1
|
Lee S, Poojari CS, Maznichenko A, Roesel D, Swiderska I, Pohl P, Hub JS, Roke S. Dynamic Second Harmonic Imaging of Proton Translocation Through Water Needles in Lipid Membranes. J Am Chem Soc 2024; 146:19818-19827. [PMID: 38991220 PMCID: PMC11273352 DOI: 10.1021/jacs.4c02810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 07/13/2024]
Abstract
Proton translocation through lipid membranes is a fundamental process in the field of biology. Several theoretical models have been developed and presented over the years to explain the phenomenon, yet the exact mechanism is still not well understood. Here, we show that proton translocation is directly related to membrane potential fluctuations. Using high-throughput wide-field second harmonic (SH) microscopy, we report apparently universal transmembrane potential fluctuations in lipid membrane systems. Molecular simulations and free energy calculations suggest that H+ permeation proceeds predominantly across a thin, membrane-spanning water needle and that the transient transmembrane potential drives H+ ions across the water needle. This mechanism differs from the transport of other cations that require completely open pores for transport and follows naturally from the well-known Grotthuss mechanism for proton transport in bulk water. Furthermore, SH imaging and conductivity measurements reveal that the rate of proton transport depends on the structure of the hydrophobic core of bilayer membranes.
Collapse
Affiliation(s)
- Seonwoo Lee
- Laboratory
for fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI),
and Institute of Materials Science (IMX), School of Engineering (STI),
and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Chetan S. Poojari
- Theoretical
Physics and Center for Biophysics, Saarland
University, Saarbrücken 66123, Germany
| | - Anna Maznichenko
- Institute
of Biophysics, Johannes Kepler University
Linz, Gruberstraße 40, Linz 4020, Austria
| | - David Roesel
- Laboratory
for fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI),
and Institute of Materials Science (IMX), School of Engineering (STI),
and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Iwona Swiderska
- Laboratory
for fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI),
and Institute of Materials Science (IMX), School of Engineering (STI),
and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Peter Pohl
- Institute
of Biophysics, Johannes Kepler University
Linz, Gruberstraße 40, Linz 4020, Austria
| | - Jochen S. Hub
- Theoretical
Physics and Center for Biophysics, Saarland
University, Saarbrücken 66123, Germany
| | - Sylvie Roke
- Laboratory
for fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI),
and Institute of Materials Science (IMX), School of Engineering (STI),
and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| |
Collapse
|
2
|
Neelam, Singh H. 1H, 15N and 13C resonance assignments of S2A mutant of human carbonic anhydrase II. BIOMOLECULAR NMR ASSIGNMENTS 2024; 18:45-49. [PMID: 38520652 DOI: 10.1007/s12104-024-10166-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/22/2024] [Indexed: 03/25/2024]
Abstract
In preparation for a detailed exploration of the structural and functional aspects of the Ser2Ala mutant of human carbonic anhydrase II, we present here almost complete sequence-specific resonance assignments for 1H, 15N, and 13C. The mutation of serine to alanine at position 2, located in the N-terminal region of the enzyme, significantly alters the hydrophilic nature of the site, rendering it hydrophobic. Consequently, there is an underlying assumption that this mutation would repel water from the site. However, intriguingly, comparative analysis of the mutant structure with the wild type reveals minimal discernible differences. These assignments serve as the basis for in-depth studies on histidine dynamics, protonation states, and its intricate role in protein-water interactions and catalysis.
Collapse
Affiliation(s)
- Neelam
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Berhampur, Odisha, 760010, India
| | - Himanshu Singh
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Berhampur, Odisha, 760010, India.
| |
Collapse
|
3
|
Savin AV, Kivshar YS. Stabilization of hydrogen-bonded molecular chains by carbon nanotubes. CHAOS (WOODBURY, N.Y.) 2024; 34:043111. [PMID: 38572948 DOI: 10.1063/5.0197401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024]
Abstract
We study numerically nonlinear dynamics of several types of molecular systems composed of hydrogen-bonded chains placed inside carbon nanotubes with open edges. We demonstrate that carbon nanotubes provide a stabilization mechanism for quasi-one-dimensional molecular chains via the formation of their secondary structures. In particular, a polypeptide chain (Gly)N placed inside a carbon nanotube can form a stable helical chain (310-, α-, π-, and β-helix) with parallel chains of hydrogen-bonded peptide groups. A chain of hydrogen fluoride molecules ⋯FH⋯FH⋯FH can form a hydrogen-bonded zigzag chain. Remarkably, we demonstrate that for molecular complexes (Gly)N∈CNT and (FH)N∈CNT, the hydrogen-bonded chains will remain stable even at T=500 K. Thus, our results suggest that the use of carbon nanotubes with encapsulated hydrogen fluoride molecules may be important for the realization of high proton conductivity at high temperatures.
Collapse
Affiliation(s)
- Alexander V Savin
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
- Academic Department of Innovational Materials and Technologies Chemistry, Plekhanov Russian University of Economics, Moscow 117997, Russia
| | - Yuri S Kivshar
- Nonlinear Physics Center, Research School of Physics, Australian National University, Canberra, ACT 2601, Australia
| |
Collapse
|
4
|
Fidalgo-Marijuan A, Ruiz de Larramendi I, Barandika G. Superprotonic Conductivity in a Metalloporphyrin-Based SMOF (Supramolecular Metal-Organic Framework). NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:398. [PMID: 38470729 PMCID: PMC10934030 DOI: 10.3390/nano14050398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024]
Abstract
Metal-organic frameworks and supramolecular metal-organic frameworks (SMOFs) exhibit great potential for a broad range of applications taking advantage of the high surface area and pore sizes and tunable chemistry. In particular, metalloporphyrin-based MOFs and SMOFs are becoming of great importance in many fields due to the bioessential functions of these macrocycles that are being mimicked. On the other hand, during the last years, proton-conducting materials have aroused much interest, and those presenting high conductivity values are potential candidates to play a key role in some solid-state electrochemical devices such as batteries and fuel cells. In this way, using metalloporphyrins as building units we have obtained a new crystalline material with formula [H(bipy)]2[(MnTPPS)(H2O)2]·2bipy·14H2O, where bipy is 4,4'-bipyidine and TPPS4- is the meso-tetra(4-sulfonatephenyl) porphyrin. The crystal structure shows a zig-zag water chain along the [100] direction located between the sulfonate groups of the porphyrin. Taking into account those structural features, the compound was tested for proton conduction by complex electrochemical impedance spectroscopy (EIS). The as-obtained conductivity is 1 × 10-2 S·cm-1 at 40 °C and 98% relative humidity, which is a remarkably high value.
Collapse
Affiliation(s)
- Arkaitz Fidalgo-Marijuan
- Department of Organic and Inorganic Chemistry, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain;
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Idoia Ruiz de Larramendi
- Department of Organic and Inorganic Chemistry, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain;
| | - Gotzone Barandika
- Department of Organic and Inorganic Chemistry, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain;
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, Barrio Sarriena s/n, 48940 Leioa, Spain
| |
Collapse
|
5
|
DeCoursey TE. Transcendent Aspects of Proton Channels. Annu Rev Physiol 2024; 86:357-377. [PMID: 37931166 PMCID: PMC10938948 DOI: 10.1146/annurev-physiol-042222-023242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
A handful of biological proton-selective ion channels exist. Some open at positive or negative membrane potentials, others open at low or high pH, and some are light activated. This review focuses on common features that result from the unique properties of protons. Proton conduction through water or proteins differs qualitatively from that of all other ions. Extraordinary proton selectivity is needed to ensure that protons permeate and other ions do not. Proton selectivity arises from a proton pathway comprising a hydrogen-bonded chain that typically includes at least one titratable amino acid side chain. The enormously diverse functions of proton channels in disparate regions of the phylogenetic tree can be summarized by considering the chemical and electrical consequences of proton flux across membranes. This review discusses examples of cells in which proton efflux serves to increase pHi, decrease pHo, control the membrane potential, generate action potentials, or compensate transmembrane movement of electrical charge.
Collapse
Affiliation(s)
- Thomas E DeCoursey
- Department of Physiology & Biophysics, Rush University, Chicago, Illinois, USA;
| |
Collapse
|
6
|
Urui T, Hayashi K, Mizuno M, Inoue K, Kandori H, Mizutani Y. Cis- Trans Reisomerization Preceding Reprotonation of the Retinal Chromophore Is Common to the Schizorhodopsin Family: A Simple and Rational Mechanism for Inward Proton Pumping. J Phys Chem B 2024; 128:744-754. [PMID: 38204413 DOI: 10.1021/acs.jpcb.3c07510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
The creation of unidirectional ion transporters across membranes represents one of the greatest challenges in chemistry. Proton-pumping rhodopsins are composed of seven transmembrane helices with a retinal chromophore bound to a lysine side chain via a Schiff base linkage and provide valuable insights for designing such transporters. What makes these transporters particularly intriguing is the discovery of both outward and inward proton-pumping rhodopsins. Surprisingly, despite sharing identical overall structures and membrane topologies, these proteins facilitate proton transport in opposite directions, implying an underlying rational mechanism that can transport protons in different directions within similar protein structures. In this study, we unraveled this mechanism by examining the chromophore structures of deprotonated intermediates in schizorhodopsins, a recently discovered subfamily of inward proton-pumping rhodopsins, using time-resolved resonance Raman spectroscopy. The photocycle of schizorhodopsins revealed the cis-trans thermal isomerization that precedes reprotonation at the Schiff base of the retinal chromophore. Notably, this order has not been observed in other proton-pumping rhodopsins, but here, it was observed in all seven schizorhodopsins studied across the archaeal domain, strongly suggesting that cis-trans thermal isomerization preceding reprotonation is a universal feature of the schizorhodopsin family. Based on these findings, we propose a structural basis for the remarkable order of events crucial for facilitating inward proton transport. The mechanism underlying inward proton transport by schizorhodopsins is straightforward and rational. The insights obtained from this study hold great promise for the design of transmembrane unidirectional ion transporters.
Collapse
Affiliation(s)
- Taito Urui
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kouhei Hayashi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| |
Collapse
|
7
|
Demchenko AP. Proton transfer reactions: from photochemistry to biochemistry and bioenergetics. BBA ADVANCES 2023. [DOI: 10.1016/j.bbadva.2023.100085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
|
8
|
Pennathur AK, Tseng C, Salazar N, Dawlaty JM. Controlling Water Delivery to an Electrochemical Interface with Surfactants. J Am Chem Soc 2023; 145:2421-2429. [PMID: 36688713 DOI: 10.1021/jacs.2c11503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Most electrochemical reactions require delivery of protons, often from water, to surface-adsorbed species. However, water also acts as a competitor to many such processes by directly reacting with the electrode, which necessitates using water in small amounts. Controlling the water content and structure near the surface is an important frontier in directing the reactivity and selectivity of electrochemical reactions. Surfactants accumulate near surfaces, and therefore, they can be used as agents to control interfacial water. Using mid-IR spectro-electrochemistry, we show that a modest concentration (1 mM) of the cationic surfactant CTAB in mixtures of 10 M water in an organic solvent (dDMSO) has a large effect on the interfacial water concentration, changing it by up to ∼35% in the presence of an applied potential. The major cause of water content change is displacement due to the accumulation or depletion of surfactants driven by potential. Two forces drive the surfactants to the electrode: the applied potential and the hydrophobic interactions with the water in the bulk. We have quantified their competition by varying the water content in the bulk. To our knowledge, for the first time, we have identified the electrochemical equivalent of the hydrophobic drive. For our system, a change in applied potential of 1 V has the same effect as adding a 0.55 mole fraction of water to the bulk. This work illustrates the significance of surfactants in the partitioning of water between the bulk and the surface and paves the way toward engineering interfacial water structures for controlling electrochemical reactions.
Collapse
Affiliation(s)
- Anuj K Pennathur
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Cindy Tseng
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Noemi Salazar
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jahan M Dawlaty
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| |
Collapse
|
9
|
Yan T, Liu S, Xu J, Sun H, Yu S, Liu J. Unimolecular Helix-Based Transmembrane Nanochannel with a Smallest Luminal Cavity of 1 Å Expressing High Proton Selectivity and Transport Activity. NANO LETTERS 2021; 21:10462-10468. [PMID: 34860025 DOI: 10.1021/acs.nanolett.1c03858] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Natural protein channels have evolved with exquisite structures to transport ions selectively and rapidly. Learning from nature to construct biomimetic artificial channels is always challenging. Herein we present a unimolecular transmembrane proton channel by quinoline-derived helix, which exhibited highly selective and ultrafast proton transport behaviors. This helix-based channel possesses a small luminal cavity of 1 Å in diameter, which could efficiently reject the permeation of cations, anions or water molecules but only permits the translocation of protons owing to the size effect. The proton flow rate exceeded 107 H+ s-1 channel-1 and reached the same magnitude with gramicidin A. Mechanism investigation revealed that the directionally arrayed NH-chain inside the synthetic channel played a pivotal role during the proton flux. This work not only presented a helix-based channel with the smallest observable nanopore, but also unveiled an unexplored pathway for realizing efficient transport of protons via the consecutive NH-chain.
Collapse
Affiliation(s)
- Tengfei Yan
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China
| | - Shengda Liu
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China
| | - Jiayun Xu
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China
| | - Hongcheng Sun
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China
| | - Shuangjiang Yu
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China
| | - Junqiu Liu
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China
- College of Chemistry, State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, China
| |
Collapse
|
10
|
Kell DB. A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation. Adv Microb Physiol 2021; 78:1-177. [PMID: 34147184 DOI: 10.1016/bs.ampbs.2021.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.
Collapse
Affiliation(s)
- Douglas B Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative, Biology, University of Liverpool, Liverpool, United Kingdom; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
| |
Collapse
|
11
|
Morelli AM, Ravera S, Panfoli I. The aerobic mitochondrial ATP synthesis from a comprehensive point of view. Open Biol 2020; 10:200224. [PMID: 33081639 PMCID: PMC7653358 DOI: 10.1098/rsob.200224] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Most of the ATP to satisfy the energetic demands of the cell is produced by the F1Fo-ATP synthase (ATP synthase) which can also function outside the mitochondria. Active oxidative phosphorylation (OxPhos) was shown to operate in the photoreceptor outer segment, myelin sheath, exosomes, microvesicles, cell plasma membranes and platelets. The mitochondria would possess the exclusive ability to assemble the OxPhos molecular machinery so to share it with the endoplasmic reticulum (ER) and eventually export the ability to aerobically synthesize ATP in true extra-mitochondrial districts. The ER lipid rafts expressing OxPhos components is indicative of the close contact of the two organelles, bearing different evolutionary origins, to maximize the OxPhos efficiency, exiting in molecular transfer from the mitochondria to the ER. This implies that its malfunctioning could trigger a generalized oxidative stress. This is consistent with the most recent interpretations of the evolutionary symbiotic process whose necessary prerequisite appears to be the presence of the internal membrane system inside the eukaryote precursor, of probable archaeal origin allowing the engulfing of the α-proteobacterial precursor of mitochondria. The process of OxPhos in myelin is here studied in depth. A model is provided contemplating the biface arrangement of the nanomotor ATP synthase in the myelin sheath.
Collapse
Affiliation(s)
- Alessandro Maria Morelli
- Pharmacy Department (DIFAR), Biochemistry Laboratory, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Silvia Ravera
- Experimental Medicine Department (DIMES), University of Genova, Via De Toni, 14, 16132 Genova, Italy
| | - Isabella Panfoli
- Pharmacy Department (DIFAR), Biochemistry Laboratory, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| |
Collapse
|
12
|
Lee JW. Protonic conductor: better understanding neural resting and action potential. J Neurophysiol 2020; 124:1029-1044. [PMID: 32816602 DOI: 10.1152/jn.00281.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
With the employment of the transmembrane electrostatic proton localization theory with a new membrane potential equation, neural resting and action potential is now much better understood as the voltage contributed by the localized protons/cations at a neural liquid- membrane interface. Accordingly, the neural resting/action potential is essentially a protonic/cationic membrane capacitor behavior. It is now understood with a newly formulated action potential equation: when action potential is <0 (negative number), the localized protons/cations charge density at the liquid-membrane interface along the periplasmic side is >0 (positive number); when the action potential is >0, the concentration of the localized protons and localized nonproton cations is <0, indicating a "depolarization" state. The nonlinear curve of the localized protons/cations charge density in the real-time domain of an action potential spike appears as an inverse mirror image to the action potential. The newly formulated action potential equation provides biophysical insights for neuron electrophysiology, which may represent a complementary development to the classic Goldman-Hodgkin-Katz equation. With the use of the action potential equation, the biological significance of axon myelination is now also elucidated as to provide protonic insulation and prevent any ions both inside and outside of the neuron from interfering with the action potential signal, so that the action potential can quickly propagate along the axon with minimal (e.g., 40 times less) energy requirement.NEW & NOTEWORTHY The newly formulated action potential equation provides biophysical insights for neuron electrophysiology, which may represent a complementary development to the classic Goldman-Hodgkin-Katz equation. The nonlinear curve of the localized protons/cations charge density in the real-time domain of an action potential spike appears as an inverse mirror image to the action potential. The biological significance of axon myelination is now elucidated as to provide protonic insulation and prevent any ions from interfering with action potential signal.
Collapse
Affiliation(s)
- James Weifu Lee
- Department of Chemistry & Biochemistry, Old Dominion University, Norfolk, Virginia
| |
Collapse
|
13
|
Liu Q, Li Z, Wang D, Li Z, Peng X, Liu C, Zheng P. Metal Organic Frameworks Modified Proton Exchange Membranes for Fuel Cells. Front Chem 2020; 8:694. [PMID: 32850683 PMCID: PMC7432281 DOI: 10.3389/fchem.2020.00694] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 07/06/2020] [Indexed: 01/04/2023] Open
Abstract
Proton exchange membrane fuel cells (PEMFCs) have received considerable interest due to their low operating temperature and high energy conversion rate. However, their practical implement suffers from significant performance challenge. In particular, proton exchange membrane (PEM) as the core component of PEMFCs, have shown a strong correlation between its properties (e.g., proton conductivity, dimensional stability) and the performance of fuel cells. Metal-organic frameworks (MOFs) as porous inorganic-organic hybrid materials have attracted extensive attention in gas storage, gas separation and reaction catalysis. Recently, the MOFs-modified PEMs have shown outstanding performance, which have great merit in commercial application. This manuscript presents an overview of the recent progress in the modification of PEMs with MOFs, with a special focus on the modification mechanism of MOFs on the properties of composite membranes. The characteristics of different types of MOFs in modified application were summarized.
Collapse
Affiliation(s)
- Quanyi Liu
- College of Civil Aviation Safety Engineering, Civil Aviation Flight University of China, Guanghan, China
| | - Zekun Li
- College of Civil Aviation Safety Engineering, Civil Aviation Flight University of China, Guanghan, China
| | - Donghui Wang
- College of Civil Aviation Safety Engineering, Civil Aviation Flight University of China, Guanghan, China
| | - Zhifa Li
- College of Civil Aviation Safety Engineering, Civil Aviation Flight University of China, Guanghan, China
| | - Xiaoliang Peng
- College of Civil Aviation Safety Engineering, Civil Aviation Flight University of China, Guanghan, China
| | - Chuanbang Liu
- College of Civil Aviation Safety Engineering, Civil Aviation Flight University of China, Guanghan, China
| | - Penglun Zheng
- College of Civil Aviation Safety Engineering, Civil Aviation Flight University of China, Guanghan, China
| |
Collapse
|
14
|
A common coupling mechanism for A-type heme-copper oxidases from bacteria to mitochondria. Proc Natl Acad Sci U S A 2020; 117:9349-9355. [PMID: 32291342 PMCID: PMC7196763 DOI: 10.1073/pnas.2001572117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We present a comprehensive investigation of mitochondrial DNA-encoded variants of cytochrome c oxidase (CcO) that harbor mutations within their core catalytic subunit I, designed to interrogate the presently disputed functions of the three putative proton channels. We assess overall respiratory competence, specific CcO catalytic activity, and, most importantly, proton/electron (H+/e−) stoichiometry from adenosine diphosphate to oxygen ratio measurements on preparations of intact mitochondria. We unequivocally show that yeast mitochondrial CcO uses the D-channel to translocate protons across its hydrophilic core, providing direct evidence in support of a common proton pumping mechanism across all members of the A-type heme-copper oxidase superfamily, independent of their bacterial or mitochondrial origin. Mitochondria metabolize almost all the oxygen that we consume, reducing it to water by cytochrome c oxidase (CcO). CcO maximizes energy capture into the protonmotive force by pumping protons across the mitochondrial inner membrane. Forty years after the H+/e− stoichiometry was established, a consensus has yet to be reached on the route taken by pumped protons to traverse CcO’s hydrophobic core and on whether bacterial and mitochondrial CcOs operate via the same coupling mechanism. To resolve this, we exploited the unique amenability to mitochondrial DNA mutagenesis of the yeast Saccharomyces cerevisiae to introduce single point mutations in the hydrophilic pathways of CcO to test function. From adenosine diphosphate to oxygen ratio measurements on preparations of intact mitochondria, we definitely established that the D-channel, and not the H-channel, is the proton pump of the yeast mitochondrial enzyme, supporting an identical coupling mechanism in all forms of the enzyme.
Collapse
|
15
|
Morelli AM, Ravera S, Calzia D, Panfoli I. An update of the chemiosmotic theory as suggested by possible proton currents inside the coupling membrane. Open Biol 2020; 9:180221. [PMID: 30966998 PMCID: PMC6501646 DOI: 10.1098/rsob.180221] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Understanding how biological systems convert and store energy is a primary purpose of basic research. However, despite Mitchell's chemiosmotic theory, we are far from the complete description of basic processes such as oxidative phosphorylation (OXPHOS) and photosynthesis. After more than half a century, the chemiosmotic theory may need updating, thanks to the latest structural data on respiratory chain complexes. In particular, up-to date technologies, such as those using fluorescence indicators following proton displacements, have shown that proton translocation is lateral rather than transversal with respect to the coupling membrane. Furthermore, the definition of the physical species involved in the transfer (proton, hydroxonium ion or proton currents) is still an unresolved issue, even though the latest acquisitions support the idea that protonic currents, difficult to measure, are involved. Moreover, FoF1-ATP synthase ubiquitous motor enzyme has the peculiarity (unlike most enzymes) of affecting the thermodynamic equilibrium of ATP synthesis. It seems that the concept of diffusion of the proton charge expressed more than two centuries ago by Theodor von Grotthuss is to be taken into consideration to resolve these issues. All these uncertainties remind us that also in biology it is necessary to consider the Heisenberg indeterminacy principle, which sets limits to analytical questions.
Collapse
Affiliation(s)
- Alessandro Maria Morelli
- 1 Pharmacy Department, Biochemistry Lab, University of Genova , Viale Benedetto XV 3, 16132 Genova , Italy
| | - Silvia Ravera
- 2 Experimental Medicine Department, University of Genova , Via De Toni 14, 16132 Genova , Italy
| | - Daniela Calzia
- 1 Pharmacy Department, Biochemistry Lab, University of Genova , Viale Benedetto XV 3, 16132 Genova , Italy
| | - Isabella Panfoli
- 2 Experimental Medicine Department, University of Genova , Via De Toni 14, 16132 Genova , Italy
| |
Collapse
|
16
|
Malkamäki A, Meunier B, Reidelbach M, Rich PR, Sharma V. The H channel is not a proton transfer path in yeast cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:717-723. [PMID: 31374214 DOI: 10.1016/j.bbabio.2019.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/24/2019] [Accepted: 07/29/2019] [Indexed: 10/26/2022]
Abstract
Cytochrome c oxidases (CcOs) in the respiratory chains of mitochondria and bacteria are primary consumers of molecular oxygen, converting it to water with the concomitant pumping of protons across the membrane to establish a proton electrochemical gradient. Despite a relatively well understood proton pumping mechanism of bacterial CcOs, the role of the H channel in mitochondrial forms of CcO remains debated. Here, we used site-directed mutagenesis to modify a central residue of the lower span of the H channel, Q413, in the genetically tractable yeast Saccharomyces cerevisiae. Exchange of Q413 to several different amino acids showed no effect on rates and efficiencies of respiratory cell growth, and redox potential measurements indicated minimal electrostatic interaction between the 413 locus and the nearest redox active component heme a. These findings clearly exclude a primary role of this section of the H channel in proton pumping in yeast CcO. In agreement with the experimental data, atomistic molecular dynamics simulations and continuum electrostatic calculations on wildtype and mutant yeast CcOs highlight potential bottlenecks in proton transfer through this route. Our data highlight the preference for neutral residues in the 413 locus, precluding sufficient hydration for formation of a proton conducting wire.
Collapse
Affiliation(s)
- Aapo Malkamäki
- Department of Physics, P. O. Box 64, University of Helsinki, 00014 Helsinki, Finland
| | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, Université Paris Saclay, 91198 Gif sur Yvette, France
| | - Marco Reidelbach
- Department of Physics, P. O. Box 64, University of Helsinki, 00014 Helsinki, Finland
| | - Peter R Rich
- Department of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
| | - Vivek Sharma
- Department of Physics, P. O. Box 64, University of Helsinki, 00014 Helsinki, Finland; Institute of Biotechnology, P. O. Box 56, University of Helsinki, 00014 Helsinki, Finland.
| |
Collapse
|
17
|
Maréchal A, Hartley AM, Warelow TP, Meunier B, Rich PR. Comparison of redox and ligand binding behaviour of yeast and bovine cytochrome c oxidases using FTIR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:705-711. [PMID: 29852141 PMCID: PMC6094048 DOI: 10.1016/j.bbabio.2018.05.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/18/2018] [Accepted: 05/24/2018] [Indexed: 11/20/2022]
Abstract
Redox and CO photolysis FTIR spectra of yeast cytochrome c oxidase WT and mutants are compared to those from bovine and P. denitrificans CcOs in order to establish common functional features. All display changes that can be assigned to their E242 (bovine numbering) equivalent and to weakly H-bonded water molecules. The additional redox-sensitive band reported at 1736 cm−1 in bovine CcO and previously assigned to D51 is absent from yeast CcO and couldn't be restored by introduction of a D residue at the equivalent position of the yeast protein. Redox spectra of yeast CcO also show much smaller changes in the amide I region, which may relate to structural differences in the region around D51 and the subunit I/II interface. Redox-induced FTIR difference spectra of WT and mutant yeast CcO are presented. Functionally-relevant features are compared with other A1-type haem copper oxidases. On oxidoreduction, all show perturbations of bovine residue E242 Introduction of bovine D51 in yeast doesn't result in an additional IR redox band. On photolysis of the FR-CO form all show perturbations of E242 and water molecules
Collapse
Affiliation(s)
- Amandine Maréchal
- Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK; Department of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
| | - Andrew M Hartley
- Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Thomas P Warelow
- Department of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Peter R Rich
- Department of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
| |
Collapse
|
18
|
DeCoursey TE. Voltage and pH sensing by the voltage-gated proton channel, H V1. J R Soc Interface 2018; 15:20180108. [PMID: 29643227 PMCID: PMC5938591 DOI: 10.1098/rsif.2018.0108] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 03/19/2018] [Indexed: 12/15/2022] Open
Abstract
Voltage-gated proton channels are unique ion channels, membrane proteins that allow protons but no other ions to cross cell membranes. They are found in diverse species, from unicellular marine life to humans. In all cells, their function requires that they open and conduct current only under certain conditions, typically when the electrochemical gradient for protons is outwards. Consequently, these proteins behave like rectifiers, conducting protons out of cells. Their activity has electrical consequences and also changes the pH on both sides of the membrane. Here we summarize what is known about the way these proteins sense the membrane potential and the pH inside and outside the cell. Currently, it is hypothesized that membrane potential is sensed by permanently charged arginines (with very high pKa) within the protein, which results in parts of the protein moving to produce a conduction pathway. The mechanism of pH sensing appears to involve titratable side chains of particular amino acids. For this purpose their pKa needs to be within the operational pH range. We propose a 'counter-charge' model for pH sensing in which electrostatic interactions within the protein are selectively disrupted by protonation of internally or externally accessible groups.
Collapse
Affiliation(s)
- Thomas E DeCoursey
- Department of Physiology & Biophysics, Rush University, 1750 West Harrison, Chicago, IL 60612, USA
| |
Collapse
|
19
|
Sung T, Namgung SD, Lee J, Choe IR, Nam KT, Kwon JY. Effects of proton conduction on dielectric properties of peptides. RSC Adv 2018; 8:34047-34055. [PMID: 35548794 PMCID: PMC9086689 DOI: 10.1039/c8ra06121a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 09/26/2018] [Indexed: 12/02/2022] Open
Abstract
Peptides have been overlooked for their use in the field of electronics, even though they are one of the most commonly found bio-induced materials, and are not only easy to mass-produce but also exhibit a high dielectric constant. Additionally, unlike proteins, which are gaining considerable interest with materials researchers, peptides are much simpler, rendering their original characteristics easier to maintain without significant alteration of their structure. On the other hand, proteins tend to deform due to their susceptibility to environmental changes. Combining such superb dielectric properties with their relatively stable nature, peptides could be utilized as a component of electronic devices ranging from basic capacitors to more complex thin-film transistors. In this paper, a peptide chain (YYACAYY) composed of tyrosine, alanine, and cysteine was extensively studied using an impedance analyzer to determine its innate charge movement mechanism in order to extend our understanding of the electric properties of peptides. The movement of mobile protons inside the peptide insulator was found to be the source of the high relative permittivity of the peptide insulator, and the dielectric constant of the peptide insulator was found to be over 17 in humid conditions. By widening the understanding of the dielectric properties of the peptide insulator, it is expected that the peptide can be further utilized as an insulator in various electronic devices. Mobile protons affect dielectric properties of peptides by forming an electrical double layer.![]()
Collapse
Affiliation(s)
- Taehoon Sung
- School of Integrated Technology
- Yonsei University
- Incheon 21983
- Republic of Korea
- Yonsei Institute of Convergence Technology
| | - Seok Daniel Namgung
- School of Integrated Technology
- Yonsei University
- Incheon 21983
- Republic of Korea
- Yonsei Institute of Convergence Technology
| | - Jaehun Lee
- Department of Materials Science and Engineering
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Ik Rang Choe
- Department of Materials Science and Engineering
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Ki Tae Nam
- Department of Materials Science and Engineering
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Jang-Yeon Kwon
- School of Integrated Technology
- Yonsei University
- Incheon 21983
- Republic of Korea
- Yonsei Institute of Convergence Technology
| |
Collapse
|
20
|
Mitochondrial cytochrome c oxidase: catalysis, coupling and controversies. Biochem Soc Trans 2017; 45:813-829. [PMID: 28620043 DOI: 10.1042/bst20160139] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 01/04/2023]
Abstract
Mitochondrial cytochrome c oxidase is a member of a diverse superfamily of haem-copper oxidases. Its mechanism of oxygen reduction is reviewed in terms of the cycle of catalytic intermediates and their likely chemical structures. This reaction cycle is coupled to the translocation of protons across the inner mitochondrial membrane in which it is located. The likely mechanism by which this occurs, derived in significant part from studies of bacterial homologues, is presented. These mechanisms of catalysis and coupling, together with current alternative proposals of underlying mechanisms, are critically reviewed.
Collapse
|
21
|
Hori Y, Ida T, Mizuno M. Potential energy construction in the diabatic picture for quantum mechanical rate constants of intermolecular proton transfer. Phys Chem Chem Phys 2017. [DOI: 10.1039/c7cp03024j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We propose a simple method for potential construction in the diabatic picture and the estimation of thermal rate constants for intermolecular proton transfer reactions using quantum dynamics simulations carried out on the constructed potentials.
Collapse
Affiliation(s)
- Yuta Hori
- Chemistry Course
- Division of Material Chemistry
- Graduate School of Natural Science and Technology
- Kanazawa University
- Kanazawa 920-1192
| | - Tomonori Ida
- Chemistry Course
- Division of Material Chemistry
- Graduate School of Natural Science and Technology
- Kanazawa University
- Kanazawa 920-1192
| | - Motohiro Mizuno
- Chemistry Course
- Division of Material Chemistry
- Graduate School of Natural Science and Technology
- Kanazawa University
- Kanazawa 920-1192
| |
Collapse
|
22
|
Panfoli I, Ponassi M, Ravera S, Calzia D, Beitia M, Morelli A, Rosano C. Tracking protons from respiratory chain complexes to ATP synthase c-subunit: The critical role of serine and threonine residues. Biochem Biophys Res Commun 2016; 482:922-927. [PMID: 27890618 DOI: 10.1016/j.bbrc.2016.11.134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 11/24/2016] [Indexed: 01/09/2023]
Abstract
F1Fo-ATP synthase is a multisubunit enzyme responsible for the synthesis of ATP. Among its multiple subunits (8 in E. coli, 17 in yeast S. cerevisiae, 16 in vertebrates), two subunits a and c are known to play a central role controlling the H+ flow through the inner mitochondrial membrane which allows the subsequent synthesis of ATP, but the pathway followed by H+ within the two proteins is still a matter of debate. In fact, even though the structure of ATP synthase is now well defined, the molecular mechanisms determining the function of both F1 and FO domains are still largely unknown. In this study, we propose a pathway for proton migration along the ATP synthase by hydrogen-bonded chain mechanism, with a key role of serine and threonine residues, by X-ray diffraction data on the subunit a of E. coli Fo.
Collapse
Affiliation(s)
- Isabella Panfoli
- Biochemistry Laboratory, Dept. of Pharmacy, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Marco Ponassi
- Proteomics Lab, IRCCS AOU San Martino - IST, National Institute for Cancer Research, Largo R. Benzi 10, 16132 Genova, Italy
| | - Silvia Ravera
- Biochemistry Laboratory, Dept. of Pharmacy, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Daniela Calzia
- Biochemistry Laboratory, Dept. of Pharmacy, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Maider Beitia
- Department of Nursing I, Medicine and Nursing Faculty, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain; Department of Physiology, Medicine and Nursing Faculty, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain; BioCruces Research Institute, Barakaldo, Bizkaia, Spain
| | - Alessandro Morelli
- Biochemistry Laboratory, Dept. of Pharmacy, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Camillo Rosano
- Proteomics Lab, IRCCS AOU San Martino - IST, National Institute for Cancer Research, Largo R. Benzi 10, 16132 Genova, Italy.
| |
Collapse
|
23
|
Taraphder S, Maupin CM, Swanson JJ, Voth GA. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II. J Phys Chem B 2016; 120:8389-404. [PMID: 27063577 PMCID: PMC5003118 DOI: 10.1021/acs.jpcb.6b02166] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/06/2016] [Indexed: 11/28/2022]
Abstract
The role of protein dynamics in enzyme catalysis is one of the most highly debated topics in enzymology. The main controversy centers around what may be defined as functionally significant conformational fluctuations and how, if at all, these fluctuations couple to enzyme catalyzed events. To shed light on this debate, the conformational dynamics along the transition path surmounting the highest free energy barrier have been herein investigated for the rate limiting proton transport event in human carbonic anhydrase (HCA) II. Special attention has been placed on whether the motion of an excess proton is correlated with fluctuations in the surrounding protein and solvent matrix, which may be rare on the picosecond and subpicosecond time scales of molecular motions. It is found that several active site residues, which do not directly participate in the proton transport event, have a significant impact on the dynamics of the excess proton. These secondary participants are shown to strongly influence the active site environment, resulting in the creation of water clusters that are conducive to fast, moderately slow, or slow proton transport events. The identification and characterization of these secondary participants illuminates the role of protein dynamics in the catalytic efficiency of HCA II.
Collapse
Affiliation(s)
- Srabani Taraphder
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - C. Mark Maupin
- Department
of Chemical and Biological Engineering, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United
States
| | - Jessica
M. J. Swanson
- Department
of Chemistry, Institute for Biophysical Dynamics, James Frank Institute,
and Computation Institute, University of
Chicago, 5735 South Ellis
Avenue, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department
of Chemistry, Institute for Biophysical Dynamics, James Frank Institute,
and Computation Institute, University of
Chicago, 5735 South Ellis
Avenue, Chicago, Illinois 60637, United States
| |
Collapse
|
24
|
Abstract
The mechanism of proton exchange in a metal-ligand enzyme active site mimic (compound 1) is described through amide hydrogen-deuterium exchange kinetics. The type and ratio of cationic guest to host in solution affect the rate of isotope exchange, suggesting that the rate of exchange is driven by a host whose cavity is occupied by water. Rate constants for acid-, base-, and water-mediated proton exchange vary by orders of magnitude depending on the guest, and differ by up to 200 million-fold relative to an alanine polypeptide. These results suggest that the unusual microenvironment of the cavity of 1 can dramatically alter the reactivity of associated water by magnitudes comparable to that of enzymes.
Collapse
|
25
|
Si W, Xin P, Li ZT, Hou JL. Tubular Unimolecular Transmembrane Channels: Construction Strategy and Transport Activities. Acc Chem Res 2015; 48:1612-9. [PMID: 26017272 DOI: 10.1021/acs.accounts.5b00143] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Lipid bilayer membranes separate living cells from their environment. Membrane proteins are responsible for the processing of ion and molecular inputs and exports, sensing stimuli and signals across the bilayers, which may operate in a channel or carrier mechanism. Inspired by these wide-ranging functions of membrane proteins, chemists have made great efforts in constructing synthetic mimics in order to understand the transport mechanisms, create materials for separation, and develop therapeutic agents. Since the report of an alkylated cyclodextrin for transporting Cu(2+) and Co(2+) by Tabushi and co-workers in 1982, chemists have constructed a variety of artificial transmembrane channels by making use of either the multimolecular self-assembly or unimolecular strategy. In the context of the design of unimolecular channels, important advances have been made, including, among others, the tethering of natural gramicidin A or alamethicin and the modification of various macrocycles such as crown ethers, cyclodextrins, calixarenes, and cucurbiturils. Many of these unimolecular channels exhibit high transport ability for metal ions, particularly K(+) and Na(+). Concerning the development of artificial channels based on macrocyclic frameworks, one straightforward and efficient approach is to introduce discrete chains to reinforce their capability to insert into bilayers. Currently, this approach has found the widest applications in the systems of crown ethers and calixarenes. We envisioned that for macrocycle-based unimolecular channels, control of the arrangement of the appended chains in the upward and/or downward direction would favor the insertion of the molecular systems into bilayers, while the introduction of additional interactions among the chains would further stabilize a tubular conformation. Both factors should be helpful for the formation of new efficient channels. In this Account, we discuss our efforts in designing new unimolecular artificial channels from tubular pillar[n]arenes by extending their lengths with various ester, hydrazide, and short peptide chains. We have utilized well-defined pillar[5]arene and pillar[6]arene as rigid frameworks that allow the appended chains to afford extended tubular structures. We demonstrate that the hydrazide and peptide chains form intramolecular N-H···O═C hydrogen bonds that enhance the tubular conformation of the whole molecule. The new pillar[n]arene derivatives have been successfully applied as unimolecular channels for the selective transport of protons, water, and amino acids and the voltage-gated transport of K(+). We also show that aromatic hydrazide helices and macrocycles appended with peptide chains are able to mediate the selective transport of NH4(+).
Collapse
Affiliation(s)
- Wen Si
- Department
of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Pengyang Xin
- Department
of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Zhan-Ting Li
- Department
of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Jun-Li Hou
- Department
of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
| |
Collapse
|
26
|
Abstract
The main properties of the voltage-gated proton channel (HV1) are described in this review, along with what is known about how the channel protein structure accomplishes its functions. Just as protons are unique among ions, proton channels are unique among ion channels. Their four transmembrane helices sense voltage and the pH gradient and conduct protons exclusively. Selectivity is achieved by the unique ability of H3O(+) to protonate an Asp-Arg salt bridge. Pathognomonic sensitivity of gating to the pH gradient ensures HV1 channel opening only when acid extrusion will result, which is crucial to most of its biological functions. An exception occurs in dinoflagellates in which influx of H(+) through HV1 triggers the bioluminescent flash. Pharmacological interventions that promise to ameliorate cancer, asthma, brain damage in ischemic stroke, Alzheimer's disease, autoimmune diseases, and numerous other conditions await future progress.
Collapse
Affiliation(s)
- Thomas E. DeCoursey
- Department of Molecular Biophysics and Physiology, Rush University, 1750 West Harrison, Chicago IL, 60612 USA
| |
Collapse
|
27
|
Mattle D, Zhang L, Sitsel O, Pedersen LT, Moncelli MR, Tadini-Buoninsegni F, Gourdon P, Rees DC, Nissen P, Meloni G. A sulfur-based transport pathway in Cu+-ATPases. EMBO Rep 2015; 16:728-40. [PMID: 25956886 PMCID: PMC4467857 DOI: 10.15252/embr.201439927] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/13/2015] [Accepted: 03/31/2015] [Indexed: 11/09/2022] Open
Abstract
Cells regulate copper levels tightly to balance the biogenesis and integrity of copper centers in vital enzymes against toxic levels of copper. PIB -type Cu(+)-ATPases play a central role in copper homeostasis by catalyzing the selective translocation of Cu(+) across cellular membranes. Crystal structures of a copper-free Cu(+)-ATPase are available, but the mechanism of Cu(+) recognition, binding, and translocation remains elusive. Through X-ray absorption spectroscopy, ATPase activity assays, and charge transfer measurements on solid-supported membranes using wild-type and mutant forms of the Legionella pneumophila Cu(+)-ATPase (LpCopA), we identify a sulfur-lined metal transport pathway. Structural analysis indicates that Cu(+) is bound at a high-affinity transmembrane-binding site in a trigonal-planar coordination with the Cys residues of the conserved CPC motif of transmembrane segment 4 (C382 and C384) and the conserved Met residue of transmembrane segment 6 (M717 of the MXXXS motif). These residues are also essential for transport. Additionally, the studies indicate essential roles of other conserved intramembranous polar residues in facilitating copper binding to the high-affinity site and subsequent release through the exit pathway.
Collapse
Affiliation(s)
- Daniel Mattle
- Centre for Membrane Pumps in Cells and Disease - PUMPkin, Department of Molecular Biology and Genetics, Danish National Research Foundation Aarhus University, Aarhus C, Denmark Division of Chemistry and Chemical Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Limei Zhang
- Division of Chemistry and Chemical Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Oleg Sitsel
- Centre for Membrane Pumps in Cells and Disease - PUMPkin, Department of Molecular Biology and Genetics, Danish National Research Foundation Aarhus University, Aarhus C, Denmark
| | - Lotte Thue Pedersen
- Centre for Membrane Pumps in Cells and Disease - PUMPkin, Department of Molecular Biology and Genetics, Danish National Research Foundation Aarhus University, Aarhus C, Denmark
| | - Maria Rosa Moncelli
- Department of Chemistry 'Ugo Schiff', University of Florence, Sesto Fiorentino, Italy
| | | | - Pontus Gourdon
- Centre for Membrane Pumps in Cells and Disease - PUMPkin, Department of Molecular Biology and Genetics, Danish National Research Foundation Aarhus University, Aarhus C, Denmark
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Poul Nissen
- Centre for Membrane Pumps in Cells and Disease - PUMPkin, Department of Molecular Biology and Genetics, Danish National Research Foundation Aarhus University, Aarhus C, Denmark
| | - Gabriele Meloni
- Centre for Membrane Pumps in Cells and Disease - PUMPkin, Department of Molecular Biology and Genetics, Danish National Research Foundation Aarhus University, Aarhus C, Denmark Division of Chemistry and Chemical Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| |
Collapse
|
28
|
Weinberger A, Tanasescu R, Stefaniu C, Fedotenko LA, Favarger F, Ishikawa T, Brezesinski G, Marques CM, Zumbuehl A. Bilayer properties of 1,3-diamidophospholipids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:1879-1884. [PMID: 25642598 DOI: 10.1021/la5041745] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A series of 1,3-diamido phosphocholines was synthesized, and their potential to form stable bilayers was investigated. Large and giant unilamellar vesicles produced from these new lipids form a wide variety of faceted liposomes. Factors such as cooling rates and the careful choice of the liposome preparation method influence the formation of facets. Interdigitation was hypothesized as a main factor for the stabilization of facets and effectively monitored by small-angle X-ray scattering measurements.
Collapse
Affiliation(s)
- Andreas Weinberger
- Department of Chemistry, University of Fribourg , Chemin du Musée 9, 1700 Fribourg, Switzerland
| | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Li X, Yan L, Yue B. Maleimide: a potential building block for the design of proton exchange membranes studied by ab initio molecular dynamics simulations. RSC Adv 2015. [DOI: 10.1039/c5ra14272e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Ab initio molecular dynamics (AIMD) simulations are applied to the study of proton transport in solid state maleimide.
Collapse
Affiliation(s)
- Xuejiao Li
- Department of Chemistry
- College of Sciences
- Shanghai University
- Shanghai 20044
- China
| | - Liuming Yan
- Department of Chemistry
- College of Sciences
- Shanghai University
- Shanghai 20044
- China
| | - Baohua Yue
- Department of Chemistry
- College of Sciences
- Shanghai University
- Shanghai 20044
- China
| |
Collapse
|
30
|
Ishigami I, Hikita M, Egawa T, Yeh SR, Rousseau DL. Proton translocation in cytochrome c oxidase: insights from proton exchange kinetics and vibrational spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:98-108. [PMID: 25268561 DOI: 10.1016/j.bbabio.2014.09.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/11/2014] [Accepted: 09/20/2014] [Indexed: 11/19/2022]
Abstract
Cytochrome c oxidase is the terminal enzyme in the electron transfer chain. It reduces oxygen to water and harnesses the released energy to translocate protons across the inner mitochondrial membrane. The mechanism by which the oxygen chemistry is coupled to proton translocation is not yet resolved owing to the difficulty of monitoring dynamic proton transfer events. Here we summarize several postulated mechanisms for proton translocation, which have been supported by a variety of vibrational spectroscopic studies. We recently proposed a proton translocation model involving proton accessibility to the regions near the propionate groups of the heme a and heme a3 redox centers of the enzyme based by hydrogen/deuterium (H/D) exchange Raman scattering studies (Egawa et al., PLoS ONE 2013). To advance our understanding of this model and to refine the proton accessibility to the hemes, the H/D exchange dependence of the heme propionate group vibrational modes on temperature and pH was measured. The H/D exchange detected at the propionate groups of heme a3 takes place within a few seconds under all conditions. In contrast, that detected at the heme a propionates occurs in the oxidized but not the reduced enzyme and the H/D exchange is pH-dependent with a pKa of ~8.0 (faster at high pH). Analysis of the thermodynamic parameters revealed that, as the pH is varied, entropy/enthalpy compensation held the free energy of activation in a narrow range. The redox dependence of the possible proton pathways to the heme groups is discussed. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
Collapse
Affiliation(s)
- Izumi Ishigami
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Masahide Hikita
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Tsuyoshi Egawa
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Denis L Rousseau
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| |
Collapse
|
31
|
Solís-Calero C, Ortega-Castro J, Hernández-Laguna A, Muñoz F. DFT study of the mechanism of the reaction of aminoguanidine with methylglyoxal. J Mol Model 2014; 20:2202. [PMID: 24705776 DOI: 10.1007/s00894-014-2202-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/04/2014] [Indexed: 11/28/2022]
Abstract
We have studied the mechanism of the reaction between aminoguanidine (AG) and methylglyoxal (MG) by carrying out Dmol3/DFT calculations, obtaining intermediates, transition-state structures, and free-energy profiles for all of the elementary steps of the reaction. Designed models included explicit water solvent, which forms hydrogen-bond networks around the reactants and intermediate molecules, facilitating intramolecular proton transfer in some steps of the reaction mechanism. The reaction take place in four steps, namely: (1) formation of a guanylhydrazone-acetylcarbinol adduct by condensation of AG and MG; (2) dehydration of the adduct; (3) formation of an 1,2,4-triazine derivative by ring closure; and (4) dehydration with the formation of 5-methyl 3-amino-1,2,4-triazine as the final product. From a microkinetic point of view, the first dehydration step was found to be the rate-determining step for the reaction, with the reaction having an apparent activation energy of 12.65 kcal mol⁻¹. Additionally, some analogous structures of intermediates and transition states for the reaction between AG and 2,3-dicarbonyl-phosphatidylethanolamine, a possible intermediate in Amadori-glycated phosphatidylethanolamine (Amadori-PE) autooxidation, were obtained to evaluate the reaction above a phosphatidylethanolamine (PE) surface. Our results are in agreement with experimental results obtaining by other authors, showing that AG is efficient at trapping dicarbonyl compounds such as methylglyoxal, and by extension these compounds joined to biomolecules such as PE in environments such as surfaces and their aqueous surroundings.
Collapse
Affiliation(s)
- Christian Solís-Calero
- Departament de Química, Institut d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122, Palma de Mallorca, Spain
| | | | | | | |
Collapse
|
32
|
DeCoursey TE, Hosler J. Philosophy of voltage-gated proton channels. J R Soc Interface 2014; 11:20130799. [PMID: 24352668 PMCID: PMC3899857 DOI: 10.1098/rsif.2013.0799] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/22/2013] [Indexed: 02/02/2023] Open
Abstract
In this review, voltage-gated proton channels are considered from a mainly teleological perspective. Why do proton channels exist? What good are they? Why did they go to such lengths to develop several unique hallmark properties such as extreme selectivity and ΔpH-dependent gating? Why is their current so minuscule? How do they manage to be so selective? What is the basis for our belief that they conduct H(+) and not OH(-)? Why do they exist in many species as dimers when the monomeric form seems to work quite well? It is hoped that pondering these questions will provide an introduction to these channels and a way to logically organize their peculiar properties as well as to understand how they are able to carry out some of their better-established biological functions.
Collapse
Affiliation(s)
- Thomas E. DeCoursey
- Department of Molecular Biophysics and Physiology, Rush University, 1750 West Harrison, Chicago, IL 60612, USA
| | - Jonathan Hosler
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS 39216, USA
| |
Collapse
|
33
|
Ullrich CI, Köhler K, Baier M, Förster B, Hartung W. Neutral Red as a Redox Dye Induces K+Efflux and Current-Voltage Changes inEremosphaera, Lemna, and Guard Cells*. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1990.tb00150.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
34
|
Schulten K, Humphrey W, Logunov I, Sheves M, Xu D. Molecular Dynamics Studies of Bacteriorhodopsin's Photocycles. Isr J Chem 2013. [DOI: 10.1002/ijch.199500042] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
35
|
Decoursey TE, Cherny VV. An Electrophysiological Comparison of Voltage-Gated Proton Channels, Other Ion Channels, and Other Proton Channels. Isr J Chem 2013. [DOI: 10.1002/ijch.199900046] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
36
|
|
37
|
Rich PR, Maréchal A. Functions of the hydrophilic channels in protonmotive cytochrome c oxidase. J R Soc Interface 2013; 10:20130183. [PMID: 23864498 PMCID: PMC3730678 DOI: 10.1098/rsif.2013.0183] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 06/03/2013] [Indexed: 01/31/2023] Open
Abstract
The structures and functions of hydrophilic channels in electron-transferring membrane proteins are discussed. A distinction is made between proton channels that can conduct protons and dielectric channels that are non-conducting but can dielectrically polarize in response to the introduction of charge changes in buried functional centres. Functions of the K, D and H channels found in A1-type cytochrome c oxidases are reviewed in relation to these ideas. Possible control of function by dielectric channels and their evolutionary relation to proton channels is explored.
Collapse
Affiliation(s)
- Peter R Rich
- Glynn Laboratory of Bioenergetics, Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
| | | |
Collapse
|
38
|
Pang XF. Properties of proton transfer in hydrogen-bonded systems and its experimental evidences and applications in biology. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 112:1-32. [DOI: 10.1016/j.pbiomolbio.2012.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 11/22/2012] [Accepted: 11/27/2012] [Indexed: 11/25/2022]
|
39
|
DeCoursey TE. Voltage-gated proton channels: molecular biology, physiology, and pathophysiology of the H(V) family. Physiol Rev 2013; 93:599-652. [PMID: 23589829 PMCID: PMC3677779 DOI: 10.1152/physrev.00011.2012] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Voltage-gated proton channels (H(V)) are unique, in part because the ion they conduct is unique. H(V) channels are perfectly selective for protons and have a very small unitary conductance, both arguably manifestations of the extremely low H(+) concentration in physiological solutions. They open with membrane depolarization, but their voltage dependence is strongly regulated by the pH gradient across the membrane (ΔpH), with the result that in most species they normally conduct only outward current. The H(V) channel protein is strikingly similar to the voltage-sensing domain (VSD, the first four membrane-spanning segments) of voltage-gated K(+) and Na(+) channels. In higher species, H(V) channels exist as dimers in which each protomer has its own conduction pathway, yet gating is cooperative. H(V) channels are phylogenetically diverse, distributed from humans to unicellular marine life, and perhaps even plants. Correspondingly, H(V) functions vary widely as well, from promoting calcification in coccolithophores and triggering bioluminescent flashes in dinoflagellates to facilitating killing bacteria, airway pH regulation, basophil histamine release, sperm maturation, and B lymphocyte responses in humans. Recent evidence that hH(V)1 may exacerbate breast cancer metastasis and cerebral damage from ischemic stroke highlights the rapidly expanding recognition of the clinical importance of hH(V)1.
Collapse
Affiliation(s)
- Thomas E DeCoursey
- Dept. of Molecular Biophysics and Physiology, Rush University Medical Center HOS-036, 1750 West Harrison, Chicago, IL 60612, USA.
| |
Collapse
|
40
|
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is crucial for respiration in many aerobic organisms. In mitochondria, it oxidizes NADH from the tricarboxylic acid cycle and β-oxidation, reduces ubiquinone, and transports protons across the inner membrane, contributing to the proton-motive force. It is also a major contributor to cellular production of reactive oxygen species. The redox reaction of complex I is catalyzed in the hydrophilic domain; it comprises NADH oxidation by a flavin mononucleotide, intramolecular electron transfer along a chain of iron-sulfur clusters, and ubiquinone reduction. Redox-coupled proton translocation in the membrane domain requires long-range energy transfer through the protein complex, and the molecular mechanisms that couple the redox and proton-transfer half-reactions are currently unknown. This review evaluates extant data on the mechanisms of energy transduction and superoxide production by complex I, discusses contemporary mechanistic models, and explores how mechanistic studies may contribute to understanding the roles of complex I dysfunctions in human diseases.
Collapse
Affiliation(s)
- Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, Cambridge, CB2 0XY, United Kingdom.
| |
Collapse
|
41
|
Mattle D, Sitsel O, Autzen HE, Meloni G, Gourdon P, Nissen P. On allosteric modulation of P-type Cu(+)-ATPases. J Mol Biol 2013; 425:2299-308. [PMID: 23500486 DOI: 10.1016/j.jmb.2013.03.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/04/2013] [Accepted: 03/04/2013] [Indexed: 11/17/2022]
Abstract
P-type ATPases perform active transport of various compounds across biological membranes and are crucial for ion homeostasis and the asymmetric composition of lipid bilayers. Although their functional cycle share principles of phosphoenzyme intermediates, P-type ATPases also show subclass-specific sequence motifs and structural elements that are linked to transport specificity and mechanistic modulation. Here we provide an overview of the Cu(+)-transporting ATPases (of subclass PIB) and compare them to the well-studied sarco(endo)plasmic reticulum Ca(2+)-ATPase (of subclass PIIA). Cu(+) ions in the cell are delivered by soluble chaperones to Cu(+)-ATPases, which expose a putative "docking platform" at the intracellular interface. Cu(+)-ATPases also contain heavy-metal binding domains providing a basis for allosteric control of pump activity. Database analysis of Cu(+) ligating residues questions a two-site model of intramembranous Cu(+) binding, and we suggest an alternative role for the proposed second site in copper translocation and proton exchange. The class-specific features demonstrate that topological diversity in P-type ATPases may tune a general energy coupling scheme to the translocation of compounds with remarkably different properties.
Collapse
Affiliation(s)
- Daniel Mattle
- Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | | | | | | | | | | |
Collapse
|
42
|
Meech R. A contribution to the history of the proton channel. WILEY INTERDISCIPLINARY REVIEWS. MEMBRANE TRANSPORT AND SIGNALING 2012; 1:533-557. [PMID: 23365805 PMCID: PMC3556693 DOI: 10.1002/wmts.59] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The low numbers of hydrogen ions in physiological solutions encouraged the assumption that H(+) currents flowing through conductive pathways would be so small as to be unmeasurable even if theoretically possible. Evidence for an H(+)-based action potential in the luminescent dinoflagellate Noctiluca and for an H(+)-conducting channel created by the secretions of the bacterium Bacillus brevis, did little to alter this perception. The clear demonstration of H(+) conduction in molluscan neurons might have provided the breakthrough but the new pathway was without an easily demonstrable function, and escaped general attention. Indeed the extreme measures that must be taken to successfully isolate H(+) currents meant that it was some years before proton channels were identified in mammalian cells. However, with the general availability of patch-clamp techniques and evidence for an important role in mammalian neutrophils, the stage was set for a series of structure/function studies with the potential to make the proton channel the best understood channel of all. In addition, widespread genomic searches have established that proton channels play important roles in processes ranging from fertilization of the human ovum to the progression of breast cancer. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Collapse
Affiliation(s)
- Robert Meech
- School of Physiology & Pharmacology, University of Bristol, Medical Sciences Building, University WalkBristol BS8 1TD, UK
| |
Collapse
|
43
|
A comparative DFT study of the Schiff base formation from acetaldehyde and butylamine, glycine and phosphatidylethanolamine. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1263-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
44
|
Peng Y, Voth GA. Expanding the view of proton pumping in cytochrome c oxidase through computer simulation. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1817:518-25. [PMID: 22178790 PMCID: PMC4120846 DOI: 10.1016/j.bbabio.2011.11.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 11/23/2011] [Accepted: 11/24/2011] [Indexed: 01/01/2023]
Abstract
In cytochrome c oxidase (CcO), a redox-driven proton pump, protons are transported by the Grotthuss shuttling via hydrogen-bonded water molecules and protonatable residues. Proton transport through the D-pathway is a complicated process that is highly sensitive to alterations in the amino acids or the solvation structure in the channel, both of which can inhibit proton pumping and enzymatic activity. Simulations of proton transport in the hydrophobic cavity showed a clear redox state dependence. To study the mechanism of proton pumping in CcO, multi-state empirical valence bond (MS-EVB) simulations have been conducted, focusing on the proton transport through the D-pathway and the hydrophobic cavity next to the binuclear center. The hydration structures, transport pathways, effects of residues, and free energy surfaces of proton transport were revealed in these MS-EVB simulations. The mechanistic insight gained from them is herein reviewed and placed in context for future studies.
Collapse
Affiliation(s)
- Yuxing Peng
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
| | - Gregory A. Voth
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
| |
Collapse
|
45
|
Xu HR, Zhang QC, Zhao HX, Long LS, Huang RB, Zheng LS. Anisotropy of proton transport in an organic–inorganic compound [(C6H10N2)2(SO4)2·3H2O]n (C6H10N2 = phenylenediammonium dication). Chem Commun (Camb) 2012; 48:4875-7. [DOI: 10.1039/c2cc30896g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
46
|
Si W, Chen L, Hu XB, Tang G, Chen Z, Hou JL, Li ZT. Selective Artificial Transmembrane Channels for Protons by Formation of Water Wires. Angew Chem Int Ed Engl 2011; 50:12564-8. [DOI: 10.1002/anie.201106857] [Citation(s) in RCA: 316] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Indexed: 11/08/2022]
|
47
|
Si W, Chen L, Hu XB, Tang G, Chen Z, Hou JL, Li ZT. Selective Artificial Transmembrane Channels for Protons by Formation of Water Wires. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106857] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
48
|
Abstract
Water molecules confined to pores with sub-nanometre diameters form single-file hydrogen-bonded chains. In such nanoscale confinement, water has unusual physical properties that are exploited in biology and hold promise for a wide range of biomimetic and nanotechnological applications. The latter can be realized by carbon and boron nitride nanotubes which confine water in a relatively non-specific way and lend themselves to the study of intrinsic properties of single-file water. As a consequence of strong water-water hydrogen bonds, many characteristics of single-file water are conserved in biological and synthetic pores despite differences in their atomistic structures. Charge transport and orientational order in water chains depend sensitively on and are mainly determined by electrostatic effects. Thus, mimicking functions of biological pores with apolar pores and corresponding external fields gives insight into the structure-function relation of biological pores and allows the development of technical applications beyond the molecular devices found in living systems. In this Perspective, we revisit results for single-file water in apolar pores, and examine the similarities and the differences between these simple systems and water in more complex pores.
Collapse
Affiliation(s)
- Jürgen Köfinger
- Laboratory of Chemical Physics, Bldg. 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | | |
Collapse
|
49
|
Varanasi L, Hosler J. Alternative initial proton acceptors for the D pathway of Rhodobacter sphaeroides cytochrome c oxidase. Biochemistry 2011; 50:2820-8. [PMID: 21344856 DOI: 10.1021/bi102002v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To characterize protein structures that control proton uptake, we assayed forms of cytochrome c oxidase (CcO) containing a carboxyl or a thiol group in line with the initial, internal waters of the D pathway for proton transfer in the presence and absence of subunit III. Subunit III provides approximately half of the protein surrounding the entry region of the D pathway. The N139D/D132N mutant contains a carboxyl group 6 Å within the D pathway and lacks the normal, surface-exposed proton acceptor, Asp-132. With subunit III, the steady-state activity of this mutant is slow, but once subunit III is removed, its activity is the same as that of wild-type CcO lacking subunit III (∼1800 H+/s). Thus, a carboxyl group∼25% within the pathway enhances proton uptake even though the carboxyl has no direct contact with bulk solvent. Protons from solvent apparently move to internal Asp-139 through a short file of waters, normally blocked by subunit III. Cys-139 also supports rapid steady-state proton uptake, demonstrating that an anion other than a carboxyl can attract and transfer protons into the D pathway. When both Asp-132 and Asp/Cys-139 are present, the removal of subunit III increases CcO activity to rates greater than that of normal CcO because of simultaneous proton uptake by two initial acceptors. The results show how the environment of the initial proton acceptor for the D pathway in these CcO forms dictates the pH range of CcO activity, with implications for the function of Asp-132, the normal proton acceptor.
Collapse
Affiliation(s)
- Lakshman Varanasi
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | | |
Collapse
|
50
|
Solís-Calero C, Ortega-Castro J, Muñoz F. Reactivity of a phospholipid monolayer model under periodic boundary conditions: a density functional theory study of the Schiff base formation between phosphatidylethanolamine and acetaldehyde. J Phys Chem B 2010; 114:15879-85. [PMID: 21077587 DOI: 10.1021/jp1088367] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A mechanism for the formation of the Schiff base between an acetaldehyde and an amine-phospholipid monolayer model based on Dmol3/density functional theory calculations under periodic boundary conditions was constructed. This is the first time such a system has been modeled to examine its chemical reactivity at this computation level. Each unit cell contains two phospholipid molecules, one acetaldehyde molecule, and nine water molecules. One of the amine-phospholipid molecules in the cell possesses a neutral amino group that is used to model the nucleophilic attack on the carboxyl group of acetaldehyde, whereas the other has a charged amino group acting as a proton donor. The nine water molecules form a hydrogen bond network along the polar heads of the phospholipids that facilitates very fast proton conduction at the interface. Using periodic boundary conditions afforded proton transfer between different cells. The reaction takes place in two steps, namely, (1) formation of a carbinolamine and (2) its dehydration to the Schiff base. The carbinolamine is the primary reaction intermediate, and dehydration is the rate-determining step of the process, consistent with available experimental evidence for similar reactions. On the basis of the results, the cell membrane surface environment may boost phospholipid glycation via a neighboring catalyst effect.
Collapse
Affiliation(s)
- Christian Solís-Calero
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | | | | |
Collapse
|