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Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021; 10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.
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Affiliation(s)
- Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Anders Barth
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt UniversityDiepenbeekBelgium
| | - Benjamin Ambrose
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus UniversityAarhusDenmark
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
| | - Richard Börner
- Laserinstitut HS Mittweida, University of Applied Science MittweidaMittweidaGermany
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität MünchenPlanegg-MartinsriedGermany
| | - Timothy D Craggs
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati School of MedicineCincinnatiUnited States
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of ChicagoChicagoUnited States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical InstituteBaltimoreUnited States
| | - Christian A Hanke
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovotIsrael
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of CopenhagenCopenhagenDenmark
- Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National UniversitySeoulRepublic of Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea UniversitySeoulRepublic of Korea
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Antonino Ingargiola
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of OxfordOxfordUnited Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National LaboratoryLivermoreUnited States
| | - Nam Ki Lee
- School of Chemistry, Seoul National UniversitySeoulRepublic of Korea
| | - Tae-Hee Lee
- Department of Chemistry, Pennsylvania State UniversityUniversity ParkUnited States
| | - Edward A Lemke
- Departments of Biology and Chemistry, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular Biology (IMB)MainzGermany
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de MontpellierMontpellierFrance
| | | | - Xavier Michalet
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Evelyn Ploetz
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Nicole C Robb
- Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), University of MelbourneParkvilleAustralia
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking UniversityBeijingChina
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Claus AM Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
- Department of Physiology, CaliforniaNanoSystems Institute, University of California, Los AngelesLos AngelesUnited States
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Cerminara M, Schöne A, Ritter I, Gabba M, Fitter J. Mapping Multiple Distances in a Multidomain Protein for the Identification of Folding Intermediates. Biophys J 2020; 118:688-697. [PMID: 31916943 PMCID: PMC7002912 DOI: 10.1016/j.bpj.2019.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/13/2019] [Accepted: 12/10/2019] [Indexed: 10/27/2022] Open
Abstract
The investigation and understanding of the folding mechanism of multidomain proteins is still a challenge in structural biology. The use of single-molecule Förster resonance energy transfer offers a unique tool to map conformational changes within the protein structure. Here, we present a study following denaturant-induced unfolding transitions of yeast phosphoglycerate kinase by mapping several inter- and intradomain distances of this two-domain protein, exhibiting a quite heterogeneous behavior. On the one hand, the development of the interdomain distance during the unfolding transition suggests a classical two-state unfolding behavior. On the other hand, the behavior of some intradomain distances indicates the formation of a compact and transient molten globule intermediate state. Furthermore, different intradomain distances measured within the same domain show pronounced differences in their unfolding behavior, underlining the fact that the choice of dye attachment positions within the polypeptide chain has a substantial impact on which unfolding properties are observed by single-molecule Förster resonance energy transfer measurements. Our results suggest that, to fully characterize the complex folding and unfolding mechanism of multidomain proteins, it is necessary to monitor multiple intra- and interdomain distances because a single reporter can lead to a misleading, partial, or oversimplified interpretation.
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Affiliation(s)
- Michele Cerminara
- Forschungszentrum Jülich, Institute of Complex Systems ICS-5, Jülich, Germany.
| | - Antonie Schöne
- Forschungszentrum Jülich, Institute of Complex Systems ICS-5, Jülich, Germany
| | - Ilona Ritter
- Forschungszentrum Jülich, Institute of Complex Systems ICS-5, Jülich, Germany
| | - Matteo Gabba
- Forschungszentrum Jülich, Institute of Complex Systems ICS-5, Jülich, Germany
| | - Jörg Fitter
- Forschungszentrum Jülich, Institute of Complex Systems ICS-5, Jülich, Germany; RWTH Aachen University, I. Physikalisches Institut (IA), Aachen, Germany.
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Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
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Sannaikar M, Inamdar (Doddamani) LS, Inamdar SR. Interaction between human serum albumin and toxic free InP/ZnS QDs using multi-spectroscopic study: An excellent alternate to heavy metal based QDs. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.02.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Childers KC, Garcin ED. Structure/function of the soluble guanylyl cyclase catalytic domain. Nitric Oxide 2018; 77:53-64. [PMID: 29702251 PMCID: PMC6005667 DOI: 10.1016/j.niox.2018.04.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 02/06/2023]
Abstract
Soluble guanylyl cyclase (GC-1) is the primary receptor of nitric oxide (NO) in smooth muscle cells and maintains vascular function by inducing vasorelaxation in nearby blood vessels. GC-1 converts guanosine 5′-triphosphate (GTP) into cyclic guanosine 3′,5′-monophosphate (cGMP), which acts as a second messenger to improve blood flow. While much work has been done to characterize this pathway, we lack a mechanistic understanding of how NO binding to the heme domain leads to a large increase in activity at the C-terminal catalytic domain. Recent structural evidence and activity measurements from multiple groups have revealed a low-activity cyclase domain that requires additional GC-1 domains to promote a catalytically-competent conformation. How the catalytic domain structurally transitions into the active conformation requires further characterization. This review focuses on structure/function studies of the GC-1 catalytic domain and recent advances various groups have made in understanding how catalytic activity is regulated including small molecules interactions, Cys-S-NO modifications and potential interactions with the NO-sensor domain and other proteins.
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Affiliation(s)
- Kenneth C Childers
- University of Maryland Baltimore County, Department of Chemistry and Biochemistry, Baltimore, USA
| | - Elsa D Garcin
- University of Maryland Baltimore County, Department of Chemistry and Biochemistry, Baltimore, USA.
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Sannaikar MS, Inamdar LS, Pujar GH, Wari MN, Balasinor NH, Inamdar SR. Comprehensive study of interaction between biocompatible PEG-InP/ZnS QDs and bovine serum albumin. LUMINESCENCE 2017; 33:495-504. [DOI: 10.1002/bio.3438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/27/2017] [Accepted: 11/13/2017] [Indexed: 11/07/2022]
Affiliation(s)
- M. S. Sannaikar
- Laser Spectroscopy Programme and UGC-CPEPA, Department of Physics; Karnatak University; Dharwad Karnataka India
| | - Laxmi S. Inamdar
- Molecular Endocrinology, Reproduction and Development Laboratory, Department of Zoology; Karnatak University; Dharwad Karnataka India
| | - G. H. Pujar
- Laser Spectroscopy Programme and UGC-CPEPA, Department of Physics; Karnatak University; Dharwad Karnataka India
| | - M. N. Wari
- Laser Spectroscopy Programme and UGC-CPEPA, Department of Physics; Karnatak University; Dharwad Karnataka India
| | - Nafisa H. Balasinor
- Neuroendocrinology Department; National Institute for Research in Reproductive Health; Parel Mumbai India
| | - S. R. Inamdar
- Laser Spectroscopy Programme and UGC-CPEPA, Department of Physics; Karnatak University; Dharwad Karnataka India
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Stockmar F, Kobitski AY, Nienhaus GU. Fast Folding Dynamics of an Intermediate State in RNase H Measured by Single-Molecule FRET. J Phys Chem B 2016; 120:641-9. [PMID: 26747376 DOI: 10.1021/acs.jpcb.5b09336] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have studied the folding kinetics of the core intermediate (I) state of RNase H by using a combination of single-molecule FRET (smFRET) and hidden Markov model analysis. To measure fast dynamics in thermal equilibrium as a function of the concentration of the denaturant GdmCl, a special FRET labeled variant, RNase H 60-113, which is sensitive to folding of the protein core, was immobilized on PEGylated surfaces. Conformational transitions between the unfolded (U) state and the I state could be described by a two-state model within our experimental time resolution, with millisecond mean residence times. The I state population was always a minority species in the entire accessible range of denaturant concentrations. By introducing the measured free energy differences between the U and I states as constraints in global fits of the GdmCl dependence of FRET histograms of a differently labeled RNase H variant (RNase H 3-135), we were able to reveal the free energy differences and, thus, population ratios of all three macroscopic state ensembles, U, I and F (folded state) as a function of denaturant concentration.
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Affiliation(s)
- Florian Stockmar
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany
| | - Andrei Yu Kobitski
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany.,Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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Rahamim G, Chemerovski-Glikman M, Rahimipour S, Amir D, Haas E. Resolution of Two Sub-Populations of Conformers and Their Individual Dynamics by Time Resolved Ensemble Level FRET Measurements. PLoS One 2015; 10:e0143732. [PMID: 26699718 PMCID: PMC4689530 DOI: 10.1371/journal.pone.0143732] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/08/2015] [Indexed: 11/19/2022] Open
Abstract
Most active biopolymers are dynamic structures; thus, ensembles of such molecules should be characterized by distributions of intra- or intermolecular distances and their fast fluctuations. A method of choice to determine intramolecular distances is based on Förster resonance energy transfer (FRET) measurements. Major advances in such measurements were achieved by single molecule FRET measurements. Here, we show that by global analysis of the decay of the emission of both the donor and the acceptor it is also possible to resolve two sub-populations in a mixture of two ensembles of biopolymers by time resolved FRET (trFRET) measurements at the ensemble level. We show that two individual intramolecular distance distributions can be determined and characterized in terms of their individual means, full width at half maximum (FWHM), and two corresponding diffusion coefficients which reflect the rates of fast ns fluctuations within each sub-population. An important advantage of the ensemble level trFRET measurements is the ability to use low molecular weight small-sized probes and to determine nanosecond fluctuations of the distance between the probes. The limits of the possible resolution were first tested by simulation and then by preparation of mixtures of two model peptides. The first labeled polypeptide was a relatively rigid Pro7 and the second polypeptide was a flexible molecule consisting of (Gly-Ser)7 repeats. The end to end distance distributions and the diffusion coefficients of each peptide were determined. Global analysis of trFRET measurements of a series of mixtures of polypeptides recovered two end-to-end distance distributions and associated intramolecular diffusion coefficients, which were very close to those determined from each of the pure samples. This study is a proof of concept study demonstrating the power of ensemble level trFRET based methods in resolution of subpopulations in ensembles of flexible macromolecules.
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Affiliation(s)
- Gil Rahamim
- The Goodman Faculty of Life Sciences Bar Ilan University, Ramat Gan Israel 52900
| | | | - Shai Rahimipour
- Department of Chemistry, Bar-Ilan University, Ramat Gan Israel 52900
| | - Dan Amir
- The Goodman Faculty of Life Sciences Bar Ilan University, Ramat Gan Israel 52900
| | - Elisha Haas
- The Goodman Faculty of Life Sciences Bar Ilan University, Ramat Gan Israel 52900
- * E-mail:
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Kedia N, Bagchi S. Time resolved FRET measurement in various heterogeneous media using merocyanine dye as a donor. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 145:467-472. [PMID: 25796017 DOI: 10.1016/j.saa.2015.03.075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 02/05/2015] [Accepted: 03/05/2015] [Indexed: 06/04/2023]
Abstract
Ultrafast fluorescence resonance energy transfer (FRET) from a merocyanine dye to a Rhodamine 6G (R6G) molecule in micelles formed by the surfactants SDS and DTAB and also in a catanionic vesicle formed by SDS and DTAB has been studied by picosecond time resolved emission spectroscopy. Here the dye acts as a donor molecule and R6G acts as the acceptor molecule. Multiple timescales of FRET have been detected, namely, an ultrafast component of 100-500 ps and relatively long component (1800-3300 ps). The different time scales are attributed to different donor-acceptor distances.
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Affiliation(s)
- Niraja Kedia
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur Campus, BCKV Main P.O., Nadia, 741252, India
| | - Sanjib Bagchi
- Presidency University, 86/1, College Street, Kolkata 700 073, India.
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Mohamad NR, Marzuki NHC, Buang NA, Huyop F, Wahab RA. An overview of technologies for immobilization of enzymes and surface analysis techniques for immobilized enzymes. BIOTECHNOL BIOTEC EQ 2015; 29:205-220. [PMID: 26019635 PMCID: PMC4434042 DOI: 10.1080/13102818.2015.1008192] [Citation(s) in RCA: 700] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/07/2014] [Indexed: 01/28/2023] Open
Abstract
The current demands of sustainable green methodologies have increased the use of enzymatic technology in industrial processes. Employment of enzyme as biocatalysts offers the benefits of mild reaction conditions, biodegradability and catalytic efficiency. The harsh conditions of industrial processes, however, increase propensity of enzyme destabilization, shortening their industrial lifespan. Consequently, the technology of enzyme immobilization provides an effective means to circumvent these concerns by enhancing enzyme catalytic properties and also simplify downstream processing and improve operational stability. There are several techniques used to immobilize the enzymes onto supports which range from reversible physical adsorption and ionic linkages, to the irreversible stable covalent bonds. Such techniques produce immobilized enzymes of varying stability due to changes in the surface microenvironment and degree of multipoint attachment. Hence, it is mandatory to obtain information about the structure of the enzyme protein following interaction with the support surface as well as interactions of the enzymes with other proteins. Characterization technologies at the nanoscale level to study enzymes immobilized on surfaces are crucial to obtain valuable qualitative and quantitative information, including morphological visualization of the immobilized enzymes. These technologies are pertinent to assess efficacy of an immobilization technique and development of future enzyme immobilization strategies.
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Affiliation(s)
- Nur Royhaila Mohamad
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Skudai81310, Johor, Malaysia
| | - Nur Haziqah Che Marzuki
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Skudai81310, Johor, Malaysia
| | - Nor Aziah Buang
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Skudai81310, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biotechnology and Medical Engineering, Faculty of Bioscience and Medical Engineering, Universiti Teknologi Malaysia, Skudai81310, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Skudai81310, Johor, Malaysia
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Harriman A. Artificial light-harvesting arrays for solar energy conversion. Chem Commun (Camb) 2015; 51:11745-56. [DOI: 10.1039/c5cc03577e] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Following natures' blueprint, the concept of artificial light-harvesting antennae is discussed in terms of sophisticated molecular arrays displaying a tailored cascade of electronic energy transfer steps.
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Affiliation(s)
- Anthony Harriman
- Molecular Photonics Laboratory
- School of Chemistry
- Bedson Building
- Newcastle University
- Newcastle upon Tyne
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13
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Abstract
Engineered nanoparticles (NPs) have found widespread application in technology and medicine. Whenever they come in contact with a living organism, interactions take place between the surfaces of the NPs and biomatter, in particular proteins, which are currently not well understood. We have introduced fluorescence correlation spectroscopy (FCS) and dual-focus FCS (2fFCS) to measure protein adsorption onto small NPs (~10-30 nm diameter). FCS allows us to measure, with subnanometer precision and as a function of protein concentration, the increase in hydrodynamic radius of the NPs due to protein adsorption. Investigations of the adsorption of a number of important serum proteins onto negatively charged, carboxyl-functionalized NPs revealed a stepwise increase of the NP size due to protein binding, clearly indicating that a protein monolayer enshrouds the NP. Structure-based calculations of the protein surface potentials reveal positively charged patches through which the proteins interact electrostatically with the negatively charged NP surfaces; the observed protein layer thickness is correlated with the molecular dimensions of the proteins binding in suitable orientations.
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Affiliation(s)
- G Ulrich Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
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Liese A, Hilterhaus L. Evaluation of immobilized enzymes for industrial applications. Chem Soc Rev 2013; 42:6236-49. [DOI: 10.1039/c3cs35511j] [Citation(s) in RCA: 467] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Rieger R, Nienhaus GU. A combined single-molecule FRET and tryptophan fluorescence study of RNase H folding under acidic conditions. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.03.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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KOBITSKI ANDREIYU, NIERTH ALEXANDER, HENGESBACH MARTIN, JÄSCHKE ANDRES, HELM MARK, NIENHAUS GULRICH. EXPLORING THE FOLDING FREE ENERGY LANDSCAPE OF SMALL RNA MOLECULES BY SINGLE-PAIR FÖRSTER RESONANCE ENERGY TRANSFER. ACTA ACUST UNITED AC 2011. [DOI: 10.1142/s1793048008000873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Proteins and RNA are biological macromolecules built from linear polymers. The process by which they fold into compact, well-defined, three-dimensional architectures to perform their functional tasks is still not well understood. It can be visualized by Brownian motion of an ensemble of molecules through a rugged energy landscape in search of an energy minimum corresponding to the native state. To explore the conformational energy landscape of small RNAs, single pair Förster resonance energy transfer (spFRET) experiments on solutions as well as on surface-immobilized samples have provided new insights. In this review, we focus on our recent work on two FRET-labeled small RNAs, the Diels-Alderase (DAse) ribozyme and the human mitochondrial tRNA Lys . For both RNAs, three different conformational states can be distinguished, and the associated mean FRET efficiencies provide clues about their structural properties. The systematic variation of their free energies with the concentration of Mg 2+ counterions was analyzed quantitatively by using a thermodynamic model that separates conformational changes from Mg 2+ binding. Furthermore, time-resolved spFRET studies on immobilized DAse reveal slow interconversions between intermediate and folded states on the time scale of ~ 100 ms. The quantitative data obtained from spFRET experiments may likely assist in the further development of theories and models addressing the folding dynamics and (counterion-dependent) energetics of RNA molecules.
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Affiliation(s)
- ANDREI YU. KOBITSKI
- Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - ALEXANDER NIERTH
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - MARTIN HENGESBACH
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - ANDRES JÄSCHKE
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - MARK HELM
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - G. ULRICH NIENHAUS
- Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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17
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Rieger R, Kobitski A, Sielaff H, Nienhaus GU. Evidence of a Folding Intermediate in RNase H from Single‐Molecule FRET Experiments. Chemphyschem 2010; 12:627-33. [DOI: 10.1002/cphc.201000693] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Indexed: 11/10/2022]
Affiliation(s)
- Robert Rieger
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), 76128 Karlsruhe (Germany), Fax: (+49) 721‐608 84 80
| | - Andrei Kobitski
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), 76128 Karlsruhe (Germany), Fax: (+49) 721‐608 84 80
| | - Hendrik Sielaff
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), 76128 Karlsruhe (Germany), Fax: (+49) 721‐608 84 80
| | - G. Ulrich Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), 76128 Karlsruhe (Germany), Fax: (+49) 721‐608 84 80
- Department of Physics, University of Illinois at Urbana‐Champaign, Urbana, 61801 (USA)
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18
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Rosenkranz T, Schlesinger R, Gabba M, Fitter J. Native and Unfolded States of Phosphoglycerate Kinase Studied by Single‐Molecule FRET. Chemphyschem 2010; 12:704-10. [DOI: 10.1002/cphc.201000701] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 09/29/2010] [Indexed: 11/10/2022]
Affiliation(s)
- Tobias Rosenkranz
- Research Centre Jülich, ISB‐2: Molecular Biophysics, 52425 Jülich (Germany), Fax: (+49) 2461 61 1448
| | - Ramona Schlesinger
- Research Centre Jülich, ISB‐2: Molecular Biophysics, 52425 Jülich (Germany), Fax: (+49) 2461 61 1448
| | - Matteo Gabba
- Research Centre Jülich, ISB‐2: Molecular Biophysics, 52425 Jülich (Germany), Fax: (+49) 2461 61 1448
| | - Jörg Fitter
- Research Centre Jülich, ISB‐2: Molecular Biophysics, 52425 Jülich (Germany), Fax: (+49) 2461 61 1448
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19
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Abstract
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances in theory and experiments have resulted in a conceptual framework for describing the folding mechanisms of globular proteins. The sizes of proteins in the denatured and folded states, cooperativity of the folding transition, dispersions in the melting temperatures at the residue level, and timescales of folding are, to a large extent, determined by N, the number of residues. The intricate details of folding as a function of denaturant concentration can be predicted by using a novel coarse-grained molecular transfer model. By watching one molecule fold at a time, using single-molecule methods, investigators have established the validity of the theoretically anticipated heterogeneity in the folding routes and the N-dependent timescales for the three stages in the approach to the native state. Despite the successes of theory, of which only a few examples are documented here, we conclude that much remains to be done to solve the protein folding problem in the broadest sense.
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Affiliation(s)
- D Thirumalai
- Biophysics Program, Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA.
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20
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Zhang L, Sun Y. Molecular simulation of adsorption and its implications to protein chromatography: A review. Biochem Eng J 2010. [DOI: 10.1016/j.bej.2009.12.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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O'Brien EP, Morrison G, Brooks BR, Thirumalai D. How accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins? J Chem Phys 2009; 130:124903. [PMID: 19334885 DOI: 10.1063/1.3082151] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Single molecule Förster resonance energy transfer (FRET) experiments are used to infer the properties of the denatured state ensemble (DSE) of proteins. From the measured average FRET efficiency, <E>, the distance distribution P(R) is inferred by assuming that the DSE can be described as a polymer. The single parameter in the appropriate polymer model (Gaussian chain, wormlike chain, or self-avoiding walk) for P(R) is determined by equating the calculated and measured <E>. In order to assess the accuracy of this "standard procedure," we consider the generalized Rouse model (GRM), whose properties [<E> and P(R)] can be analytically computed, and the Molecular Transfer Model for protein L for which accurate simulations can be carried out as a function of guanadinium hydrochloride (GdmCl) concentration. Using the precisely computed <E> for the GRM and protein L, we infer P(R) using the standard procedure. We find that the mean end-to-end distance can be accurately inferred (less than 10% relative error) using <E> and polymer models for P(R). However, the value extracted for the radius of gyration (R(g)) and the persistence length (l(p)) are less accurate. For protein L, the errors in the inferred properties increase as the GdmCl concentration increases for all polymer models. The relative error in the inferred R(g) and l(p), with respect to the exact values, can be as large as 25% at the highest GdmCl concentration. We propose a self-consistency test, requiring measurements of <E> by attaching dyes to different residues in the protein, to assess the validity of describing DSE using the Gaussian model. Application of the self-consistency test to the GRM shows that even for this simple model, which exhibits an order-->disorder transition, the Gaussian P(R) is inadequate. Analysis of experimental data of FRET efficiencies with dyes at several locations for the cold shock protein, and simulations results for protein L, for which accurate FRET efficiencies between various locations were computed, shows that at high GdmCl concentrations there are significant deviations in the DSE P(R) from the Gaussian model.
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Affiliation(s)
- Edward P O'Brien
- Biophysics Program, University of Maryland, College Park, Maryland 20742, USA
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22
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Abdallah D, Whelan J, Dust JM, Hoz S, Buncel E. Energy Transfer in the Azobenzene−Naphthalene Light Harvesting System. J Phys Chem A 2009; 113:6640-7. [DOI: 10.1021/jp901596t] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dalia Abdallah
- Department of Chemistry, Queen’s University, Kingston, ON, K7L 3N6 Canada, Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON, K7K 7B4 Canada, Departments of Chemistry and Environmental Science, Sir Wilfred Grenfell College (SWGC), Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H 6P9 Canada, and Department of Chemistry, Bar Ilan University, Ramat-Gan, Israel
| | - Jamie Whelan
- Department of Chemistry, Queen’s University, Kingston, ON, K7L 3N6 Canada, Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON, K7K 7B4 Canada, Departments of Chemistry and Environmental Science, Sir Wilfred Grenfell College (SWGC), Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H 6P9 Canada, and Department of Chemistry, Bar Ilan University, Ramat-Gan, Israel
| | - Julian M. Dust
- Department of Chemistry, Queen’s University, Kingston, ON, K7L 3N6 Canada, Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON, K7K 7B4 Canada, Departments of Chemistry and Environmental Science, Sir Wilfred Grenfell College (SWGC), Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H 6P9 Canada, and Department of Chemistry, Bar Ilan University, Ramat-Gan, Israel
| | - Shmaryahu Hoz
- Department of Chemistry, Queen’s University, Kingston, ON, K7L 3N6 Canada, Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON, K7K 7B4 Canada, Departments of Chemistry and Environmental Science, Sir Wilfred Grenfell College (SWGC), Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H 6P9 Canada, and Department of Chemistry, Bar Ilan University, Ramat-Gan, Israel
| | - Erwin Buncel
- Department of Chemistry, Queen’s University, Kingston, ON, K7L 3N6 Canada, Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON, K7K 7B4 Canada, Departments of Chemistry and Environmental Science, Sir Wilfred Grenfell College (SWGC), Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H 6P9 Canada, and Department of Chemistry, Bar Ilan University, Ramat-Gan, Israel
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23
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Abstract
The structural and dynamic details of protein folding are still widely unexplored due to the enormous level of heterogeneity intrinsic to this process. The unfolded polypeptide chain can assume a vast number of possible conformations, and many complex pathways lead from the ensemble of unfolded conformations to the ensemble of native conformations in an overall funnel-shaped energy landscape. Classical experimental methods involve measurements on bulk samples and usually yield only average values characteristic of the entire molecular ensemble under study. The observation of individual molecules avoids this averaging and allows, in principle, microscopic distributions of conformations and folding trajectories to be revealed. Fluorescence-based techniques are arguably the most versatile single-molecule methods at present, and Förster resonance energy transfer (FRET) between two dye molecules specifically attached to the protein of interest provides a means of studying the inter-dye distance and, thereby, the conformation of folding polypeptide chains in real time. This chapter focuses on practical aspects and different experimental realizations for protein folding investigations by using single-molecule fluorescence.
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24
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Hengesbach M, Kobitski A, Voigts-Hoffmann F, Frauer C, Nienhaus GU, Helm M. RNA intramolecular dynamics by single-molecule FRET. ACTA ACUST UNITED AC 2008; Chapter 11:Unit 11.12. [PMID: 18819081 DOI: 10.1002/0471142700.nc1112s34] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Investigation of single RNA molecules using fluorescence resonance energy transfer (FRET) is a powerful approach to investigate dynamic and thermodynamic aspects of the folding process of a given RNA. Its application requires interdisciplinary work from the fields of chemistry, biochemistry, and physics. The present work gives detailed instructions on the synthesis of RNA molecules labeled with two fluorescent dyes interacting by FRET, as well as on their investigation by single-molecule fluorescence spectroscopy.
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Affiliation(s)
- Martin Hengesbach
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
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25
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Engel R, Westphal AH, Huberts DH, Nabuurs SM, Lindhoud S, Visser AJ, van Mierlo CP. Macromolecular Crowding Compacts Unfolded Apoflavodoxin and Causes Severe Aggregation of the Off-pathway Intermediate during Apoflavodoxin Folding. J Biol Chem 2008; 283:27383-27394. [DOI: 10.1074/jbc.m802393200] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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26
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Zinc porphyrin: a fluorescent acceptor in studies of Zn-cytochrome c unfolding by fluorescence resonance energy transfer. Proc Natl Acad Sci U S A 2008; 105:10779-84. [PMID: 18669660 DOI: 10.1073/pnas.0802737105] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
FRET between the zinc porphyrin (ZnP) chromophore in zinc-substituted cytochrome c (Zn-cyt c) and an Alexa Fluor dye attached to specific surface sites was used to characterize Zn-cyt c unfolding. The use of ZnP as a fluorescent acceptor eliminates the need to doubly label the protein with exogenous dyes to perform FRET experiments in which both donor and acceptor fluorescence is monitored. The requirement for attachment of only one dye also minimizes perturbation to the protein. This sensitive technique allowed for the determination of distances between the label placed at six different sites and ZnP through a range of denaturant concentrations. Fitting of the data to a three-state model provides distances in the unfolding intermediate. The use of ZnP as a fluorescent acceptor of energy in FRET has a significant potential for application to a range of other systems including heme-binding proteins and proteins to which a covalently attached heme tag may be added.
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27
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Affiliation(s)
- Alessandro Borgia
- Department of Chemistry, Cambridge University, Medical Research Council Centre for Protein Engineering, Cambridge, CB2 1EW, United Kingdom; ,
| | - Philip M. Williams
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, United Kingdom;
| | - Jane Clarke
- Department of Chemistry, Cambridge University, Medical Research Council Centre for Protein Engineering, Cambridge, CB2 1EW, United Kingdom; ,
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28
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Kobitski A, Hengesbach M, Helm M, Nienhaus G. Sculpting an RNA Conformational Energy Landscape by a Methyl Group Modification—A Single-Molecule FRET Study. Angew Chem Int Ed Engl 2008; 47:4326-30. [DOI: 10.1002/anie.200705675] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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29
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Kobitski A, Hengesbach M, Helm M, Nienhaus G. Ausformung einer RNA-Konformationsenergielandschaft durch eine Methylgruppenmodifikation – eine Einzelmolekül-FRET-Studie. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705675] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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Mallam AL, Jackson SE. Use of protein engineering techniques to elucidate protein folding pathways. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2008; 84:57-113. [PMID: 19121700 DOI: 10.1016/s0079-6603(08)00403-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Anna L Mallam
- Department of Chemistry, Cambridge, CB2 1EW, United Kingdom
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31
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Voigts-Hoffmann F, Hengesbach M, Kobitski AY, van Aerschot A, Herdewijn P, Nienhaus GU, Helm M. A Methyl Group Controls Conformational Equilibrium in Human Mitochondrial tRNALys. J Am Chem Soc 2007; 129:13382-3. [DOI: 10.1021/ja075520+] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Sarkar R, Narayanan SS, Pålsson LO, Dias F, Monkman A, Pal SK. Direct Conjugation of Semiconductor Nanocrystals to a Globular Protein to Study Protein-Folding Intermediates. J Phys Chem B 2007; 111:12294-8. [DOI: 10.1021/jp075239h] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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