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Li W, Zhou J, Lan Q, Ding XL, Pan XT, Ahmed SA, Ji LN, Wang K, Xia XH. Single-Molecule Electrical and Spectroscopic Profiling Protein Allostery Using a Gold Plasmonic Nanopore. NANO LETTERS 2023; 23:2586-2592. [PMID: 36942994 DOI: 10.1021/acs.nanolett.2c04848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Direct structural and dynamic characterization of protein conformers in solution is highly desirable but currently impractical. Herein, we developed a single molecule gold plasmonic nanopore system for observation of protein allostery, enabling us to monitor translocation dynamics and conformation transition of proteins by ion current detection and SERS spectrum measurement, respectively. Allosteric transition of calmodulin (CaM) was elaborately probed by the nanopore system. Two conformers of CaM were well-resolved at a single-molecule level using both the ion current blockage signal and the SERS spectra. The collected SERS spectra provided structural evidence to confirm the interaction between CaM and the gold plasmonic nanopore, which was responsible for the different translocation behaviors of the two conformers. SERS spectra revealed the amino acid residues involved in the conformational change of CaM upon calcium binding. The results demonstrated that the excellent spectral characterization furnishes a single-molecule nanopore technique with an advanced capability of direct structure analysis.
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Affiliation(s)
- Wang Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Juan Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qing Lan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xin-Lei Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiao-Tong Pan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Saud Asif Ahmed
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Li-Na Ji
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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Knoepp F, Wahl J, Andersson A, Kraut S, Sommer N, Weissmann N, Ramser K. A Microfluidic System for Simultaneous Raman Spectroscopy, Patch-Clamp Electrophysiology, and Live-Cell Imaging to Study Key Cellular Events of Single Living Cells in Response to Acute Hypoxia. SMALL METHODS 2021; 5:e2100470. [PMID: 34927935 DOI: 10.1002/smtd.202100470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/23/2021] [Indexed: 06/14/2023]
Abstract
The ability to sense changes in oxygen availability is fundamentally important for the survival of all aerobic organisms. However, cellular oxygen sensing mechanisms and pathologies remain incompletely understood and studies of acute oxygen sensing, in particular, have produced inconsistent results. Current methods cannot simultaneously measure the key cellular events in acute hypoxia (i.e., changes in redox state, electrophysiological properties, and mechanical responses) at controlled partial pressures of oxygen (pO2 ). The lack of such a comprehensive method essentially contributes to the discrepancies in the field. A sealed microfluidic system that combines i) Raman spectroscopy, ii) patch-clamp electrophysiology, and iii) live-cell imaging under precisely controlled pO2 have therefore been developed. Merging these modalities allows label-free and simultaneous observation of oxygen-dependent alterations in multiple cellular redox couples, membrane potential, and cellular contraction. This technique is adaptable to any cell type and allows in-depth insight into acute oxygen sensing processes underlying various physiologic and pathologic conditions.
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Affiliation(s)
- Fenja Knoepp
- Excellence Cluster Cardio-Pulmonary Institute (CPI), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, D-35392, Giessen, Germany
| | - Joel Wahl
- Department of Engineering Sciences and Mathematics, Luleå University of Technology, Luleå, SE-97187, Sweden
| | - Anders Andersson
- Department of Engineering Sciences and Mathematics, Luleå University of Technology, Luleå, SE-97187, Sweden
| | - Simone Kraut
- Excellence Cluster Cardio-Pulmonary Institute (CPI), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, D-35392, Giessen, Germany
| | - Natascha Sommer
- Excellence Cluster Cardio-Pulmonary Institute (CPI), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, D-35392, Giessen, Germany
| | - Norbert Weissmann
- Excellence Cluster Cardio-Pulmonary Institute (CPI), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, D-35392, Giessen, Germany
| | - Kerstin Ramser
- Department of Engineering Sciences and Mathematics, Luleå University of Technology, Luleå, SE-97187, Sweden
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Minnes L, Greetham GM, Shaw DJ, Clark IP, Fritzsch R, Towrie M, Parker AW, Henry AJ, Taylor RJ, Hunt NT. Uncovering the Early Stages of Domain Melting in Calmodulin with Ultrafast Temperature-Jump Infrared Spectroscopy. J Phys Chem B 2019; 123:8733-8739. [PMID: 31557034 PMCID: PMC7007250 DOI: 10.1021/acs.jpcb.9b08870] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
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The signaling protein
calmodulin (CaM) undergoes a well-known change
in secondary structure upon binding Ca2+, but the structural
plasticity of the Ca2+-free apo state
is linked to CaM functionality. Variable temperature studies of apo-CaM indicate two structural transitions at 46 and 58
°C that are assigned to melting of the C- and N-terminal domains,
respectively, but the molecular mechanism of domain unfolding is unknown.
We report temperature-jump time-resolved infrared (IR) spectroscopy
experiments designed to target the first steps in the C-terminal domain
melting transition of human apo-CaM. A comparison
of the nonequilibrium relaxation of apo-CaM with
the more thermodynamically stable holo-CaM, with
4 equiv of Ca2+ bound, shows that domain melting of apo-CaM begins on microsecond time scales with α-helix
destabilization. These observations enable the assignment of previously
reported dynamics of CaM on hundreds of microsecond time scales to
thermally activated melting, producing a complete mechanism for thermal
unfolding of CaM.
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Affiliation(s)
- Lucy Minnes
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , United Kingdom
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | | | - Ian P Clark
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | - Robby Fritzsch
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , United Kingdom
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | | | | | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute , University of York , Heslington, York YO10 5DD , United Kingdom
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Minnes L, Shaw DJ, Cossins BP, Donaldson PM, Greetham GM, Towrie M, Parker AW, Baker MJ, Henry AJ, Taylor RJ, Hunt NT. Quantifying Secondary Structure Changes in Calmodulin Using 2D-IR Spectroscopy. Anal Chem 2017; 89:10898-10906. [DOI: 10.1021/acs.analchem.7b02610] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Lucy Minnes
- Department
of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow, G4 0NG, United Kingdom
| | | | | | - Paul M. Donaldson
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, United Kingdom
| | - Gregory M. Greetham
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, United Kingdom
| | - Michael Towrie
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, United Kingdom
| | - Anthony W. Parker
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, United Kingdom
| | - Matthew J. Baker
- WestCHEM,
Department of Pure and Applied Chemistry, Technology and Innovation
Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, United Kingdom
| | | | | | - Neil T. Hunt
- Department
of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow, G4 0NG, United Kingdom
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The role of an l-leucine residue on the conformations of glycyl-l-leucine oligomers and its N- or C-terminal dependence: infrared absorption and Raman scattering studies. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 45:23-34. [DOI: 10.1007/s00249-015-1072-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 06/27/2015] [Accepted: 08/12/2015] [Indexed: 12/20/2022]
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Abstract
Oxidation of methionine residues in calmodulin (CaM) lowers the affinity for calcium and results in an inability to activate target proteins fully. To evaluate the structural consequences of CaM oxidation, we used infrared difference spectroscopy to identify oxidation-dependent effects on protein conformation and calcium liganding. Oxidation-induced changes include an increase in hydration of alpha-helices, as indicated in the downshift of the amide I' band of both apo-CaM and Ca(2+)-CaM, and a modification of calcium liganding by carboxylate side chains, reflected in antisymmetric carboxylate band shifts. Changes in carboxylate ligands are consistent with the model we propose: an Asp at position 1 of the EF-loop experiences diminished hydrogen bonding with the polypeptide backbone, an Asp at position 3 forms a bidentate coordination of calcium, and an Asp at position 5 forms a pseudobridging coordination with a calcium-bound water molecule. The bidentate coordination of calcium by conserved glutamates is unaffected by oxidation. The observed changes in calcium ligation are discussed in terms of the placement of methionine side chains relative to the calcium-binding sites, suggesting that varying sensitivities of binding sites to oxidation may underlie the loss of CaM function upon oxidation.
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Doody MA, Baker GA, Pandey S, Bright FV. Effects of ethanol volume percent on fluorescein-labeled spinach apo- and holocalmodulin. Anal Chem 2000; 72:227-33. [PMID: 10655658 DOI: 10.1021/ac990551b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the effects of EtOH volume percent (0-70%) on spinach apo- and holocalmodulin that have been site-selectively labeled with fluorescein (F). In these experiments, calmodulin (CaM) has one F reporter group attached to Cys-26, and this site is located immediately adjacent to one of the four primary Ca(2+)-binding sites (EF hands). The optimum analytical CaM-F sensitivity to Ca2+ occurs between approximately 10 and 30% EtOH. Our results also show that added EtOH causes changes in CaM and these changes are surprisingly different for apo- and holo-CaM. Apo-CaM-F appears to lose one of its two waters of hydration at approximately 20% EtOH and retains one water of hydration between approximately 20 and 70% EtOH. In apo-CaM-F, the semiangle that describes the range over which the fluorescein reporter group can precess remains essentially constant (42 +/- 2 degrees) between 0 and 70% EtOH. This shows that the fluorescein reporter group precessional freedom in apo-CaM-F is not affected significantly by EtOH. Holo-CaM-F also appears to lose one water of hydration at approximately 20-30% EtOH but then appears to denature as the EtOH volume percent increases. The fluorescein reporter group semiangle within holo-CaM-F decreases from 43 +/- 1 degrees in neat aqueous buffer to 36 +/- 1 degrees at 70% EtOH. This shows that holo-CaM-F is less nativelike and the EF hand "closes down" about the fluorescein reporter group in holo-CaM-F as the EtOH volume percent increases.
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Affiliation(s)
- M A Doody
- Department of Chemistry, Natural Sciences Complex, University at Buffalo, State University of New York 14260-3000, USA
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Nara M, Tanokura M, Yamamoto T, Tasumi M. A comparative study of the binding effects of Mg2+, Ca2+, Sr2+, and Cd2+ on calmodulin by fourier-transform infrared spectroscopy. ACTA ACUST UNITED AC 1995. [DOI: 10.1002/bspy.350010107] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Tsuruta H, Sano T. A fluorescence temperature-jump study on Ca2(+)-induced conformational changes in calmodulin. Biophys Chem 1990; 35:75-84. [PMID: 2328277 DOI: 10.1016/0301-4622(90)80062-c] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Calmodulin has been shown to alter its conformation so as to interact with a number of target proteins upon Ca2+ binding. A Ca2(+)-binding study of calmodulin was performed by monitoring the fluorescence of intrinsic tyrosine residues and the probe 1-anilinonaphthalene-8-sulfonate (ANS). ANS fluorescence was shown to reflect Ca2+ binding to both high- and low-affinity sites. On the one hand, tyrosine fluorescence was sensitive only to the high-affinity Ca2+ binding. Temperature-jump investigation of the ternary complex of Ca2(+)-calmodulin-ANS in combination with monitoring of ANS fluorescence demonstrated the kinetic characteristics of the conformational change. The relaxation process was attributed to Ca2(+)-induced conformational change and the rate constants of this process were evaluated. On the basis of the rate constants of the conformational change, a rapid response of calmodulin in Ca2+ signaling is suggested.
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Affiliation(s)
- H Tsuruta
- Department of Materials Science, Faculty of Science, Hiroshima University, Japan
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11
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Buccigross JM, Nelson DJ. EPR studies show that all lanthanides do not have the same order of binding to calmodulin. Biochem Biophys Res Commun 1986; 138:1243-9. [PMID: 3019337 DOI: 10.1016/s0006-291x(86)80416-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Calmodulin, spin labeled at Tyr-99, has been titrated with the lanthanides La3+, Nd3+, Eu3+, Tb3+, Er3+ and Lu3+ as well as Ca2+ and Cd2+. The titration was monitored by EPR and changes in mobility of the spin label, due to binding into the labeled site and protein conformational change, were observed. Comparison of these titration curves with theoretical binding curves for the various calmodulin-metal species, show that different lanthanides have different high affinity sites. Three basic categories were observed, with Lu3+ and Er3+ behaving like Ca2+, Eu3+ and Tb3+ binding in the opposite order from Ca2+, and La3+ and Nd3+ different from either Ca2+ or Tb3+.
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12
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Buccigross JM, O'Donnell CL, Nelson DJ. A flow-dialysis method for obtaining relative measures of association constants in calmodulin-metal-ion systems. Biochem J 1986; 235:677-84. [PMID: 3019305 PMCID: PMC1146741 DOI: 10.1042/bj2350677] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A flow-dialysis apparatus suitable for the study of high-affinity metal-binding proteins has been utilized to study calmodulin-metal exchange as a measure of relative calmodulin-metal association constants. Calmodulin labelled with radioactive 153Gd was dialysed against buffer containing various competing metal ions. The rate of label exchange was monitored by a gamma-ray scintillation detector. Competing metals used were Ca2+ and Cd2+, and the lanthanides Gd3+, Eu3+, La3+ and Lu3+. All exchange processes were first-order, and two categories of metal were found: Ca2+ and Cd2+ in one, the lanthanides comprising the other. In addition calmodulin-metal complexes with radioactive 109Cd and 45Ca released the bound label without any competing metal being added to the buffer. The kinetics of this metal loss can be described by two consecutive first-order processes, and the fraction of label associated with each rate can be determined. Studies of phosphodiesterase activation by calmodulin show Cd2+ and calmodulin to cause 80% of the maximum activation found when Ca2+ and calmodulin are used.
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Delville A, Laszlo P, Nelson DJ. Calmodulin: calcium, potassium, and magnesium ion multiple equilibria and kinetics for interconversion, including the effect of repeated stimulation. J Theor Biol 1985; 112:157-75. [PMID: 3974261 DOI: 10.1016/s0022-5193(85)80121-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Using computer simulations, with realistic values for the intrinsic thermodynamic binding constants and kinetic on and off rate constants at the four metal-binding sites, the calmodulin molecule is shown to have been optimally adjusted by evolution for biological function. Despite a very large number of potential molecular states, depending upon occupation by potassium, calcium, or magnesium ions, the system restricts itself to a small number of physiologically-significant equilibrium species. It appears to possess built-in triggers for biological processes, with rapid (approximately 20 ms time-scale), step-function shaped, changes of the populations of the CMKK, CMMK, CKKK, CMMM (and CCKK) states. The time-response of calmodulin to periodic changes in ionic levels (2 and 5 s-1) makes it quite adequate for repeated stimulations. In short, calmodulin appears as a very selective information transmitter at the molecular level.
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Aulabaugh A, Niemczura WP, Gibbons WA. High field proton NMR studies of tryptic fragments of calmodulin: a comparison with the native protein. Biochem Biophys Res Commun 1984; 118:225-32. [PMID: 6696757 DOI: 10.1016/0006-291x(84)91090-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Addition of the 600 MHz proton magnetic resonance (PMR) spectra of two calmodulin tryptic fragments, residues 1-77 and 78-148, both in the apo- and calcium-bound forms, yielded, to a first order, the corresponding spectrum of intact apo- and calcium-bound calmodulin, respectively. This plus additional data permitted: 1) assignments of resonances to a particular sequence 2) the hypothesis that the secondary and tertiary structures and the calcium binding properties are similar in the fragments and intact calmodulin 3) assignment of the two high affinity calcium sites to the sequence 78-148.
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