1
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Maughan MN, Gadberry JD, Sharpes CE, Buckley PE, Miklos AE, Furton KG, DeGreeff LE, Hall NJ, Greubel RR, Sloan KB. Calibrating canines-a universal detector calibrant for detection dogs. Front Allergy 2024; 5:1366596. [PMID: 38533355 PMCID: PMC10963624 DOI: 10.3389/falgy.2024.1366596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024] Open
Abstract
Since the advent of the Universal Detector Calibrant (UDC) by scientists at Florida International University in 2013, this tool has gone largely unrecognized and under-utilized by canine scent detection practitioners. The UDC is a chemical that enables reliability testing of biological and instrumental detectors. Training a biological detector, such as a scent detection canine, to respond to a safe, non-target, and uncommon compound has significant advantages. For example, if used prior to a search, the UDC provides the handler with the ability to confirm the detection dog is ready to work without placing target odor on site (i.e., a positive control), thereby increasing handler confidence in their canine and providing documentation of credibility that can withstand legal scrutiny. This review describes the UDC, summarizes its role in canine detection science, and addresses applications for UDC within scent detection canine development, training, and testing.
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Affiliation(s)
| | | | | | - Patricia E. Buckley
- Biochemistry Branch, U.S. Army DEVCOM Chemical Biological Center, Aberdeen Proving Ground, MD, United States
| | - Aleksandr E. Miklos
- Biochemistry Branch, U.S. Army DEVCOM Chemical Biological Center, Aberdeen Proving Ground, MD, United States
| | - Kenneth G. Furton
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States
| | - Lauryn E. DeGreeff
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States
- Formerly of the U.S. Naval Research Laboratory, Washington, DC, United States
| | - Nathaniel J. Hall
- Department of Animal and Food Science, Texas Tech University, Lubbock, TX, United States
| | | | - Katylynn B. Sloan
- Technical Services Division, United States Secret Service, Washington, DC, United States
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2
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Beabout K, Ehrenworth Breedon AM, Blum SM, Miklos AE, Lux MW, Chávez JL, Goodson MS. Detection of Bile Acids in Complex Matrices Using a Transcription Factor-Based Biosensor. ACS Biomater Sci Eng 2023; 9:5151-5162. [PMID: 36475595 DOI: 10.1021/acsbiomaterials.2c01006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bile acids play an important role in digestion and human health, are found throughout the gastrointestinal tract, and are excreted in feces. Therefore, bile acids are promising biomarkers for monitoring health and detecting fecal contamination in water sources. Here, we engineered a bile acid sensor by expressing the transcription factor BreR, a TetR-like repressor from Vibrio cholorae, in Escherichia coli. The sensor was further optimized by screening a promoter library. To further characterize the BreR sensor and increase its utility, we moved expression to a cell-free expression (CFE) system, resulting in an approximately 3 orders of magnitude increase in deoxycholic acid sensitivity. We next optimized this sensor to detect bile acids in fecal water, wastewater, and serum and transferred the CFE sensor to a paper-based assay to enhance fieldability.
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Affiliation(s)
- Kathryn Beabout
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
- UES, Inc., Dayton, Ohio 45432, United States
| | - Amy M Ehrenworth Breedon
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
- UES, Inc., Dayton, Ohio 45432, United States
| | - Steven M Blum
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
| | - Aleksandr E Miklos
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
| | - Matthew W Lux
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
| | - Jorge L Chávez
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Michael S Goodson
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
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3
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McDonald ND, Rhea KA, Berk KL, Zacharko JL, Miklos AE. Cell-Free Protein Systems from Yersinia pestis are Functional and Growth-Temperature Dependent. ACS Synth Biol 2021; 10:3604-3607. [PMID: 34854671 DOI: 10.1021/acssynbio.1c00505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cellular lysates capable of transcription and translation have become valuable tools for prototyping genetic circuits, screening engineered functional parts, and producing biological components. Here we report that lysates derived from Yersinia pestis CO92- are functional and can utilize both the E. coli σ70 and the bacteriophage T7 promoter systems to produce green fluorescent protein (GFP). Because of the natural lifestyle of Y. pestis, lysates were produced from cultures grown at 21 °C, 26 °C, and 37 °C to mimic the infection cycle. Regardless of the promoter system the GFP production from 37 °C was the most productive and the 26 °C lysate was the least. When reactions are initiated with 5 nM of DNA, the GFP output of the 37 °C lysate is comparable with the productivity of other non-E. coli systems. The data we present demonstrate that, without genetic modification to enhance productivity, cell-free extracts from Y. pestis are functional and dependent on the temperature at which the bacterium was grown.
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Affiliation(s)
- Nathan D. McDonald
- U.S. Army DEVCOM Chemical Biological Center, Aberdeen Proving Ground, Edgewood Area, Maryland 21010, United States
| | - Katherine A. Rhea
- U.S. Army DEVCOM Chemical Biological Center, Aberdeen Proving Ground, Edgewood Area, Maryland 21010, United States
| | - Kimberly L. Berk
- U.S. Army DEVCOM Chemical Biological Center, Aberdeen Proving Ground, Edgewood Area, Maryland 21010, United States
| | - Julie L. Zacharko
- U.S. Army DEVCOM Chemical Biological Center, Aberdeen Proving Ground, Edgewood Area, Maryland 21010, United States
| | - Aleksandr E. Miklos
- U.S. Army DEVCOM Chemical Biological Center, Aberdeen Proving Ground, Edgewood Area, Maryland 21010, United States
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4
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Phillips DA, Zacharoff LA, Hampton CM, Chong GW, Malanoski AP, Metskas LA, Xu S, Bird LJ, Eddie BJ, Miklos AE, Jensen GJ, Drummy LF, El-Naggar MY, Glaven SM. A bacterial membrane sculpting protein with BAR domain-like activity. eLife 2021; 10:60049. [PMID: 34643180 PMCID: PMC8687657 DOI: 10.7554/elife.60049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/12/2021] [Indexed: 11/13/2022] Open
Abstract
Bin/Amphiphysin/RVS (BAR) domain proteins belong to a superfamily of coiled-coil proteins influencing membrane curvature in eukaryotes and are associated with vesicle biogenesis, vesicle-mediated protein trafficking, and intracellular signaling. Here, we report a bacterial protein with BAR domain-like activity, BdpA, from Shewanella oneidensis MR-1, known to produce redox-active membrane vesicles and micrometer-scale outer membrane extensions (OMEs). BdpA is required for uniform size distribution of membrane vesicles and influences scaffolding of OMEs into a consistent diameter and curvature. Cryo-TEM reveals that a strain lacking BdpA produces lobed, disordered OMEs rather than membrane tubules or narrow chains produced by the wild-type strain. Overexpression of BdpA promotes OME formation during planktonic growth of S. oneidensis where they are not typically observed. Heterologous expression results in OME production in Marinobacter atlanticus and Escherichia coli. Based on the ability of BdpA to alter membrane architecture in vivo, we propose that BdpA and its homologs comprise a newly identified class of bacterial BAR domain-like proteins.
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Affiliation(s)
- Daniel A Phillips
- Oak Ridge Institute for Science and Education / US Army DEVCOM Chemical Biological Center, Aberdeen Proving Grounds, United States
| | - Lori A Zacharoff
- Department of Physics and Astronomy, University of Southern California, Los Angeles, United States
| | - Cheri M Hampton
- Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, Dayton, United States
| | - Grace W Chong
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Anthony P Malanoski
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, United States
| | - Lauren Ann Metskas
- Biological Sciences, Chemistry, California Institute of Technology, Pasadena, United States
| | - Shuai Xu
- Department of Physics and Astronomy, University of Southern California, Los Angeles, United States
| | - Lina J Bird
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, United States
| | - Brian J Eddie
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, United States
| | - Aleksandr E Miklos
- BioSciences Division, BioChemistry Branch, US Army DEVCOM Chemical Biological Center, Aberdeen Proving Ground, United States
| | - Grant J Jensen
- Biology and Bioengineering, California Institute of Technology, Pasadena, United States
| | - Lawrence F Drummy
- Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, Dayton, United States
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, Biological Sciences, and Chemistry, University of Southern California, Los Angeles, United States
| | - Sarah M Glaven
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, United States
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5
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Hofmann ER, Davidson C, Chen H, Zacharko M, Dorton JE, Kilper GK, Graves C, Miklos AE, Rhea K, Ma J, Goodwin BG, Sozhamannan S. Blind Spot: A Braille Patterned Novel Multiplex Lateral Flow Immunoassay Sensor Array for the Detection of Biothreat Agents. ACS Omega 2021; 6:22700-22708. [PMID: 34514241 PMCID: PMC8427625 DOI: 10.1021/acsomega.1c02938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/10/2021] [Indexed: 05/15/2023]
Abstract
Lateral flow immunoassays (LFIs) are simple, point-of-care diagnostic devices used for detecting biological agents or other analytes of interest in a sample. LFIs are predominantly singleplex assays, interrogating one target analyte at a time. There is a need for multiplex LFI devices, e.g., a syndromic panel to differentiate pathogens causing diseases exhibiting similar symptoms. Multiplex LFI devices would be especially valuable in instances where sample quantity is limiting and reducing assay time and costs is critical. There are limitations to the design parameters and performance characteristics of a multiplex LFI assay with many horizontal test lines due to constraints in capillary flow dynamics. To address some of the performance issues, we have developed a spot array multiplex LFI using Braille format (hence called Blind Spot) and a sensor, MACAW (Modular Automated Colorimetric Analyses Widget), that can analyze and interpret the results. As a proof of concept, we created a multiplex toxin panel, for detecting three toxins, using two letter codes for each. The results indicated that the six-plex, triple toxin assay performs as well as singleplex assays. The sensor-based calls are better compared to human interpretation in discriminating and interpreting ambiguous test results correctly especially at lower antigen concentrations and from strips with blemishes.
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Affiliation(s)
- E. Randal Hofmann
- EXCET,
Inc., Springfield, Virginia 22150, United States
- US
Army Combat Capabilities Development Command, Chemical Biological
Center, Edgewood, Maryland 21010, United States
| | | | - Hsiu Chen
- Maxim
Biomedical, Inc., Rockville, Maryland 20850, United States
| | - Melody Zacharko
- US
Army Combat Capabilities Development Command, Chemical Biological
Center, Edgewood, Maryland 21010, United States
| | | | | | | | - Aleksandr E. Miklos
- US
Army Combat Capabilities Development Command, Chemical Biological
Center, Edgewood, Maryland 21010, United States
| | - Katherine Rhea
- EXCET,
Inc., Springfield, Virginia 22150, United States
- US
Army Combat Capabilities Development Command, Chemical Biological
Center, Edgewood, Maryland 21010, United States
| | - Joe Ma
- Maxim
Biomedical, Inc., Rockville, Maryland 20850, United States
| | - Bruce G. Goodwin
- Defense
Biological Product Assurance Office (DBPAO), Joint Program Executive
Office (JPEO) for Chemical, Biological, Radiological and Nuclear Defense
(CBRND) Joint Project Lead (JPL) CBRND Enabling Biotechnologies (EB), Frederick, Maryland 21704, United States
| | - Shanmuga Sozhamannan
- Defense
Biological Product Assurance Office (DBPAO), Joint Program Executive
Office (JPEO) for Chemical, Biological, Radiological and Nuclear Defense
(CBRND) Joint Project Lead (JPL) CBRND Enabling Biotechnologies (EB), Frederick, Maryland 21704, United States
- Logistics
Management Institute, Tysons, Virginia 22102, United States
- . Phone: 301 619 8430
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6
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Blum SM, Lee MS, Mgboji GE, Funk VL, Beabout K, Harbaugh SV, Roth PA, Liem AT, Miklos AE, Emanuel PA, Walper SA, Chávez JL, Lux MW. Impact of Porous Matrices and Concentration by Lyophilization on Cell-Free Expression. ACS Synth Biol 2021; 10:1116-1131. [PMID: 33843211 DOI: 10.1021/acssynbio.0c00634] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cell-free expression systems have drawn increasing attention as a tool to achieve complex biological functions outside of the cell. Several applications of the technology involve the delivery of functionality to challenging environments, such as field-forward diagnostics or point-of-need manufacturing of pharmaceuticals. To achieve these goals, cell-free reaction components are preserved using encapsulation or lyophilization methods, both of which often involve an embedding of components in porous matrices like paper or hydrogels. Previous work has shown a range of impacts of porous materials on cell-free expression reactions. Here, we explored a panel of 32 paperlike materials and 5 hydrogel materials for the impact on reaction performance. The screen included a tolerance to lyophilization for reaction systems based on both cell lysates and purified expression components. For paperlike materials, we found that (1) materials based on synthetic polymers were mostly incompatible with cell-free expression, (2) lysate-based reactions were largely insensitive to the matrix for cellulosic and microfiber materials, and (3) purified systems had an improved performance when lyophilized in cellulosic but not microfiber matrices. The impact of hydrogel materials ranged from completely inhibitory to a slight enhancement. The exploration of modulating the rehydration volume of lyophilized reactions yielded reaction speed increases using an enzymatic colorimetric reporter of up to twofold with an optimal ratio of 2:1 lyophilized reaction to rehydration volume for the lysate system and 1.5:1 for the purified system. The effect was independent of the matrices assessed. Testing with a fluorescent nonenzymatic reporter and no matrix showed similar improvements in both yields and reaction speeds for the lysate system and yields but not reaction speeds for the purified system. We finally used these observations to show an improved performance of two sensors that span reaction types, matrix, and reporters. In total, these results should enhance efforts to develop field-forward applications of cell-free expression systems.
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Affiliation(s)
- Steven M. Blum
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
| | - Marilyn S. Lee
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
| | - Glory E. Mgboji
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee 37830-6209, United States
| | - Vanessa L. Funk
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
| | - Kathryn Beabout
- UES, Inc., Dayton, Ohio 45432, United States
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Svetlana V. Harbaugh
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Pierce A. Roth
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
- DCS Corporation, 4696 Millenium Drive, Suite 450, Belcamp, Maryland 21017, United States
| | - Alvin T. Liem
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
- DCS Corporation, 4696 Millenium Drive, Suite 450, Belcamp, Maryland 21017, United States
| | - Aleksandr E. Miklos
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
| | - Peter A. Emanuel
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
| | - Scott A. Walper
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Jorge Luis Chávez
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Matthew W. Lux
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
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7
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Berk KL, Blum SM, Funk VL, Sun Y, Yang IY, Gostomski MV, Roth PA, Liem AT, Emanuel PA, Hogan ME, Miklos AE, Lux MW. Rapid Visual Authentication Based on DNA Strand Displacement. ACS Appl Mater Interfaces 2021; 13:19476-19486. [PMID: 33852293 DOI: 10.1021/acsami.1c02429] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Novel ways to track and verify items of a high value or security is an ever-present need. Taggants made from deoxyribonucleic acid (DNA) have several advantageous properties, such as high information density and robust synthesis; however, existing methods require laboratory techniques to verify, limiting applications. Here, we leverage DNA nanotechnology to create DNA taggants that can be validated in the field in seconds to minutes with a simple equipment. The system is driven by toehold-mediated strand-displacement reactions where matching oligonucleotide sequences drive the generation of a fluorescent signal through the potential energy of base pairing. By pooling different "input" oligonucleotide sequences in a taggant and spatially separating "reporter" oligonucleotide sequences on a paper ticket, unique, sequence-driven patterns emerge for different taggant formulations. Algorithmically generated oligonucleotide sequences show no crosstalk and ink-embedded taggants maintain activity for at least 99 days at 60 °C (equivalent to nearly 2 years at room temperature). The resulting fluorescent signals can be analyzed by the eye or a smartphone when paired with a UV flashlight and filtered glasses.
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Affiliation(s)
- Kimberly L Berk
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
| | - Steven M Blum
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
| | - Vanessa L Funk
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
| | - Yuhua Sun
- Applied DNA Sciences, Stony Brook, New York 11790, United States
| | - In-Young Yang
- Applied DNA Sciences, Stony Brook, New York 11790, United States
| | - Mark V Gostomski
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
| | - Pierce A Roth
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
- DCS Corporation, Belcamp, Maryland 21017, United States
| | - Alvin T Liem
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
- DCS Corporation, Belcamp, Maryland 21017, United States
| | - Peter A Emanuel
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
| | - Michael E Hogan
- Applied DNA Sciences, Stony Brook, New York 11790, United States
| | - Aleksandr E Miklos
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
| | - Matthew W Lux
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
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8
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Cole SD, Miklos AE, Chiao AC, Sun ZZ, Lux MW. Methodologies for preparation of prokaryotic extracts for cell-free expression systems. Synth Syst Biotechnol 2020; 5:252-267. [PMID: 32775710 PMCID: PMC7398980 DOI: 10.1016/j.synbio.2020.07.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/19/2022] Open
Abstract
Cell-free systems that mimic essential cell functions, such as gene expression, have dramatically expanded in recent years, both in terms of applications and widespread adoption. Here we provide a review of cell-extract methods, with a specific focus on prokaryotic systems. Firstly, we describe the diversity of Escherichia coli genetic strains available and their corresponding utility. We then trace the history of cell-extract methodology over the past 20 years, showing key improvements that lower the entry level for new researchers. Next, we survey the rise of new prokaryotic cell-free systems, with associated methods, and the opportunities provided. Finally, we use this historical perspective to comment on the role of methodology improvements and highlight where further improvements may be possible.
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Affiliation(s)
- Stephanie D. Cole
- US Army Combat Capabilities Development Command Chemical Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
| | - Aleksandr E. Miklos
- US Army Combat Capabilities Development Command Chemical Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
| | - Abel C. Chiao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Synvitrobio Inc., San Francisco, CA, USA
| | - Zachary Z. Sun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Synvitrobio Inc., San Francisco, CA, USA
| | - Matthew W. Lux
- US Army Combat Capabilities Development Command Chemical Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
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9
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Davidson CE, Dixon MM, Williams BR, Kilper GK, Lim SH, Martino RA, Rhodes P, Hulet MS, Miles RW, Samuels AC, Emanuel PA, Miklos AE. Detection of Chemical Warfare Agents by Colorimetric Sensor Arrays. ACS Sens 2020; 5:1102-1109. [PMID: 32212640 DOI: 10.1021/acssensors.0c00042] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We report the successful use of colorimetric arrays to identify chemical warfare agents (CWAs). Methods were developed to interpret and analyze a 73-indicator array with an entirely automated workflow. Using a cross-validated first-nearest-neighbor algorithm for assessing detection and identification performances on 632 exposures, at 30 min postexposure we report, on average, 78% correct chemical identification, 86% correct class-level identification, and 96% correct red light/green light (agent versus non-agent) detection. Of 174 total independent agent test exposures, 164 were correctly identified from a 30 min exposure in the red light/green light context, yielding a 94% correct identification of CWAs. Of 149 independent non-agent exposures, 139 were correctly identified at 30 min in the red light/green light context, yielding a 7% false alarm rate. We find that this is a promising approach for the development of a miniaturized, field-portable analytical equipment suitable for soldiers and first responders.
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Affiliation(s)
- Charles E. Davidson
- Science and Technology Corporation, 111 C Bata Boulevard, Belcamp, Maryland 21017, United States
| | - Melissa M. Dixon
- U.S. Army CCDC Chemical Biological Center, Aberdeen Proving Ground, Aberdeen, Maryland 21010, United States
| | - Barry R. Williams
- Leidos, 3465 Box Hill Corporate Center Drive, Abingdon, Maryland 21009, United States
| | - Gary K. Kilper
- Excet, 6225 Brandon Avenue, Suite 360, Springfield, Virginia 22150, United States
| | - Sung H. Lim
- iSense, 855 Maude Avenue, Mountain View, California 94043, United States
| | - Raymond A. Martino
- iSense, 855 Maude Avenue, Mountain View, California 94043, United States
| | - Paul Rhodes
- iSense, 855 Maude Avenue, Mountain View, California 94043, United States
| | - Melissa S. Hulet
- Leidos, 3465 Box Hill Corporate Center Drive, Abingdon, Maryland 21009, United States
| | - Ronald W. Miles
- U.S. Army CCDC Chemical Biological Center, Aberdeen Proving Ground, Aberdeen, Maryland 21010, United States
| | - Alan C. Samuels
- U.S. Army CCDC Chemical Biological Center, Aberdeen Proving Ground, Aberdeen, Maryland 21010, United States
| | - Peter A. Emanuel
- U.S. Army CCDC Chemical Biological Center, Aberdeen Proving Ground, Aberdeen, Maryland 21010, United States
| | - Aleksandr E. Miklos
- U.S. Army CCDC Chemical Biological Center, Aberdeen Proving Ground, Aberdeen, Maryland 21010, United States
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10
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Lee J, Der BS, Karamitros CS, Li W, Marshall NM, Lungu OI, Miklos AE, Xu J, Kang TH, Lee CH, Tan B, Hughes RA, Jung ST, Ippolito GC, Gray JJ, Zhang Y, Kuhlman B, Georgiou G, Ellington AD. Computer-based Engineering of Thermostabilized Antibody Fragments. AIChE J 2020; 66:e16864. [PMID: 32336757 PMCID: PMC7181397 DOI: 10.1002/aic.16864] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We used the molecular modeling program Rosetta to identify clusters of amino acid substitutions in antibody fragments (scFvs and scAbs) that improve global protein stability and resistance to thermal deactivation. Using this methodology, we increased the melting temperature (Tm) and resistance to heat treatment of an antibody fragment that binds to the Clostridium botulinum hemagglutinin protein (anti-HA33). Two designed antibody fragment variants with two amino acid replacement clusters, designed to stabilize local regions, were shown to have both higher Tm compared to the parental scFv and importantly, to retain full antigen binding activity after 2 hours of incubation at 70 °C. The crystal structure of one thermostabilized scFv variants was solved at 1.6 Å and shown to be in close agreement with the RosettaAntibody model prediction.
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Affiliation(s)
- Jiwon Lee
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755
| | - Bryan S. Der
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | | | - Wenzong Li
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Nicholas M. Marshall
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Oana I. Lungu
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Aleksandr E. Miklos
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, APGEA, MD 21010
| | - Jianqing Xu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MA 21218
| | - Tae Hyun Kang
- Biopharmaceutical Chemistry Major, School of Applied Chemistry, Kookmin University, Seongbuk-gu, Seoul 02707, Republic of Korea
| | - Chang-Han Lee
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Bing Tan
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Randall A. Hughes
- US Army Research Laboratory, Austin, TX 78712,Applied Research Laboratories, The University of Texas at Austin, Austin, TX 78712
| | - Sang Taek Jung
- Department of Biomedical Science, Graduate School of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Gregory C. Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MA 21218
| | - Yan Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | - George Georgiou
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712,Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712,Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712,To whom correspondence should be addressed: George Georgiou () and Andrew D. Ellington ()
| | - Andrew D. Ellington
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712,Department of Chemistry, The University of Texas at Austin, Austin, TX 78712,To whom correspondence should be addressed: George Georgiou () and Andrew D. Ellington ()
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11
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Rajagopalan S, Wang C, Yu K, Kuzin AP, Richter F, Lew S, Miklos AE, Matthews ML, Seetharaman J, Su M, Hunt JF, Cravatt BF, Baker D. Design of activated serine-containing catalytic triads with atomic-level accuracy. Nat Chem Biol 2014; 10:386-91. [PMID: 24705591 PMCID: PMC4048123 DOI: 10.1038/nchembio.1498] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 03/10/2014] [Indexed: 01/07/2023]
Abstract
A challenge in the computational design of enzymes is that multiple properties, including substrate binding, transition state stabilization and product release, must be simultaneously optimized, and this has limited the absolute activity of successful designs. Here, we focus on a single critical property of many enzymes: the nucleophilicity of an active site residue that initiates catalysis. We design proteins with idealized serine-containing catalytic triads and assess their nucleophilicity directly in native biological systems using activity-based organophosphate probes. Crystal structures of the most successful designs show unprecedented agreement with computational models, including extensive hydrogen bonding networks between the catalytic triad (or quartet) residues, and mutagenesis experiments demonstrate that these networks are critical for serine activation and organophosphate reactivity. Following optimization by yeast display, the designs react with organophosphate probes at rates comparable to natural serine hydrolases. Co-crystal structures with diisopropyl fluorophosphate bound to the serine nucleophile suggest that the designs could provide the basis for a new class of organophosphate capture agents.
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Affiliation(s)
- Sridharan Rajagopalan
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Chu Wang
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Kai Yu
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Alexandre P. Kuzin
- Northeast Structural Genomics Consortium, Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Florian Richter
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Graduate program in Biological Physics, Structure and Design, University of Washington, Seattle, Washington 98195, USA
| | - Scott Lew
- Northeast Structural Genomics Consortium, Department of Biological Sciences, Columbia University, New York, New York 10027
| | | | - Megan L. Matthews
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jayaraman Seetharaman
- Northeast Structural Genomics Consortium, Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Min Su
- Northeast Structural Genomics Consortium, Department of Biological Sciences, Columbia University, New York, New York 10027
| | - John. F. Hunt
- Northeast Structural Genomics Consortium, Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Benjamin F. Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Graduate program in Biological Physics, Structure and Design, University of Washington, Seattle, Washington 98195, USA,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
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12
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Der BS, Kluwe C, Miklos AE, Jacak R, Lyskov S, Gray JJ, Georgiou G, Ellington AD, Kuhlman B. Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability. PLoS One 2013; 8:e64363. [PMID: 23741319 PMCID: PMC3669367 DOI: 10.1371/journal.pone.0064363] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/11/2013] [Indexed: 12/29/2022] Open
Abstract
Reengineering protein surfaces to exhibit high net charge, referred to as “supercharging”, can improve reversibility of unfolding by preventing aggregation of partially unfolded states. Incorporation of charged side chains should be optimized while considering structural and energetic consequences, as numerous mutations and accumulation of like-charges can also destabilize the native state. A previously demonstrated approach deterministically mutates flexible polar residues (amino acids DERKNQ) with the fewest average neighboring atoms per side chain atom (AvNAPSA). Our approach uses Rosetta-based energy calculations to choose the surface mutations. Both protocols are available for use through the ROSIE web server. The automated Rosetta and AvNAPSA approaches for supercharging choose dissimilar mutations, raising an interesting division in surface charging strategy. Rosetta-supercharged variants of GFP (RscG) ranging from −11 to −61 and +7 to +58 were experimentally tested, and for comparison, we re-tested the previously developed AvNAPSA-supercharged variants of GFP (AscG) with +36 and −30 net charge. Mid-charge variants demonstrated ∼3-fold improvement in refolding with retention of stability. However, as we pushed to higher net charges, expression and soluble yield decreased, indicating that net charge or mutational load may be limiting factors. Interestingly, the two different approaches resulted in GFP variants with similar refolding properties. Our results show that there are multiple sets of residues that can be mutated to successfully supercharge a protein, and combining alternative supercharge protocols with experimental testing can be an effective approach for charge-based improvement to refolding.
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Affiliation(s)
- Bryan S. Der
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Christien Kluwe
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Aleksandr E. Miklos
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
- Applied Research Laboratories, University of Texas at Austin, Austin, Texas, United States of America
| | - Ron Jacak
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - George Georgiou
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Andrew D. Ellington
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
- Applied Research Laboratories, University of Texas at Austin, Austin, Texas, United States of America
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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13
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Abstract
As the availability of DNA sequence information has grown, so has the need to replicate DNA sequences synthetically. Synthetically produced DNA sequences allow the researcher to exert greater control over model systems and allow for the combinatorial design and construction of novel metabolic and regulatory pathways, as well as optimized protein-coding sequences for biotechnological applications. This utility has made synthetically produced DNA a hallmark of the molecular biosciences and a mainstay of synthetic biology. However, synthetically produced DNA has a significant shortcoming in that it typically has an error rate that is orders of magnitude higher when compared to DNA sequences derived directly from a biological source. This relatively high error rate adds to the cost and labor necessary to obtain sequence-verified clones from synthetically produced DNA sequences. This unit describes a protocol to enrich error-free sequences from a population of error-rich DNA via treatment with CEL I (Surveyor) endonuclease. This method is a straightforward and quick way of reducing the error content of synthetic DNA pools and reliably reduces the error rates by >6-fold per round of treatment.
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Affiliation(s)
- Randall A Hughes
- The University of Texas at Austin, Applied Research Laboratories, Department of Chemistry and Biochemistry, Center for Systems and Synthetic Biology, Austin, Texas, USA
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14
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Abstract
The availability of custom synthetic gene-length DNA products removes numerous bottlenecks in research efforts, making gene synthesis an increasingly common commercial service. However, the assembly of synthetic oligonucleotides into large, custom DNA constructs is not especially difficult, and performing "in-house" gene synthesis has time and cost advantages. This unit will treat both the concerns of design and physical assembly in gene synthesis, including how to design DNA sequences for synthesis and the design of overlapping oligonucleotide schemes to ensure facile assembly into the final product. Assembly is accomplished using a reliable series of PCR reactions, with a troubleshooting assembly protocol included, which not only assembles difficult sequences but allows identification of the source of a failure down to a pair of oligonucleotides.
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Affiliation(s)
- Aleksandr E Miklos
- The University of Texas at Austin, Applied Research Laboratories, Department of Chemistry and Biochemistry, Center for Systems and Synthetic Biology, Austin, Texas, USA
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15
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Miklos AE, Kluwe C, Der BS, Pai S, Sircar A, Hughes RA, Berrondo M, Xu J, Codrea V, Buckley PE, Calm AM, Welsh HS, Warner CR, Zacharko MA, Carney JP, Gray JJ, Georgiou G, Kuhlman B, Ellington AD. Structure-based design of supercharged, highly thermoresistant antibodies. ACTA ACUST UNITED AC 2012; 19:449-55. [PMID: 22520751 DOI: 10.1016/j.chembiol.2012.01.018] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 01/02/2012] [Accepted: 01/23/2012] [Indexed: 10/28/2022]
Abstract
Mutation of surface residues to charged amino acids increases resistance to aggregation and can enable reversible unfolding. We have developed a protocol using the Rosetta computational design package that "supercharges" proteins while considering the energetic implications of each mutation. Using a homology model, a single-chain variable fragment antibody was designed that has a markedly enhanced resistance to thermal inactivation and displays an unanticipated ≈30-fold improvement in affinity. Such supercharged antibodies should prove useful for assays in resource-limited settings and for developing reagents with improved shelf lives.
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Affiliation(s)
- Aleksandr E Miklos
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
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16
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Romero PA, Stone E, Lamb C, Chantranupong L, Krause A, Miklos AE, Hughes RA, Fechtel B, Ellington AD, Arnold FH, Georgiou G. SCHEMA-designed variants of human Arginase I and II reveal sequence elements important to stability and catalysis. ACS Synth Biol 2012; 1:221-8. [PMID: 22737599 DOI: 10.1021/sb300014t] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Arginases catalyze the divalent cation-dependent hydrolysis of L-arginine to urea and L-ornithine. There is significant interest in using arginase as a therapeutic antineogenic agent against L-arginine auxotrophic tumors and in enzyme replacement therapy for treating hyperargininemia. Both therapeutic applications require enzymes with sufficient stability under physiological conditions. To explore sequence elements that contribute to arginase stability we used SCHEMA-guided recombination to design a library of chimeric enzymes composed of sequence fragments from the two human isozymes Arginase I and II. We then developed a novel active learning algorithm that selects sequences from this library that are both highly informative and functional. Using high-throughput gene synthesis and our two-step active learning algorithm, we were able to rapidly create a small but highly informative set of seven enzymatically active chimeras that had an average variant distance of 40 mutations from the closest parent arginase. Within this set of sequences, linear regression was used to identify the sequence elements that contribute to the long-term stability of human arginase under physiological conditions. This approach revealed a striking correlation between the isoelectric point and the long-term stability of the enzyme to deactivation under physiological conditions.
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Affiliation(s)
| | | | | | | | - Andreas Krause
- Department of Computer Science, Swiss Federal Institute of Technology, Zurich, Switzerland
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17
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Xu J, Miklos AE, Hughes R, Kuhlman B, Georgiou G, Ellington AD, Gray JJ. A Systematic Computational Method to Predict and Enhance Antibody-Antigen Binding in the Absence of Antibody Crystal Structures. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.3382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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18
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Alicea I, Marvin JS, Miklos AE, Ellington AD, Looger LL, Schreiter ER. Structure of the Escherichia coli phosphonate binding protein PhnD and rationally optimized phosphonate biosensors. J Mol Biol 2011; 414:356-69. [PMID: 22019591 DOI: 10.1016/j.jmb.2011.09.047] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 09/25/2011] [Accepted: 09/28/2011] [Indexed: 12/17/2022]
Abstract
The phnD gene of Escherichia coli encodes the periplasmic binding protein of the phosphonate (Pn) uptake and utilization pathway. We have crystallized and determined structures of E. coli PhnD (EcPhnD) in the absence of ligand and in complex with the environmentally abundant 2-aminoethylphosphonate (2AEP). Similar to other bacterial periplasmic binding proteins, 2AEP binds near the center of mass of EcPhnD in a cleft formed between two lobes. Comparison of the open, unliganded structure with the closed 2AEP-bound structure shows that the two lobes pivot around a hinge by ~70° between the two states. Extensive hydrogen bonding and electrostatic interactions stabilize 2AEP, which binds to EcPhnD with low nanomolar affinity. These structures provide insight into Pn uptake by bacteria and facilitated the rational design of high signal-to-noise Pn biosensors based on both coupled small-molecule dyes and autocatalytic fluorescent proteins.
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Affiliation(s)
- Ismael Alicea
- Department of Chemistry, University of Puerto Rico, Río Piedras, San Juan, Puerto Rico 00931
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19
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Abstract
DNA synthesis techniques and technologies are quickly becoming a cornerstone of modern molecular biology and play a pivotal role in the field of synthetic biology. The ability to synthesize whole genes, novel genetic pathways, and even entire genomes is no longer the dream it was 30 years ago. Using little more than a thermocycler, commercially synthesized oligonucleotides, and DNA polymerases, a standard molecular biology laboratory can synthesize several kilobase pairs of synthetic DNA in a week using existing techniques. Herein, we review the techniques used in the generation of synthetic DNA, from the chemical synthesis of oligonucleotides to their assembly into long, custom sequences. Software and websites to facilitate the execution of these approaches are explored, and applications of DNA synthesis techniques to gene expression and synthetic biology are discussed. Finally, an example of automated gene synthesis from our own laboratory is provided.
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Affiliation(s)
- Randall A Hughes
- Applied Research Laboratories, The University of Texas at Austin, Austin, Texas, USA
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20
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Cuneo MJ, Changela A, Miklos AE, Beese LS, Krueger JK, Hellinga HW. Structural analysis of a periplasmic binding protein in the tripartite ATP-independent transporter family reveals a tetrameric assembly that may have a role in ligand transport. J Biol Chem 2008; 283:32812-20. [PMID: 18723845 DOI: 10.1074/jbc.m803595200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Several bacterial solute transport mechanisms involve members of the periplasmic binding protein (PBP) superfamily that bind and deliver ligand to integral membrane transport proteins in the ATP-binding cassette, tripartite tricarboxylate transporter, or tripartite ATP-independent (TRAP) families. PBPs involved in ATP-binding cassette transport systems have been well characterized, but only a few PBPs involved in TRAP transport have been studied. We have measured the thermal stability, determined the oligomerization state by small angle x-ray scattering, and solved the x-ray crystal structure to 1.9 A resolution of a TRAP-PBP (open reading frame tm0322) from the hyperthermophilic bacterium Thermotoga maritima (TM0322). The overall fold of TM0322 is similar to other TRAP transport related PBPs, although the structural similarity of backbone atoms (2.5-3.1 A root mean square deviation) is unusually low for PBPs within the same group. Individual monomers within the tetrameric asymmetric unit of TM0322 exhibit high root mean square deviation (0.9 A) to each other as a consequence of conformational heterogeneity in their binding pockets. The gel filtration elution profile and the small angle x-ray scattering analysis indicate that TM0322 assembles as dimers in solution that in turn assemble into a dimer of dimers in the crystallographic asymmetric unit. Tetramerization has been previously observed in another TRAP-PBP (the Rhodobacter sphaeroides alpha-keto acid-binding protein) where quaternary structure formation is postulated to be an important requisite for the transmembrane transport process.
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Affiliation(s)
- Matthew J Cuneo
- Department of Biochemistry, Duke University, Medical Center, Durham, North Carolina 27710, USA
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