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Park CS, Iwabata K, Sridhar U, Tsuei M, Singh K, Kim YK, Thayumanavan S, Abbott NL. A New Strategy for Reporting Specific Protein Binding Events at Aqueous-Liquid Crystal Interfaces in the Presence of Non-Specific Proteins. ACS APPLIED MATERIALS & INTERFACES 2020; 12:7869-7878. [PMID: 31825195 PMCID: PMC7368459 DOI: 10.1021/acsami.9b16867] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Aqueous-liquid crystal (LC) interfaces offer promise as responsive interfaces at which biomolecular recognition events can be amplified into macroscopic signals. However, the design of LC interfaces that distinguish between specific and non-specific protein interactions remains an unresolved challenge. Herein, we report the synthesis of amphiphilic monomers, dimers, and trimers conjugated to sulfonamide ligands via triazole rings, their assembly at aqueous-LC interfaces, and the orientational response of LCs to the interactions of carbonic anhydrase II (CAII) and serum albumin with the oligomer-decorated LC interfaces. Of six oligomers synthesized, only dimers without amide methylation were found to assemble at aqueous interfaces of nematic 4-cyano-4'-pentylbiphenyl (5CB) to induce perpendicular LC orientations. At dimer-decorated LC interfaces, we found that concentrations of CAII less than 4 μM did not measurably perturb the LC but prevented non-specific adsorption and penetration of serum albumin into the dimer-decorated interface that otherwise triggered bright, globular LC optical domains. These experiments and others (including competitive adsorption of CAII, BSA, and lysozyme) support our hypothesis that specific binding of CAII to the dimer prevents LC anchoring transitions triggered by non-specific adsorption of serum albumin. We illustrate the utility of the approach by reporting (i) the relative activity of two small-molecule inhibitors (6-ethoxy-2-benzothiazolesulfonamide and benzenesulfonamide) of CAII to sulfonamide and (ii) proteolytic digestion of a protein (CAII) by thermolysin. Overall, the results in this paper provide new insight into the interactions of proteins at aqueous-LC interfaces and fresh ideas for either blocking non-specific interactions of proteins at surfaces or reporting specific binding events at LC interfaces in the presence of non-specific proteins.
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Affiliation(s)
- Chul Soon Park
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kazuki Iwabata
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Uma Sridhar
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Michael Tsuei
- Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Khushboo Singh
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Young-ki Kim
- Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Korea
| | - S. Thayumanavan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Nicholas L. Abbott
- Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
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Nakahara Y, Higashi M, Funayama R, Horii Y, Osuga H, Sakamoto H, Oda M, Kado S, Kimura K. Evaluation of Stretching Properties of [7]Thiaheterohelicene Framework Called “Molecular Spring” Using AFM Force Measurements and Electrostatic State Calculations. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20140346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yoshio Nakahara
- Department of Applied Chemistry, Faculty of Systems Engineering, Wakayama University
| | - Minako Higashi
- Department of Applied Chemistry, Faculty of Systems Engineering, Wakayama University
| | - Ryoto Funayama
- Department of Applied Chemistry, Faculty of Systems Engineering, Wakayama University
| | - Yasuo Horii
- Department of Applied Chemistry, Faculty of Systems Engineering, Wakayama University
| | - Hideji Osuga
- Department of Applied Chemistry, Faculty of Systems Engineering, Wakayama University
| | - Hidefumi Sakamoto
- Department of Applied Chemistry, Faculty of Systems Engineering, Wakayama University
| | - Masato Oda
- Department of Applied Chemistry, Faculty of Systems Engineering, Wakayama University
| | - Shinpei Kado
- Department of Applied Chemistry, Faculty of Systems Engineering, Wakayama University
| | - Keiichi Kimura
- Department of Applied Chemistry, Faculty of Systems Engineering, Wakayama University
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Ros I, Placido T, Amendola V, Marinzi C, Manfredi N, Comparelli R, Striccoli M, Agostiano A, Abbotto A, Pedron D, Pilot R, Bozio R. SERS Properties of Gold Nanorods at Resonance with Molecular, Transverse, and Longitudinal Plasmon Excitations. PLASMONICS (NORWELL, MASS.) 2014; 9:581-593. [PMID: 24834019 PMCID: PMC4018483 DOI: 10.1007/s11468-014-9669-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 01/22/2014] [Indexed: 05/29/2023]
Abstract
The amplification of Raman signals of the heteroaromatic cation 1-(N-methylpyrid-4-yl)-2-(N-methylpyrrol-2-yl)ethylene (PEP+)) bound to Au nanorods (NRs) was investigated at different excitation wavelengths to study the effect of the laser resonance with the absorption band of the PEP+ moiety and with the two plasmon oscillation modes of the NR. Two different PEP+ derivatives, differing in the length of the alkyl chain bearing the anchoring group, were used as target molecules. Raman spectra obtained exciting at 514 or at 785 nm (i.e., exciting the transverse or the longitudinal plasmon band) present a higher intensity than that at 488 nm suggesting a higher Raman amplification when the laser excitation wavelength is resonant with one of the two plasmon modes. Moreover, considering results of Discrete Dipole Approximation (DDA) calculations of the local field generated at the NR surface when either the transverse or the longitudinal plasmon modes are excited, we deduced that the resonance condition of the 514-nm laser excitation with the absorption band of the dye strongly contributes to the amplification of the Raman signal.
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Affiliation(s)
- Ida Ros
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
- INSTM, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Tiziana Placido
- Department of Chemistry, University of Bari, Via Orabona 4, Bari, 70126 Italy
| | - Vincenzo Amendola
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Chiara Marinzi
- Department of Materials Science and INSTM, University of Milano-Bicocca, Via Cozzi 53, 20125 Milano, Italy
| | - Norberto Manfredi
- Department of Materials Science and INSTM, University of Milano-Bicocca, Via Cozzi 53, 20125 Milano, Italy
| | - Roberto Comparelli
- CNR-IPCF Division of Bari, c/o Department of Chemistry, University of Bari, Via Orabona 4, Bari, 70126 Italy
| | - Marinella Striccoli
- CNR-IPCF Division of Bari, c/o Department of Chemistry, University of Bari, Via Orabona 4, Bari, 70126 Italy
| | - Angela Agostiano
- Department of Chemistry, University of Bari, Via Orabona 4, Bari, 70126 Italy
- CNR-IPCF Division of Bari, c/o Department of Chemistry, University of Bari, Via Orabona 4, Bari, 70126 Italy
| | - Alessandro Abbotto
- Department of Materials Science and INSTM, University of Milano-Bicocca, Via Cozzi 53, 20125 Milano, Italy
| | - Danilo Pedron
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Roberto Pilot
- Department of Chemical Sciences, University of Padova and INSTM, Via Marzolo 1, 35131 Padova, Italy
| | - Renato Bozio
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
- INSTM, University of Padova, Via Marzolo 1, 35131 Padova, Italy
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Wakayama J, Sugiyama S. Evaluation of Temperature Effect on the Interaction between β-Lactoglobulin and Anti-β-lactoglobulin Antibody by Atomic Force Microscopy. Biochemistry 2011; 51:32-42. [DOI: 10.1021/bi201245k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun’ichi Wakayama
- Nano-Biotechnology Laboratory, Food
Engineering Division, National Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Shigeru Sugiyama
- Nano-Biotechnology Laboratory, Food
Engineering Division, National Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
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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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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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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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Lynch S, Baker H, Byker SG, Zhou D, Sinniah K. Single molecule force spectroscopy on G-quadruplex DNA. Chemistry 2009; 15:8113-6. [PMID: 19603437 DOI: 10.1002/chem.200901390] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Susanna Lynch
- Chemistry & Biochemistry, Calvin College, 1726 Knollcrest Circle SE, Grand Rapids, MI 49546, USA
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Abstract
Single-molecule force-clamp spectroscopy offers a novel platform for mechanically denaturing proteins by applying a constant force to a polyprotein. A powerful emerging application of the technique is that, by introducing a disulfide bond in each protein module, the chemical kinetics of disulfide bond cleavage under different stretching forces can be probed at the single-bond level. Even at forces much lower than that which can rupture the chemical bond, the breaking of the S-S bond at the presence of various chemical reducing agents is significantly accelerated. Our previous work demonstrated that the rate of thiol/disulfide exchange reaction is force-dependent and well-described by an Arrhenius term of the form r = A(exp((FΔx(r) - E(a))/k(B)T)[nucleophile]). From Arrhenius fits to the force dependency of the reduction rate, we measured the bond elongation parameter, Δx(r), along the reaction coordinate to the transition state of the S(N)2 reaction cleaved by different nucleophiles and enzymes, never before observed by any other technique. For S-S cleavage by various reducing agents, obtaining the Δx(r) value can help depicting the energy landscapes and elucidating the mechanisms of the reactions at the single-molecule level. Small nucleophiles, such as 1,4-dl-dithiothreitol (DTT), tris(2-carboxyethyl)phosphine (TCEP), and l-cysteine, react with the S-S bond with monotonically increasing rates under the applied force, while thioredoxin enzymes exhibit both stretching-favored and -resistant reaction-rate regimes. These measurements demonstrate the power of the single-molecule force-clamp spectroscopy approach in providing unprecedented access to chemical reactions.
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Porter-Peden L, Kamper SG, Wal MV, Blankespoor R, Sinniah' K. Estimating kinetic and thermodynamic parameters from single molecule enzyme-inhibitor interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:11556-11561. [PMID: 18808161 PMCID: PMC2586077 DOI: 10.1021/la801477a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We report the application of recently developed microscopic models to estimate the apparent kinetic and thermodynamic parameters in a single molecule force spectroscopy study of the carbonic anhydrase enzyme and a complementary sulfonamide inhibitor. The most probable rupture force for the enzyme-inhibitor interaction shows a nonlinear dependency on the log-loading rate. Estimates for the kinetic and thermodynamic parameters were obtained by fitting the nonlinear dependency to linear cubic potential and cusp potential models and compared to the standard Bell-Evans model. The reliability of the estimated parameters was verified by modeling the experimental rupture force distributions by the theoretically predicted distributions at rupture. We also report that linkers that are attached to the enzyme and inhibitor show appreciable effects on the apparent kinetic and thermodynamic parameters.
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Affiliation(s)
| | | | | | | | - Kumar Sinniah'
- CORRESPONDING AUTHOR FOOTNOTE Prof. Kumar Sinniah, Calvin College, Department of Chemistry & Biochemistry, 3201 Burton Street SE, Grand Rapids, MI 49546. Phone: (616) 526-6058, Fax: (616) 526-6501;
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