Biophysical journal最新文献_第10页

FTIR study of light-induced proton transfer and Ca²⁺ binding in T82D mutant of TAT rhodopsin. TAT rhodopsin 的 T82D 突变体中光诱导质子转移和 Ca2+ 结合的傅立叶变换红外光谱（FTIR）研究。

IF 3.2 3区生物学

Biophysical journal Pub Date : 2024-12-17 Epub Date: 2024-08-08 DOI: 10.1016/j.bpj.2024.08.005

Teppei Sugimoto, Kota Katayama, Hideki Kandori

{"title":"FTIR study of light-induced proton transfer and Ca2+ binding in T82D mutant of TAT rhodopsin.","authors":"Teppei Sugimoto, Kota Katayama, Hideki Kandori","doi":"10.1016/j.bpj.2024.08.005","DOIUrl":"10.1016/j.bpj.2024.08.005","url":null,"abstract":"Proton transfer reactions play important functional roles in many proteins, such as enzymes and transporters, which is also the case in rhodopsins. In fact, functional expression of rhodopsins accompanies intramolecular proton transfer reactions in many cases. One of the exceptional cases can be seen in the protonated form of marine bacterial TAT rhodopsin, which isomerizes the retinal by light but returns to the original state within 10-5 s. Thus, light energy is converted into heat without any function. In contrast, the T82D mutant of TAT rhodopsin conducts the light-induced deprotonation of the Schiff base at high pH. In this article, we report the structural analysis of T82D by means of difference Fourier transform infrared (FTIR) spectroscopy. In the light-induced difference FTIR spectra at 77 K, we observed little hydrogen out-of-plane vibrations for T82D as well as the wild-type (WT), suggesting that the planar chromophore structure itself is not the origin of the reversion from the K intermediate in WT TAT rhodopsin. Upon relaxation of the K intermediate, T82D forms the following intermediate, such as M, whereas K of WT returns to the original state. Present FTIR analysis revealed the proton transfer from the Schiff base to D82 in T82D upon formation of the M intermediate. It is accompanied by the second proton transfer from E54 to the Schiff base, forming the N intermediate, particularly in membranes. The equilibrium between the M and N intermediates corresponds to the protonation equilibrium between E54 and the Schiff base. We also found that Ca2+ binding takes place in T82D as well as WT but with 6 times lower affinity. An altered hydrogen-bonding network would be the origin of low affinity in T82D, where deprotonation of E54 is involved in the Ca2+ binding.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"4245-4255"},"PeriodicalIF":3.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141905801","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Nernst equilibrium, rectification, and saturation: Insights into ion channel behavior. 奈氏平衡、整流和饱和：离子通道行为透视。

IF 3.2 3区生物学

Biophysical journal Pub Date : 2024-12-17 Epub Date: 2024-10-30 DOI: 10.1016/j.bpj.2024.10.016

Ryan Carlsen, Hannah Weckel-Dahman, Jessica M J Swanson

{"title":"Nernst equilibrium, rectification, and saturation: Insights into ion channel behavior.","authors":"Ryan Carlsen, Hannah Weckel-Dahman, Jessica M J Swanson","doi":"10.1016/j.bpj.2024.10.016","DOIUrl":"10.1016/j.bpj.2024.10.016","url":null,"abstract":"The dissipation of electrochemical gradients through ion channels plays a central role in biology. Herein we use voltage-responsive kinetic models of ion channels to explore how electrical and chemical potentials differentially influence ion transport properties. These models demonstrate how electrically driven flux is greater than the Nernstian equivalent chemically driven flux yet still perfectly cancels when the two gradients oppose each other. We find that the location and relative stability of ion-binding sites dictates rectification properties by shifting the location of the most voltage-sensitive transitions. However, these rectification properties invert when bulk concentrations increase relative to the binding-site stabilities, moving the rate-limiting steps from uptake into a relatively empty channel to release from an ion-blocked full channel. Additionally, the origin of channel saturation is shown to depend on the free energy of uptake relative to bulk concentrations. Collectively these insights provide a framework for interpreting and predicting how channel properties manifest in electrochemical transport behavior.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"4304-4315"},"PeriodicalIF":3.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proton diffusion on the surface of mixed lipid membranes highlights the role of membrane composition. 混合脂膜表面的质子扩散凸显了膜成分的作用。

IF 3.2 3区生物学

Biophysical journal Pub Date : 2024-12-17 Epub Date: 2024-07-02 DOI: 10.1016/j.bpj.2024.07.002

Ambili Ramanthrikkovil Variyam, Mateusz Rzycki, Anna Yucknovsky, Alexei A Stuchebrukhov, Dominik Drabik, Nadav Amdursky

{"title":"Proton diffusion on the surface of mixed lipid membranes highlights the role of membrane composition.","authors":"Ambili Ramanthrikkovil Variyam, Mateusz Rzycki, Anna Yucknovsky, Alexei A Stuchebrukhov, Dominik Drabik, Nadav Amdursky","doi":"10.1016/j.bpj.2024.07.002","DOIUrl":"10.1016/j.bpj.2024.07.002","url":null,"abstract":"Proton circuits within biological membranes, the foundation of natural bioenergetic systems, are significantly influenced by the lipid compositions of different biological membranes. In this study, we investigate the influence of mixed lipid membrane composition on the proton transfer (PT) properties on the surface of the membrane. We track the excited-state PT (ESPT) process from a tethered probe to the membrane with timescales and length scales of PT relevant to bioenergetic systems. Two processes can happen during ESPT: the initial PT from the probe to the membrane at short timescales, followed by diffusion of dissociated protons around the probe on the membrane, and the possible geminate recombination with the probe at longer timescales. Here, we use membranes composed of mixtures of phosphatidylcholine (PC) and phosphatidic acid (PA). We show that the changes in the ESPT properties are not monotonous with the concentration of the lipid mixture; at a low concentration of PA in PC, we find that the membrane is a poor proton acceptor. Molecular dynamics simulations indicate that the membrane is more structured at this specific lipid mixture, with the least number of defects. Accordingly, we suggest that the structure of the membrane is an important factor in facilitating PT. We further show that the composition of the membrane affects the geminate proton diffusion around the probe, whereas, on a timescale of tens of nanoseconds, the dissociated proton is mostly lateral restricted to the membrane plane in PA membranes, while in PC, the diffusion is less restricted by the membrane.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"4200-4210"},"PeriodicalIF":3.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11700359/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141496991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Searching for proton transfer channels in respiratory complex I. 寻找呼吸复合体 I 中的质子转移通道

IF 3.2 3区生物学

Biophysical journal Pub Date : 2024-12-17 Epub Date: 2024-08-07 DOI: 10.1016/j.bpj.2024.07.041

Panyue Wang, Jackson Demaray, Stanislav Moroz, Alexei A Stuchebrukhov

{"title":"Searching for proton transfer channels in respiratory complex I.","authors":"Panyue Wang, Jackson Demaray, Stanislav Moroz, Alexei A Stuchebrukhov","doi":"10.1016/j.bpj.2024.07.041","DOIUrl":"10.1016/j.bpj.2024.07.041","url":null,"abstract":"We have explored a strategy to identify potential proton transfer channels using computational analysis of a protein structure based on Voronoi partitioning and applied it for the analysis of proton transfer pathways in redox-driven proton-pumping respiratory complex I. The analysis results in a network of connected voids/channels, which represent the dual structure of the protein; we then hydrated the identified channels using our water placement program Dowser++. Many theoretical water molecules found in the channels perfectly match the observed experimental water molecules in the structure; some other predicted water molecules have not been resolved in the experiments. The channels are of varying cross sections. Some channels are big enough to accommodate water molecules that are suitable to conduct protons; others are too narrow to hold water but require only minor conformational changes to accommodate proton transfer. We provide a preliminary analysis of the proton conductivity of the network channels, classifying the proton transfer channels as open, closed, and partially open, and discuss possible conformational changes that can modulate, i.e., open and close, the channels.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"4233-4244"},"PeriodicalIF":3.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11700350/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141878305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dimerization is required for the glycosylation of S1-S2 linker of sea urchin voltage-gated proton channel Hv1. 海胆电压门控质子通道 Hv1 的 S1-S2 连接器糖基化需要二聚化。

IF 3.2 3区生物学

Biophysical journal Pub Date : 2024-12-17 Epub Date: 2024-07-31 DOI: 10.1016/j.bpj.2024.07.034

Yoshifumi Okochi, Yuka Jinno, Yasushi Okamura

{"title":"Dimerization is required for the glycosylation of S1-S2 linker of sea urchin voltage-gated proton channel Hv1.","authors":"Yoshifumi Okochi, Yuka Jinno, Yasushi Okamura","doi":"10.1016/j.bpj.2024.07.034","DOIUrl":"10.1016/j.bpj.2024.07.034","url":null,"abstract":"Multimerization of ion channels is essential for establishing the ion-selective pathway and tuning the gating regulated by membrane potential, second messengers, and temperature. Voltage-gated proton channel, Hv1, consists of voltage-sensor domain and coiled-coil domain. Hv1 forms dimer, whereas voltage-dependent channel activity is self-contained in monomer unlike many ion channels, which assemble to form ion-conductive pathways among multiple subunits. Dimerization of Hv1 is necessary for cooperative gating, but other roles of dimerization in physiological aspects are still largely unclear. In this study, we show that dimerization of Hv1 takes place in ER. Sea urchin Hv1 (Strongylocentrotus purpuratus Hv1: SpHv1) was glycosylated in the consensus sequence for N-linked glycosylation within the S1-S2 extracellular loop. However, glycosylation was not observed in the monomeric SpHv1 that lacks the coiled-coil domain. A version of mHv1 in which the S1-S2 loop was replaced by that of SpHv1 showed glycosylation and its monomeric form was not glycosylated. Tandem dimer of monomeric SpHv1 underwent glycosylation, suggesting that dimerization of Hv1 is required for glycosylation. Moreover, when monomeric Hv1 has a dilysine motif in the C-terminal end, which is known to act as a retrieval signal from Golgi to ER, prolonging the time of residency in ER, it was glycosylated. Overall, our results suggest that monomeric SpHv1 does not stay long in ER, thereby escaping glycosylation, while the dimerization causes the proteins to stay longer in ER. Thus, the findings highlight the novel significance of dimerization of Hv1: regulation of biogenesis and maturation of the proteins in intracellular compartments.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"4221-4232"},"PeriodicalIF":3.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141858923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Effects of pH on opioid receptor activation and implications for drug design. pH 值对阿片受体活化的影响及其对药物设计的意义。

IF 3.2 3区生物学

Biophysical journal Pub Date : 2024-12-17 Epub Date: 2024-07-05 DOI: 10.1016/j.bpj.2024.07.007

Christoph Stein

引用次数: 0

How and when to measure mitochondrial inner membrane potentials. 如何以及何时测量线粒体内膜电位？

IF 3.2 3区生物学

Biophysical journal Pub Date : 2024-12-17 Epub Date: 2024-03-07 DOI: 10.1016/j.bpj.2024.03.011

Alicia J Kowaltowski, Fernando Abdulkader

{"title":"How and when to measure mitochondrial inner membrane potentials.","authors":"Alicia J Kowaltowski, Fernando Abdulkader","doi":"10.1016/j.bpj.2024.03.011","DOIUrl":"10.1016/j.bpj.2024.03.011","url":null,"abstract":"The scientific literature on mitochondria has increased significantly over the years due to findings that these organelles have widespread roles in the onset and progression of pathological conditions such as metabolic disorders, neurodegenerative and cardiovascular diseases, inflammation, and cancer. Researchers have extensively explored how mitochondrial properties and functions are modified in different models, often using fluorescent inner mitochondrial membrane potential (ΔΨm) probes to assess functional mitochondrial aspects such as protonmotive force and oxidative phosphorylation. This review provides an overview of existing techniques to measure ΔpH and ΔΨm, highlighting their advantages, limitations, and applications. It discusses drawbacks of ΔΨm probes, especially when used without calibration, and conditions where alternative methods should replace ΔΨm measurements for the benefit of the specific scientific objectives entailed. Studies investigating mitochondria and their vast biological roles would be significantly advanced by the understanding of the correct applications as well as limitations of protonmotive force measurements and use of fluorescent ΔΨm probes, adopting more precise, artifact-free, sensitive, and quantitative measurements of mitochondrial functionality.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"4150-4157"},"PeriodicalIF":3.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11700358/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140058620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Interaction with stomatin directs human proton channels into cholesterol-dependent membrane domains. 与 stomatin 的相互作用引导人类质子通道进入胆固醇依赖膜域。

IF 3.2 3区生物学

Biophysical journal Pub Date : 2024-12-17 Epub Date: 2024-03-05 DOI: 10.1016/j.bpj.2024.03.003

Artem G Ayuyan, Vladimir V Cherny, Gustavo Chaves, Boris Musset, Fredric S Cohen, Thomas E DeCoursey

{"title":"Interaction with stomatin directs human proton channels into cholesterol-dependent membrane domains.","authors":"Artem G Ayuyan, Vladimir V Cherny, Gustavo Chaves, Boris Musset, Fredric S Cohen, Thomas E DeCoursey","doi":"10.1016/j.bpj.2024.03.003","DOIUrl":"10.1016/j.bpj.2024.03.003","url":null,"abstract":"Many membrane proteins are modulated by cholesterol. Here we report profound effects of cholesterol depletion and restoration on the human voltage-gated proton channel, hHV1, in excised patches but negligible effects in the whole-cell configuration. Despite the presence of a putative cholesterol-binding site, a CARC motif in hHV1, mutation of this motif did not affect cholesterol effects. The murine HV1 lacks a CARC sequence but displays similar cholesterol effects. These results argue against a direct effect of cholesterol on the HV1 protein. However, the data are fully explainable if HV1 preferentially associates with cholesterol-dependent lipid domains, or \"rafts.\" The rafts would be expected to concentrate in the membrane/glass interface and to be depleted from the electrically accessible patch membrane. This idea is supported by evidence that HV1 channels can diffuse between seal and patch membranes when suction is applied. Simultaneous truncation of the large intracellular N and C termini of hHV1 greatly attenuated the cholesterol effect, but C truncation alone did not; this suggests that the N terminus is the region of attachment to lipid domains. Searching for abundant raft-associated proteins led to stomatin. Co-immunoprecipitation experiment results were consistent with hHV1 binding to stomatin. The stomatin-mediated association of HV1 with cholesterol-dependent lipid domains provides a mechanism for cells to direct HV1 to subcellular locations where it is needed, such as the phagosome in leukocytes.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"4180-4190"},"PeriodicalIF":3.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140038629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An affordable convertible: Engineering proton transfer pathways in microbial rhodopsins. 经济实惠的敞篷车--微生物红蛋白中质子转移途径的工程设计。

IF 3.2 3区生物学

Biophysical journal Pub Date : 2024-12-17 Epub Date: 2024-08-22 DOI: 10.1016/j.bpj.2024.08.014

Leonid S Brown

引用次数: 0

Zinc inhibits the voltage-gated proton channel HCNL1. 锌抑制电压门控质子通道 HCNL1。

IF 3.2 3区生物学

Biophysical journal Pub Date : 2024-12-17 Epub Date: 2024-08-28 DOI: 10.1016/j.bpj.2024.08.018

Makoto F Kuwabara, Joschua Klemptner, Julia Muth, Emilia De Martino, Dominik Oliver, Thomas K Berger

{"title":"Zinc inhibits the voltage-gated proton channel HCNL1.","authors":"Makoto F Kuwabara, Joschua Klemptner, Julia Muth, Emilia De Martino, Dominik Oliver, Thomas K Berger","doi":"10.1016/j.bpj.2024.08.018","DOIUrl":"10.1016/j.bpj.2024.08.018","url":null,"abstract":"Voltage-gated ion channels allow ion flux across biological membranes in response to changes in the membrane potential. HCNL1 is a recently discovered voltage-gated ion channel that selectively conducts protons through its voltage-sensing domain (VSD), reminiscent of the well-studied depolarization-activated Hv1 proton channel. However, HCNL1 is activated by hyperpolarization, allowing the influx of protons, which leads to an intracellular acidification in zebrafish sperm. Zinc ions (Zn2+) are important cofactors in many proteins and essential for sperm physiology. Proton channels such as Hv1 and Otopetrin1 are inhibited by Zn2+. We investigated the effect of Zn2+ on heterologously expressed HCNL1 channels using electrophysiological and fluorometric techniques. Extracellular Zn2+ inhibits HCNL1 currents with an apparent half-maximal inhibition (IC50) of 26 μM. Zn2+ slows voltage-dependent current kinetics, shifts the voltage-dependent activation to more negative potentials, and alters hyperpolarization-induced conformational changes of the voltage sensor. Our data suggest that extracellular Zn2+ inhibits HCNL1 currents by multiple mechanisms, including modulation of channel gating. Two histidine residues located at the extracellular side of the VSD might weakly contribute to Zn2+ coordination: mutants with either histidine replaced with alanine show modest shifts of the IC50 values to higher concentrations. Interestingly, Zn2+ inhibits HCNL1 at even lower concentrations from the intracellular side (IC50 ≈ 0.5 μM). A histidine residue at the intracellular end of S1 (position 50) is important for Zn2+ binding: much higher Zn2+ concentrations are required to inhibit the mutant HCNL1-H50A (IC50 ≈ 106 μM). We anticipate that Zn2+ will be a useful ion to study the structure-function relationship of HCNL1 as well as the physiological role of HCNL1 in zebrafish sperm.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"4256-4265"},"PeriodicalIF":3.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142104008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0