1
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Yousefi A, Zheng Z, Zargarbashi S, Assadipapari M, Hickman GJ, Parmenter CD, Bueno-Alejo CJ, Sanderson G, Craske D, Xu L, Perry CC, Rahmani M, Ying C. Structural Flexibility and Disassembly Kinetics of Single Ferritin Molecules Using Optical Nanotweezers. ACS NANO 2024; 18:15617-15626. [PMID: 38850556 PMCID: PMC11191739 DOI: 10.1021/acsnano.4c01221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024]
Abstract
Ferritin, a spherical protein shell assembled from 24 subunits, functions as an efficient iron storage and release system through its channels. Understanding how various chemicals affect the structural behavior of ferritin is crucial for unravelling the origins of iron-related diseases in living organisms including humans. In particular, the influence of chemicals on ferritin's dynamics and iron release is barely explored at the single-protein level. Here, by employing optical nanotweezers using double-nanohole (DNH) structures, we examined the effect of ascorbic acid (reducing reagent) and pH on individual ferritin's conformational dynamics. The dynamics of ferritin increased as the concentration of ascorbic acid approached saturation. At pH 2.0, ferritin exhibited significant structural fluctuations and eventually underwent a stepwise disassembly into fragments. This work demonstrated the disassembly pathway and kinetics of a single ferritin molecule in solution. We identified four critical fragments during its disassembly pathway, which are 22-mer, 12-mer, tetramer, and dimer subunits. Moreover, we present single-molecule evidence of the cooperative disassembly of ferritin. Interrogating ferritin's structural change in response to different chemicals holds importance for understanding their roles in iron metabolism, hence facilitating further development of medical treatments for its associated diseases.
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Affiliation(s)
- Arman Yousefi
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118NS, United
Kingdom
| | - Ze Zheng
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118NS, United
Kingdom
| | - Saaman Zargarbashi
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118NS, United
Kingdom
| | - Mahya Assadipapari
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118NS, United
Kingdom
| | - Graham J. Hickman
- School
of Science and Technology, Nottingham Trent
University, Nottingham NG11 8NS, United Kingdom
| | | | - Carlos J. Bueno-Alejo
- School
of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Gabriel Sanderson
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118NS, United
Kingdom
| | - Dominic Craske
- School
of Science and Technology, Nottingham Trent
University, Nottingham NG11 8NS, United Kingdom
| | - Lei Xu
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118NS, United
Kingdom
| | - Carole C. Perry
- Interdisciplinary
Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom
| | - Mohsen Rahmani
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118NS, United
Kingdom
| | - Cuifeng Ying
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118NS, United
Kingdom
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2
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Chu J, Romero A, Taulbee J, Aran K. Development of Single Molecule Techniques for Sensing and Manipulation of CRISPR and Polymerase Enzymes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300328. [PMID: 37226388 PMCID: PMC10524706 DOI: 10.1002/smll.202300328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/20/2023] [Indexed: 05/26/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and polymerases are powerful enzymes and their diverse applications in genomics, proteomics, and transcriptomics have revolutionized the biotechnology industry today. CRISPR has been widely adopted for genomic editing applications and Polymerases can efficiently amplify genomic transcripts via polymerase chain reaction (PCR). Further investigations into these enzymes can reveal specific details about their mechanisms that greatly expand their use. Single-molecule techniques are an effective way to probe enzymatic mechanisms because they may resolve intermediary conformations and states with greater detail than ensemble or bulk biosensing techniques. This review discusses various techniques for sensing and manipulation of single biomolecules that can help facilitate and expedite these discoveries. Each platform is categorized as optical, mechanical, or electronic. The methods, operating principles, outputs, and utility of each technique are briefly introduced, followed by a discussion of their applications to monitor and control CRISPR and Polymerases at the single molecule level, and closing with a brief overview of their limitations and future prospects.
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Affiliation(s)
- Josephine Chu
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Andres Romero
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Jeffrey Taulbee
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Kiana Aran
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
- Cardea, San Diego, CA, 92121, USA
- University of California Berkeley, Berkeley, CA, 94720, USA
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3
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Yousefi A, Ying C, Parmenter CD, Assadipapari M, Sanderson G, Zheng Z, Xu L, Zargarbashi S, Hickman GJ, Cousins RB, Mellor CJ, Mayer M, Rahmani M. Optical Monitoring of In Situ Iron Loading into Single, Native Ferritin Proteins. NANO LETTERS 2023; 23:3251-3258. [PMID: 37053043 PMCID: PMC10141409 DOI: 10.1021/acs.nanolett.3c00042] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Ferritin is a protein that stores and releases iron to prevent diseases associated with iron dysregulation in plants, animals, and bacteria. The conversion between iron-loaded holo-ferritin and empty apo-ferritin is an important process for iron regulation. To date, studies of ferritin have used either ensemble measurements to quantify the characteristics of a large number of proteins or single-molecule approaches to interrogate labeled or modified proteins. Here we demonstrate the first real-time study of the dynamics of iron ion loading and biomineralization within a single, unlabeled ferritin protein. Using optical nanotweezers, we trapped single apo- and holo-ferritins indefinitely, distinguished one from the other, and monitored their structural dynamics in real time. The study presented here deepens the understanding of the iron uptake mechanism of ferritin proteins, which may lead to new therapeutics for iron-related diseases.
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Affiliation(s)
- Arman Yousefi
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118 NS, United
Kingdom
| | - Cuifeng Ying
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118 NS, United
Kingdom
- Email
for C.Y.:
| | | | - Mahya Assadipapari
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118 NS, United
Kingdom
| | - Gabriel Sanderson
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118 NS, United
Kingdom
| | - Ze Zheng
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118 NS, United
Kingdom
| | - Lei Xu
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118 NS, United
Kingdom
| | - Saaman Zargarbashi
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118 NS, United
Kingdom
| | - Graham J. Hickman
- School
of Science and Technology, Nottingham Trent
University, Nottingham NG11 8NS, United
Kingdom
| | - Richard B. Cousins
- Nanoscale
and Microscale Research Centre, University
of Nottingham, Nottingham NG7 2RD, United
Kingdom
| | - Christopher J. Mellor
- School
of Physics and Astronomy, University of
Nottingham, Nottingham NG7 2RD, United
Kingdom
| | - Michael Mayer
- Adolphe
Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| | - Mohsen Rahmani
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118 NS, United
Kingdom
- Email for M.R.:
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4
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Gokulu IS, Banta S. Biotechnology applications of proteins functionalized with DNA oligonucleotides. Trends Biotechnol 2023; 41:575-585. [PMID: 36115723 DOI: 10.1016/j.tibtech.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 10/14/2022]
Abstract
The functionalization of proteins with DNA through the formation of covalent bonds enables a wide range of biotechnology advancements. For example, single-molecule analytical methods rely on bioconjugated DNA as elastic biolinkers for protein immobilization. Labeling proteins with DNA enables facile protein identification, as well as spatial and temporal organization and control of protein within DNA-protein networks. Bioconjugation reactions can target native, engineered, and non-canonical amino acids (NCAAs) within proteins. In addition, further protein engineering via the incorporation of peptide tags and self-labeling proteins can also be used for conjugation reactions. The selection of techniques will depend on application requirements such as yield, selectivity, conjugation position, potential for steric hindrance, cost, commercial availability, and potential impact on protein function.
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Affiliation(s)
- Ipek Simay Gokulu
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA.
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5
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Sun H, Wang J. Novel perspective for protein-drug interaction analysis: atomic force microscope. Analyst 2023; 148:454-474. [PMID: 36398684 DOI: 10.1039/d2an01591a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Proteins are major drug targets, and drug-target interaction identification and analysis are important factors for drug discovery. Atomic force microscopy (AFM) is a powerful tool making it possible to image proteins with nanometric resolution and probe intermolecular forces under physiological conditions. We review recent studies conducted in the field of target protein drug discovery using AFM-based analysis technology, including drug-driven changes in nanomechanical properties of protein morphology and interactions. Underlying mechanisms (including thermodynamic and kinetic parameters) of the drug-target interaction and drug-modulating protein-protein interaction (PPI) on the surfaces of models or living cells are discussed. Furthermore, challenges and the outlook for the field are likewise discussed. Overall, this insight into the mechanical properties of protein-drug interactions provides an unprecedented information framework for rational drug discovery in the pharmaceutical field.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
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6
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Riccardi M, Martin OJF. Electromagnetic Forces and Torques: From Dielectrophoresis to Optical Tweezers. Chem Rev 2023; 123:1680-1711. [PMID: 36719985 PMCID: PMC9951227 DOI: 10.1021/acs.chemrev.2c00576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Indexed: 02/02/2023]
Abstract
Electromagnetic forces and torques enable many key technologies, including optical tweezers or dielectrophoresis. Interestingly, both techniques rely on the same physical process: the interaction of an oscillating electric field with a particle of matter. This work provides a unified framework to understand this interaction both when considering fields oscillating at low frequencies─dielectrophoresis─and high frequencies─optical tweezers. We draw useful parallels between these two techniques, discuss the different and often unstated assumptions they are based upon, and illustrate key applications in the fields of physical and analytical chemistry, biosensing, and colloidal science.
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Affiliation(s)
- Marco Riccardi
- Nanophotonics and Metrology Laboratory, Swiss Federal Institute of Technology Lausanne (EPFL), EPFL-STI-NAM, Station 11, CH-1015Lausanne, Switzerland
| | - Olivier J. F. Martin
- Nanophotonics and Metrology Laboratory, Swiss Federal Institute of Technology Lausanne (EPFL), EPFL-STI-NAM, Station 11, CH-1015Lausanne, Switzerland
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7
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Mukherjee S, Mepperi J, Sahu P, Barman DK, Kotamarthi HC. Single-Molecule Optical Tweezers As a Tool for Delineating the Mechanisms of Protein-Processing Mechanoenzymes. ACS OMEGA 2023; 8:87-97. [PMID: 36643560 PMCID: PMC9835622 DOI: 10.1021/acsomega.2c06044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Mechanoenzymes convert chemical energy from the hydrolysis of nucleotide triphosphates to mechanical energy for carrying out cellular functions ranging from DNA unwinding to protein degradation. Protein-processing mechanoenzymes either remodel the protein structures or translocate them across cellular compartments in an energy-dependent manner. Optical-tweezer-based single-molecule force spectroscopy assays have divulged information on details of chemo-mechanical coupling, directed motion, as well as mechanical forces these enzymes are capable of generating. In this review, we introduce the working principles of optical tweezers as a single-molecule force spectroscopy tool and assays developed to decipher the properties such as unfolding kinetics, translocation velocities, and step sizes by protein remodeling mechanoenzymes. We focus on molecular motors involved in protein degradation and disaggregation, i.e., ClpXP, ClpAP, and ClpB, and insights provided by single-molecule assays on kinetics and stepping dynamics during protein unfolding and translocation. Cellular activities such as protein synthesis, folding, and translocation across membranes are also energy dependent, and the recent single-molecule studies decoding the role of mechanical forces on these processes have been discussed.
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8
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Valencia Ramirez A, Bonneux G, Terfort A, Losada-Pérez P, Renner FU. Nanomechanical Stability of Laterally Heterogeneous Films of Corrosion Inhibitor Molecules Obtained by Microcontact Printing on Au Model Substrates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15614-15621. [PMID: 36484233 DOI: 10.1021/acs.langmuir.2c02276] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Self-assembled monolayers of corrosion inhibitors of the mercaptobenzimidazole family, SH-BimH, SH-BimH-5NH2, and SH-BimH-5OMe, were formed on template-stripped ultraflat Au surfaces using microcontact printing, and subsequently analyzed using X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and AFM-force spectroscopy (AFM-FS) using a quantitative imaging (QI) mode. Printing of all used inhibitor molecules resulted in clear patterns and in slightly more compact films compared to immersion. The stability of the monolayers is further probed by AFM-FS. Adhesion values of laterally heterogeneous inhibitor-modified surfaces compared to bare Au surfaces, nonpatterned areas, and fully covered surfaces are analyzed and discussed. Microcontact printing confers a superior nanomechanical stability to imidazole-modified films of the printed surface patches as compared to homogeneously covered surfaces by immersion into the inhibitor solution.
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Affiliation(s)
- Andrea Valencia Ramirez
- Institute for Materials Research, Hasselt University, Diepenbeek 3590, Belgium
- Division IMOMEC, IMEC vzw, Diepenbeek 3590, Belgium
| | - Gilles Bonneux
- Institute for Materials Research, Hasselt University, Diepenbeek 3590, Belgium
- Division IMOMEC, IMEC vzw, Diepenbeek 3590, Belgium
| | - Andreas Terfort
- Institute of Inorganic and Analytical Chemistry, Goethe-University, Frankfurt am Main 60438, Germany
| | - Patricia Losada-Pérez
- Experimental Soft Matter and Thermal Physics Laboratory, Université Libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Frank Uwe Renner
- Institute for Materials Research, Hasselt University, Diepenbeek 3590, Belgium
- Division IMOMEC, IMEC vzw, Diepenbeek 3590, Belgium
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9
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Pramanik U, Nandy A, Khamari L, Mukherjee S. Structure and Transition Dynamics of Intrinsically Disordered Proteins Probed by Single-Molecule Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:12764-12772. [PMID: 36217309 DOI: 10.1021/acs.langmuir.2c02409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Intrinsically disordered proteins (IDPs) are a class of proteins that do not follow the unanimated perspective of the structure-function paradigm. IDPs enunciate the dynamics of motions which are often difficult to characterize by a particular experimental or theoretical approach. The chameleon nature of the IDPs is a result of an alteration or transition in their conformation upon binding with ligands. Experimental investigations via ensemble-average approaches to probe this randomness are often difficult to synchronize. Thus, to sense the substates of different conformational ensembles of IDPs, researchers have often targeted approaches based on single-molecule measurements. In this Perspective, we will discuss various single-molecule approaches to explore the conformational transitions of IDPs in different scenarios, the outcome, challenges, and future prospects.
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Affiliation(s)
- Ushasi Pramanik
- Department of ChemistryIISER Bhopal, Bhopal Bypass Road, Bhauri, Bhopal462 066, Madhya Pradesh, India
| | - Atanu Nandy
- Department of ChemistryIISER Bhopal, Bhopal Bypass Road, Bhauri, Bhopal462 066, Madhya Pradesh, India
| | - Laxmikanta Khamari
- Department of ChemistryIISER Bhopal, Bhopal Bypass Road, Bhauri, Bhopal462 066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of ChemistryIISER Bhopal, Bhopal Bypass Road, Bhauri, Bhopal462 066, Madhya Pradesh, India
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10
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Liao S, Sun M, Zhan J, Xu M, Yao L. Advances in the Biological Application of Force-Induced Remnant Magnetization Spectroscopy. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072072. [PMID: 35408471 PMCID: PMC9000611 DOI: 10.3390/molecules27072072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022]
Abstract
Biomolecules participate in various physiological and pathological processes through intermolecular interactions generally driven by non-covalent forces. In the present review, the force-induced remnant magnetization spectroscopy (FIRMS) is described and illustrated as a novel method to measure non-covalent forces. During the FIRMS measurement, the molecular magnetic probes are magnetized to produce an overall magnetization signal. The dissociation under the interference of external force yields a decrease in the magnetic signal, which is recorded and collected by atomic magnetometer in a spectrum to study the biological interactions. Furthermore, the recent FIRMS development with various external mechanical forces and magnetic probes is summarized.
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Affiliation(s)
- Shuyu Liao
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China; (S.L.); (M.S.); (J.Z.); (M.X.)
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengxue Sun
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China; (S.L.); (M.S.); (J.Z.); (M.X.)
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinxiu Zhan
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China; (S.L.); (M.S.); (J.Z.); (M.X.)
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Xu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China; (S.L.); (M.S.); (J.Z.); (M.X.)
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Yao
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China; (S.L.); (M.S.); (J.Z.); (M.X.)
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
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11
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Abstract
Single molecule Förster resonance energy transfer (smFRET) is a unique biophysical approach for studying conformational dynamics in biomacromolecules. Photon-by-photon hidden Markov modeling (H2MM) is an analysis tool that can quantify FRET dynamics of single biomolecules, even if they occur on the sub-millisecond timescale. However, dye photophysical transitions intertwined with FRET dynamics may cause artifacts. Here, we introduce multi-parameter H2MM (mpH2MM), which assists in identifying FRET dynamics based on simultaneous observation of multiple experimentally-derived parameters. We show the importance of using mpH2MM to decouple FRET dynamics caused by conformational changes from photophysical transitions in confocal-based smFRET measurements of a DNA hairpin, the maltose binding protein, MalE, and the type-III secretion system effector, YopO, from Yersinia species, all exhibiting conformational dynamics ranging from the sub-second to microsecond timescales. Overall, we show that using mpH2MM facilitates the identification and quantification of biomolecular sub-populations and their origin. In this work, the authors demonstrate the application of multi-parameter photon-by-photon hidden Markov modeling (mpH2MM) on alternating laser excitation (ALEX)-based smFRET measurements. The utility of mpH2MM in identifying and quantifying dynamic biomolecular sub-populations is demonstrated in three different systems.
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12
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Nie J, Tian F, Zheng B, Wang Z, Zheng P. Exploration of Metal-Ligand Coordination Bonds in Proteins by Single-molecule Force Spectroscopy. CHEM LETT 2021. [DOI: 10.1246/cl.210307] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jingyuan Nie
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Fang Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Ziyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
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13
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Pulling the springs of a cell by single-molecule force spectroscopy. Emerg Top Life Sci 2021; 5:77-87. [PMID: 33284963 DOI: 10.1042/etls20200254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 11/17/2022]
Abstract
The fundamental unit of the human body comprises of the cells which remain embedded in a fibrillar network of extracellular matrix proteins which in turn provides necessary anchorage the cells. Tissue repair, regeneration and reprogramming predominantly involve a traction force mediated signalling originating in the ECM and travelling deep into the cell including the nucleus via circuitry of spring-like filamentous proteins like microfilaments or actin, intermediate filaments and microtubules to elicit a response in the form of mechanical movement as well as biochemical changes. The 'springiness' of these proteins is highlighted in their extension-contraction behaviour which is manifested as an effect of differential traction force. Atomic force microscope (AFM) provides the magic eye to visualize and quantify such force-extension/indentation events in these filamentous proteins as well as in whole cells. In this review, we have presented a summary of the current understanding and advancement of such measurements by AFM based single-molecule force spectroscopy in the context of cytoskeletal and nucleoskeletal proteins which act in tandem to facilitate mechanotransduction.
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14
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Cheirdaris DG. Force Spectroscopy in Mechanical Protein Domains Unfolding. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1339:187-193. [DOI: 10.1007/978-3-030-78787-5_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Martínez‐Tong DE, Pomposo JA, Verde‐Sesto E. Triggering Forces at the Nanoscale: Technologies for Single‐Chain Mechanical Activation and Manipulation. Macromol Rapid Commun 2020; 42:e2000654. [DOI: 10.1002/marc.202000654] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/14/2020] [Indexed: 01/05/2023]
Affiliation(s)
- Daniel E. Martínez‐Tong
- Departamento de Polímeros y Materiales Avanzados: Física, Química y Tecnología University of the Basque Country (UPV/EHU) P. Manuel Lardizábal 3 Donostia‐San Sebastián 20018 Spain
- Centro de Física de Materiales (UPV/EHU‐CSIC) P. Manuel Lardizábal 5 San Sebastián 20018 Spain
| | - José A. Pomposo
- Departamento de Polímeros y Materiales Avanzados: Física, Química y Tecnología University of the Basque Country (UPV/EHU) P. Manuel Lardizábal 3 Donostia‐San Sebastián 20018 Spain
- Centro de Física de Materiales (CFM) (CSIC‐UPV/EHU)—Materials Physics Center (MPC) Paseo Manuel de Lardizábal 5 Donostia‐San Sebastián 20018 Spain
- IKERBASQUE—Basque Foundation for Science Plaza Euskadi 5 Bilbao 48009 Spain
| | - Ester Verde‐Sesto
- Centro de Física de Materiales (CFM) (CSIC‐UPV/EHU)—Materials Physics Center (MPC) Paseo Manuel de Lardizábal 5 Donostia‐San Sebastián 20018 Spain
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