to divert the permeant ions and trap them in off-axis cryptic sites above the SF, a mechanism we term a "molecular-lid". Our study provides an atomic description of the "lid" K⁺ blocking mode and offers valuable insights for the design of therapeutics based on venom peptides.

Mechanisms of ligand binding

Many processes in chemistry and biology involve interactions of a ligand with its molecular target. Interest in the mechanism governing such interactions has dominated theoretical and experimental analysis for over a century. The interpretation of molecular recognition has evolved from a simple rigid body association of the ligand with its target to appreciation of the key role played by conformational transitions. Two conceptually distinct descriptions have had a profound impact on our understanding of mechanisms of ligand binding. The first description, referred to as induced fit, assumes that conformational changes follow the initial binding step to optimize the complex between the ligand and its target. The second description, referred to as conformational selection, assumes that the free target exists in multiple conformations in equilibrium and that the ligand selects the optimal one for binding. Both descriptions can be merged into more complex reaction schemes that better describe the functional repertoire of macromolecular systems. This review deals with basic mechanisms of ligand binding, with special emphasis on induced fit, conformational selection, and their mathematical foundations to provide rigorous context for the analysis and interpretation of experimental data. We show that conformational selection is a surprisingly versatile mechanism that includes induced fit as a mathematical special case and even captures kinetic properties of more complex reaction schemes. These features make conformational selection a dominant mechanism of molecular recognition in biology, consistent with the rich conformational landscape accessible to biological macromolecules being unraveled by structural biology.

Visualization of structural dynamics of protein disulfide isomerase enzymes in catalysis of oxidative folding and reductive unfolding

Time-resolved single-molecule observations by high-speed atomic force microscopy (HS-AFM), have greatly advanced our understanding of how proteins operate to fulfill their unique functions. Using this device, we succeeded in visualizing two members of the protein disulfide isomerase family (PDIs) that act to catalyze oxidative folding and reductive unfolding in the endoplasmic reticulum (ER). ERdj5, an ER-resident disulfide reductase that promotes ER-associated degradation, reduces nonnative disulfide bonds of misfolded proteins utilizing the dynamics of its N-terminal and C-terminal clusters. With unfolded substrates, canonical PDI assembles to form a face-to-face dimer with a central hydrophobic cavity and multiple redox-active sites to accelerate oxidative folding inside the cavity. Altogether, PDIs exert highly dynamic mechanisms to ensure the protein quality control in the ER.

Recent advances in bioimaging with high-speed atomic force microscopy

Among various microscopic techniques for characterizing protein structures and functions, high-speed atomic force microscopy (HS-AFM) is a unique technique in that it allows direct visualization of structural changes and molecular interactions of proteins without any labeling in a liquid environment. Since the development of the HS-AFM was first reported in 2001, it has been applied to analyze the dynamics of various types of proteins, including motor proteins, membrane proteins, DNA-binding proteins, amyloid proteins, and artificial proteins. This method has now become a versatile tool indispensable for biophysical research. This short review summarizes some bioimaging applications of HS-AFM reported in the last few years and novel applications of HS-AFM utilizing the unique ability of AFM to gain mechanical properties of samples in addition to structural information.

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.

Queueing arrival and release mechanism for K+ permeation through a potassium channel

The mechanism underlying ion permeation through potassium channels still remains controversial. K+ ions permeate across a narrow selectivity filter (SF) in a single file. Conventional scenarios assume that K+ ions are tightly bound in the SF, and, thus, they are displaced from their energy well by ion-ion repulsion with an incoming ion. This tight coupling between entering and exiting ions has been called the "knock-on" mechanism. However, this paradigm is contradicted by experimental data measuring the water-ion flux coupling ratio, demonstrating fewer ion occupancies. Here, the results of molecular dynamics simulations of permeation through the KcsA potassium channel revealed an alternative mechanism. In the aligned ions in the SF (an ion queue), the outermost K+ was readily and spontaneously released toward the extracellular space, and the affinity of the relevant ion was ~ 50 mM. Based on this low-affinity regime, a simple queueing mechanism described by loose coupling of entering and exiting ions is proposed.

Allosteric Cooperativity in Proton Energy Conversion in A1-Type Cytochrome c Oxidase

Cytochrome c oxidase (CcO), the Cu_A, heme a, heme a₃, Cu_B enzyme of respiratory chain, converts the free energy released by aerobic cytochrome c oxidation into a membrane electrochemical proton gradient (ΔμH⁺). ΔμH⁺ derives from the membrane anisotropic arrangement of dioxygen reduction to two water molecules and transmembrane proton pumping from a negative (N) space to a positive (P) space separated by the membrane. Spectroscopic, potentiometric, and X-ray crystallographic analyses characterize allosteric cooperativity of dioxygen binding and reduction with protonmotive conformational states of CcO. These studies show that allosteric cooperativity stabilizes the favorable conformational state for conversion of redox energy into a transmembrane ΔμH⁺.