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Article ; Online: Morphology Control of Self-Assembled Copper Coordination Polymers for Glucose Assays.

Van Houten, Justin / Dosajh, Advikaa / Gulati, Shriya / Bhullar, Gurjap / Copeman, Christopher / Ogata, Alana F

Langmuir : the ACS journal of surfaces and colloids

2024

Abstract: Low-cost analytical assays enable accessible detection of clinically and environmentally important analytes; however, common enzyme-based assays suffer from high production and storage costs. Catalytically active synthetic materials serve as replacements ...

Abstract	Low-cost analytical assays enable accessible detection of clinically and environmentally important analytes; however, common enzyme-based assays suffer from high production and storage costs. Catalytically active synthetic materials serve as replacements for natural enzymes, but development of cost-effective, highly efficient synthetic strategies remains a challenge. Here, we utilized a facile synthesis for copper bipyridine coordination polymers (CuBpyCPs) and investigated structure-function relationships to achieve optimal catalytic properties for a glucose assay. We demonstrated the manipulation of CuBpyCP morphology, resulting in nanoscale petal-like structures and microscale high-index faceted structures, and identified three pure crystal morphologies exhibiting a comparable catalytic activity (
Language	English
Publishing date	2024-02-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2005937-1
ISSN	1520-5827 ; 0743-7463
ISSN (online)	1520-5827
ISSN	0743-7463
DOI	10.1021/acs.langmuir.3c02979
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Article ; Online: Single-molecule studies reveal method for tuning the heterogeneous activity of alkaline phosphatase.

Gilboa, Tal / Ogata, Alana F / Reilly, Charles B / Walt, David R

Biophysical journal

2022 Volume 121, Issue 11, Page(s) 2027–2034

Abstract: Single-molecule-enzymology (SME) methods have enabled the observation of heterogeneous catalytic activities within a single enzyme population. Heterogeneous activity is hypothesized to originate from conformational changes in the enzyme that result from ... ...

Abstract	Single-molecule-enzymology (SME) methods have enabled the observation of heterogeneous catalytic activities within a single enzyme population. Heterogeneous activity is hypothesized to originate from conformational changes in the enzyme that result from changes in the local environment leading to catalytically active substates. Here, we use SME to investigate the mechanisms of heterogeneous activity exhibited by tissue nonspecific alkaline phosphatase (TNSALP), which reveals two subpopulations with different catalytic activities. We show the effect of pH and temperature on the distribution of TNSALP activity and confirm the presence of two subpopulations attributed to half- and fully active TNSALP substates. We provide mechanistic insight about protein structure using molecular dynamic simulations and show pH- and temperature-dependent conformational transitions that corroborate experimentally observed changes in TNSALP activity. These results show the utility of SME to understand heterogeneous enzyme activity and demonstrate a simple approach using pH and temperature to tune catalytic activity within an enzyme population.
MeSH term(s)	Alkaline Phosphatase/chemistry ; Alkaline Phosphatase/metabolism ; Animals ; COS Cells ; Chlorocebus aethiops ; Hypophosphatasia
Chemical Substances	Alkaline Phosphatase (EC 3.1.3.1)
Language	English
Publishing date	2022-05-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2022.05.005
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Article ; Online: Single-Molecule Enzymology for Diagnostics: Profiling Alkaline Phosphatase Activity in Clinical Samples.

Gilboa, Tal / Ogata, Alana F / Walt, David R

Chembiochem : a European journal of chemical biology

2021 Volume 23, Issue 1, Page(s) e202100358

Abstract: Enzymes can be used as biomarkers for a variety of diseases. However, profiling enzyme activity in clinical samples is challenging due to the heterogeneity in enzyme activity, and the low abundance of the target enzyme in biofluids. Single-molecule ... ...

Abstract	Enzymes can be used as biomarkers for a variety of diseases. However, profiling enzyme activity in clinical samples is challenging due to the heterogeneity in enzyme activity, and the low abundance of the target enzyme in biofluids. Single-molecule methods can overcome these challenges by providing information on the distribution of enzyme activities in a sample. Here, we describe the concept of using the single-molecule enzymology (SME) method to analyze enzymatic activity in clinical samples. We present recent work focused on measuring alkaline phosphatase isotypes in serum samples using SME. Future work will involve improving and simplifying this technology, and applying it to other enzymes for diagnostics.
MeSH term(s)	Alkaline Phosphatase/analysis ; Alkaline Phosphatase/metabolism ; Biomarkers/analysis ; Biomarkers/metabolism ; Cardiovascular Diseases/diagnostic imaging ; Cardiovascular Diseases/metabolism ; Humans ; Neoplasms/diagnostic imaging ; Neoplasms/metabolism ; Neurodegenerative Diseases/diagnostic imaging ; Neurodegenerative Diseases/metabolism ; Optical Imaging ; Single Molecule Imaging
Chemical Substances	Biomarkers ; Alkaline Phosphatase (EC 3.1.3.1)
Language	English
Publishing date	2021-09-12
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2020469-3
ISSN	1439-7633 ; 1439-4227
ISSN (online)	1439-7633
ISSN	1439-4227
DOI	10.1002/cbic.202100358
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Article ; Online: Ultrasensitive Detection of Enzymatic Activity Using Single Molecule Arrays.

Wang, Xu / Ogata, Alana F / Walt, David R

Journal of the American Chemical Society

2020 Volume 142, Issue 35, Page(s) 15098–15106

Abstract: Enzyme assays are important for many applications including clinical diagnostics, functional proteomics, and drug discovery. Current methods for enzymatic activity measurement often suffer from low analytical sensitivity. We developed an ultrasensitive ... ...

Abstract	Enzyme assays are important for many applications including clinical diagnostics, functional proteomics, and drug discovery. Current methods for enzymatic activity measurement often suffer from low analytical sensitivity. We developed an ultrasensitive method for the detection of enzymatic activity using Single Molecule Arrays (eSimoa). The eSimoa assay is accomplished by conjugating substrates to paramagnetic beads and measuring the conversion of substrates to products using single molecule analysis. We demonstrated the eSimoa method for the detection of protein kinases, telomerase, histone H3 methyltransferase SET7/9, and polypeptide
MeSH term(s)	Cell Line ; Enzyme Assays ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Histone Methyltransferases/antagonists & inhibitors ; Histone Methyltransferases/metabolism ; Humans ; N-Acetylgalactosaminyltransferases/antagonists & inhibitors ; N-Acetylgalactosaminyltransferases/metabolism ; Protein Kinases/metabolism ; Single Molecule Imaging ; Telomerase/antagonists & inhibitors ; Telomerase/metabolism ; Polypeptide N-acetylgalactosaminyltransferase
Chemical Substances	Enzyme Inhibitors ; Histone Methyltransferases (EC 2.1.1.-) ; N-Acetylgalactosaminyltransferases (EC 2.4.1.-) ; Protein Kinases (EC 2.7.-) ; Telomerase (EC 2.7.7.49)
Language	English
Publishing date	2020-08-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.0c06599
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Article: Ultrasensitive Detection of Enzymatic Activity Using Single Molecule Arrays

Wang, Xu / Ogata, Alana F / Walt, David R

Journal of the American Chemical Society. 2020 Aug. 14, v. 142, no. 35

2020

Abstract	Enzyme assays are important for many applications including clinical diagnostics, functional proteomics, and drug discovery. Current methods for enzymatic activity measurement often suffer from low analytical sensitivity. We developed an ultrasensitive method for the detection of enzymatic activity using Single Molecule Arrays (eSimoa). The eSimoa assay is accomplished by conjugating substrates to paramagnetic beads and measuring the conversion of substrates to products using single molecule analysis. We demonstrated the eSimoa method for the detection of protein kinases, telomerase, histone H3 methyltransferase SET7/9, and polypeptide N-acetylgalactosaminyltransferase with unprecedented sensitivity. In addition, we tested enzyme inhibition and performed theoretical calculations for the binding of inhibitor to its target enzyme and show the need for an ultrasensitive enzymatic assay to evaluate the potency of tight binding inhibitors. The eSimoa assay was successfully used to determine inhibition constants of both bosutinib and dasatinib. Due to the ultrasensitivity of this method, we also were able to measure the kinase activities at the single cell level. We show that the eSimoa assay is a simple, fast, and highly sensitive approach, which can be easily extended to detect a variety of other enzymes, providing a promising platform for enzyme-related fundamental research and inhibitor screening.
Keywords	detection limit ; diagnostic techniques ; drugs ; enzyme activity ; enzyme inhibition ; histones ; methyltransferases ; polypeptides ; protein kinases ; proteomics ; telomerase
Language	English
Dates of publication	2020-0814
Size	p. 15098-15106.
Publishing place	American Chemical Society
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.0c06599
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Sequential Protein Capture in Multiplex Single Molecule Arrays: A Strategy for Eliminating Assay Cross-Reactivity.

Gilboa, Tal / Maley, Adam M / Ogata, Alana F / Wu, Connie / Walt, David R

Advanced healthcare materials

2020 Volume 10, Issue 4, Page(s) e2001111

Abstract: Measurements of multiple biomolecules within the same biological sample are important for many clinical applications to enable accurate disease diagnosis or classification. These disease-related biomarkers often exist at very low levels in biological ... ...

Abstract	Measurements of multiple biomolecules within the same biological sample are important for many clinical applications to enable accurate disease diagnosis or classification. These disease-related biomarkers often exist at very low levels in biological fluids, necessitating ultrasensitive measurement methods. Single-molecule arrays (Simoa), a bead-based digital enzyme-linked immunosorbent assay, is the current state of the art for ultrasensitive protein detection and can detect sub-femtomolar protein concentrations, but its ability to achieve high-order multiplexing without cross-reactivity remains a challenge. Here, a sequential protein capture approach for multiplex Simoa assays is implemented to eliminate cross-reactivity between binding reagents by sequentially capturing each protein analyte and then incubating each capture bead with only its corresponding detection antibody. This strategy not only reduces cross-reactivity to background levels and significantly improves measurement accuracies, but also enables higher-order multiplexing. As a proof of concept, the sequential multiplex Simoa assay is used to measure five different cytokines in plasma samples from Coronavirus Disease 2019 (COVID-19) patients. The ultrasensitive sequential multiplex Simoa assays will enable the simultaneous measurements of multiple low-abundance analytes in a time- and cost-effective manner and will prove especially critical in many cases where sample volumes are limited.
MeSH term(s)	Biological Assay ; COVID-19/blood ; COVID-19/virology ; Calibration ; Cross Reactions/immunology ; Cytokines/blood ; Humans ; Proteins/analysis ; Reproducibility of Results ; SARS-CoV-2/physiology
Chemical Substances	Cytokines ; Proteins
Keywords	covid19
Language	English
Publishing date	2020-09-06
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649576-4
ISSN	2192-2659 ; 2192-2640
ISSN (online)	2192-2659
ISSN	2192-2640
DOI	10.1002/adhm.202001111
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Article ; Online: Severe Acute Respiratory Syndrome Coronavirus 2 Antigens as Targets of Antibody Responses.

Ogata, Alana F / Lazarovits, Roey / Uwamanzu-Nna, Augusta / Gilboa, Tal / Cheng, Chi-An / Walt, David R

Clinics in laboratory medicine

2021 Volume 42, Issue 1, Page(s) 97–109

Abstract: Humoral immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during acute infection and convalescence has been widely studied since March 2020. In this review, the authors summarize literature on humoral responses to SARS-CoV-2 ... ...

Abstract	Humoral immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during acute infection and convalescence has been widely studied since March 2020. In this review, the authors summarize literature on humoral responses to SARS-CoV-2 antigens with a focus on spike, nucleocapsid, and the receptor-binding domain as targets of antibody responses. They highlight serologic studies during acute SARS-CoV-2 infection and discuss the clinical relevance of antibody levels in COVID-19 progression. Antibody responses in pediatric COVID-19 patients are also reviewed. Finally, the authors discuss antibody responses during convalescence and their role in protection from SARS-CoV-2 reinfection.
MeSH term(s)	Antibodies, Viral ; Antibody Formation ; COVID-19 ; Child ; Humans ; Immunity, Humoral ; SARS-CoV-2
Chemical Substances	Antibodies, Viral
Language	English
Publishing date	2021-11-03
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	604580-7
ISSN	1557-9832 ; 0272-2712
ISSN (online)	1557-9832
ISSN	0272-2712
DOI	10.1016/j.cll.2021.10.002
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Jg. 1995 - 2021: Lesesall (1.OG)
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Article: Role of Molecular Modification and Protein Folding in the Nucleation and Growth of Protein-Metal-Organic Frameworks.

Carpenter, Brooke P / Talosig, A Rain / Mulvey, Justin T / Merham, Jovany G / Esquivel, Jamie / Rose, Ben / Ogata, Alana F / Fishman, Dmitry A / Patterson, Joseph P

Chemistry of materials : a publication of the American Chemical Society

2022 Volume 34, Issue 18, Page(s) 8336–8344

Abstract: Metal-organic frameworks (MOFs) are a class of porous nanomaterials that have been extensively studied as enzyme immobilization substrates. During in situ immobilization, MOF nucleation is driven by biomolecules with low isoelectric points. Investigation ...

Abstract	Metal-organic frameworks (MOFs) are a class of porous nanomaterials that have been extensively studied as enzyme immobilization substrates. During in situ immobilization, MOF nucleation is driven by biomolecules with low isoelectric points. Investigation of how biomolecules control MOF self-assembly mechanisms on the molecular level is key to designing nanomaterials with desired physical and chemical properties. Here, we demonstrate how molecular modifications of bovine serum albumin (BSA) with fluorescein isothiocyanate (FITC) can affect MOF crystal size, morphology, and encapsulation efficiency. Final crystal properties are characterized using scanning electron microscopy (SEM), powder X-ray diffraction (PXRD), fluorescent microscopy, and fluorescence spectroscopy. To probe MOF self-assembly, in situ experiments were performed using cryogenic transmission electron microscopy (cryo-TEM) and X-ray diffraction (XRD). Biophysical characterization of BSA and FITC-BSA was performed using ζ potential, mass spectrometry, circular dichroism studies, fluorescence spectroscopy, and Fourier transform infrared (FTIR) spectroscopy. The combined data reveal that protein folding and stability within amorphous precursors are contributing factors in the rate, extent, and mechanism of crystallization. Thus, our results suggest molecular modifications as promising methods for fine-tuning protein@MOFs' nucleation and growth.
Language	English
Publishing date	2022-09-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	1500399-1
ISSN	1520-5002 ; 0897-4756
ISSN (online)	1520-5002
ISSN	0897-4756
DOI	10.1021/acs.chemmater.2c01903
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Article ; Online: Direct Observation of Amorphous Precursor Phases in the Nucleation of Protein-Metal-Organic Frameworks.

Ogata, Alana F / Rakowski, Alexander M / Carpenter, Brooke P / Fishman, Dmitry A / Merham, Jovany G / Hurst, Paul J / Patterson, Joseph P

Journal of the American Chemical Society

2020 Volume 142, Issue 3, Page(s) 1433–1442

Abstract: Protein-metal-organic frameworks (p-MOFs) are a prototypical example of how synthetic biological hybrid systems can be used to develop next-generation materials. Controlling p-MOF formation enables the design of hybrid materials with enhanced biological ... ...

Abstract	Protein-metal-organic frameworks (p-MOFs) are a prototypical example of how synthetic biological hybrid systems can be used to develop next-generation materials. Controlling p-MOF formation enables the design of hybrid materials with enhanced biological activity and high stability. However, such control is yet to be fully realized due to an insufficient understanding of the governing nucleation and growth mechanisms in p-MOF systems. The structural evolution of p-MOFs was probed by cryo-transmission electron microscopy, revealing nonclassical pathways via dissolution-recrystallization of highly hydrated amorphous particles and solid-state transformation of a protein-rich amorphous phase. On the basis of these data, we propose a general description of p-MOF crystallization which is best characterized by particle aggregation and colloidal theory for future synthetic strategies.
MeSH term(s)	Cryoelectron Microscopy ; Crystallization ; Metal-Organic Frameworks/chemistry ; Proteins/chemistry
Chemical Substances	Metal-Organic Frameworks ; Proteins
Language	English
Publishing date	2020-01-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.9b11371
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Article ; Online: Rapid, Wet Chemical Fabrication of Radial Junction Electroluminescent Wires.

Qiao, Shaopeng / Ogata, Alana F / Jha, Gaurav / Chattopadhyay, Aurnov / Penner, Reginald M

ACS applied materials & interfaces

2018 Volume 10, Issue 41, Page(s) 35344–35353

Abstract: A wet chemical process involving two electrodeposition steps followed by a solution casting step, the "EESC" process, is described for the fabrication of electroluminescent, radial junction wires. EESC is demonstrated by assembling three well-studied ... ...

Abstract	A wet chemical process involving two electrodeposition steps followed by a solution casting step, the "EESC" process, is described for the fabrication of electroluminescent, radial junction wires. EESC is demonstrated by assembling three well-studied nanocrystalline (or amorphous) materials: Au, CdSe, and poly(3,4-ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS). The tri-layered device architecture produced by EESC minimizes the influence of an electrically resistive CdSe emitter layer by using a highly conductive gold nanowire that serves as both a current collector and a negative electrode. Hole injection, at a high barrier CdSe-PEDOT:PSS interface (ϕ
Language	English
Publishing date	2018-10-04
Publishing country	United States
Document type	Journal Article
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.8b10855
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