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Huang TC, Liang KH, Chang TJ, Hung KF, Wang ML, Cheng YF, Liao YT, Yang DM. Structure-based approaches against COVID-19. J Chin Med Assoc 2024; 87:139-141. [PMID: 38305483 DOI: 10.1097/jcma.0000000000001043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has had a major impact on human life. This review highlights the versatile roles of both classical and modern structure-based approaches for COVID-19. X-ray crystallography, nuclear magnetic resonance spectroscopy, and cryogenic electron microscopy are the three cornerstones of classical structural biology. These technologies have helped provide fundamental and detailed knowledge regarding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the related human host proteins as well as enabled the identification of its target sites, facilitating the cessation of its transmission. Further progress into protein structure modeling was made using modern structure-based approaches derived from homology modeling and integrated with artificial intelligence (AI), facilitating advanced computational simulation tools to actively guide the design of new vaccines and the development of anti-SARS-CoV-2 drugs. This review presents the practical contributions and future directions of structure-based approaches for COVID-19.
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Affiliation(s)
- Ta-Chou Huang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Kung-Hao Liang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Institute of Biomedical Informatics, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Tai-Jay Chang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Laboratory of Genome Research, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Kai-Feng Hung
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Mong-Lien Wang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Yen-Fu Cheng
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Yi-Ting Liao
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - De-Ming Yang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
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Liu Z, Gu KK, Shelby ML, Gilbile D, Lyubimov AY, Russi S, Cohen AE, Narayanasamy SR, Botha S, Kupitz C, Sierra RG, Poitevin F, Gilardi A, Lisova S, Coleman MA, Frank M, Kuhl TL. A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography. Acta Crystallogr D Struct Biol 2023; 79:944-952. [PMID: 37747292 PMCID: PMC10565732 DOI: 10.1107/s2059798323007027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 08/07/2023] [Indexed: 09/26/2023] Open
Abstract
Over the past two decades, serial X-ray crystallography has enabled the structure determination of a wide range of proteins. With the advent of X-ray free-electron lasers (XFELs), ever-smaller crystals have yielded high-resolution diffraction and structure determination. A crucial need to continue advancement is the efficient delivery of fragile and micrometre-sized crystals to the X-ray beam intersection. This paper presents an improved design of an all-polymer microfluidic `chip' for room-temperature fixed-target serial crystallography that can be tailored to broadly meet the needs of users at either synchrotron or XFEL light sources. The chips are designed to be customized around different types of crystals and offer users a friendly, quick, convenient, ultra-low-cost and robust sample-delivery platform. Compared with the previous iteration of the chip [Gilbile et al. (2021), Lab Chip, 21, 4831-4845], the new design eliminates cleanroom fabrication. It has a larger imaging area to volume, while maintaining crystal hydration stability for both in situ crystallization or direct crystal slurry loading. Crystals of two model proteins, lysozyme and thaumatin, were used to validate the effectiveness of the design at both synchrotron (lysozyme and thaumatin) and XFEL (lysozyme only) facilities, yielding complete data sets with resolutions of 1.42, 1.48 and 1.70 Å, respectively. Overall, the improved chip design, ease of fabrication and high modifiability create a powerful, all-around sample-delivery tool that structural biologists can quickly adopt, especially in cases of limited sample volume and small, fragile crystals.
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Affiliation(s)
- Zhongrui Liu
- Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA
| | - Kevin K. Gu
- Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA
| | - Megan L. Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Deepshika Gilbile
- Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA
| | - Artem Y. Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sankar Raju Narayanasamy
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Raymond G. Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Fredric Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Antonio Gilardi
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Matthew A. Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- Department of Radiation Oncology, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Matthias Frank
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Tonya L. Kuhl
- Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA
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5
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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, Ros A. Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme. LAB ON A CHIP 2023; 23:3016-3033. [PMID: 37294576 PMCID: PMC10503405 DOI: 10.1039/d3lc00176h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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.
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Affiliation(s)
- Diandra Doppler
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Alice Grieco
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain.
| | - Sahba Zaare
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Rebecca Jernigan
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Jose Domingo Meza-Aguilar
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Mohammad T Rabbani
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Abhik Manna
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Roberto C Alvarez
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Konstantinos Karpos
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Garrett Nelson
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Jay-How Yang
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Jackson Carrion
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Katherine Morin
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Gihan K Ketawala
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Angel L Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
| | - Miguel Angel Ruiz-Fresneda
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain.
| | - Juan Luis Pacheco-Garcia
- Departamento de Química Física, Universidad de Granada, Av. Fuentenueva s/n, 18071 Granada, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain.
| | - Reza Nazari
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Raymond Sierra
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Mark S Hunter
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Alexander Batyuk
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Christopher J Kupitz
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Robert E Sublett
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Stella Lisova
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Valerio Mariani
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, 955 Main St, Buffalo, NY, 14203, USA
| | - Sabine Botha
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Richard A Kirian
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Jose Manuel Martin-Garcia
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain.
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
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