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Your search keyword '"Machen, Alexandra"' showing total 19 results
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19 results on '"Machen, Alexandra"'

1. Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)

Author

Dampalla, Chamandi S., Miller, Matthew J., Kim, Yunjeong, Zabiegala, Alexandria, Nguyen, Harry Nhat, Madden, Trent K., Thurman, Hayden A., Machen, Alexandra J., Cooper, Anne, Liu, Lijun, Battaile, Kevin P., Lovell, Scott, Chang, Kyeong-Ok, and Groutas, William C.

Published
2023
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5. Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies

Author

Dampalla, Chamandi S., primary, Nguyen, Harry Nhat, additional, Rathnayake, Athri D., additional, Kim, Yunjeong, additional, Perera, Krishani Dinali, additional, Madden, Trent K., additional, Thurman, Hayden A., additional, Machen, Alexandra J., additional, Kashipathy, Maithri M., additional, Liu, Lijun, additional, Battaile, Kevin P., additional, Lovell, Scott, additional, Chang, Kyeong-Ok, additional, and Groutas, William C., additional

Published
2022
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8. Caught in the Act: Anthrax Toxin Translocation Complex Reveals insight into the Lethal Factor Unfolding and Refolding mechanism

Author

Machen, Alexandra J, Fisher, Mark T, and Freudenthal, Bret D

Abstract

Translocation is essential to the anthrax toxin mechanism. Protective antigen, the translocon component of this AB toxin, forms an oligomeric pore with three key clamp sites that aid in the efficient entry of lethal factor or edema factor, the enzymatic components of the toxin, into the cell. LF and EF translocate through the protective antigen pore with the pH gradient between the endosome and the cytosol acting as the driving force. Structural details of the translocation process have remained elusive despite their biological importance. To overcome the technical challenges of studying translocation intermediates, we developed a novel method to immobilize, transition, and stabilize anthrax toxin. Here, we report a cryoEM snapshot of PA pore translocating the N-terminal domain of LF. The resulting 3.1 and 3.2 Å structures of the complex trace LF N as it unfolds near the α clamp, translocates through the Φ clamp, and begins to refold in the charge clamp. In addition, helical density inside the β barrel channel suggests LF secondary structural elements begin to refold at the charge clamp site. We conclude the anthrax toxin uses an extended β barrel to efficiently fold the enzymatic payload prior to channel exit. This refolding mechanism has broader implications for pore length of other protein translocating toxins.

Published
2020
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14. Chaperonin-Based Biolayer Interferometry To Assess the Kinetic Stability of Metastable, Aggregation-Prone Proteins

Author

Lea, Wendy A., primary, O’Neil, Pierce T., additional, Machen, Alexandra J., additional, Naik, Subhashchandra, additional, Chaudhri, Tapan, additional, McGinn-Straub, Wesley, additional, Tischer, Alexander, additional, Auton, Matthew T., additional, Burns, Joshua R., additional, Baldwin, Michael R., additional, Khar, Karen R., additional, Karanicolas, John, additional, and Fisher, Mark T., additional

Published
2016
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18. In Vitro Motility Assays for Acinetobacter Species.

Author

Biswas I, Machen A, and Mettlach J

Subjects
Acinetobacter physiology, Bacteriological Techniques, Phenotype
Abstract

Bacteria belonging to genus Acinetobacter do not encode flagella and are characterized as a non-motile organism. However, several recent studies have demonstrated that Acinetobacter spp. display two types of motility: twitching and swarming. Twitching motility requires the presence of functional type IV pili and occurs on solid surfaces under humid conditions. The extension and the retraction of the pili allows the bacterium to move and spread. In contrast the exact molecular mechanism for swarming motility in Acinetobacter spp. is currently unknown; but it requires semisolid surfaces and humid conditions. Motility has been associated with the bacterial virulence; however, motility appears to be highly dependent on the experimental conditions and the isolate understudy. In this chapter we attempt to provide detailed methods for twitching and swarming motilities that are specific for Acinetobacter spp.

Published
2019
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19. Constructing Kinetically Controlled Denaturation Isotherms of Folded Proteins Using Denaturant-Pulse Chaperonin Binding.

Author

O'Neil PT, Machen AJ, Thompson JA, Wang W, Hoang QQ, Baldwin MR, Khar KR, Karanicolas J, and Fisher MT

Subjects
Biosensing Techniques, Cell Line, Data Analysis, Kinetics, Protein Aggregates, Protein Binding, Proteins metabolism, Software, User-Computer Interface, Protein Denaturation, Protein Folding, Proteins chemistry, Temperature
Abstract

Methods to assess the kinetic stability of proteins, particularly those that are aggregation prone, are very useful in establishing ligand induced stabilizing effects. Because aggregation prone proteins are by nature difficult to work with, most solution based methods are compromised by this inherent instability. Here, we describe a label-free method that examines the denaturation of immobilized proteins where the dynamic unfolded protein populations are captured and detected by chaperonin binding.

Published
2019
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