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Confocal Laser Scanning Microscopy and Fluorescence Correlation Methods for the Evaluation of Molecular Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1310:1-30. [PMID: 33834430 DOI: 10.1007/978-981-33-6064-8_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Confocal laser scanning microscopy (CLSM) and related microscopic techniques allow a unique and versatile approach to image and analyze living cells due to their specificity and high sensitivity. Among confocal related techniques, fluorescence correlation methods, such as fluorescence correlation spectroscopy (FCS) and dual-color fluorescence cross-correlation spectroscopy (FCCS), are highly sensitive biophysical methods for analyzing the complex dynamic events of molecular diffusion and interaction change in live cells as well as in solution by exploiting the characteristics of fluorescence signals. Analytical and quantitative information from FCS and FCCS coupled with fluorescence images obtained from CLSM can now be applied in convergence science such as drug delivery and nanomedicine, as well as in basic cell biology. In this chapter, a brief introduction into the physical parameters that can be obtained from FCS and FCCS is first provided. Secondly, experimental examples of the methods for evaluating the parameters is presented. Finally, two potential FCS and FCCS applications for convergence science are introduced in more detail.
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Oasa S, Mikuni S, Yamamoto J, Kurosaki T, Yamashita D, Kinjo M. Relationship Between Homodimeric Glucocorticoid Receptor and Transcriptional Regulation Assessed via an In Vitro Fluorescence Correlation Spectroscopy-Microwell System. Sci Rep 2018; 8:7488. [PMID: 29748590 PMCID: PMC5945783 DOI: 10.1038/s41598-018-25393-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 04/19/2018] [Indexed: 12/17/2022] Open
Abstract
Glucocorticoid receptor (GR) is a hormone-activated transcription regulatory protein involved in metabolism as well as adrenocortical responses to psychosocial stress. Ligand-activated GR localizes to the nucleus, where GR homodimers regulate gene transcription via direct binding to glucocorticoid response elements (GREs). The role of GR homodimers in transcriptional activation has not yet been elucidated. In this study, we determined the concentration of GR homodimer, and its dissociation constant (Kd), at the single-cell level, by using fluorescence correlation spectroscopy (FCS) combined with a microwell system. Results from dissociation constant analysis and diffusion analysis suggested that GR forms complexes with other proteins as well as homodimers. We determined the relationship between the concentration of GR homodimer and transcriptional activity using a triple-color FCS-microwell system-based fluorescent reporter assay. The binding affinity of GR to GREs was analyzed via fluorescence cross-correlation spectroscopy (FCCS). Our findings indicate that the GR homodimer is essential for activating target gene transcription.
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Affiliation(s)
- Sho Oasa
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Shintaro Mikuni
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Johtaro Yamamoto
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Tsumugi Kurosaki
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Daisuke Yamashita
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan.
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Marchenkov V, Marchenko N, Kaysheva A, Kotova N, Kashparov I, Semisotnov G. Dataset concerning GroEL chaperonin interaction with proteins. Data Brief 2016; 6:619-24. [PMID: 26909376 PMCID: PMC4735476 DOI: 10.1016/j.dib.2016.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 12/28/2015] [Accepted: 01/06/2016] [Indexed: 11/21/2022] Open
Abstract
GroEL chaperonin is well-known to interact with a wide variety of polypeptide chains. Here we show the data related to our previous work (http://dx.doi.org/10.1016/j.pep.2015.11.020[1]), and concerning the interaction of GroEL with native (lysozyme, α-lactalbumin) and denatured (lysozyme, α-lactalbumin and pepsin) proteins in solution. The use of affinity chromatography on the base of denatured pepsin for GroEL purification from fluorescent impurities is represented as well.
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Harada K, Mikuni S, Beppu H, Niimi H, Abe S, Hano N, Yamagata K, Kinjo M, Kitajima I. A rapid and high-throughput quantitation assay of the nuclear factor κB activity using fluorescence correlation spectroscopy in the setting of clinical laboratories. PLoS One 2013; 8:e75579. [PMID: 24124497 PMCID: PMC3790820 DOI: 10.1371/journal.pone.0075579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/14/2013] [Indexed: 11/30/2022] Open
Abstract
Background Transcription factor nuclear factor-κB (NF-κB) plays a key role in the regulation of immune responses to inflammation. However, convenient assay systems to quantitate the NF-κB activity level in a timely manner are not available in the setting of clinical laboratories. Therefore, we developed a novel and high-throughput quantitative assay based on fluorescence correlation spectroscopy (FCS) to detect the NF-κB activity level in cellular nuclear extracts and evaluated the performance of this method. The basic principle of this assay is to calculate the binding fraction of NF-κB to fluorescent-labeled DNA probes, which contain NF-κB binding sites. Methods Non-fluorescent competitive probes are employed to normalize the influence of the viscosity of the nuclear extracts between samples and to eliminate the influence of nonspecific binding of the fluorescent probes. To confirm accurate quantitation, human recombinant NF-κB p50 was mixed into U937 cell nuclear extracts, and the binding fraction of the fluorescent probes to NF-κB in the mixture was calculated for quantitation. To evaluate whether this method can be applied to measure the NF-κB activity in human lymphocytes, the NF-κB activity levels of systemic inflammatory response syndrome patients during perioperative periods were measured. Results The percentage recovery was 88.9%. The coefficients of variation of the intra-assay were approximately 10%. NF-κB activity levels during the perioperative period can were successfully measured. The assay time for the FCS measurement was within 20 minutes. Conclusions This assay system can be used to quantitate NF-κB activity levels in a timely manner in the setting of hospital laboratories.
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Affiliation(s)
- Kenu Harada
- Department of Clinical Laboratory and Molecular Pathology, Graduate School of Medicine and Pharmaceutical Science for Research, University of Toyama, Toyama, Japan
| | - Shintaro Mikuni
- Department of Advanced Optical Imaging Research, Research Center for Cooperative Projects, Graduated School of Medicine, Hokkaido University, Sapporo, Japan
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Hideyuki Beppu
- Department of Clinical Laboratory and Molecular Pathology, Graduate School of Medicine and Pharmaceutical Science for Research, University of Toyama, Toyama, Japan
| | - Hideki Niimi
- Department of Clinical Laboratory and Molecular Pathology, Graduate School of Medicine and Pharmaceutical Science for Research, University of Toyama, Toyama, Japan
| | - Shigeki Abe
- Sysmex Corporation BMA Laboratory, Kobe, Japan
| | - Nobuko Hano
- Sysmex Corporation BMA Laboratory, Kobe, Japan
| | | | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Isao Kitajima
- Department of Clinical Laboratory and Molecular Pathology, Graduate School of Medicine and Pharmaceutical Science for Research, University of Toyama, Toyama, Japan
- * E-mail:
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Lyu ZX, Shao Q, Gao YQ, Zhao XS. Direct observation of the uptake of outer membrane proteins by the periplasmic chaperone Skp. PLoS One 2012; 7:e46068. [PMID: 23049938 PMCID: PMC3458824 DOI: 10.1371/journal.pone.0046068] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 08/28/2012] [Indexed: 11/18/2022] Open
Abstract
The transportation of membrane proteins through the aqueous subcellular space is an important and challenging process. Its molecular mechanism and the associated structural change are poorly understood. Periplasmic chaperones, such as Skp in Escherichia coli, play key roles in the transportation and protection of outer membrane proteins (OMPs) in Gram-negative bacteria. The molecular mechanism through which Skp interacts with and protects OMPs remains mysterious. Here, a combined experimental and molecular dynamics simulation study was performed to gain the structural and dynamical information in the process of OMPs and Skp binding. Stopped-flow experiments on site specific mutated and labeled Skp and several OMPs, namely OmpC, the transmembrane domain of OmpA, and OmpF, allowed us to obtain the mechanism of OMP entering the Skp cavity, and molecular dynamics simulations yielded detailed molecular interactions responsible for this process. Both experiment and simulation show that the entrance of OMP into Skp is a highly directional process, which is initiated by the interaction between the N-terminus of OMP and the bottom “tentacle” domain of Skp. The opening of the more flexible tentacle of Skp, the non-specific electrostatic interactions between OMP and Skp, and the constant formation and breaking of salt bridges between Skp and its substrate together allow OMP to enter Skp and gradually “climb” into the Skp cavity in the absence of an external energy supply.
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Affiliation(s)
- Zhi-Xin Lyu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, Biodynamic Optical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Qiang Shao
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- * E-mail: (YQG); (XSZ)
| | - Xin Sheng Zhao
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, Biodynamic Optical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- * E-mail: (YQG); (XSZ)
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Shahzad A, Knapp M, Lang I, Köhler G. The use of fluorescence correlation spectroscopy (FCS) as an alternative biomarker detection technique: a preliminary study. J Cell Mol Med 2011; 15:2706-11. [PMID: 21306559 PMCID: PMC4373439 DOI: 10.1111/j.1582-4934.2011.01272.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Accepted: 01/27/2011] [Indexed: 11/30/2022] Open
Abstract
Biomarkers are essential part of daily medical practice. Currently, biomarkers are being used both for diagnostic and prognostic purposes. There are many approaches e.g. ELISA by which biomarker levels are detected from patient samples. However, all these approaches are laborious, time consuming and expensive. There is therefore a general need for exploring new technique which can overcome these drawbacks. Here, we present a preliminary study for detection of serum biomarkers by fluorescence correlation spectroscopy (FCS) based diagnostic technique. FCS is a technique basically used for spatial and temporal analysis of molecular interactions of extremely low-concentration biomolecules in solution. FCS is able to measure diffusion time of the fluorescent molecules passing through the open detection volume and it can also measure the average number of fluorescent molecules passing through the detection volume. Because diffusion speed is correlated with shape and molecular mass of the fluorescent molecule, this property makes it possible to study the complex formation between a small fluorescently labelled and a large unlabelled molecule. In this preliminary study, we utilize this FCS property for detection of serum biomarker. Further studies on various pathological serum samples are warranted to explore further aspects of this technique.
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Affiliation(s)
- Aamir Shahzad
- Max F. Perutz Laboratories, Department of Structural Biology and Biomolecular Chemistry, University of Vienna, Vienna, Austria.
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Lee JI, Sato M, Ushida K, Mochida J. Measurement of diffusion in articular cartilage using fluorescence correlation spectroscopy. BMC Biotechnol 2011; 11:19. [PMID: 21366913 PMCID: PMC3061899 DOI: 10.1186/1472-6750-11-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 03/02/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fluorescence correlation spectroscopy (FCS) provides information about translational diffusion of fluorescent molecules in tiny detection volumes at the single-molecule level. In normal states, cartilage tissue lacks vascularity, so chondrocyte metabolism depends on diffusion for molecular exchanges. The abundant extracellular matrix (ECM) of cartilage is maintained by a limited number of chondrocytes. ECM plays an important role in the regulation of chondrocyte functions. In this study, FCS was used to measure diffusion behaviors of albumin, the major protein of the intra-articular space, using normal and degenerated cartilage. Preliminary investigation of fluorescence dyes including Alexa 488, Rhodamine 6G and Rhodamine 123 was conducted to evaluate their properties in cartilage. RESULTS The results indicate that the diffusion behaviors of fluorescently labeled albumin can be observed using FCS in both normal and chemically degenerated cartilage. CONCLUSIONS This work demonstrates the capability of FCS for direct measurement of diffusion in cartilaginous ECM. When the diffusion characteristics of fluorescent probes in ECM are clarified using FCS evaluation, FCS will be applicable as a method for early diagnosis of osteoarthritis, which is accompanied by increased abnormalities of ECM and also as tool for evaluating bio-engineered artificial cartilage for autologous chondrocyte implantation.
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Affiliation(s)
- Jeong Ik Lee
- Department of Orthopaedic Surgery, Surgical Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
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Kawai-Noma S, Pack CG, Kojidani T, Asakawa H, Hiraoka Y, Kinjo M, Haraguchi T, Taguchi H, Hirata A. In vivo evidence for the fibrillar structures of Sup35 prions in yeast cells. ACTA ACUST UNITED AC 2010; 190:223-31. [PMID: 20643880 PMCID: PMC2930275 DOI: 10.1083/jcb.201002149] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Correlative light and electron microscopy provides support for the linear amalgamation of yeast prion proteins. Yeast prion [PSI+] is caused by aggregated structures of the Sup35 protein. Although Sup35 forms typical amyloid fibrils in vitro, there is no direct evidence for the fibrillar structures of Sup35 in vivo. We analyzed [PSI+] cells in which Sup35 fused with green fluorescent protein (GFP) formed aggregates visible by fluorescence microscopy using thin-section electron microscopy (EM). Rapid-freeze EM combined with an immunogold-labeling technique as well as correlative light EM, which allows high-resolution imaging by EM of the same structure observed by light (fluorescence) microscopy, shows that the aggregates contain bundled fibrillar structures of Sup35-GFP. Additional biochemical and fluorescent correlation spectroscopy results suggest that the Sup35 oligomers diffused in the [PSI+] lysates adopt fibril-like shapes. Our findings demonstrate that [PSI+] cells contain Sup35 fibrillar structures closely related to those formed in vitro and provide insight into the molecular mechanism by which Sup35 aggregates are assembled and remodeled in [PSI+] cells.
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Affiliation(s)
- Shigeko Kawai-Noma
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
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Shahzad A, Köhler G, Knapp M, Gaubitzer E, Puchinger M, Edetsberger M. Emerging applications of fluorescence spectroscopy in medical microbiology field. J Transl Med 2009; 7:99. [PMID: 19941643 PMCID: PMC2787503 DOI: 10.1186/1479-5876-7-99] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 11/26/2009] [Indexed: 12/03/2022] Open
Abstract
There are many diagnostic techniques and methods available for diagnosis of medically important microorganisms like bacteria, viruses, fungi and parasites. But, almost all these techniques and methods have some limitations or inconvenience. Most of these techniques are laborious, time consuming and with chances of false positive or false negative results. It warrants the need of a diagnostic technique which can overcome these limitations and problems. At present, there is emerging trend to use Fluorescence spectroscopy as a diagnostic as well as research tool in many fields of medical sciences. Here, we will critically discuss research studies which propose that Fluorescence spectroscopy may be an excellent diagnostic as well as excellent research tool in medical microbiology field with high sensitivity and specificity.
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Affiliation(s)
- Aamir Shahzad
- Max F, Perutz Laboratories, Department of Structural Biology and Biomolecular Chemistry, University of Vienna, Vienna, Austria.
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Jiang Y, Wang Q, Cohen AE, Douglas N, Frydman J, Moerner WE. Hardware-based anti-Brownian electrokinetic trap (ABEL trap) for single molecules: Control loop simulations and application to ATP binding stoichiometry in multi-subunit enzymes. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2008; 7038:1-12. [PMID: 19823693 DOI: 10.1117/12.798093] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The hardware-based Anti-Brownian ELectrokinetic trap (ABEL trap) features a feedback latency as short as 25 µs, suitable for trapping single protein molecules in aqueous solution. The performance of the feedback control loop is analyzed to extract estimates of the position variance for various controller designs. Preliminary data are presented in which the trap is applied to the problem of determining the distribution of numbers of ATP bound for single chaperonin multi-subunit enzymes.
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Affiliation(s)
- Yan Jiang
- Department of Chemistry, Stanford University, Stanford, California 94305
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Konno H, Murakami-Fuse T, Fujii F, Koyama F, Ueoka-Nakanishi H, Pack CG, Kinjo M, Hisabori T. The regulator of the F1 motor: inhibition of rotation of cyanobacterial F1-ATPase by the epsilon subunit. EMBO J 2006; 25:4596-604. [PMID: 16977308 PMCID: PMC1589999 DOI: 10.1038/sj.emboj.7601348] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Accepted: 08/22/2006] [Indexed: 11/09/2022] Open
Abstract
The chloroplast-type F(1) ATPase is the key enzyme of energy conversion in chloroplasts, and is regulated by the endogenous inhibitor epsilon, tightly bound ADP, the membrane potential and the redox state of the gamma subunit. In order to understand the molecular mechanism of epsilon inhibition, we constructed an expression system for the alpha(3)beta(3)gamma subcomplex in thermophilic cyanobacteria allowing thorough investigation of epsilon inhibition. epsilon Inhibition was found to be ATP-independent, and different to that observed for bacterial F(1)-ATPase. The role of the additional region on the gamma subunit of chloroplast-type F(1)-ATPase in epsilon inhibition was also determined. By single molecule rotation analysis, we succeeded in assigning the pausing angular position of gamma in epsilon inhibition, which was found to be identical to that observed for ATP hydrolysis, product release and ADP inhibition, but distinctly different from the waiting position for ATP binding. These results suggest that the epsilon subunit of chloroplast-type ATP synthase plays an important regulator for the rotary motor enzyme, thus preventing wasteful ATP hydrolysis.
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Affiliation(s)
- Hiroki Konno
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan
- ATP System Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Corporation (JST), Nagatsuta-cho, Midori-ku, Yokohama, Japan
| | - Tomoe Murakami-Fuse
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan
- ATP System Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Corporation (JST), Nagatsuta-cho, Midori-ku, Yokohama, Japan
| | - Fumihiko Fujii
- Laboratory of Supramolecular Biophysics, Research Institute for Electronic Science, Hokkaido University, Kita-ku, Sapporo, Hokkaido, Japan
| | - Fumie Koyama
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan
- ATP System Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Corporation (JST), Nagatsuta-cho, Midori-ku, Yokohama, Japan
| | - Hanayo Ueoka-Nakanishi
- ATP System Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Corporation (JST), Nagatsuta-cho, Midori-ku, Yokohama, Japan
| | - Chan-Gi Pack
- Laboratory of Supramolecular Biophysics, Research Institute for Electronic Science, Hokkaido University, Kita-ku, Sapporo, Hokkaido, Japan
| | - Masataka Kinjo
- Laboratory of Supramolecular Biophysics, Research Institute for Electronic Science, Hokkaido University, Kita-ku, Sapporo, Hokkaido, Japan
| | - Toru Hisabori
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan
- ATP System Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Corporation (JST), Nagatsuta-cho, Midori-ku, Yokohama, Japan
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-Ku, Yokohama, Kanagawa 226-8503, Japan. Tel.: +81 45 924 5234; Fax: +81 45 924 5277; E-mail:
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Oyama R, Takashima H, Yonezawa M, Doi N, Miyamoto-Sato E, Kinjo M, Yanagawa H. Protein-protein interaction analysis by C-terminally specific fluorescence labeling and fluorescence cross-correlation spectroscopy. Nucleic Acids Res 2006; 34:e102. [PMID: 16914444 PMCID: PMC1904107 DOI: 10.1093/nar/gkl477] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Here, we describe novel puromycin derivatives conjugated with iminobiotin and a fluorescent dye that can be linked covalently to the C-terminus of full-length proteins during cell-free translation. The iminobiotin-labeled proteins can be highly purified by affinity purification with streptavidin beads. We confirmed that the purified fluorescence-labeled proteins are useful for quantitative protein–protein interaction analysis based on fluorescence cross-correlation spectroscopy (FCCS). The apparent dissociation constants of model protein pairs such as proto-oncogenes c-Fos/c-Jun and archetypes of the family of Ca2+-modulated calmodulin/related binding proteins were in accordance with the reported values. Further, detailed analysis of the interactions of the components of polycomb group complex, Bmi1, M33, Ring1A and RYBP, was successfully conducted by means of interaction assay for all combinatorial pairs. The results indicate that FCCS analysis with puromycin-based labeling and purification of proteins is effective and convenient for in vitro protein–protein interaction assay, and the method should contribute to a better understanding of protein functions by using the resource of available nucleotide sequences.
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Affiliation(s)
| | | | | | | | | | - Masataka Kinjo
- Research Institute for Electronic Science, Hokkaido UniversitySapporo 060-0812, Japan
| | - Hiroshi Yanagawa
- To whom correspondence should be addressed. Tel: +81 45 566 1775; Fax: +81 45 566 1440;
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Tokuriki N, Kinjo M, Negi S, Hoshino M, Goto Y, Urabe I, Yomo T. Protein folding by the effects of macromolecular crowding. Protein Sci 2004; 13:125-33. [PMID: 14691228 PMCID: PMC2286514 DOI: 10.1110/ps.03288104] [Citation(s) in RCA: 164] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Unfolded states of ribonuclease A were used to investigate the effects of macromolecular crowding on macromolecular compactness and protein folding. The extent of protein folding and compactness were measured by circular dichroism spectroscopy, fluorescence correlation spectroscopy, and NMR spectroscopy in the presence of polyethylene glycol (PEG) or Ficoll as the crowding agent. The unfolded state of RNase A in a 2.4 M urea solution at pH 3.0 became native in conformation and compactness by the addition of 35% PEG 20000 or Ficoll 70. In addition, the effects of macromolecular crowding on inert macromolecule compactness were investigated by fluorescence correlation spectroscopy using Fluorescence-labeled PEG as a test macromolecule. The size of Fluorescence-labeled PEG decreased remarkably with an increase in the concentration of PEG 20000 or Ficoll 70. These results show that macromolecules are favored compact conformations in the presence of a high concentration of macromolecules and indicate the importance of a crowded environment for the folding and stabilization of globular proteins. Furthermore, the magnitude of the effects on macromolecular crowding by the different sizes of background molecules was investigated. RNase A and Fluorescence-labeled PEG did not become compact, and had folded conformation by the addition of PEG 200. The effect of the chemical potential on the compaction of a test molecule in relation to the relative sizes of the test and background molecules is also discussed.
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Affiliation(s)
- Nobuhiko Tokuriki
- Department of Biotechnology, Graduate School of Engineering, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
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Hom EFY, Verkman AS. Analysis of coupled bimolecular reaction kinetics and diffusion by two-color fluorescence correlation spectroscopy: enhanced resolution of kinetics by resonance energy transfer. Biophys J 2002; 83:533-46. [PMID: 12080140 PMCID: PMC1302167 DOI: 10.1016/s0006-3495(02)75189-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In two-color fluorescence correlation spectroscopy (TCFCS), the fluorescence intensities of two fluorescently-labeled species are cross-correlated over time and can be used to identify static and dynamic interactions. Generally, fluorophore labels are chosen that do not undergo Förster resonance energy transfer (FRET). Here, a general TCFCS theory is presented that accounts for the possibility of FRET between reactants in the reversible bimolecular reaction, [reaction: see text] where k(f) and k(b) are forward and reverse rate constants, respectively (dissociation constant K(d) = k(b)/k(f)). Using this theory, we systematically investigated the influence on the correlation function of FRET, reaction rates, reactant concentrations, diffusion, and component visibility. For reactants of comparable size and an energy-transfer efficiency of approximately 90%, experimentally measurable cross-correlation functions should be sensitive to reaction kinetics for K(d) > 10(-8) M and k(f) >or= approximately 10(7) M(-1)s(-1). Measured auto-correlation functions corresponding to donor and acceptor labels are generally less sensitive to reaction kinetics, although for the acceptor, this sensitivity increases as the visibility of the donor increases relative to the acceptor. In the absence of FRET or a significant hydrodynamic difference between reactant species, there is little effect of reaction kinetics on the shape of auto- and cross-correlation functions. Our results suggest that a subset of biologically relevant association-dissociation kinetics can be measured by TCFCS and that FRET can be advantageous in enhancing these effects.
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Affiliation(s)
- Erik F Y Hom
- The Graduate Group in Biophysics, Department of Medicine, Cardiovascular Research Institute, University of California, San Francisco, California 94143-0521, USA.
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