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Botha S, Fromme P. Review of serial femtosecond crystallography including the COVID-19 pandemic impact and future outlook. Structure 2023; 31:1306-1319. [PMID: 37898125 PMCID: PMC10842180 DOI: 10.1016/j.str.2023.10.005] [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] [Received: 07/18/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/30/2023]
Abstract
Serial femtosecond crystallography (SFX) revolutionized macromolecular crystallography over the past decade by enabling the collection of X-ray diffraction data from nano- or micrometer sized crystals while outrunning structure-altering radiation damage effects at room temperature. The serial manner of data collection from millions of individual crystals coupled with the femtosecond duration of the ultrabright X-ray pulses enables time-resolved studies of macromolecules under near-physiological conditions to unprecedented temporal resolution. In 2020 the rapid spread of the coronavirus SARS-CoV-2 resulted in a global pandemic of coronavirus disease-2019. This led to a shift in how serial femtosecond experiments were performed, along with rapid funding and free electron laser beamtime availability dedicated to SARS-CoV-2-related studies. This review outlines the current state of SFX research, the milestones that were achieved, the impact of the global pandemic on this field as well as an outlook into exciting future directions.
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Affiliation(s)
- Sabine Botha
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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2
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Yoder N, Jalali-Yazdi F, Noreng S, Houser A, Baconguis I, Gouaux E. Light-coupled cryo-plunger for time-resolved cryo-EM. J Struct Biol 2020; 212:107624. [PMID: 32950604 DOI: 10.1016/j.jsb.2020.107624] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 12/26/2022]
Abstract
Proteins are dynamic molecules that can undergo rapid conformational rearrangements in response to stimuli. These structural changes are often critical to protein function, and thus elucidating time-dependent conformational landscapes has been a long-standing goal of structural biology. To harness the power of single particle cryo-EM methods to enable 'time-resolved' structure determination, we have developed a light-coupled cryo-plunger that pairs flash-photolysis of caged ligands with rapid sample vitrification. The 'flash-plunger' consists of a high-power ultraviolet LED coupled with focusing optics and a motorized linear actuator, enabling the user to immobilize protein targets in vitreous ice within a programmable time window - as short as tens of milliseconds - after stimulus delivery. The flash-plunger is a simple, inexpensive and flexible tool to explore short-lived conformational states previously unobtainable by conventional sample preparation methods.
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Affiliation(s)
- Nate Yoder
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Farzad Jalali-Yazdi
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Sigrid Noreng
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alexandra Houser
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Isabelle Baconguis
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA; Howard Hughes Medical Institute, Oregon Health & Science University, Portland, OR 97239, USA.
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The Eye, Oxidative Damage and Polyunsaturated Fatty Acids. Nutrients 2018; 10:nu10060668. [PMID: 29795004 PMCID: PMC6024720 DOI: 10.3390/nu10060668] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/17/2018] [Accepted: 05/22/2018] [Indexed: 12/12/2022] Open
Abstract
Polyunsaturated fatty acids (PUFA) are known to have numerous beneficial effects, owing to their anti-inflammatory and antioxidant properties. From a metabolic standpoint, the mitochondria play a fundamental role in cellular homeostasis, and oxidative stress can affect their functioning. Indeed, the mitochondria are the main source of ROS, and an imbalance between ROS and antioxidant defenses leads to oxidative stress. In addition, aging, the decline of cellular functions, and continual exposure to light underlie many diseases, particularly those of the eye. Long-term exposure to insults, such as UV light, visible light, ionizing radiation, chemotherapeutics, and environmental toxins, contribute to oxidative damage in ocular tissues and expose the aging eye to considerable risk of pathological consequences of oxidative stress. Ample antioxidant defenses responsible for scavenging free radicals are essential for redox homeostasis in the eye, indeed, eye tissues, starting from the tear film, which normally are exposed to high oxygen levels, have strong antioxidant defenses that are efficient for protecting against ROS-related injuries. On the contrary, instead, the trabecular meshwork is not directly exposed to light and its endothelial cells are poorly equipped with antioxidant defenses. All this makes the eye a target organ of oxidative damage. This review focuses on the role of the polyunsaturated fatty acids in the human eye, particularly in such pathologies as dry eye, glaucoma, and macular degeneration, in which dietary PUFA supplementation can be a valid therapeutic aid.
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Klán P, Šolomek T, Bochet CG, Blanc A, Givens R, Rubina M, Popik V, Kostikov A, Wirz J. Photoremovable protecting groups in chemistry and biology: reaction mechanisms and efficacy. Chem Rev 2013; 113:119-91. [PMID: 23256727 PMCID: PMC3557858 DOI: 10.1021/cr300177k] [Citation(s) in RCA: 1238] [Impact Index Per Article: 112.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Indexed: 02/06/2023]
Affiliation(s)
- Petr Klán
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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Plattner H, Sehring IM, Mohamed IK, Miranda K, De Souza W, Billington R, Genazzani A, Ladenburger EM. Calcium signaling in closely related protozoan groups (Alveolata): non-parasitic ciliates (Paramecium, Tetrahymena) vs. parasitic Apicomplexa (Plasmodium, Toxoplasma). Cell Calcium 2012; 51:351-82. [PMID: 22387010 DOI: 10.1016/j.ceca.2012.01.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 12/20/2022]
Abstract
The importance of Ca2+-signaling for many subcellular processes is well established in higher eukaryotes, whereas information about protozoa is restricted. Recent genome analyses have stimulated such work also with Alveolates, such as ciliates (Paramecium, Tetrahymena) and their pathogenic close relatives, the Apicomplexa (Plasmodium, Toxoplasma). Here we compare Ca2+ signaling in the two closely related groups. Acidic Ca2+ stores have been characterized in detail in Apicomplexa, but hardly in ciliates. Two-pore channels engaged in Ca2+-release from acidic stores in higher eukaryotes have not been stingently characterized in either group. Both groups are endowed with plasma membrane- and endoplasmic reticulum-type Ca2+-ATPases (PMCA, SERCA), respectively. Only recently was it possible to identify in Paramecium a number of homologs of ryanodine and inositol 1,3,4-trisphosphate receptors (RyR, IP3R) and to localize them to widely different organelles participating in vesicle trafficking. For Apicomplexa, physiological experiments suggest the presence of related channels although their identity remains elusive. In Paramecium, IP3Rs are constitutively active in the contractile vacuole complex; RyR-related channels in alveolar sacs are activated during exocytosis stimulation, whereas in the parasites the homologous structure (inner membrane complex) may no longer function as a Ca2+ store. Scrutinized comparison of the two closely related protozoan phyla may stimulate further work and elucidate adaptation to parasitic life. See also "Conclusions" section.
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Affiliation(s)
- H Plattner
- Department of Biology, University of Konstanz, P.O. Box 5560, 78457 Konstanz, Germany.
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Fibich A, Apell HJ. Kinetics of luminal proton binding to the SR Ca-ATPase. Biophys J 2011; 101:1896-904. [PMID: 22004743 DOI: 10.1016/j.bpj.2011.09.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 08/23/2011] [Accepted: 09/13/2011] [Indexed: 10/16/2022] Open
Abstract
An open membrane preparation containing SR Ca-ATPase was prepared from sarcoplasmic-reticulum vesicles to study the ion binding kinetics in the P-E(2) conformation. Because Ca(2+) and H(+) binding are electrogenic reactions, fluorescent styryl dyes could be used to determine changes in the binding site occupation in equilibrium titration experiments and time-resolved relaxation processes triggered by a pH jump. By photo release from caged proton the pH of the electrolyte could be decreased in a step of 0.1 pH units by a single ultraviolet-laser flash. Analysis of the pH-jump induced relaxation process in the P-E(2) conformation showed that three Ca-ATPase-specific processes could be identified, fast H(+) binding (τ < 100 μs) and pH-insensitive conformational relaxations after the release of the Ca(2+) ion (τ ∼160 ms), and a slow process (τ ∼3.4 s) whose origin could not be unambiguously revealed. The Ca(2+)-binding affinity in the P-E(2) conformation was reduced with increasing pH, a behavior that can be explained by a reversible transition of the empty P-E(2) state to an inactivated state of the ion pump. All findings are interpreted in the framework of the Post-Albers pump cycle introduced previously, supplemented by an additional transition to an inhibited state of the ion pump.
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Affiliation(s)
- Andreas Fibich
- Department of Biology, University of Konstanz, Konstanz, Germany
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Abstract
In the absence of Na(+) and K(+) ions the Na,K-ATPase shows a pH-dependent ATP hydrolysis that can be inhibited by ouabain. At pH 7.2 this activity is 5% of the maximal under physiological conditions. It could be inferred that this activity is associated with H(+) transport in both directions across the membrane and facilitates an H-only mode of the sodium pump under such unphysiological conditions. By the analysis of experiments with reconstituted proteoliposomes an overall electroneutral transport mode has been proven. The stoichiometry was determined to be 2 H(+)/2 H(+)/1 ATP and is comparable to what is known from the closely related H,K-ATPase. By time-resolved ATP-concentration jump experiments it was found that at no time was the third, Na(+)-specific binding site of the pump occupied by protons. A modified Post-Albers pump cycle is proposed, with H(+) ions as congeners for Na(+) and K(+), by which all experiments performed can be explained.
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Affiliation(s)
- Hans-Jürgen Apell
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany.
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Habeck M, Cirri E, Katz A, Karlish SJ, Apell HJ. Investigation of Electrogenic Partial Reactions in Detergent-Solubilized Na,K-ATPase. Biochemistry 2009; 48:9147-55. [DOI: 10.1021/bi901148k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael Habeck
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Erica Cirri
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Adriana Katz
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Steven J. Karlish
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hans-Jürgen Apell
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
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Kjelstrup S, Barragán D, Bedeaux D. Coefficients for active transport and thermogenesis of Ca2+-ATPase isoforms. Biophys J 2009; 96:4376-86. [PMID: 19486662 DOI: 10.1016/j.bpj.2009.02.070] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 02/03/2009] [Accepted: 02/05/2009] [Indexed: 11/28/2022] Open
Abstract
Coefficients for active transport of ions and heat in vesicles with Ca(2+)-ATPase from sarcoplasmic reticulum are defined in terms of a newly proposed thermodynamic theory and calculated using experiments reported in the literature. The coefficients characterize in a quantitative manner different performances of the enzyme isoforms. Four enzyme isoforms are examined, namely from white and red muscle tissue, from blood platelets, and from brown adipose mitochondria. The results indicate that the isoforms have a somewhat specialized function. White muscle tissue and brown adipose tissue have the same active transport coefficient ratio, but the activity level of the enzyme in white muscle is higher than in brown adipose tissue. The thermogenesis ratio is high in both white muscle and brown adipose tissue, in agreement with a specific role in nonshivering thermogenesis. Other isoforms do not have this ability to generate heat. A calcium-dependence of the coefficients is found, which can be understood as being in accordance with the role of this ion as a messenger in muscle contraction as well as in thermogenesis. The investigation points to new experiments related to structure as well as to function of the isoforms.
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Affiliation(s)
- Signe Kjelstrup
- Centre for Advanced Study, at The Norwegian Academy of Science and Letters, Oslo, Norway.
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Cherepanov AV, Doroshenko EV, Matysik J, de Vries S, De Groot HJM. A view on phosphate ester photochemistry by time-resolved solid state NMR. Intramolecular redox reaction of caged ATP. Phys Chem Chem Phys 2008; 10:6820-8. [PMID: 19015786 DOI: 10.1039/b806677a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The light-driven intramolecular redox reaction of adenosine-5'-triphosphate-[P3-(1-(2-nitrophenyl)-ethyl)]ester (caged ATP) has been studied in frozen aqueous solution using time-resolved solid state NMR spectroscopy under continuous illumination conditions. Cleavage of the phosphate ester bond leads to 0.3, 1.36, and 6.06 ppm downfield shifts of the alpha-, beta-, and gamma-phosphorus resonances of caged ATP, respectively. The observed rate of ATP formation is 2.4 +/- 0.2 h(-1) at 245 K. The proton released in the reaction binds to the triphosphate moiety of the nascent ATP, causing the upfield shifts of the 31P resonances. Analyses of the reaction kinetics indicate that bond cleavage and proton release are two sequential processes in the solid state, suggesting that the 1-hydroxy,1-(2-nitrosophenyl)-ethyl carbocation intermediate is involved in the reaction. The beta-phosphate oxygen atom of ATP is protonated first, indicating its proximity to the reaction center, possibly within hydrogen bonding distance. The residual linewidth kinetics are interpreted in terms of chemical exchange processes, hydrogen bonding of the beta-phosphate oxygen atom and evolution of the hydrolytic equilibrium at the triphosphate moiety of the nascent ATP. Photoreaction of caged ATP in situ gives an opportunity to study structural kinetics and catalysis of ATP-dependent enzymes by NMR spectroscopy in rotating solids.
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Affiliation(s)
- Alexey V Cherepanov
- Biophysical Organic Chemistry/Solid State NMR group, Leiden Institute of Chemistry, Faculty of Mathematics and Natural Sciences, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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Kjelstrup S, de Meis L, Bedeaux D, Simon JM. Is the Ca2+-ATPase from sarcoplasmic reticulum also a heat pump? EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 38:59-67. [PMID: 18679670 DOI: 10.1007/s00249-008-0358-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 06/27/2008] [Accepted: 07/03/2008] [Indexed: 10/21/2022]
Abstract
We calculate, using the first law of thermodynamics, the membrane heat fluxes during active transport of Ca(2+) in the Ca(2+)-ATPase in leaky and intact vesicles, during ATP hydrolysis or synthesis conditions. The results show that the vesicle interior may cool down during hydrolysis and Ca(2+)-uptake, and heat up during ATP synthesis and Ca(2+)-efflux. The heat flux varies with the SERCA isoform. Electroneutral processes and rapid equilibration of water were assumed. The results are consistent with the second law of thermodynamics for the overall processes. The expression for the heat flux and experimental data, show that important contributions come from the enthalpy of hydrolysis for the medium in question, and from proton transport between the vesicle interior and exterior. The analysis give quantitative support to earlier proposals that certain, but not all, Ca(2+)-ATPases, not only act as Ca(2+)-pumps, but also as heat pumps. It can thus help explain why SERCA 1 type enzymes dominate in tissues where thermal regulation is important, while SERCA 2 type enzymes, with their lower activity and better ability to use the energy from the reaction to pump ions, dominate in tissues where this is not an issue.
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Affiliation(s)
- Signe Kjelstrup
- Centre of Advanced Study, Norwegian Academy of Science and Letters, Drammensveien 78, Oslo, Norway.
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Zafar S, Hussain A, Liu Y, Lewis D, Inesi G. Specificity of ligand binding to transport sites: Ca2+ binding to the Ca2+ transport ATPase and its dependence on H+ and Mg2+. Arch Biochem Biophys 2008; 476:87-94. [PMID: 18485884 PMCID: PMC2756220 DOI: 10.1016/j.abb.2008.04.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Accepted: 04/14/2008] [Indexed: 10/22/2022]
Abstract
Ligand binding to transport sites constitutes the initial step in the catalytic cycle of transport ATPases. Here, we consider the well characterized Ca2+ ATPase of sarcoplasmic reticulum (SERCA) and describe a series of Ca2+ binding isotherms obtained by equilibrium measurements in the presence of various H+ and Mg2+ concentrations. We subject the isotherms to statistical mechanics analysis, using a model based on a minimal number of mechanistic steps. The analysis allows satisfactory fits and yields information on occupancy of the specific Ca2+ sites under various conditions. It also provides a fundamental method for analysis of binding specificity to transport sites under equilibrium conditions that lead to tightly coupled catalytic activation.
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Affiliation(s)
- Sufi Zafar
- T.J. Watson Research Center, IBM, Route 134, P.O. Box 218, Yorktown Heights, NY 10598, USA
| | - Arif Hussain
- Greenebaum Cancer Center, University of Maryland Medical Center, Baltimore, MD 21201, USA
| | - Yueyong Liu
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA
| | - David Lewis
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA
| | - G. Inesi
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA
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A F, C J, H-J A. Properties of the SR Ca-ATPase in an Open Microsomal Membrane Preparation. Open Biochem J 2008; 2:91-9. [PMID: 18949080 PMCID: PMC2570558 DOI: 10.2174/1874091x00802010091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Revised: 05/16/2008] [Accepted: 05/26/2008] [Indexed: 11/22/2022] Open
Abstract
SR vesicles isolated from rabbit muscle were treated by a SDS incubation and subsequent dialysis to obtain open membrane fragments that allow a direct access to the luminal membrane surface and especially to the ion-binding sites in the P-E(2) conformation of the Ca-ATPase. The open membrane fragments showed about 80% of the enzyme activity in the untreated membranes. Pump function was investigated by using electrochromic styryl dyes. The kinetic properties of cytoplasmic ion binding showed no significant differences between the Ca-ATPases in SR vesicles and in membrane fragments. From pH-dependent Ca(2+) binding it could be deduced that due to the SDS treatment the density of negatively charged lipid was increased by one elementary charge per 12 lipid molecules. Major differences between Ca-ATPase from SR vesicles and membrane fragments were the respective fluorescence amplitudes. This effect is, however, produced by dye-lipid interaction and not by pump function. It was demonstrated that time-resolved kinetics may be study by the use of caged compounds such as caged ATP or caged calcium also in the case of the membrane fragments.
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Affiliation(s)
- Fibich A
- Department of Biology, University of Konstanz, Konstanz Germany
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Tadini-Buoninsegni F, Bartolommei G, Moncelli MR, Fendler K. Charge transfer in P-type ATPases investigated on planar membranes. Arch Biochem Biophys 2008; 476:75-86. [PMID: 18328799 DOI: 10.1016/j.abb.2008.02.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 02/19/2008] [Accepted: 02/20/2008] [Indexed: 11/18/2022]
Abstract
Planar lipid bilayers, e.g., black lipid membranes (BLM) and solid supported membranes (SSM), have been employed to investigate charge movements during the reaction cycle of P-type ATPases. The BLM/SSM method allows a direct measurement of the electrical currents generated by the cation transporter following chemical activation by a substrate concentration jump. The electrical current transients provides information about the reaction mechanism of the enzyme. In particular, the BLM/SSM technique allows identification of electrogenic steps which in turn may be used to localize ion translocation during the reaction cycle of the pump. In addition, using the high time resolution of the technique, especially when rapid activation via caged ATP is employed, rate constants of electrogenic and electroneutral steps can be determined. In the present review, we will discuss the main results obtained by the BLM and SSM methods and how they have contributed to unravel the transport mechanism of P-type ATPases.
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