8 results on '"Karpos K"'
Search Results
2. Rhodopsin's Ultra-Fast Activation Dynamics in Bilayer and Micelle Environments
- Author
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Salas-Estrada, Leslie A., primary, Grant, Thomas D., additional, Perera, Suchithranga M., additional, Struts, Andrey V., additional, Chawla, Udeep, additional, Xu, Xiaolin, additional, Fried, Steven D., additional, Weerasinghe, Nipuna, additional, Mendez, D., additional, Alvarez, R., additional, Karpos, K., additional, Lisova, S., additional, Zaare, S., additional, Nazari, R., additional, Zatsepsin, N.A., additional, Singharoy, Abhishek, additional, Boutet, S., additional, Carbajo, S., additional, Hunter, M.S., additional, Liang, M., additional, Seaberg, M.D., additional, Fromme, Raimund, additional, Fromme, Petra, additional, Kirian, Richard A., additional, Brown, Michael F., additional, and Grossfield, Alan, additional more...
- Published
- 2020
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Catalog
3. Comprehensive characterization of gas dynamic virtual nozzles for x-ray free-electron laser experiments.
- Author
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Karpos K, Zaare S, Manatou D, Alvarez RC, Krishnan V, Ottmar C, Gilletti J, Pableo A, Doppler D, Ansari A, Nazari R, Ros A, and Kirian RA
- Abstract
We introduce a hardware-software system for rapidly characterizing liquid microjets for x-ray diffraction experiments. An open-source python-based software package allows for programmatic and automated data collection and analysis. We show how jet speed, length, and diameter are influenced by nozzle geometry, gas flow rate, liquid viscosity, and liquid flow rate. We introduce "jet instability" and "jet probability" metrics to help quantify the suitability of a given nozzle for x-ray diffraction experiments. Among our observations were pronounced improvements in jet stability and reliability when using asymmetric needle-tipped nozzles, which allowed for the production of microjects smaller than 250 nm in diameter, traveling faster than 120 m/s., Competing Interests: The authors have no conflicts to disclose., (© 2024 Author(s).) more...
- Published
- 2024
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4. Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme.
- Author
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Doppler D, Sonker M, Egatz-Gomez A, Grieco A, Zaare S, Jernigan R, Meza-Aguilar JD, Rabbani MT, Manna A, Alvarez RC, Karpos K, Cruz Villarreal J, Nelson G, Yang JH, Carrion J, Morin K, Ketawala GK, Pey AL, Ruiz-Fresneda MA, Pacheco-Garcia JL, Hermoso JA, Nazari R, Sierra R, Hunter MS, Batyuk A, Kupitz CJ, Sublett RE, Lisova S, Mariani V, Boutet S, Fromme R, Grant TD, Botha S, Fromme P, Kirian RA, Martin-Garcia JM, and Ros A more...
- Subjects
- Humans, Crystallography, X-Ray, Injections, NAD(P)H Dehydrogenase (Quinone), Proteins chemistry, Lasers
- Abstract
Droplet injection strategies are a promising tool to reduce the large amount of sample consumed in serial femtosecond crystallography (SFX) measurements at X-ray free electron lasers (XFELs) with continuous injection approaches. Here, we demonstrate a new modular microfluidic droplet injector (MDI) design that was successfully applied to deliver microcrystals of the human NAD(P)H:quinone oxidoreductase 1 (NQO1) and phycocyanin. We investigated droplet generation conditions through electrical stimulation for both protein samples and implemented hardware and software components for optimized crystal injection at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Stanford Linac Coherent Light Source (LCLS). Under optimized droplet injection conditions, we demonstrate that up to 4-fold sample consumption savings can be achieved with the droplet injector. In addition, we collected a full data set with droplet injection for NQO1 protein crystals with a resolution up to 2.7 Å, leading to the first room-temperature structure of NQO1 at an XFEL. NQO1 is a flavoenzyme associated with cancer, Alzheimer's and Parkinson's disease, making it an attractive target for drug discovery. Our results reveal for the first time that residues Tyr128 and Phe232, which play key roles in the function of the protein, show an unexpected conformational heterogeneity at room temperature within the crystals. These results suggest that different substates exist in the conformational ensemble of NQO1 with functional and mechanistic implications for the enzyme's negative cooperativity through a conformational selection mechanism. Our study thus demonstrates that microfluidic droplet injection constitutes a robust sample-conserving injection method for SFX studies on protein crystals that are difficult to obtain in amounts necessary for continuous injection, including the large sample quantities required for time-resolved mix-and-inject studies. more...
- Published
- 2023
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5. Electrically stimulated droplet injector for reduced sample consumption in serial crystallography.
- Author
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Sonker M, Doppler D, Egatz-Gomez A, Zaare S, Rabbani MT, Manna A, Cruz Villarreal J, Nelson G, Ketawala GK, Karpos K, Alvarez RC, Nazari R, Thifault D, Jernigan R, Oberthür D, Han H, Sierra R, Hunter MS, Batyuk A, Kupitz CJ, Sublett RE, Poitevin F, Lisova S, Mariani V, Tolstikova A, Boutet S, Messerschmidt M, Meza-Aguilar JD, Fromme R, Martin-Garcia JM, Botha S, Fromme P, Grant TD, Kirian RA, and Ros A more...
- Abstract
With advances in X-ray free-electron lasers (XFELs), serial femtosecond crystallography (SFX) has enabled the static and dynamic structure determination for challenging proteins such as membrane protein complexes. In SFX with XFELs, the crystals are typically destroyed after interacting with a single XFEL pulse. Therefore, thousands of new crystals must be sequentially introduced into the X-ray beam to collect full data sets. Because of the serial nature of any SFX experiment, up to 99% of the sample delivered to the X-ray beam during its "off-time" between X-ray pulses is wasted due to the intrinsic pulsed nature of all current XFELs. To solve this major problem of large and often limiting sample consumption, we report on improvements of a revolutionary sample-saving method that is compatible with all current XFELs. We previously reported 3D-printed injection devices coupled with gas dynamic virtual nozzles (GDVNs) capable of generating samples containing droplets segmented by an immiscible oil phase for jetting crystal-laden droplets into the path of an XFEL. Here, we have further improved the device design by including metal electrodes inducing electrowetting effects for improved control over droplet generation frequency to stimulate the droplet release to matching the XFEL repetition rate by employing an electrical feedback mechanism. We report the improvements in this electrically triggered segmented flow approach for sample conservation in comparison with a continuous GDVN injection using the microcrystals of lysozyme and 3-deoxy-D-manno-octulosonate 8-phosphate synthase and report the segmented flow approach for sample injection applied at the Macromolecular Femtosecond Crystallography instrument at the Linear Coherent Light Source for the first time., Competing Interests: A.E.G., J.C.V., and A.R. hold a patent on electrical droplet stimulation in a 3D-printed device., (© 2022 The Authors.) more...
- Published
- 2022
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6. Co-flow injection for serial crystallography at X-ray free-electron lasers.
- Author
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Doppler D, Rabbani MT, Letrun R, Cruz Villarreal J, Kim DH, Gandhi S, Egatz-Gomez A, Sonker M, Chen J, Koua FHM, Yang J, Youssef M, Mazalova V, Bajt S, Shelby ML, Coleman MA, Wiedorn MO, Knoska J, Schön S, Sato T, Hunter MS, Hosseinizadeh A, Kuptiz C, Nazari R, Alvarez RC, Karpos K, Zaare S, Dobson Z, Discianno E, Zhang S, Zook JD, Bielecki J, de Wijn R, Round AR, Vagovic P, Kloos M, Vakili M, Ketawala GK, Stander NE, Olson TL, Morin K, Mondal J, Nguyen J, Meza-Aguilar JD, Kodis G, Vaiana S, Martin-Garcia JM, Mariani V, Schwander P, Schmidt M, Messerschmidt M, Ourmazd A, Zatsepin N, Weierstall U, Bruce BD, Mancuso AP, Grant T, Barty A, Chapman HN, Frank M, Fromme R, Spence JCH, Botha S, Fromme P, Kirian RA, and Ros A more...
- Abstract
Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macro-molecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX., (© Diandra Doppler et al. 2022.) more...
- Published
- 2022
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7. The modified Shriners Hospitals for Children Greenville (mSHCG) multi-segment foot model provides clinically acceptable measurements of ankle and midfoot angles: A dual fluoroscopy study.
- Author
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Roach KE, Foreman KB, MacWilliams BA, Karpos K, Nichols J, and Anderson AE
- Subjects
- Ankle Joint anatomy & histology, Biomechanical Phenomena, Fluoroscopy, Foot anatomy & histology, Humans, Range of Motion, Articular, Reference Standards, Reproducibility of Results, Young Adult, Ankle Joint diagnostic imaging, Foot diagnostic imaging, Physical Therapy Modalities, Walking physiology
- Abstract
Background: Several multi-segment foot models have been developed to evaluate foot and ankle motion using skin-marker motion analysis. However, few multi-segment models have been evaluated against a reference standard to establish kinematic accuracy., Research Question: How accurately do skin-markers estimate foot and ankle motion for the modified Shriners Hospitals for Children Greenville (mSHCG) multi-segment foot model when compared against the reference standard, dual fluoroscopy (DF), during gait, in asymptomatic participants?, Methods: Five participants walked overground as full-body skin-marker trajectory data and DF images of the foot and shank were simultaneously acquired. Using the mSHCG model, ankle and midfoot angles were calculated throughout stance for both motion analysis techniques. Statistical parametric mapping assessed differences in joint angles and marker positions between skin-marker and DF motion analysis techniques. Paired t tests, and linear regression models were used to compare joint angles and range of motion (ROM) calculated from the two techniques., Results: In the coronal plane, the skin-marker model significantly overestimated ROM (p = 0.028). Further, the DF model midfoot ROM was significantly positively related to differences between DF and skin-marker midfoot angles (p = 0.035, adjusted R
2 = 0.76). In the sagittal plane, skin-markers underestimated ankle angles by as much as 7.26°, while midfoot angles were overestimated by as much as 9.01°. However, DF and skin-marker joint angles were not significantly different over stance. Skin-markers on the tibia, calcaneus, and fifth metatarsal had significantly different positions than the DF markers along the direction of walking for isolated portions that were less than 10 % of stance. Euclidean distances between DF and skin-markers positions were less than 9.36 mm., Significance: As the accuracy of the mSHCG model was formerly unknown, the results of this study provide ranges of confidence for key angles calculated by this model., (Copyright © 2021 Elsevier B.V. All rights reserved.) more...- Published
- 2021
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8. 3D printing of gas-dynamic virtual nozzles and optical characterization of high-speed microjets.
- Author
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Nazari R, Zaare S, Alvarez RC, Karpos K, Engelman T, Madsen C, Nelson G, Spence JCH, Weierstall U, Adrian RJ, and Kirian RA
- Abstract
Gas dynamic virtual nozzles (GDVNs) produce microscopic flow-focused liquid jets and droplets and play an important role at X-ray free-electron laser (XFEL) facilities where they are used to steer a stream of hydrated biomolecules into an X-ray focus during diffraction measurements. Highly stable and reproducible microjet and microdroplets are desired, as are flexible fabrication methods that enable integrated mixing microfluidics, droplet triggering mechanisms, laser illumination, and other customized features. In this study, we develop the use of high-resolution 3D nano-printing for the production of monolithic, asymmetric GDVN designs that are difficult to fabricate by other means. We also develop a dual-pulsed nanosecond image acquisition and analysis platform for the characterization of GDVN performance, including jet speed, length, diameter, and directionality, among others. We show that printed GDVNs can form microjets with very high degree of reproducibility, down to sub-micron diameters, and with water jet speeds beyond 170 m/s. more...
- Published
- 2020
- Full Text
- View/download PDF
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