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Zoccante A, Cara E, Ferrarese Lupi F, Hönicke P, Kayser Y, Beckhoff B, Klapetek P, Marchi D, Cossi M. The thermodynamics of self-assembled monolayer formation: a computational and experimental study of thiols on a flat gold surface. Phys Chem Chem Phys 2024; 26:18799-18807. [PMID: 38938190 DOI: 10.1039/d4cp01322k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
A methodology based on molecular dynamics simulations is presented to determine the chemical potential of thiol self-assembled monolayers on a gold surface. The thiol de-solvation and then the monolayer formation are described by thermodynamic integration with a gradual decoupling of one molecule from the environment, with the necessary corrections to account for standard state changes. The procedure is applied both to physisorbed undissociated thiol molecules and to chemisorbed dissociated thiyl radicals, considering in the latter case the possible chemical potential of the produced hydrogen. We considered monolayers formed by either 7-mercapto-4-methylcoumarin (MMC) or 3-mercapto-propanoic acid (MPA) on a flat gold surface: the free energy profiles with respect to the monolayer density are consistent with a transition from a very stable lying-down phase at low densities to a standing-up phase at higher densities, as expected. The maximum densities of thermodynamically stable monolayers are compared to experimental measures performed with reference-free grazing-incidence X-ray fluorescence (RF-GIXRF) on the same systems, finding a better agreement in the case of chemisorbed thiyl radicals.
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Affiliation(s)
- Alberto Zoccante
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, via T. Michel 11, I-15121 Alessandria, Italy.
| | - Eleonora Cara
- Istituto Nazionale di Ricerca Metrologica (INRiM), Strada delle Cacce, 91, 10135 Torino, Italy
| | - Federico Ferrarese Lupi
- Istituto Nazionale di Ricerca Metrologica (INRiM), Strada delle Cacce, 91, 10135 Torino, Italy
| | - Philipp Hönicke
- Physikalisch-Technische Bundesanstalt (PTB), Abbestr. 2-12, 10587 Berlin, Germany
- Helmholtz-Zentrum Berlin, Hahn-Meitner Platz 1, 14109 Berlin, Germany
| | - Yves Kayser
- Physikalisch-Technische Bundesanstalt (PTB), Abbestr. 2-12, 10587 Berlin, Germany
- Max-Planck-Institut für chemische Energiekonversion Mulheim an der Ruhr, Nordrhein-Westfalen, DE, Germany
| | - Burkhard Beckhoff
- Physikalisch-Technische Bundesanstalt (PTB), Abbestr. 2-12, 10587 Berlin, Germany
| | - Petr Klapetek
- Department of Nanometrology, Czech Metrology Institute (CMI), Okružní 31, 638 00 Brno, Czech Republic
| | - Davide Marchi
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, via T. Michel 11, I-15121 Alessandria, Italy.
| | - Maurizio Cossi
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, via T. Michel 11, I-15121 Alessandria, Italy.
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Thiagarajan S, Price E, Connors L, Dettman A, Koh AS. Study of n-Alkanethiol Self-Assembly Behavior on Iron Particles: Effect of Alkyl Chain Length and Adsorption Solvent on Resulting Iron-Based Magnetorheological Fluids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:13506-13521. [PMID: 36279502 DOI: 10.1021/acs.langmuir.2c02014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Self-assembled monolayers (SAMs) of organic molecules on metal surfaces are a type of inexpensive surface coating often used to improve metal substrate properties for sensors, electrochemistry, and nanofabrication applications. Iron, specifically, is one of the most commonly used metals, both as a pure metal and as an alloy due to its high conductivity, strong ferromagnetism, and low cost. However, magnetorheological fluids, which have shown impressive energy dampening in fields from civil infrastructure to biomedical devices utilizing iron dispersions, have suffered from low reliability and efficiency due to iron particle oxidation, corrosion, and settling. To understand the effect of self-assembled monolayers on iron and both the adsorbed particle's resistance against aggregation and performance impact, this work performs an in-depth study on alkanethiol-based self-assembled monolayers on iron particles. Adsorption of alkanethiols and the generation of SAMs on micron-sized iron particles were evaluated as a function of adsorption solvent polarity and alkanethiol chain length. Maximum alkanethiol loading, determined from appropriate isotherms, was found to strongly be a function of both parameters. Alkanethiol adsorption increased with increasing alkyl chain length and increasing solvent log P values in polar solvents. With respect to magnetorheologically relevant parameters, alkanethiol adsorption did not show any significant effect on both the magnetic properties of iron (as particles) and fluid on-state yield stress. The colloidal stability of n-alkanethiol adsorbed iron-based magnetorheological fluids (MRFs) was a function of both n-alkanethiol chain length and the iron particle adsorption solvent. MRFs composed of hexadecanethiol adsorbed iron prepared in polar solvents like methanol and ethanol showed excellent sedimentation stability compared to all other MRFs prepared in this study.
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Affiliation(s)
- Sandhiya Thiagarajan
- Department of Chemical and Biological Engineering, University of Alabama, Tuscaloosa, Alabama35487, United States
| | - Emma Price
- Department of Chemical and Biological Engineering, University of Alabama, Tuscaloosa, Alabama35487, United States
| | - Lela Connors
- Department of Chemical and Biological Engineering, University of Alabama, Tuscaloosa, Alabama35487, United States
| | - Aubrey Dettman
- Department of Mechanical Engineering, University of Alabama, Tuscaloosa, Alabama35487, United States
| | - Amanda S Koh
- Department of Chemical and Biological Engineering, University of Alabama, Tuscaloosa, Alabama35487, United States
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3
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Pérez-Domínguez S, Caballero-Mancebo S, Marcuello C, Martínez-Júlvez M, Medina M, Lostao A. Nanomechanical Study of Enzyme: Coenzyme Complexes: Bipartite Sites in Plastidic Ferredoxin-NADP+ Reductase for the Interaction with NADP+. Antioxidants (Basel) 2022; 11:antiox11030537. [PMID: 35326186 PMCID: PMC8944804 DOI: 10.3390/antiox11030537] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/04/2022] Open
Abstract
Plastidic ferredoxin-NADP+ reductase (FNR) transfers two electrons from two ferredoxin or flavodoxin molecules to NADP+, generating NADPH. The forces holding the Anabaena FNR:NADP+ complex were analyzed by dynamic force spectroscopy, using WT FNR and three C-terminal Y303 variants, Y303S, Y303F, and Y303W. FNR was covalently immobilized on mica and NADP+ attached to AFM tips. Force–distance curves were collected for different loading rates and specific unbinding forces were analyzed under the Bell–Evans model to obtain the mechanostability parameters associated with the dissociation processes. The WT FNR:NADP+ complex presented a higher mechanical stability than that reported for the complexes with protein partners, corroborating the stronger affinity of FNR for NADP+. The Y303 mutation induced changes in the FNR:NADP+ interaction mechanical stability. NADP+ dissociated from WT and Y303W in a single event related to the release of the adenine moiety of the coenzyme. However, two events described the Y303S:NADP+ dissociation that was also a more durable complex due to the strong binding of the nicotinamide moiety of NADP+ to the catalytic site. Finally, Y303F shows intermediate behavior. Therefore, Y303, reported as crucial for achieving catalytically competent active site geometry, also regulates the concerted dissociation of the bipartite nucleotide moieties of the coenzyme.
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Affiliation(s)
- Sandra Pérez-Domínguez
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; (S.P.-D.); (S.C.-M.); (C.M.)
| | - Silvia Caballero-Mancebo
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; (S.P.-D.); (S.C.-M.); (C.M.)
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; (S.P.-D.); (S.C.-M.); (C.M.)
- Laboratorio de Microscopías Avanzadas (LMA), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC Joint Unit), Universidad de Zaragoza, 50018 Zaragoza, Spain;
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC Joint Unit), Universidad de Zaragoza, 50018 Zaragoza, Spain;
- Correspondence: (M.M.); (A.L.); Tel.: +34-976762476 (M.M.); +34-876555357 (A.L.)
| | - Anabel Lostao
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; (S.P.-D.); (S.C.-M.); (C.M.)
- Laboratorio de Microscopías Avanzadas (LMA), Universidad de Zaragoza, 50018 Zaragoza, Spain
- Fundación ARAID, 50018 Zaragoza, Spain
- Correspondence: (M.M.); (A.L.); Tel.: +34-976762476 (M.M.); +34-876555357 (A.L.)
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4
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Dissecting the cytochrome c 2-reaction centre interaction in bacterial photosynthesis using single molecule force spectroscopy. Biochem J 2019; 476:2173-2190. [PMID: 31320503 PMCID: PMC6688529 DOI: 10.1042/bcj20170519] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 11/17/2022]
Abstract
The reversible docking of small, diffusible redox proteins onto a membrane protein complex is a common feature of bacterial, mitochondrial and photosynthetic electron transfer (ET) chains. Spectroscopic studies of ensembles of such redox partners have been used to determine ET rates and dissociation constants. Here, we report a single-molecule analysis of the forces that stabilise transient ET complexes. We examined the interaction of two components of bacterial photosynthesis, cytochrome c 2 and the reaction centre (RC) complex, using dynamic force spectroscopy and PeakForce quantitative nanomechanical imaging. RC-LH1-PufX complexes, attached to silicon nitride AFM probes and maintained in a photo-oxidised state, were lowered onto a silicon oxide substrate bearing dispersed, immobilised and reduced cytochrome c 2 molecules. Microscale patterns of cytochrome c 2 and the cyan fluorescent protein were used to validate the specificity of recognition between tip-attached RCs and surface-tethered cytochrome c 2 Following the transient association of photo-oxidised RC and reduced cytochrome c 2 molecules, retraction of the RC-functionalised probe met with resistance, and forces between 112 and 887 pN were required to disrupt the post-ET RC-c 2 complex, depending on the retraction velocities used. If tip-attached RCs were reduced instead, the probability of interaction with reduced cytochrome c 2 molecules decreased 5-fold. Thus, the redox states of the cytochrome c 2 haem cofactor and RC 'special pair' bacteriochlorophyll dimer are important for establishing a productive ET complex. The millisecond persistence of the post-ET cytochrome c 2[oxidised]-RC[reduced] 'product' state is compatible with rates of cyclic photosynthetic ET, at physiologically relevant light intensities.
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Müller H, Metzler M, Barth N, Conings B, Boyen HG, Jacob T, Kibler LA. Electrocatalytic Behavior of Pd and Pt Nanoislands Deposited onto 4,4′-Dithiodipyridine SAMs on Au(111). Electrocatalysis (N Y) 2018. [DOI: 10.1007/s12678-018-0467-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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6
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Kradolfer S, Lipiec E, Baldacchini C, Bizzarri AR, Cannistraro S, Zenobi R. Vibrational Changes Induced by Electron Transfer in Surface Bound Azurin Metalloprotein Studied by Tip-Enhanced Raman Spectroscopy and Scanning Tunneling Microscopy. ACS NANO 2017; 11:12824-12831. [PMID: 29202236 DOI: 10.1021/acsnano.7b07768] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The copper protein azurin, due to the peculiar coupling of its optical and vibronic properties with electron transfer (ET) and its biorecognition capabilities, is a very promising candidate for bioelectronic, bio-optoelectronic and biosensor applications. However, a complete understanding of the fundamental processes relating azurin ET and its optical and vibronic characteristics with the charge transport mechanisms occurring in proteins bound to a conductive surface, the typical scenario for a biosensor or bioelectronic component, is still lacking. We studied azurin proteins bound to a gold electrode surface by scanning tunneling microscopy combined with tip-enhanced Raman spectroscopy (STM-TERS). Robust TER spectra were obtained, and the protein's vibronic response under optical excitation in resonance with its ligand-to-metal charge transfer band was found to be affected by the tunneling parameters, indicating a direct involvement of the active site vibrations in the electron transport process.
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Affiliation(s)
- Stefan Kradolfer
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
| | - Ewelina Lipiec
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
- The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences 31-342 Krakow, Poland
| | - Chiara Baldacchini
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia , I-01100 Viterbo, Italy
- Institute of Agro-Environmental and Forest Biology, CNR , I-05010 Porano, Italy
| | - Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia , I-01100 Viterbo, Italy
| | - Salvatore Cannistraro
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia , I-01100 Viterbo, Italy
| | - Renato Zenobi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
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7
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Stan RC, Kros A, Akkilic N, Sanghamitra NJ, Appel J. Direct wiring of the azurin redox center to gold electrodes investigated by protein film voltammetry. J Electroanal Chem (Lausanne) 2017. [DOI: 10.1016/j.jelechem.2017.01.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Baldacchini C, Bizzarri AR, Cannistraro S. Electron transfer, conduction and biorecognition properties of the redox metalloprotein Azurin assembled onto inorganic substrates. Eur Polym J 2016. [DOI: 10.1016/j.eurpolymj.2016.04.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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9
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Das P, Reches M. Review insights into the interactions of amino acids and peptides with inorganic materials using single molecule force spectroscopy. Biopolymers 2015; 104:480-94. [DOI: 10.1002/bip.22655] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/18/2015] [Accepted: 03/30/2015] [Indexed: 01/11/2023]
Affiliation(s)
- Priyadip Das
- Institute of Chemistry, The Hebrew University of Jerusalem; 91904 Jerusalem Israel
- The Center for Nanoscience and Nanotechnology; The Hebrew University of Jerusalem; 91904 Jerusalem Israel
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10
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Casalini S, Dumitru AC, Leonardi F, Bortolotti CA, Herruzo ET, Campana A, de Oliveira RF, Cramer T, Garcia R, Biscarini F. Multiscale sensing of antibody-antigen interactions by organic transistors and single-molecule force spectroscopy. ACS NANO 2015; 9:5051-62. [PMID: 25868724 DOI: 10.1021/acsnano.5b00136] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Antibody-antigen (Ab-Ag) recognition is the primary event at the basis of many biosensing platforms. In label-free biosensors, these events occurring at solid-liquid interfaces are complex and often difficult to control technologically across the smallest length scales down to the molecular scale. Here a molecular-scale technique, such as single-molecule force spectroscopy, is performed across areas of a real electrode functionalized for the immunodetection of an inflammatory cytokine, viz. interleukin-4 (IL4). The statistical analysis of force-distance curves allows us to quantify the probability, the characteristic length scales, the adhesion energy, and the time scales of specific recognition. These results enable us to rationalize the response of an electrolyte-gated organic field-effect transistor (EGOFET) operated as an IL4 immunosensor. Two different strategies for the immobilization of IL4 antibodies on the Au gate electrode have been compared: antibodies are bound to (i) a smooth film of His-tagged protein G (PG)/Au; (ii) a 6-aminohexanethiol (HSC6NH2) self-assembled monolayer on Au through glutaraldehyde. The most sensitive EGOFET (concentration minimum detection level down to 5 nM of IL4) is obtained with the first functionalization strategy. This result is correlated to the highest probability (30%) of specific binding events detected by force spectroscopy on Ab/PG/Au electrodes, compared to 10% probability on electrodes with the second functionalization. Specifically, this demonstrates that Ab/PG/Au yields the largest areal density of oriented antibodies available for recognition. More in general, this work shows that specific recognition events in multiscale biosensors can be assessed, quantified, and optimized by means of a nanoscale technique.
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Affiliation(s)
- Stefano Casalini
- †Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Andra C Dumitru
- ‡Instituto de Ciencia de Materiales de Madrid (CSIC), 28049 Madrid, Spain
| | | | - Carlo A Bortolotti
- †Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Elena T Herruzo
- ‡Instituto de Ciencia de Materiales de Madrid (CSIC), 28049 Madrid, Spain
| | - Alessandra Campana
- ⊥"Alma Mater Studiorum", Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Rafael F de Oliveira
- †Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
- #Unesp, Postgraduate Program in Materials Science and Technology, São Paulo State University, 17033-360, Bauru, SP Brazil
| | - Tobias Cramer
- ∞"Alma Mater Studiorum", Dipartimento di Fisica e Astronomia, Università di Bologna, Viale Berti Pichat 6/2, 40127 Bologna, Italy
| | - Ricardo Garcia
- ‡Instituto de Ciencia de Materiales de Madrid (CSIC), 28049 Madrid, Spain
| | - Fabio Biscarini
- †Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
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11
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González-Fernández D, Torneiro M, López-Quintela MA, Lazzari M. Copolymers with acetyl-protected thiol pendant groups as highly efficient stabilizing agents for gold surfaces. RSC Adv 2015. [DOI: 10.1039/c4ra12458h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We showed the potential of novel multifunctional sulfur-containing polymers as model ligands for the preparation of sub-5 nm gold nanoparticles.
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Affiliation(s)
- Daniel González-Fernández
- Centre for Research in Biological Chemistry and Molecular Materials (CIQUS)
- University of Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
- Dept. of Organic Chemistry
| | - Mercedes Torneiro
- Dept. of Organic Chemistry
- Faculty of Chemistry
- University of Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - M. Arturo López-Quintela
- Dept. of Physical Chemistry
- Faculty of Chemistry
- University of Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Massimo Lazzari
- Centre for Research in Biological Chemistry and Molecular Materials (CIQUS)
- University of Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
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12
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Santini S, Bizzarri AR, Yamada T, Beattie CW, Cannistraro S. Binding of azurin to cytochromec551 as investigated by surface plasmon resonance and fluorescence. J Mol Recognit 2014; 27:124-30. [DOI: 10.1002/jmr.2346] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 12/02/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Simona Santini
- Biophysics and Nanoscience Centre, CNISM, Dipartimento DEB; Università della Tuscia; Viterbo Italy
| | - Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, CNISM, Dipartimento DEB; Università della Tuscia; Viterbo Italy
| | - Tohru Yamada
- Department of Surgery, Division of Surgical Oncology; University of Illinois; Chicago IL USA
| | - Craig W. Beattie
- Department of Surgery, Division of Surgical Oncology; University of Illinois; Chicago IL USA
| | - Salvatore Cannistraro
- Biophysics and Nanoscience Centre, CNISM, Dipartimento DEB; Università della Tuscia; Viterbo Italy
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Caprioli F, Decker F. A new simple method to heal defects and to improve electrode passivity of aromatic SAMs on gold. J Electroanal Chem (Lausanne) 2013. [DOI: 10.1016/j.jelechem.2013.09.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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Chen P, Keller AM, Joshi CP, Martell DJ, Andoy NM, Benítez JJ, Chen TY, Santiago AG, Yang F. Single-molecule dynamics and mechanisms of metalloregulators and metallochaperones. Biochemistry 2013; 52:7170-83. [PMID: 24053279 DOI: 10.1021/bi400597v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Understanding how cells regulate and transport metal ions is an important goal in the field of bioinorganic chemistry, a frontier research area that resides at the interface of chemistry and biology. This Current Topic reviews recent advances from the authors' group in using single-molecule fluorescence imaging techniques to identify the mechanisms of metal homeostatic proteins, including metalloregulators and metallochaperones. It emphasizes the novel mechanistic insights into how dynamic protein-DNA and protein-protein interactions offer efficient pathways via which MerR-family metalloregulators and copper chaperones can fulfill their functions. This work also summarizes other related single-molecule studies of bioinorganic systems and provides an outlook toward single-molecule imaging of metalloprotein functions in living cells.
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Affiliation(s)
- Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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15
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Safenkova IV, Zherdev AV, Dzantievf BB. Application of atomic force microscopy for characteristics of single intermolecular interactions. BIOCHEMISTRY (MOSCOW) 2013; 77:1536-52. [PMID: 23379527 DOI: 10.1134/s000629791213010x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Atomic force microscopy (AFM) can be used to make measurements in vacuum, air, and water. The method is able to gather information about intermolecular interaction forces at the level of single molecules. This review encompasses experimental and theoretical data on the characterization of ligand-receptor interactions by AFM. The advantage of AFM in comparison with other methods developed for the characterization of single molecular interactions is its ability to estimate not only rupture forces, but also thermodynamic and kinetic parameters of the rupture of a complex. The specific features of force spectroscopy applied to ligand-receptor interactions are examined in this review from the stage of the modification of the substrate and the cantilever up to the processing and interpretation of the data. We show the specificities of the statistical analysis of the array of data based on the results of AFM measurements, and we discuss transformation of data into thermodynamic and kinetic parameters (kinetic dissociation constant, Gibbs free energy, enthalpy, and entropy). Particular attention is paid to the study of polyvalent interactions, where the definition of the constants is hampered due to the complex stoichiometry of the reactions.
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Affiliation(s)
- I V Safenkova
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, 119071, Russia.
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16
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An investigation of the effects of self-assembled monolayers on protein crystallisation. Int J Mol Sci 2013; 14:12329-45. [PMID: 23749116 PMCID: PMC3709788 DOI: 10.3390/ijms140612329] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/16/2013] [Accepted: 06/03/2013] [Indexed: 12/02/2022] Open
Abstract
Most protein crystallisation begins from heterogeneous nucleation; in practice, crystallisation typically occurs in the presence of a solid surface in the solution. The solid surface provides a nucleation site such that the energy barrier for nucleation is lower on the surface than in the bulk solution. Different types of solid surfaces exhibit different surface energies, and the nucleation barriers depend on the characteristics of the solid surfaces. Therefore, treatment of the solid surface may alter the surface properties to increase the chance to obtain protein crystals. In this paper, we propose a method to modify the glass cover slip using a self-assembled monolayer (SAM) of functional groups (methyl, sulfydryl and amino), and we investigated the effect of each SAM on protein crystallisation. The results indicated that both crystallisation success rate in a reproducibility study, and crystallisation hits in a crystallisation screening study, were increased using the SAMs, among which, the methyl-modified SAM demonstrated the most significant improvement. These results illustrated that directly modifying the crystallisation plates or glass cover slips to create surfaces that favour heterogeneous nucleation can be potentially useful in practical protein crystallisation, and the utilisation of a SAM containing a functional group can be considered a promising technique for the treatment of the surfaces that will directly contact the crystallisation solution.
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17
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Saito H, Iwayama M, Mizukami T, Kang J, Tateno M, Nagao H. Molecular dynamics study on binding free energy of Azurin–Cytochrome c551 complex. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2012.12.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Bizzarri AR. Steered Molecular Dynamics Simulations of the Electron Transfer Complex between Azurin and Cytochrome c551. J Phys Chem B 2011; 115:1211-9. [DOI: 10.1021/jp107933k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, CNISM, Facolta’ di Scienze, Università della Tuscia, Largo dell’Università, I-01100 Viterbo, Italy
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19
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Samanta D, Sarkar A. Immobilization of bio-macromolecules on self-assembled monolayers: methods and sensor applications. Chem Soc Rev 2011; 40:2567-92. [DOI: 10.1039/c0cs00056f] [Citation(s) in RCA: 313] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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20
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Funari G, Domenici F, Nardinocchi L, Puca R, D'Orazi G, Bizzarri AR, Cannistraro S. Interaction of p53 with Mdm2 and azurin as studied by atomic force spectroscopy. J Mol Recognit 2010; 23:343-51. [PMID: 19941302 DOI: 10.1002/jmr.999] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Azurin, a bacterial protein, can be internalized in cancer cells and induce apoptosis. Such anticancer effect is coupled to the formation of a complex with the tumour-suppressor p53. The mechanism by which azurin stabilizes p53 and the binding sites of their complex are still under investigation. It is also known that the predominant mechanism for p53 down-regulation implies its association to Mdm2, the main ubiquitin ligase affecting its stability. However, the p53/Mdm2 interaction, occurring at the level of both their N-terminal domains, has been characterized so far by experiments involving only partial domains of these proteins. The relevance of the p53/Mdm2 complex as a possible target of the anticancer therapies requires a deeper study of this complex as made up of the two entire proteins. Moreover, the apparent antagonist action of azurin against Mdm2, with respect of p53 regulation, might suggest the possibility that azurin binds p53 at the same site of Mdm2, preventing in such a way p53 and Mdm2 from association and thus p53 from degradation. By following the interaction of the two entire proteins by atomic force spectroscopy, we have assessed the formation of a specific complex between p53 and Mdm2. We found for it a binding strength and a dissociation rate constant typical of dynamical protein-protein interactions and we observed that azurin, even if capable to bind p53, does not compete with Mdm2 for the same binding site on p53. The formation of the p53/Mdm2/azurin ternary complex might suggest an alternative anti-cancer mechanism adopted by azurin.
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Affiliation(s)
- Gloria Funari
- Biophysics and Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Viterbo, Italy
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21
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Sisquella X, de Pourcq K, Alguacil J, Robles J, Sanz F, Anselmetti D, Imperial S, Fernàndez-Busquets X. A single-molecule force spectroscopy nanosensor for the identification of new antibiotics and antimalarials. FASEB J 2010; 24:4203-17. [PMID: 20634351 DOI: 10.1096/fj.10-155507] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
An important goal of nanotechnology is the application of individual molecule handling techniques to the discovery of potential new therapeutic agents. Of particular interest is the search for new inhibitors of metabolic routes exclusive of human pathogens, such as the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway essential for the viability of most human pathogenic bacteria and of the malaria parasite. Using atomic force microscopy single-molecule force spectroscopy (SMFS), we have probed at the single-molecule level the interaction of 1-deoxy-D-xylulose 5-phosphate synthase (DXS), which catalyzes the first step of the MEP pathway, with its two substrates, pyruvate and glyceraldehyde-3-phosphate. The data obtained in this pioneering SMFS analysis of a bisubstrate enzymatic reaction illustrate the substrate sequentiality in DXS activity and allow for the calculation of catalytic parameters with single-molecule resolution. The DXS inhibitor fluoropyruvate has been detected in our SMFS competition experiments at a concentration of 10 μM, improving by 2 orders of magnitude the sensitivity of conventional enzyme activity assays. The binding of DXS to pyruvate is a 2-step process with dissociation constants of k(off) = 6.1 × 10(-4) ± 7.5 × 10(-3) and 1.3 × 10(-2) ± 1.0 × 10(-2) s(-1), and reaction lengths of x(β) = 3.98 ± 0.33 and 0.52 ± 0.23 Å. These results constitute the first quantitative report on the use of nanotechnology for the biodiscovery of new antimalarial enzyme inhibitors and open the field for the identification of compounds represented only by a few dozens of molecules in the sensor chamber.
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Affiliation(s)
- Xavier Sisquella
- Nanotechnology Platform, Barcelona Science Park, Barcelona, Spain
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22
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Grumelli D, Méndez De Leo LP, Bonazzola C, Zamlynny V, Calvo EJ, Salvarezza RC. Methylene blue incorporation into alkanethiol SAMs on Au(111): effect of hydrocarbon chain ordering. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:8226-8232. [PMID: 20356031 DOI: 10.1021/la904594p] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A detailed polarization modulation infrared reflection absorption spectroscopy, scanning tunneling microscopy, and electrochemical study on methylene blue (MB) incorporation into alkanethiolate self-assembled monolayers (SAMs) on Au(111) is reported. Results show that the amount of MB incorporated in the SAMs reaches a maximum for intermediate hydrocarbon chain lengths (C10-C12). Well-ordered SAMs of long alkanethiols (C > C12) hinder the incorporation of the MB molecules into the SAM. On the other hand, less ordered SAMs of short alkanethiols (C < or = C6) are not efficient to retain the MB incorporated through the defects. For C12 the amount of incorporated MB increases as the SAM disorder is increased. This information is essential to the design of efficient thiol-based Au vectors for transport and delivery of molecules as well as thiol-based Au devices for molecular sensing.
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Affiliation(s)
- Doris Grumelli
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, 1900 La Plata, Buenos Aires, Argentina.
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23
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Vericat C, Vela ME, Benitez G, Carro P, Salvarezza RC. Self-assembled monolayers of thiols and dithiols on gold: new challenges for a well-known system. Chem Soc Rev 2010; 39:1805-34. [PMID: 20419220 DOI: 10.1039/b907301a] [Citation(s) in RCA: 775] [Impact Index Per Article: 55.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Self-assembled monolayers (SAMs) of alkanethiols and dialkanethiols on gold are key elements for building many systems and devices with applications in the wide field of nanotechnology. Despite the progress made in the knowledge of these fascinating two-dimensional molecular systems, there are still several "hot topics" that deserve special attention in order to understand and to control their physical and chemistry properties at the molecular level. This critical review focuses on some of these topics, including the nature of the molecule-gold interface, whose chemistry and structure remain elusive, the self-assembly process on planar and irregular surfaces, and on nanometre-sized objects, and the chemical reactivity and thermal stability of these systems in ambient and aqueous solutions, an issue which seriously limits their technological applications (375 references).
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Affiliation(s)
- C Vericat
- Instituto de Investigaciones Fisicoquímicas Teóricasy Aplicadas (INIFTA), Universidad Nacional de La Plata-CONICET, Sucursal 4 Casilla de Correo 16, (1900) La Plata, Argentina
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24
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Bizzarri AR, Di Agostino S, Andolfi L, Cannistraro S. A combined atomic force microscopy imaging and docking study to investigate the complex between p53 DNA binding domain and Azurin. J Mol Recognit 2010; 22:506-15. [PMID: 19642109 DOI: 10.1002/jmr.975] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The tumor suppressor p53 interacts with the redox copper protein Azurin (AZ) forming a complex which is of some relevance in biomedicine and cancer therapy. To obtain information on the spatial organization of this complex when it is immobilized on a substrate, we have used tapping mode-atomic force microscopy (TM-AFM) imaging combined with computational docking. The vertical dimension and the bearing volume of the DNA binding domain (DBD) of p53, anchored to functionalized gold substrate through exposed lysine residues, alone and after deposing AZ, have been measured by TM-AFM. By a computational docking approach, a three-dimensional model for the DBD of p53, before and after addition of AZ, have been predicted. Then we have calculated the possible arrangements of these biomolecular systems on gold substrate by finding a good agreement with the related experimental distribution of the height. The potentiality of the approach combining TM-AFM imaging and computational docking for the study of biomolecular complexes immobilized on substrates is briefly discussed.
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Affiliation(s)
- Anna Rita Bizzarri
- Biophysics & Nanoscience Centre, CNISM, Facolta' di Scienze, Università della Tuscia, I-01100 Viterbo, Italy.
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25
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Bizzarri AR, Cannistraro S. The application of atomic force spectroscopy to the study of biological complexes undergoing a biorecognition process. Chem Soc Rev 2010; 39:734-49. [DOI: 10.1039/b811426a] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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26
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Bizzarri AR, Cannistraro S. Atomic Force Spectroscopy in Biological Complex Formation: Strategies and Perspectives. J Phys Chem B 2009; 113:16449-64. [DOI: 10.1021/jp902421r] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Largo dell’Università, 01100 Viterbo, Italy
| | - Salvatore Cannistraro
- Biophysics and Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Largo dell’Università, 01100 Viterbo, Italy
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27
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Léger C, Bertrand P. Direct Electrochemistry of Redox Enzymes as a Tool for Mechanistic Studies. Chem Rev 2008; 108:2379-438. [DOI: 10.1021/cr0680742] [Citation(s) in RCA: 594] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Taranta M, Bizzarri AR, Cannistraro S. Probing the interaction between p53 and the bacterial protein azurin by single molecule force spectroscopy. J Mol Recognit 2008; 21:63-70. [DOI: 10.1002/jmr.869] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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29
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Bonanni B, Andolfi L, Bizzarri AR, Cannistraro S. Functional Metalloproteins Integrated with Conductive Substrates: Detecting Single Molecules and Sensing Individual Recognition Events. J Phys Chem B 2007; 111:5062-75. [PMID: 17425359 DOI: 10.1021/jp070035m] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the past decade, there has been significant interest in the integration of biomaterials with electronic elements: combining biological functions of biomolecules with nanotechnology offers new perspectives for implementation of ultrasensitive hybrid nanodevices. In particular, great attention has been devoted to redox metalloproteins, since they possess unique characteristics, such as electron-transfer capability, possibility of gating redox activity, and nanometric size, which make them appealing for bioelectronics applications at the nanoscale. The reliable connection of redox proteins to electrodes, aimed at ensuring good electrical contact with the conducting substrate besides preserving protein functionality, is a fundamental step for designing a hybrid nanodevice and calls for a full characterization of the immobilized proteins, possibly at the single-molecule level. Here, we describe how a multitechnique approach, based on several scanning probe microscopy techniques, may provide a comprehensive characterization of different metalloproteins on metal electrodes, disclosing unique information not only about morphological properties of the adsorbed molecules but also about the effectiveness of electrical coupling with the conductive substrate, or even concerning the preserved biorecognition capability upon adsorption. We also show how the success of an immobilization strategy, which is of primary importance for optimal integration of metalloproteins with a metal electrode, can be promptly assessed by means of the proposed approach. Besides the characterization aspect, the complementary employment of the proposed techniques deserves major potentialities for ultrasensitive detection of adsorbed biomolecules. In particular, it is shown how sensing of single metalloproteins may be optimized by monitoring the most appropriate observable. Additionally, we suggest how the combination of several experimental techniques might offer increased versatility, real-time response, and wide applicability as a detection method, once a reproducible correlation among signals coming from different single-molecule techniques is established.
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Affiliation(s)
- B Bonanni
- Biophysics and Nanoscience Centre, CNISM, and CNR-INFM Facoltà di Scienze, Università della Tuscia, Largo dell'Università, I-01100 Viterbo, Italy
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30
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Bizzarri AR, Brunori E, Bonanni B, Cannistraro S. Docking and molecular dynamics simulation of the Azurin–Cytochrome c551 electron transfer complex. J Mol Recognit 2007; 20:122-31. [PMID: 17407190 DOI: 10.1002/jmr.820] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We coupled protein-protein docking procedure with molecular dynamics (MD) simulation to investigate the electron transfer (ET) complex Azurin-Cytochrome c551 whose transient character makes difficult a direct experimental investigation. The ensemble of complexes generated by the docking algorithm are filtered according to both the distance between the metal ions in the redox centres of the two proteins and to the involvement of suitable residues at the interface. The resulting best complex (BC) is characterized by a distance of 1.59 nm and involves Val23 and Ile59 of Cytochrome c551. The ET properties have been evaluated in the framework of the Pathways model and compared with experimental data. A 60 ns long MD simulation, carried on at full hydration, evidenced that the two protein molecules retain their mutual spatial positions upon forming the complex. An analysis of the ET properties of the complex, monitored at regular time intervals, has revealed that several different ET paths are possible, with the occasional intervening of water molecules. Furthermore, the temporal evolution of the geometric distance between the two redox centres is characterized by very fast fluctuations around an average value of 1.6 nm, with periodic jumps at 2 nm with a frequency of about 70 MHz. Such a behaviour is discussed in connection with a nonlinear dynamics of protein systems and its possible implications in the ET process are explored.
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Affiliation(s)
- Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, CNISM, Università della Tuscia, Largo dell'Università, I-01100 Viterbo, Italy.
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