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Wasilewski T, Neubauer D, Wojciechowski M, Szulczyński B, Gębicki J, Kamysz W. Evaluation of Linkers' Influence on Peptide-Based Piezoelectric Biosensors' Sensitivity to Aldehydes in the Gas Phase. Int J Mol Sci 2023; 24:10610. [PMID: 37445789 DOI: 10.3390/ijms241310610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Recent findings qualified aldehydes as potential biomarkers for disease diagnosis. One of the possibilities is to use electrochemical biosensors in point-of-care (PoC), but these need further development to overcome some limitations. Currently, the primary goal is to enhance their metrological parameters in terms of sensitivity and selectivity. Previous findings indicate that peptide OBPP4 (KLLFDSLTDLKKKMSEC-NH2) is a promising candidate for further development of aldehyde-sensitive biosensors. To increase the affinity of a receptor layer to long-chain aldehydes, a structure stabilization of the peptide active site via the incorporation of different linkers was studied. Indeed, the incorporation of linkers improved sensitivity to and binding of aldehydes in comparison to that of the original peptide-based biosensor. The tendency to adopt disordered structures was diminished owing to the implementation of suitable linkers. Therefore, to improve the metrological characteristics of peptide-based piezoelectric biosensors, linkers were added at the C-terminus of OBPP4 peptide (KLLFDSLTDLKKKMSE-linker-C-NH2). Those linkers consist of proteinogenic amino acids from group one: glycine, L-proline, L-serine, and non proteinogenic amino acids from group two: β-alanine, 4-aminobutyric acid, and 6-aminohexanoic acid. Linkers were evaluated with in silico studies, followed by experimental verification. All studied linkers enhanced the detection of aldehydes in the gas phase. The highest difference in frequency (60 Hz, nonanal) was observed between original peptide-based biosensors and ones based on peptides modified with the GSGSGS linker. It allowed evaluation of the limit of detection for nonanal at the level of 2 ppm, which is nine times lower than that of the original peptide. The highest sensitivity values were also obtained for the GSGSGS linker: 0.3312, 0.4281, and 0.4676 Hz/ppm for pentanal, octanal, and nonanal, respectively. An order of magnitude increase in sensitivity was observed for the six linkers used. Generally, the linker's rigidity and the number of amino acid residues are much more essential for biosensors' metrological characteristics than the amino acid sequence itself. It was found that the longer the linkers, the better the effect on docking efficiency.
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Affiliation(s)
- Tomasz Wasilewski
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland
| | - Damian Neubauer
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland
| | - Marek Wojciechowski
- Department of Pharmaceutical Technology and Biochemistry, Chemical Faculty, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Bartosz Szulczyński
- Department of Process Engineering and Chemical Technology, Chemical Faculty, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Jacek Gębicki
- Department of Process Engineering and Chemical Technology, Chemical Faculty, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Wojciech Kamysz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland
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2
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Clark RA, Yawitz T, Luchs L, Conrad T, Bartlebaugh O, Boyd H, Hargittai B. Tripeptide Self-Assembled Monolayers as Biocompatible Surfaces for Cytochrome c Electrochemistry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:1414-1424. [PMID: 36688667 DOI: 10.1021/acs.langmuir.2c02682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Biocompatible tripeptide self-assembled monolayers (SAMs) are designed with a carboxylate group on the terminal amino acid (glutamate, aspartate, or amino adipate) to electrostatically attract the lysine groups around the heme crevice in horse heart cytochrome c (cyt c), creating an electroactive protein/tripeptide/Au interfacial structure. Exposing the peptide/Au electrode to cyt c resulted in an 11 ± 3 pmol/cm2 electroactive protein surface coverage. Topographical images of the interfacial structure are obtained down to single-protein resolution by atomic force microscopy. Uniform protein monolayer assemblies are formed on the Au electrode with no major surface roughness changes. The cyt c/peptide/Au electrode systems were examined electrochemically to probe surface charge effects on the redox thermodynamics and kinetics of cyt c. Neutralization of protein surface charge due to adsorption on anionic COOH-terminated SAMs was found to change the formal potential, as determined by cyclic voltammetry. The cyt c/peptide/Au electrodes exhibit formal potentials shifted to more positive values, have a surface carboxylic acid pKa of 6 or higher, and produce effective cyt c surface charges (Zox) of -6 to -14. The Marcus theory is utilized to determine the protein electron transfer rates, which are ∼5 times faster for cyt c/tripeptide/Au compared to cyt c/11-mercaptoundecanoic acid SAMs of similar chain lengths.
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Affiliation(s)
- Rose A Clark
- Department of Chemistry, Saint Francis University, 169 Lakeview Drive, P.O. Box 600, Loretto, Pennsylvania15940, United States
| | - Tanner Yawitz
- Department of Chemistry, Saint Francis University, 169 Lakeview Drive, P.O. Box 600, Loretto, Pennsylvania15940, United States
| | - Logan Luchs
- Department of Chemistry, Saint Francis University, 169 Lakeview Drive, P.O. Box 600, Loretto, Pennsylvania15940, United States
| | - Tiffany Conrad
- Department of Chemistry, Saint Francis University, 169 Lakeview Drive, P.O. Box 600, Loretto, Pennsylvania15940, United States
| | - Owen Bartlebaugh
- Department of Chemistry, Saint Francis University, 169 Lakeview Drive, P.O. Box 600, Loretto, Pennsylvania15940, United States
| | - Hannah Boyd
- Department of Chemistry, Saint Francis University, 169 Lakeview Drive, P.O. Box 600, Loretto, Pennsylvania15940, United States
| | - Balazs Hargittai
- Department of Chemistry, Saint Francis University, 169 Lakeview Drive, P.O. Box 600, Loretto, Pennsylvania15940, United States
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3
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Grabarek A, Walczak Ł, Cyganik P. Odd-Even Effect in Peptide SAMs-Competition of Secondary Structure and Molecule-Substrate Interaction. J Phys Chem B 2021; 125:10964-10971. [PMID: 34554757 PMCID: PMC8503877 DOI: 10.1021/acs.jpcb.1c06625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Peptide-based self-assembled
monolayers (SAMs) are well known to
be crucial for biocompatible surface formation on inorganic substrates
applied for implants, biosensors, or tissue engineering. Moreover,
recently these bioinspired nanostructures are also considered
particularly interesting for molecular electronics applications due
to their surprisingly high conductance and thickness-independent capacitance,
which make them a very promising element of organic field-effect transistors
(OFETs). Our structural analysis conducted for a series of prototypic
homooligopeptides based on glycine (Gly) with cysteine (Cys) as a
substrate bonding group chemisorbed on Au and Ag metal substrates
(GlynCys/Au(Ag), n =
1–9) exhibits the formation by these monolayers secondary structure
close to β-sheet conformation with pronounced odd–even structural effect strongly affecting packing density and conformation
of molecules in the monolayer, which depend on the length of molecules
and the type of metal substrate. Our experiments indicate that the
origin of these structural effects is related to the either cooperative
or competitive relationship between the type of secondary structure
formed by these molecules and the directional character of their chemical
bonding to the metal substrate. The current analysis opens up the
opportunity for the rational design of these biologically inspired
nanostructures, which is crucial both for mentioned biological and
electronic applications.
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Affiliation(s)
- Agnieszka Grabarek
- Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Krakow, Poland
| | - Łukasz Walczak
- Science & Research Division, PREVAC sp. z o.o., Raciborska 61, 44-362 Rogow, Poland
| | - Piotr Cyganik
- Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Krakow, Poland
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4
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Noriega R. Measuring the Multiscale Dynamics, Structure, and Function of Biomolecules at Interfaces. J Phys Chem B 2021; 125:5667-5675. [PMID: 34042455 DOI: 10.1021/acs.jpcb.1c01546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The individual and collective structure and properties of biomolecules can change dramatically when they are localized at an interface. However, the small spatial extent of interfacial regions poses challenges to the detailed characterization of multiscale processes that dictate the structure and function of large biological units such as peptides, proteins, or nucleic acids. This Perspective surveys a broad set of tools that provide new opportunities to probe complex, dynamic interfaces across the vast range of temporal regimes that connect molecular-scale events to macroscopic observables. An emphasis is placed on the integration over multiple time scales, the use of complementary techniques, and the incorporation of external stimuli to control interfacial properties with spatial, temporal, and chemical specificity.
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Affiliation(s)
- Rodrigo Noriega
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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5
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Blasi D, Sarcina L, Tricase A, Stefanachi A, Leonetti F, Alberga D, Mangiatordi GF, Manoli K, Scamarcio G, Picca RA, Torsi L. Enhancing the Sensitivity of Biotinylated Surfaces by Tailoring the Design of the Mixed Self-Assembled Monolayer Synthesis. ACS OMEGA 2020; 5:16762-16771. [PMID: 32685844 PMCID: PMC7364725 DOI: 10.1021/acsomega.0c01717] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/18/2020] [Indexed: 05/04/2023]
Abstract
Thiolated self-assembled monolayers (SAMs) are typically used to anchor on a gold surface biomolecules serving as recognition elements for biosensor applications. Here, the design and synthesis of N-(2-hydroxyethyl)-3-mercaptopropanamide (NMPA) in biotinylated mixed SAMs is proposed as an alternative strategy with respect to on-site multistep functionalization of SAMs prepared from solutions of commercially available thiols. In this study, the mixed SAM deposited from a 10:1 solution of 3-mercaptopropionic acid (3MPA) and 11-mercaptoundecanoic acid (11MUA) is compared to that resulting from a 10:1 solution of NMPA:11MUA. To this end, surface plasmon resonance (SPR) and attenuated total reflectance infrared (ATR-IR) experiments have been carried out on both mixed SAMs after biotinylation. The study demonstrated how the fine tuning of the SAM features impacts directly on both the biofunctionalization steps, i.e., the biotin anchoring, and the biorecognition properties evaluated upon exposure to streptavidin analyte. Higher affinity for the target analyte with reduced nonspecific binding and lower detection limit has been demonstrated when NMPA is chosen as the more abundant starting thiol. Molecular dynamics simulations complemented the experimental findings providing a molecular rationale behind the performance of the biotinylated mixed SAMs. The present study confirms the importance of the functionalization design for the development of a highly performing biosensor.
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Affiliation(s)
- Davide Blasi
- CSGI,
Unità di Bari, Unità
di Bari, Via Orabona 4, 70125 Bari, Italy
| | - Lucia Sarcina
- Dipartimento
di Chimica, Università degli Studi
di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy
| | - Angelo Tricase
- Dipartimento
di Chimica, Università degli Studi
di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy
| | - Angela Stefanachi
- Dipartimento
di Farmacia − Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy
| | - Francesco Leonetti
- Dipartimento
di Farmacia − Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy
| | | | | | - Kyriaki Manoli
- CSGI,
Unità di Bari, Unità
di Bari, Via Orabona 4, 70125 Bari, Italy
- Dipartimento
di Chimica, Università degli Studi
di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy
| | - Gaetano Scamarcio
- Dipartimento
di Fisica “M. Merlin”, Università
degli Studi di Bari Aldo Moro, Via Amendola 173, 70126 Bari, Italy
- IFN
CNR, Sede secondaria di Bari, Via Amendola 173, 70126 Bari, Italy
| | - Rosaria Anna Picca
- CSGI,
Unità di Bari, Unità
di Bari, Via Orabona 4, 70125 Bari, Italy
- Dipartimento
di Chimica, Università degli Studi
di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy
| | - Luisa Torsi
- CSGI,
Unità di Bari, Unità
di Bari, Via Orabona 4, 70125 Bari, Italy
- Dipartimento
di Chimica, Università degli Studi
di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy
- Physics
and Center for Functional Materials, Faculty of Science and Engineering, Åbo Akademi University, Porthansgatan 3, 20500 Åbo, Finland
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6
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Bar L, Dejeu J, Lartia R, Bano F, Richter RP, Coche-Guérente L, Boturyn D. Impact of Antigen Density on Recognition by Monoclonal Antibodies. Anal Chem 2020; 92:5396-5403. [DOI: 10.1021/acs.analchem.0c00092] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Laure Bar
- University of Grenoble-Alpes, CNRS, DCM UMR 5250, 570 rue de la chimie, CS 40700, 38058 Grenoble Cedex 9, France
| | - Jérôme Dejeu
- University of Grenoble-Alpes, CNRS, DCM UMR 5250, 570 rue de la chimie, CS 40700, 38058 Grenoble Cedex 9, France
| | - Rémy Lartia
- University of Grenoble-Alpes, CNRS, DCM UMR 5250, 570 rue de la chimie, CS 40700, 38058 Grenoble Cedex 9, France
| | - Fouzia Bano
- University of Leeds, School of Biomedical Sciences, Faculty of Biological Sciences, School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, Astbury Center for Structural Molecular Biology, and Bragg Centre for Materials Research, Leeds LS2 9JT, United Kingdom
| | - Ralf P. Richter
- University of Leeds, School of Biomedical Sciences, Faculty of Biological Sciences, School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, Astbury Center for Structural Molecular Biology, and Bragg Centre for Materials Research, Leeds LS2 9JT, United Kingdom
| | - Liliane Coche-Guérente
- University of Grenoble-Alpes, CNRS, DCM UMR 5250, 570 rue de la chimie, CS 40700, 38058 Grenoble Cedex 9, France
| | - Didier Boturyn
- University of Grenoble-Alpes, CNRS, DCM UMR 5250, 570 rue de la chimie, CS 40700, 38058 Grenoble Cedex 9, France
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7
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Sen R, Tagore S, De RK. Cluster Quality based Non-Reductional (CQNR) oversampling technique and effector protein predictor based on 3D structure (EPP3D) of proteins. Comput Biol Med 2019; 112:103374. [DOI: 10.1016/j.compbiomed.2019.103374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/26/2019] [Accepted: 07/26/2019] [Indexed: 11/28/2022]
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8
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9
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Vega-Figueroa K, Santillán J, Ortiz-Gómez V, Ortiz-Quiles EO, Quiñones-Colón BA, Castilla-Casadiego DA, Almodóvar J, Bayro MJ, Rodríguez-Martínez JA, Nicolau E. Aptamer-Based Impedimetric Assay of Arsenite in Water: Interfacial Properties and Performance. ACS OMEGA 2018; 3:1437-1444. [PMID: 29503970 PMCID: PMC5830693 DOI: 10.1021/acsomega.7b01710] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/23/2018] [Indexed: 06/08/2023]
Abstract
In this work, we explore the use of electrochemical methods (i.e., impedance) along with the arsenic-specific aptamer (ArsSApt) to fabricate and study the interfacial properties of an arsenic (As(III)) sensor. The ArsSApt layer was self-assembled on a gold substrate, and upon binding of As(III), a detectable change in the impedimetric signal was recorded because of conformational changes at the interfacial layer. These interfacial changes are linearly correlated with the concentration of arsenic present in the system. This target-induced signal was utilized for the selective detection of As(III) with a linear dynamic range of 0.05-10 ppm and minimum detectable concentrations of ca. 0.8 μM. The proposed system proved to be successful mainly because of the combination of a highly sensitive electrochemical platform and the recognized specificity of the ArsSApt toward its target molecule. Also, the interaction between the ArsSApt and the target molecule (i.e., arsenic) was explored in depth. The obtained results in this work are aimed at proving the development of a simple and environmentally benign sensor for the detection of As(III) as well as in elucidating the possible interactions between the ArsSApt and arsenic molecules.
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Affiliation(s)
- Karlene Vega-Figueroa
- Department
of Biology and Department of Physics, University of Puerto
Rico, Rio Piedras Campus, P.O. Box 23346, San Juan, Puerto Rico 00931-3346, United States
- Molecular
Sciences Research Center, University of
Puerto Rico, 1390 Ponce
De Leon Avenue, Suite 2, San Juan, Puerto Rico 00931-3346, United States
| | - Jaime Santillán
- Department
of Biology and Department of Physics, University of Puerto
Rico, Rio Piedras Campus, P.O. Box 23346, San Juan, Puerto Rico 00931-3346, United States
- Molecular
Sciences Research Center, University of
Puerto Rico, 1390 Ponce
De Leon Avenue, Suite 2, San Juan, Puerto Rico 00931-3346, United States
| | - Valerie Ortiz-Gómez
- Department
of Biology and Department of Physics, University of Puerto
Rico, Rio Piedras Campus, P.O. Box 23346, San Juan, Puerto Rico 00931-3346, United States
- Molecular
Sciences Research Center, University of
Puerto Rico, 1390 Ponce
De Leon Avenue, Suite 2, San Juan, Puerto Rico 00931-3346, United States
| | - Edwin O. Ortiz-Quiles
- Department
of Chemistry, University of Puerto Rico, Rio Piedras Campus, 17 Ave. Universidad
Ste. 1701, San Juan, Puerto
Rico 00925-2537, United
States
- Molecular
Sciences Research Center, University of
Puerto Rico, 1390 Ponce
De Leon Avenue, Suite 2, San Juan, Puerto Rico 00931-3346, United States
| | - Beatriz A. Quiñones-Colón
- Department
of Chemical Engineering, University of Puerto
Rico Mayaguez, Call Box 9000, Mayaguez, Puerto Rico 00681-9000, United States
| | - David A. Castilla-Casadiego
- Department
of Chemical Engineering, University of Puerto
Rico Mayaguez, Call Box 9000, Mayaguez, Puerto Rico 00681-9000, United States
| | - Jorge Almodóvar
- Department
of Chemical Engineering, University of Puerto
Rico Mayaguez, Call Box 9000, Mayaguez, Puerto Rico 00681-9000, United States
| | - Marvin J. Bayro
- Department
of Chemistry, University of Puerto Rico, Rio Piedras Campus, 17 Ave. Universidad
Ste. 1701, San Juan, Puerto
Rico 00925-2537, United
States
- Molecular
Sciences Research Center, University of
Puerto Rico, 1390 Ponce
De Leon Avenue, Suite 2, San Juan, Puerto Rico 00931-3346, United States
| | - José A. Rodríguez-Martínez
- Department
of Biology and Department of Physics, University of Puerto
Rico, Rio Piedras Campus, P.O. Box 23346, San Juan, Puerto Rico 00931-3346, United States
- Molecular
Sciences Research Center, University of
Puerto Rico, 1390 Ponce
De Leon Avenue, Suite 2, San Juan, Puerto Rico 00931-3346, United States
| | - Eduardo Nicolau
- Department
of Chemistry, University of Puerto Rico, Rio Piedras Campus, 17 Ave. Universidad
Ste. 1701, San Juan, Puerto
Rico 00925-2537, United
States
- Molecular
Sciences Research Center, University of
Puerto Rico, 1390 Ponce
De Leon Avenue, Suite 2, San Juan, Puerto Rico 00931-3346, United States
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10
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Liu J, Chisti MM, Zeng X. General Signal Amplification Strategy for Nonfaradic Impedimetric Sensing: Trastuzumab Detection Employing a Peptide Immunosensor. Anal Chem 2017; 89:4013-4020. [PMID: 28256130 DOI: 10.1021/acs.analchem.6b04570] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A label-free and reagent-free peptide mimotope capacitive biosensor has been developed for cancer drug (trastuzumab) quantification based on nonfaradic readout. The low sensitivity issue of capacitive biosensors was overcome with two innovations: peptide mimotope mixed self-assembled monolayer (SAM) biointerface and dilution of the analysis buffer. Signal amplification was achieved through dilution of phosphate-buffered saline (PBS) to tune Cdl to dominate the overall capacitance change upon target binding, which contribution is often negligible without dilution. After 1000× dilution, the limit of detection was lowered 500-fold (0.22 μg/mL) and the sensitivity was increased 20-fold [0.04192 (μg/mL)-1] in comparison with undiluted PBS. The proposed signal amplification strategy is more straightforward and practical compared to biorecognition element engineering and other strategies. The proposed method was further applied to planar electrodes for optimizing sensing response time to less than 1 min.
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Affiliation(s)
- Juan Liu
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | | | - Xiangqun Zeng
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
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