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Bush DB, Knotts TA. The effects of antigen size, binding site valency, and flexibility on fab-antigen binding near solid surfaces. J Chem Phys 2018; 149:165102. [PMID: 30384722 DOI: 10.1063/1.5045356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Next generation antibody microarray devices have the potential to outperform current molecular detection methods and realize new applications in medicine, scientific research, and national defense. However, antibody microarrays, or arrays of antibody fragments ("fabs"), continue to evade mainstream use in part due to persistent reliability problems despite improvements to substrate design and protein immobilization strategies. Other factors could be disrupting microarray performance, including effects resulting from antigen characteristics. Target molecules embody a wide range of sizes, shapes, number of epitopes, epitope accessibility, and other physical and chemical properties. As a result, it may not be ideal for microarray designs to utilize the same substrate or immobilization strategy for all of the capture molecules. This study investigates how three antigen properties, such as size, binding site valency, and molecular flexibility, affect fab binding. The work uses an advanced, experimentally validated, coarse-grain model and umbrella sampling to calculate the free energy of ligand binding and how this energy landscape is different on the surface compared to in the bulk. The results confirm that large antigens interact differently with immobilized fabs compared to smaller antigens. Analysis of the results shows that despite these differences, tethering fabs in an upright orientation on hydrophilic surfaces is the best configuration for antibody microarrays.
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Affiliation(s)
- Derek B Bush
- Department of Chemical Engineering, Brigham Young University Provo, Provo, Utah 84602, USA
| | - Thomas A Knotts
- Department of Chemical Engineering, Brigham Young University Provo, Provo, Utah 84602, USA
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Bush DB, Knotts TA. Probing the effects of surface hydrophobicity and tether orientation on antibody-antigen binding. J Chem Phys 2017; 146:155103. [DOI: 10.1063/1.4980083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Derek B. Bush
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84602, USA
| | - Thomas A. Knotts
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84602, USA
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Shon HK, Son JG, Lee KB, Kim J, Kim MS, Choi IS, Lee TG. Chemical Imaging Analysis of the Micropatterns of Proteins and Cells Using Cluster Ion Beam-based Time-of-Flight Secondary Ion Mass Spectrometry and Principal Component Analysis. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.3.815] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Wei S, Knotts TA. Effects of tethering a multistate folding protein to a surface. J Chem Phys 2011; 134:185101. [PMID: 21568530 DOI: 10.1063/1.3589863] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Protein/surface interactions are important in a variety of fields and devices, yet fundamental understanding of the relevant phenomena remains fragmented due to resolution limitations of experimental techniques. Molecular simulation has provided useful answers, but such studies have focused on proteins that fold through a two-state process. This study uses simulation to show how surfaces can affect proteins which fold through a multistate process by investigating the folding mechanism of lysozyme (PDB ID: 7LZM). The results demonstrate that in the bulk 7LZM folds through a process with four stable states: the folded state, the unfolded state, and two stable intermediates. The folding mechanism remains the same when the protein is tethered to a surface at most residues; however, in one case the folding mechanism changes in such a way as to eliminate one of the intermediates. An analysis of the molecular configurations shows that tethering at this site is advantageous for protein arrays because the active site is both presented to the bulk phase and stabilized. Taken as a whole, the results offer hope that rational design of protein arrays is possible once the behavior of the protein on the surface is ascertained.
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Affiliation(s)
- Shuai Wei
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84602, USA
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Su J, Rajapaksha TW, Peter ME, Mrksich M. Assays of Endogenous Caspase Activities: A Comparison of Mass Spectrometry and Fluorescence Formats. Anal Chem 2006; 78:4945-51. [PMID: 16841915 DOI: 10.1021/ac051974i] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper describes a label-free assay for measuring endogenous caspase protease activities in cell lysates. The assay format, termed SAMDI-MS (self-assembled monolayers for matrix assisted laser desorption ionization time-of-flight mass spectrometry), is based on the enzymatic modification of peptides immobilized to monolayer substrates, followed by direct detection of the products with mass spectrometry. Monolayers presenting peptide substrates for either caspase-3 or -8 were treated with lysates from Jurkat cells that were stimulated with staurosporine and SKW6.4 cells that were stimulated with LzCD95L. In both cases, the SAMDI assays reported on the activation of endogenous caspase enzymes with levels of detection that are similar to those observed using the commonly employed fluorogenic assays. The use of longer peptide substrates, which are not compatible with the fluorogenic assays, provided for a better resolution of the two caspase activities. This work is significant because it demonstrates that the SAMDI assay can be used to measure endogenous enzyme activities and because it avoids the loss of activity and specificity that often accompany label-dependent assay formats.
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Affiliation(s)
- Jing Su
- Howard Hughes Medical Institute and Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA
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Michel R, Castner DG. Advances in time-of-flight secondary ion mass spectrometry analysis of protein films. SURF INTERFACE ANAL 2006. [DOI: 10.1002/sia.2382] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Wagner MS, McArthur SL, Shen M, Horbett TA, Castner DG. Limits of detection for time of flight secondary ion mass spectrometry (ToF-SIMS) and X-ray photoelectron spectroscopy (XPS): detection of low amounts of adsorbed protein. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2003; 13:407-28. [PMID: 12160301 DOI: 10.1163/156856202320253938] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Characterization of biomaterial surfaces requires analytical techniques that are capable of detecting a wide concentration range of adsorbed protein. This range includes detection of low amounts of adsorbed protein (<10 ng/cm2) that may be present on non-fouling biomaterials. X-ray Photoelectron Spectroscopy (XPS) and Time of Flight Secondary Ion Mass Spectrometry (ToF-SIMS) are surface sensitive techniques capable of detecting adsorbed proteins. We have investigated the lower limits of detection of both XPS and ToF-SIMS on four model substrates each presenting unique challenges for analysis by XPS and ToF-SIMS: mica, poly(tetrafluoroethylene), allyl amine plasma polymer and heptyl amine plasma polymer. The detection limit for XPS ranged from 10 ng/cm2 of fibrinogen (on mica) to 200 ng/cm2 (on allyl amine plasma polymers). The detection limit for ToF-SIMS ranged from 0.1 ng/cm2 of fibrinogen to 100 ng/cm2, depending on the substrate and data analysis. Optimal conditions provided detection limits between 0.1 ng/cm2 and 15 ng/cm2 on all of the substrates used in this study. While both techniques were shown to be effective in detecting protein, the sensitivity of both XPS and ToF-SIMS was shown to be dependent on substrate surface chemistry and the organization of the adsorbed protein film. This study specifically highlights the applicability of ToF-SIMS in the characterization of low level protein adsorption.
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Affiliation(s)
- Matthew S Wagner
- Department of Chemical Engineering, National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Seattle 98195-1750, USA
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Merrett K, Cornelius RM, McClung WG, Unsworth LD, Sheardown H. Surface analysis methods for characterizing polymeric biomaterials. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2003; 13:593-621. [PMID: 12182547 DOI: 10.1163/156856202320269111] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Surface properties have an enormous effect on the success or failure of a biomaterial device, thus signifying the considerable importance of and the need for adequate characterization of the biomaterial surface. Microscopy techniques used in the analysis of biomaterial surfaces include scanning electron microscopy, transmission electron microscopy, atomic force microscopy, and confocal microscopy. Spectroscopic techniques include X-ray photoelectron spectroscopy, Fourier Transform infrared attenuated total reflection and secondary ion mass spectrometry. The measurement of contact angles, although one of the earlier techniques developed remains a very useful tool in the evaluation of surface hydrophobicity/hydrophilicity. This paper provides a brief, easy to understand synopsis of these and other techniques including emerging techniques, which are proving useful in the analysis of the surface properties of polymeric biomaterials. Cautionary statements have been made, numerous authors referenced and examples used to show the specific type of information that can be acquired from the different techniques used in the characterization of polymeric biomaterials surfaces.
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Affiliation(s)
- K Merrett
- Department of Chemical Engineering, University of Ottawa, ON, Canada
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Bourdos N, Kollmer F, Benninghoven A, Ross M, Sieber M, Galla HJ. Analysis of lung surfactant model systems with time-of-flight secondary ion mass spectrometry. Biophys J 2000; 79:357-69. [PMID: 10866961 PMCID: PMC1300939 DOI: 10.1016/s0006-3495(00)76297-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
An often-used model lung surfactant containing dipalmitoylphosphatidylcholine (DPPC), dipalmitoylphosphatidylglycerol (DPPG), and the surfactant protein C (SP-C) was analyzed as Langmuir-Blodgett film by spatially resolved time-of-flight secondary ion mass spectrometry (TOF-SIMS) to directly visualize the formation and composition of domains. Binary lipid and lipid/SP-C systems were probed for comparison. TOF-SIMS spectra revealed positive secondary ions (SI) characteristic for DPPC and SP-C, but not for DPPG. SI mapping results in images with domain structures in DPPC/DPPG and DPPG/SP-C, but not in DPPC/SP-C films. We are able to distinguish between the fluid and condensed areas probably due to a matrix effect. These findings correspond with other imaging techniques, fluorescence light microscopy (FLM), scanning force microscopy (SFM), and silver decoration. The ternary mixture DPPC/DPPG/SP-C transferred from the collapse region exhibited SP-C-rich domains surrounding pure lipid areas. The results obtained are in full accordance with our earlier SFM picture of layered protrusions that serve as a compressed reservoir for surfactant material during expansion. Our study demonstrates once more that SP-C plays a unique role in the respiration process.
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Affiliation(s)
- N Bourdos
- Institut für Biochemie, Westfälische Wilhelms-Universität, D-48149 Münster, Germany
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Trevor JL, Mencer DE, Lykke KR, Pellin MJ, Hanley L. Surface Mass Spectrometry of Biotinylated Self-Assembled Monolayers. Anal Chem 1997; 69:4331-8. [DOI: 10.1021/ac970283m] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jennifer L. Trevor
- Materials Science and Chemistry Divisions, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, and Department of Chemistry, The Pennsylvania State UniversityHazelton, Hazelton, Pennsylvania 18533
| | - Donald E. Mencer
- Materials Science and Chemistry Divisions, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, and Department of Chemistry, The Pennsylvania State UniversityHazelton, Hazelton, Pennsylvania 18533
| | - Keith R. Lykke
- Materials Science and Chemistry Divisions, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, and Department of Chemistry, The Pennsylvania State UniversityHazelton, Hazelton, Pennsylvania 18533
| | - Michael J. Pellin
- Materials Science and Chemistry Divisions, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, and Department of Chemistry, The Pennsylvania State UniversityHazelton, Hazelton, Pennsylvania 18533
| | - Luke Hanley
- Materials Science and Chemistry Divisions, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, and Department of Chemistry, The Pennsylvania State UniversityHazelton, Hazelton, Pennsylvania 18533
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Abstract
In a survey, the analytical tools to characterise and optimise properties and stabilities of interfaces in thin film biosensors are discussed. After an introduction to microscopic and spectroscopic techniques and different transducers, case studies are presented. They concern bioaffinity sensors with particular emphasis on biomimetic recognition structures, catalytic sensors, transmembrane sensors, cell sensors, and the ambitious goal of addressing individual biomolecular function units.
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Affiliation(s)
- W Göpel
- Institute of Physical and Theoretical Chemistry, University of Tübingen, Germany
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