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Myers MD, Ryazantsev S, Hicke L, Payne GS. Calmodulin Promotes N-BAR Domain-Mediated Membrane Constriction and Endocytosis. Dev Cell 2016; 37:162-73. [PMID: 27093085 DOI: 10.1016/j.devcel.2016.03.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 02/15/2016] [Accepted: 03/16/2016] [Indexed: 10/21/2022]
Abstract
Membrane remodeling by BAR (Bin, Amphiphysin, RVS) domain-containing proteins, such as endophilins and amphiphysins, is integral to the process of endocytosis. However, little is known about the regulation of endocytic BAR domain activity. We have identified an interaction between the yeast Rvs167 N-BAR domain and calmodulin. Calmodulin-binding mutants of Rvs167 exhibited defects in endocytic vesicle release. In vitro, calmodulin enhanced membrane tubulation and constriction by wild-type Rvs167 but not calmodulin-binding-defective mutants. A subset of mammalian N-BAR domains bound calmodulin, and co-expression of calmodulin with endophilin A2 potentiated tubulation in vivo. These studies reveal a conserved role for calmodulin in regulating the intrinsic membrane-sculpting activity of endocytic N-BAR domains.
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Affiliation(s)
- Margaret D Myers
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sergey Ryazantsev
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Linda Hicke
- Molecular Genetics and Microbiology, College of Natural Sciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Gregory S Payne
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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2
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Anderson JH, Tester DJ, Will ML, Ackerman MJ. Whole-Exome Molecular Autopsy After Exertion-Related Sudden Unexplained Death in the Young. ACTA ACUST UNITED AC 2016; 9:259-65. [DOI: 10.1161/circgenetics.115.001370] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/21/2016] [Indexed: 11/16/2022]
Affiliation(s)
- Jason H. Anderson
- From the Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine (J.H.A., M.J.A.), Department of Molecular Pharmacology and Experimental Therapeutics/Windland Smith Rice Sudden Death Genomics Laboratory (D.J.T., M.L.W., M.J.A.), and Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic, Rochester, MN (M.J.A.)
| | - David J. Tester
- From the Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine (J.H.A., M.J.A.), Department of Molecular Pharmacology and Experimental Therapeutics/Windland Smith Rice Sudden Death Genomics Laboratory (D.J.T., M.L.W., M.J.A.), and Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic, Rochester, MN (M.J.A.)
| | - Melissa L. Will
- From the Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine (J.H.A., M.J.A.), Department of Molecular Pharmacology and Experimental Therapeutics/Windland Smith Rice Sudden Death Genomics Laboratory (D.J.T., M.L.W., M.J.A.), and Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic, Rochester, MN (M.J.A.)
| | - Michael J. Ackerman
- From the Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine (J.H.A., M.J.A.), Department of Molecular Pharmacology and Experimental Therapeutics/Windland Smith Rice Sudden Death Genomics Laboratory (D.J.T., M.L.W., M.J.A.), and Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic, Rochester, MN (M.J.A.)
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Marshall CB, Nishikawa T, Osawa M, Stathopulos PB, Ikura M. Calmodulin and STIM proteins: Two major calcium sensors in the cytoplasm and endoplasmic reticulum. Biochem Biophys Res Commun 2015; 460:5-21. [PMID: 25998729 DOI: 10.1016/j.bbrc.2015.01.106] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 01/22/2015] [Indexed: 01/22/2023]
Abstract
The calcium (Ca(2+)) ion is a universal signalling messenger which plays vital physiological roles in all eukaryotes. To decode highly regulated intracellular Ca(2+) signals, cells have evolved a number of sensor proteins that are ideally adapted to respond to a specific range of Ca(2+) levels. Among many such proteins, calmodulin (CaM) is a multi-functional cytoplasmic Ca(2+) sensor with a remarkable ability to interact with and regulate a plethora of structurally diverse target proteins. CaM achieves this 'multi-talented' functionality through two EF-hand domains, each with an independent capacity to bind targets, and an adaptable flexible linker. By contrast, stromal interaction molecule-1 and -2 (STIMs) have evolved for a specific role in endoplasmic reticulum (ER) Ca(2+) sensing using EF-hand machinery analogous to CaM; however, whereas CaM structurally adjusts to dissimilar binding partners, STIMs use the EF-hand machinery to self-regulate the stability of the Ca(2+) sensing domain. The molecular mechanisms underlying the Ca(2+)-dependent signal transduction by CaM and STIMs have revealed a remarkable repertoire of actions and underscore the flexibility of nature in molecular evolution and adaption to discrete Ca(2+) levels. Recent genomic sequencing efforts have uncovered a number of disease-associated mutations in both CaM and STIM1. This article aims to highlight the most recent key structural and functional findings in the CaM and STIM fields, and discusses how these two Ca(2+) sensor proteins execute their biological functions.
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Affiliation(s)
- Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Tadateru Nishikawa
- Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo, 113-0033, Japan
| | - Peter B Stathopulos
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, M5G 1L7, Canada.
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Distinctive malfunctions of calmodulin mutations associated with heart RyR2-mediated arrhythmic disease. Biochim Biophys Acta Gen Subj 2015; 1850:2168-76. [PMID: 26164367 DOI: 10.1016/j.bbagen.2015.07.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/22/2015] [Accepted: 07/02/2015] [Indexed: 01/11/2023]
Abstract
Calmodulin (CaM) is a cytoplasmic calcium sensor that interacts with the cardiac ryanodine receptor (RyR2), a large Ca(2+) channel complex that mediates Ca(2+) efflux from the sarcoplasmic reticulum (SR) to activate cardiac muscle contraction. Direct CaM association with RyR2 is an important physiological regulator of cardiac muscle excitation-contraction coupling and defective CaM-RyR2 protein interaction has been reported in cases of heart failure. Recent genetic studies have identified CaM missense mutations in patients with a history of severe cardiac arrhythmogenic disorders that present divergent clinical features, including catecholaminergic polymorphic ventricular tachycardia (CPVT), long QT syndrome (LQTS) and idiopathic ventricular fibrillation (IVF). Herein, we describe how two CPVT- (N54I & N98S) and three LQTS-associated (D96V, D130G & F142L) CaM mutations result in alteration of their biochemical and biophysical properties. Ca(2+)-binding studies indicate that the CPVT-associated CaM mutations, N54I & N98S, exhibit the same or a 3-fold reduced Ca(2+)-binding affinity, respectively, versus wild-type CaM, whereas the LQTS-associated CaM mutants, D96V, D130G & F142L, display more profoundly reduced Ca(2+)-binding affinity. In contrast, all five CaM mutations confer a disparate RyR2 interaction and modulation of [(3)H]ryanodine binding to RyR2, regardless of CPVT or LQTS association. Our findings suggest that the clinical presentation of CPVT or LQTS associated with these five CaM mutations may involve both altered intrinsic Ca(2+)-binding as well as defective interaction with RyR2.
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Tamura K, Hayashi S. Linear Response Path Following: A Molecular Dynamics Method To Simulate Global Conformational Changes of Protein upon Ligand Binding. J Chem Theory Comput 2015; 11:2900-17. [PMID: 26575728 DOI: 10.1021/acs.jctc.5b00120] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Molecular functions of proteins are often fulfilled by global conformational changes that couple with local events such as the binding of ligand molecules. High molecular complexity of proteins has, however, been an obstacle to obtain an atomistic view of the global conformational transitions, imposing a limitation on the mechanistic understanding of the functional processes. In this study, we developed a new method of molecular dynamics (MD) simulation called the linear response path following (LRPF) to simulate a protein's global conformational changes upon ligand binding. The method introduces a biasing force based on a linear response theory, which determines a local reaction coordinate in the configuration space that represents linear coupling between local events of ligand binding and global conformational changes and thus provides one with fully atomistic models undergoing large conformational changes without knowledge of a target structure. The overall transition process involving nonlinear conformational changes is simulated through iterative cycles consisting of a biased MD simulation with an updated linear response force and a following unbiased MD simulation for relaxation. We applied the method to the simulation of global conformational changes of the yeast calmodulin N-terminal domain and successfully searched out the end conformation. The atomistically detailed trajectories revealed a sequence of molecular events that properly lead to the global conformational changes and identified key steps of local-global coupling that induce the conformational transitions. The LRPF method provides one with a powerful means to model conformational changes of proteins such as motors and transporters where local-global coupling plays a pivotal role in their functional processes.
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Affiliation(s)
- Koichi Tamura
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
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Marsman RF, Barc J, Beekman L, Alders M, Dooijes D, van den Wijngaard A, Ratbi I, Sefiani A, Bhuiyan ZA, Wilde AAM, Bezzina CR. A mutation in CALM1 encoding calmodulin in familial idiopathic ventricular fibrillation in childhood and adolescence. J Am Coll Cardiol 2013; 63:259-66. [PMID: 24076290 DOI: 10.1016/j.jacc.2013.07.091] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/24/2013] [Accepted: 07/01/2013] [Indexed: 10/26/2022]
Abstract
OBJECTIVES This study aimed to identify the genetic defect in a family with idiopathic ventricular fibrillation (IVF) manifesting in childhood and adolescence. BACKGROUND Although sudden cardiac death in the young is rare, it frequently presents as the first clinical manifestation of an underlying inherited arrhythmia syndrome. Gene discovery for IVF is important as it enables the identification of individuals at risk, because except for arrhythmia, IVF does not manifest with identifiable clinical abnormalities. METHODS Exome sequencing was carried out on 2 family members who were both successfully resuscitated from a cardiac arrest. RESULTS We characterized a family presenting with a history of ventricular fibrillation (VF) and sudden death without electrocardiographic or echocardiographic abnormalities at rest. Two siblings died suddenly at the ages of 9 and 10 years, and another 2 were resuscitated from out-of-hospital cardiac arrest with documented VF at ages 10 and 16 years, respectively. Exome sequencing identified a missense mutation affecting a highly conserved residue (p.F90L) in the CALM1 gene encoding calmodulin. This mutation was also carried by 1 of the siblings who died suddenly, from whom DNA was available. The mutation was present in the mother and in another sibling, both asymptomatic but displaying a marginally prolonged QT interval during exercise. CONCLUSIONS We identified a mutation in CALM1 underlying IVF manifesting in childhood and adolescence. The causality of the mutation is supported by previous studies demonstrating that F90 mediates the direct interaction of CaM with target peptides. Our approach highlights the utility of exome sequencing in uncovering the genetic defect even in families with a small number of affected individuals.
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Affiliation(s)
- Roos F Marsman
- Department of Clinical and Experimental Cardiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Julien Barc
- Department of Clinical and Experimental Cardiology, Academic Medical Center, Amsterdam, the Netherlands; ICIN-Netherlands Heart Institute, Utrecht, the Netherlands
| | - Leander Beekman
- Department of Clinical and Experimental Cardiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Marielle Alders
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, the Netherlands
| | - Dennis Dooijes
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Arthur van den Wijngaard
- Department of Clinical Genetics, Cardiovascular Research Institute Maastricht, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Ilham Ratbi
- Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohamed V Souissi, Rabat, Morocco
| | - Abdelaziz Sefiani
- Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohamed V Souissi, Rabat, Morocco
| | - Zahurul A Bhuiyan
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, the Netherlands; Laboratoire de Génétique Moléculaire, Service de Génétique Médicale, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Arthur A M Wilde
- Department of Clinical and Experimental Cardiology, Academic Medical Center, Amsterdam, the Netherlands; Princess Al Jawhara Albrahim Centre of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Connie R Bezzina
- Department of Clinical and Experimental Cardiology, Academic Medical Center, Amsterdam, the Netherlands.
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Kuttner YY, Nagar T, Engel S. Surface dynamics in allosteric regulation of protein-protein interactions: modulation of calmodulin functions by Ca2+. PLoS Comput Biol 2013; 9:e1003028. [PMID: 23592972 PMCID: PMC3617199 DOI: 10.1371/journal.pcbi.1003028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 02/25/2013] [Indexed: 11/19/2022] Open
Abstract
Knowledge of the structural basis of protein-protein interactions (PPI) is of fundamental importance for understanding the organization and functioning of biological networks and advancing the design of therapeutics which target PPI. Allosteric modulators play an important role in regulating such interactions by binding at site(s) orthogonal to the complex interface and altering the protein's propensity for complex formation. In this work, we apply an approach recently developed by us for analyzing protein surfaces based on steered molecular dynamics simulation (SMD) to the study of the dynamic properties of functionally distinct conformations of a model protein, calmodulin (CaM), whose ability to interact with target proteins is regulated by the presence of the allosteric modulator Ca(2+). Calmodulin is a regulatory protein that acts as an intracellular Ca(2+) sensor to control a wide variety of cellular processes. We demonstrate that SMD analysis is capable of pinpointing CaM surfaces implicated in the recognition of both the allosteric modulator Ca(2+) and target proteins. Our analysis of changes in the dynamic properties of the CaM backbone elicited by Ca(2+) binding yielded new insights into the molecular mechanism of allosteric regulation of CaM-target interactions.
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Affiliation(s)
- Yosef Y. Kuttner
- Bioinformatics Core Facility, National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tal Nagar
- Bioinformatics Core Facility, National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Stanislav Engel
- Department of Clinical Biochemistry and Pharmacology, National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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8
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Nakashima K, Ishida H, Nakatomi A, Yazawa M. Specific conformation and Ca(2+)-binding mode of yeast calmodulin: insight into evolutionary development. J Biochem 2012; 152:27-35. [PMID: 22563102 DOI: 10.1093/jb/mvs048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The vertebrate calmodulin is configured with two structurally independent globular lobes in N- and C-terminus, and a flexible central linker. Distinctly, two lobes of calmodulin from Saccharomyces cerevisiae (yCaM) interact and influence the Ca(2+)-binding profile of each other. We explored this further using the mutant proteins with eliminated Ca(2+)-binding ability in one of the lobes and found that the Ca(2+)-bound N-lobe associates with the Ca(2+)-free C-lobe to gain the Ca(2+) affinity of a wild-type level. Next, analysing series of C-terminal residue truncation mutant, we found that the truncation of C-terminal three residues induce the hyper Ca(2+) affinity. These residues are also important for the general structural behaviour of calmodulin, such as Ca(2+)-induced slow mobility shift in polyacrylamide gel electrophoresis and for the ability to activate Cmk1p (yeast calmodulin kinase). These suggest: (i) when Ca(2+) occupies only N-lobe, two lobes interact and form the stable intermediate leading to a proper level of Ca(2+) affinity; (ii) the C-terminal three residues are required to prohibit abnormal stabilization of the intermediate promoting abnormally high Ca(2+) affinity and for recognition of target enzymes. A model for Ca(2+) and target bindings of yCaM is proposed. Evolutional aspect concerning the biological significance of this model was discussed.
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Affiliation(s)
- Kenichi Nakashima
- Graduate School of Science, Hokkaido University, N10-W8, Sapporo, Hokkaido 060-0810, Japan.
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Kitevski-LeBlanc JL, Evanics F, Scott Prosser R. Optimizing ¹⁹F NMR protein spectroscopy by fractional biosynthetic labeling. JOURNAL OF BIOMOLECULAR NMR 2010; 48:113-121. [PMID: 20734112 DOI: 10.1007/s10858-010-9443-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 07/27/2010] [Indexed: 05/29/2023]
Abstract
In protein NMR experiments which employ nonnative labeling, incomplete enrichment is often associated with inhomogeneous line broadening due to the presence of multiple labeled species. We investigate the merits of fractional enrichment strategies using a monofluorinated phenylalanine species, where resolution is dramatically improved over that achieved by complete enrichment. In NMR studies of calmodulin, a 148 residue calcium binding protein, ¹⁹F and ¹H-¹⁵N HSQC spectra reveal a significant extent of line broadening and the appearance of minor conformers in the presence of complete (>95%) 3-fluorophenylalanine labeling. The effects of varying levels of enrichment of 3-fluorophenylalanine (i.e. between 3 and >95%) were further studied by ¹⁹F and ¹H-¹⁵N HSQC spectra, ¹⁵N T(1) and T(2) relaxation measurements, ¹⁹F T(2) relaxation, translational diffusion and heat denaturation experiments via circular dichroism. Our results show that while several properties, including translational diffusion and thermal stability show little variation between non-fluorinated and >95% ¹⁹F labeled samples, ¹⁹F and ¹H-¹⁵N HSQC spectra show significant improvements in line widths and resolution at or below 76% enrichment. Moreover, high levels of fluorination (>80%) appear to increase protein disorder as evidenced by backbone ¹⁵N dynamics. In this study, reasonable signal to noise can be achieved between 60-76% ¹⁹F enrichment, without any detectable perturbations from labeling.
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Affiliation(s)
- Julianne L Kitevski-LeBlanc
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Rd., North Mississauga, ON L5L1C6, Canada
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Kitevski-Leblanc JL, Evanics F, Scott Prosser R. Approaches to the assignment of (19)F resonances from 3-fluorophenylalanine labeled calmodulin using solution state NMR. JOURNAL OF BIOMOLECULAR NMR 2010; 47:113-123. [PMID: 20401735 DOI: 10.1007/s10858-010-9415-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 03/24/2010] [Indexed: 05/29/2023]
Abstract
Traditional single site replacement mutations (in this case, phenylalanine to tyrosine) were compared with methods which exclusively employ (15)N and (19)F-edited two- and three-dimensional NMR experiments for purposes of assigning (19)F NMR resonances from calmodulin (CaM), biosynthetically labeled with 3-fluorophenylalanine (3-FPhe). The global substitution of 3-FPhe for native phenylalanine was tolerated in CaM as evidenced by a comparison of (1)H-(15)N HSQC spectra and calcium binding assays in the presence and absence of 3-FPhe. The (19)F NMR spectrum reveals six resolved resonances, one of which integrates to three 3-FPhe species, making for a total of eight fluorophenylalanines. Single phenylalanine to tyrosine mutants of five phenylalanine positions resulted in (19)F NMR spectra with significant chemical shift perturbations of the remaining resonances, and provided only a single definitive assignment. Although (1)H-(19)F heteronucleclear NOEs proved weak, (19)F-edited (1)H-(1)H NOESY connectivities were relatively easy to establish by making use of the (3)J(FH) coupling between the fluorine nucleus and the adjacent fluorophenylalanine delta proton. (19)F-edited NOESY connectivities between the delta protons and alpha and beta nuclei in addition to (15)N-edited (1)H, (1)H NOESY crosspeaks proved sufficient to assign 4 of 8 (19)F resonances. Controlled cleavage of the protein into two fragments using trypsin, and a repetition of the above 2D and 3D techniques resulted in unambiguous assignments of all 8 (19)F NMR resonances. Our studies suggest that (19)F-edited NOESY NMR spectra are generally adequate for complete assignment without the need to resort to mutational analysis.
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Affiliation(s)
- Julianne L Kitevski-Leblanc
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Rd. North, Mississauga, ON, L5L 1C6, Canada
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Tsai YC, Delk NA, Chowdhury NI, Braam J. Arabidopsis potential calcium sensors regulate nitric oxide levels and the transition to flowering. PLANT SIGNALING & BEHAVIOR 2007; 2:446-54. [PMID: 19517005 PMCID: PMC2634334 DOI: 10.4161/psb.2.6.4695] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Accepted: 07/05/2007] [Indexed: 05/18/2023]
Abstract
In plants, flowering is a critical developmental transition orchestrated by four regulatory pathways. Distinct alleles encoding mutant forms of the Arabidopsis potential calcium sensor CML24 cause alterations in flowering time. CML24 can act as a switch in the response to day length perception; loss-of-function cml24 mutants are late flowering under long days, whereas apparent gain of CML24 function results in early flowering. CML24 function is required for proper CONSTANS (CO) expression; components upstream of CO in the photoperiod pathway are largely unaffected in the cml24 mutants. In conjunction with CML23, a related calmodulin-like protein, CML24 also inhibits FLOWERING LOCUS C (FLC) expression and therefore impacts the autonomous regulatory pathway of the transition to flowering. Nitric oxide (NO) levels are elevated in cml23/cml24 double mutants and are largely responsible for FLC transcript accumulation. Therefore, CML23 and CML24 are potential calcium sensors that have partially overlapping function that may act to transduce calcium signals to regulate NO accumulation. In turn, NO levels influence the transition to flowering through both the photoperiod and autonomous regulatory pathways.
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Affiliation(s)
- Yu-Chang Tsai
- Biochemistry and Cell Biology; Rice University; Houston, Texas USA
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12
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Pennestri M, Melino S, Contessa GM, Casavola EC, Paci M, Ragnini-Wilson A, Cicero DO. Structural basis for the interaction of the myosin light chain Mlc1p with the myosin V Myo2p IQ motifs. J Biol Chem 2006; 282:667-79. [PMID: 17074768 DOI: 10.1074/jbc.m607016200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Calmodulin, regulatory, and essential myosin light chain are evolutionary conserved proteins that, by binding to IQ motifs of target proteins, regulate essential intracellular processes among which are efficiency of secretory vesicles release at synapsis, intracellular signaling, and regulation of cell division. The yeast Saccharomyces cerevisiae calmodulin Cmd1 and the essential myosin light chain Mlc1p share the ability to interact with the class V myosin Myo2p and Myo4 and the class II myosin Myo1p. These myosins are required for vesicle, organelle, and mRNA transport, spindle orientation, and cytokinesis. We have used the budding yeast model system to study how calmodulin and essential myosin light chain selectively regulate class V myosin function. NMR structural analysis of uncomplexed Mlc1p and interaction studies with the first three IQ motifs of Myo2p show that the structural similarities between Mlc1p and the other members of the EF-hand superfamily of calmodulin-like proteins are mainly restricted to the C-lobe of these proteins. The N-lobe of Mlc1p presents a significantly compact and stable structure that is maintained both in the free and complexed states. The Mlc1p N-lobe interacts with the IQ motif in a manner that is regulated both by the IQ motifs sequence as well as by light chain structural features. These characteristic allows a distinctive interaction of Mlc1p with the first IQ motif of Myo2p when compared with calmodulin. This finding gives us a novel view of how calmodulin and essential light chain, through a differential binding to IQ1 of class V myosin motor, regulate this activity during vegetative growth and cytokinesis.
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Affiliation(s)
- Matteo Pennestri
- Department of Chemical Science and Technology, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
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13
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Okano H, Ohya Y. Binding of calmodulin to Nuf1p is required for karyogamy in Saccharomyces cerevisiae. Mol Genet Genomics 2003; 269:649-57. [PMID: 12836012 DOI: 10.1007/s00438-003-0853-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2003] [Accepted: 04/13/2003] [Indexed: 10/26/2022]
Abstract
The role of calmodulin (CaM) during mating in Saccharomyces cerevisiae was examined by using a set of Phe-to-Ala substitutions. We identified ten CaM mutants that exhibited significantly reduced mating efficiencies when crossed to a strain of the opposite mating type harboring the same CaM mutation. Most of the mating-defective CaM mutants were bilateral, i.e., they also exhibited mating defects, albeit minor ones, when crossed to the wild type. When strains carrying different bilateral CaM mutations were mated, the mating efficiencies recovered dramatically. We termed this phenomenon "intragenic mating complementation", and classified the mating-defective CaM mutations into two intragenic mating complementation groups. Two mutant alleles belonging to different groups showed minor defects in cell adhesion and cell fusion, but exhibited severe defects in karyogamy. CaM is known to bind to the essential spindle pole body component Nuf1p. This binding appears to be important for karyogamy because the nuf1(C911R) mutation, which impairs CaM-Nuf1p binding, resulted in a severe defect in karyogamy. Indeed, the two mating-defective CaM mutations were found to compromise formation of the CaM/Nuf1p complex, and the mating defects of these two CaM mutants were suppressible by a dominant, CaM-independent, mutation in NUF1. Taken together, these results suggest that loss of CaM binding to Nuf1p causes a defect in karyogamy, thereby inhibiting productive mating.
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Affiliation(s)
- H Okano
- Bio-Mimetic Control Research Center, The Institute of Physical and Chemical Research RIKEN, Anagahora, 463-0003 Nagoya, Aichi, Japan
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14
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Ishida H, Nakashima KI, Kumaki Y, Nakata M, Hikichi K, Yazawa M. The solution structure of apocalmodulin from Saccharomyces cerevisiae implies a mechanism for its unique Ca2+ binding property. Biochemistry 2002; 41:15536-42. [PMID: 12501182 DOI: 10.1021/bi020330r] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have determined the solution structure of calmodulin (CaM) from yeast (Saccharomyces cerevisiae) (yCaM) in the apo state by using NMR spectroscopy. yCaM is 60% identical in its amino acid sequence with other CaMs, and exhibits its unique biological features. yCaM consists of two similar globular domains (N- and C-domain) containing three Ca(2+)-binding motifs, EF-hands, in accordance with the observed 3 mol of Ca(2+) binding. In the solution structure of yCaM, the conformation of the N-domain conforms well to the one of the expressed N-terminal half-domains of yCaM [Ishida, H., et al. (2000) Biochemistry 39, 13660-13668]. The conformation of the C-domain basically consists of a pair of helix-loop-helix motifs, though a segment corresponding to the forth Ca(2+)-binding site of CaM deviates in its primary structure from a typical EF-hand motif and loses the ability to bind Ca(2+). Thus, the resulting conformation of each domain is essentially identical to the corresponding domain of CaM in the apo state. A flexible linker connects the two domains as observed for CaM. Any evidence for the previously reported interdomain interaction in yCaM was not observed in the solution structure of the apo state. Hence, the interdomain interaction possibly occurs in the course of Ca(2+) binding and generates a cooperative Ca(2+) binding among all three sites. Preliminary studies on a mutant protein of yCaM, E104Q, revealed that the Ca(2+)-bound N-domain interacts with the apo C-domain and induces a large conformational change in the C-domain.
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Affiliation(s)
- Hiroaki Ishida
- Division of Biological Sciences, High-Resolution NMR Laboratory, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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Desrivières S, Cooke FT, Morales-Johansson H, Parker PJ, Hall MN. Calmodulin controls organization of the actin cytoskeleton via regulation of phosphatidylinositol (4,5)-bisphosphate synthesis in Saccharomyces cerevisiae. Biochem J 2002; 366:945-51. [PMID: 12079494 PMCID: PMC1222839 DOI: 10.1042/bj20020429] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2002] [Revised: 06/17/2002] [Accepted: 06/21/2002] [Indexed: 11/17/2022]
Abstract
Phosphoinositides regulate a wide range of cellular processes, including proliferation, survival, cytoskeleton remodelling and membrane trafficking, yet the mechanisms controlling the kinases, phosphatases and lipases that modulate phosphoinositide levels are poorly understood. In the present study, we describe a mechanism controlling MSS4, the sole phosphatidylinositol (4)-phosphate 5-kinase in Saccharomyces cerevisiae. Mutations in MSS4 and CMD1, encoding the small Ca(2+)-binding protein calmodulin, confer similar phenotypes, including loss of viability and defects in endocytosis and in organization of the actin cytoskeleton. Overexpression of MSS4 suppresses the growth and actin defects of cmd1-226, a temperature-sensitive calmodulin mutant which is defective in the organization of the actin cytoskeleton. Finally, the cmd1-226 mutant exhibits reduced levels of phosphatidylinositol (4,5)-bisphosphate. These findings suggest that calmodulin positively controls MSS4 activity and thereby the actin cytoskeleton.
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Affiliation(s)
- Sylvane Desrivières
- Division of Biochemistry, Biozentrum, University of Basel, Klingelbergstrasse 70, Switzerland
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Joseph JD, Means AR. Calcium binding is required for calmodulin function in Aspergillus nidulans. EUKARYOTIC CELL 2002; 1:119-25. [PMID: 12455978 PMCID: PMC118048 DOI: 10.1128/ec.01.1.119-125.2002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To explore the structural basis for the essential role of calmodulin (CaM) in Aspergillus nidulans, we have compared the biochemical and in vivo properties of A. nidulans CaM (AnCaM) with those of heterologous CaMs. Neither Saccharomyces cerevisiae CaM (ScCaM) nor a Ca2+ binding mutant of A. nidulans CaM (1234) interacts appreciably with A. nidulans CaM binding proteins by an overlay assay or activates two essential CaMKs, CMKA and CMKB. In contrast, although vertebrate CaM (VCaM) binds a spectrum of proteins similar to that for AnCaM, it is unable to fully activate CMKA and CMKB, displaying a higher K(CaM) and reduced Vmax for both enzymes. In correlation with the biochemical analysis, neither ScCaM nor 1234 can support A. nidulans growth in the absence of the endogenous protein, whereas VCaM only partially complements the absence of wild-type CaM. Analysis of VCaM and AnCaM chimeras demonstrates that amino acid variations in both N- and C-terminal domains contribute to the inability of VCaM to activate CMKB, but differences in the N terminus are largely responsible for the reduced activity towards CMKA. In vivo, the chimeric molecules support growth equivalently, but only to levels intermediate between those of VCaM and AnCaM, suggesting that the reduced ability to activate the CaMKs is not solely responsible for the inability of VCaM to complement the absence of the wild-type protein. Thus, not only is Ca2+ binding required for CaM function in A. nidulans, but the essential in vivo functions of A. nidulans CaM are uniquely sensitive to the subtle amino acid variations present in vertebrate CaM.
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Affiliation(s)
- James D Joseph
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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Williams KE, Cyert MS. The eukaryotic response regulator Skn7p regulates calcineurin signaling through stabilization of Crz1p. EMBO J 2001; 20:3473-83. [PMID: 11432834 PMCID: PMC125528 DOI: 10.1093/emboj/20.13.3473] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
To survive ionic, pH and pheromone stress, the yeast Saccharomyces cerevisiae activates signaling through the Ca2+-activated phosphatase calcineurin to the transcription factor Crz1p/Tcn1p. We show that the overexpression of SKN7, a response-regulator transcription factor, activates transcription from a calcineurin/Crz1p-dependent response element (CDRE). Ca2+-induced, calcineurin/Crz1p-dependent activation of several genes is reduced in skn7 mutants. Skn7p modulates CDRE-dependent transcription by affecting Crz1p protein levels. Specifically, the rate of Crz1p turnover is increased in skn7 mutants. Calcineurin, but not its phosphatase activity, is required for Skn7p-mediated Crz1p stabilization. Skn7p binds to both calcineurin and Crz1p in vitro, and we suggest that this interaction is required for Skn7p regulation of Crz1p. The DNA-binding and internal coiled-coil domains, but not the response- regulator phosphorylation of Skn7p, are necessary for Crz1p-dependent transcriptional activation and Crz1p stabilization by Skn7 in vivo. The DNA-binding domain of Skn7p is also required for binding to Crz1p and calcineurin in vitro. Thus, we propose that Skn7p protects Crz1p from degradation by binding to it and calcineurin through its DNA-binding domain.
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Affiliation(s)
| | - Martha S. Cyert
- Department of Biological Science, Stanford University, Stanford, CA 94305-5020, USA
Corresponding author e-mail:
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Ivanovska I, Rose MD. Fine structure analysis of the yeast centrin, Cdc31p, identifies residues specific for cell morphology and spindle pole body duplication. Genetics 2001; 157:503-18. [PMID: 11156974 PMCID: PMC1461518 DOI: 10.1093/genetics/157.2.503] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Centrin/Cdc31p is a Ca2+-binding protein related to calmodulin found in the MTOC of diverse organisms. In yeast, Cdc31p localizes to the SPB where it interacts with Kar1p and is required for SPB duplication. Recent findings suggest that centrin also functions elsewhere in the cell. To dissect the functions of Cdc31p, we generated cdc31 mutations chosen only for temperature sensitivity, but otherwise unbiased as to phenotype. Three phenotypes of the cdc31 mutants, temperature sensitivity, G2/M arrest, and cell lysis, were not well correlated, indicating that the mutations may differentially affect Cdc31p's interactions with other proteins. Alleles near the C-terminal region exhibited high G2/M arrest and genetic interactions with kar1-Delta17, suggesting that this region modulates an SPB-related function. Alleles causing high lysis and reduced Kic1p kinase activity mapped to the middle of the gene, suggesting disruption of a KIC1-like function and defects in activating Kic1p. A third region conferred temperature sensitivity without affecting cell lysis or G2/M arrest, suggesting that it defines a third function. Mutations in the C-terminal region were also defective for interaction with Kic1p. Mapping the alleles onto a predicted structure of Cdc31p, we have identified surfaces likely to be important for interacting with both Kar1p and Kic1p.
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Affiliation(s)
- I Ivanovska
- Department of Molecular Biology, Princeton University, Washington Rd., Princeton, NJ 08544, USA
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Ishida H, Takahashi K, Nakashima K, Kumaki Y, Nakata M, Hikichi K, Yazawa M. Solution structures of the N-terminal domain of yeast calmodulin: Ca2+-dependent conformational change and its functional implication. Biochemistry 2000; 39:13660-8. [PMID: 11076504 DOI: 10.1021/bi000582x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have determined solution structures of the N-terminal half domain (N-domain) of yeast calmodulin (YCM0-N, residues 1-77) in the apo and Ca(2+)-saturated forms by NMR spectroscopy. The Ca(2+)-binding sites of YCM0-N consist of a pair of helix-loop-helix motifs (EF-hands), in which the loops are linked by a short beta-sheet. The binding of two Ca(2+) causes large rearrangement of the four alpha-helices and exposes the hydrophobic surface as observed for vertebrate calmodulin (CaM). Within the observed overall conformational similarity in the peptide backbone, several significant conformational differences were observed between the two proteins, which originated from the 38% disagreement in amino acid sequences. The beta-sheet in apo YCM0-N is strongly twisted compared with that in the N-domain of CaM, while it turns to the normal more stable conformation on Ca(2+) binding. YCM0-N shows higher cooperativity in Ca(2+) binding than the N-domain of CaM, and the observed conformational change of the beta-sheet is a possible cause of the highly cooperative Ca(2+) binding. The hydrophobic surface on Ca(2+)-saturated YCM0-N appears less flexible due to the replacements of Met51, Met71, and Val55 in the hydrophobic surface of CaM with Leu51, Leu71, and Ile55, which is thought to be one of reasons for the poor activation of target enzymes by yeast CaM.
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Affiliation(s)
- H Ishida
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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Inoue SB, Qadota H, Arisawa M, Watanabe T, Ohya Y. Prenylation of Rho1p is required for activation of yeast 1, 3-beta-glucan synthase. J Biol Chem 1999; 274:38119-24. [PMID: 10608882 DOI: 10.1074/jbc.274.53.38119] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
One of the essential protein substrates of geranylgeranyl transferase type I in the budding yeast Saccharomyces cerevisiae is a rho-type GTPase, Rho1p, which is a regulatory subunit of 1, 3-beta-glucan synthase. Previous studies have indicated that modification of Rho1p is significantly reduced in a mutant of the beta subunit of geranylgeranyl transferase type I called cal1-1. Here we present genetic and biochemical evidence showing that modification of Rho1p is required for activity of 1,3-beta-glucan synthase. The 1,3-beta-glucan synthase activity of the cal1-1 membrane was significantly reduced compared with that of the wild-type membrane. The impaired activity was partly due to the reduced amount of Fks1p, a putative catalytic subunit of 1, 3-beta-glucan synthase, but also partly due to reduced affinity between unmodified Rho1p and Fks1p. Glutathione S-transferase (GST)-Rho1 proteins with or without the C-terminal motif required for the modification were purified and used to analyze the interaction. The modified form of GST-Rho1p was specifically able to restore the 1,3-beta-glucan synthase of the rho1-3 membrane. Gel overlay analysis indicated that an unmodified form of GST-Rho1p fails to interact with Fks1p. These results indicated that the geranylgeranylation of Rho1p is a prerequisite to the assembly and activation of 1,3-beta-glucan synthase in vitro. Increased cytoplasmic levels of divalent cations such as Ca(2+) restored both Rho1p modification and the 1,3-beta-glucan synthase activity of cal1-1, suggesting that cytoplasmic levels of the divalent cations affect geranylgeranyl transferase type I activity in vivo.
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Affiliation(s)
- S B Inoue
- Department of Mycology, Nippon Roche Research Center, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
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Abstract
The utilization of optical biosensors to study molecular interactions continues to expand. In 1998, 384 articles relating to the use of commercial biosensors were published in 130 different journals. While significant strides in new applications and methodology were made, a majority of the biosensor literature is of rather poor quality. Basic information about experimental conditions is often not presented and many publications fail to display the experimental data, bringing into question the credibility of the results. This review provides suggestions on how to collect, analyze and report biosensor data.
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Affiliation(s)
- D G Myszka
- University of Utah, Salt Lake City, UT 84132, USA.
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Abstract
Optical biosensors have made the analysis of molecular interactions rapid and convenient. The field is still young, with commercial instrumentation having been available for less than ten years. For this reason instrument development is still an important factor and the past year has seen continuing advances in instrumentation and particularly in novel sensor surfaces.
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Affiliation(s)
- R J Leatherbarrow
- Department of Chemistry, Imperial College, South Kensington, London, SW7, 2AY, UK.
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