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Abstract
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Adeno-associated
virus (AAV) has a single-stranded DNA genome encapsidated
in a small icosahedrally symmetric protein shell with 60 subunits.
AAV is the leading delivery vector in emerging gene therapy treatments
for inherited disorders, so its structure and molecular interactions
with human hosts are of intense interest. A wide array of electron
microscopic approaches have been used to visualize the virus and its
complexes, depending on the scientific question, technology available,
and amenability of the sample. Approaches range from subvolume tomographic
analyses of complexes with large and flexible host proteins to detailed
analysis of atomic interactions within the virus and with small ligands
at resolutions as high as 1.6 Å. Analyses have led to the reclassification
of glycan receptors as attachment factors, to structures with a new-found
receptor protein, to identification of the epitopes of antibodies,
and a new understanding of possible neutralization mechanisms. AAV
is now well-enough characterized that it has also become a model system
for EM methods development. Heralding a new era, cryo-EM is now also
being deployed as an analytic tool in the process development and
production quality control of high value pharmaceutical biologics,
namely AAV vectors.
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Affiliation(s)
- Scott M Stagg
- Department of Biological Sciences, Florida State University, Tallahassee, Florida 32306, United States.,Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States
| | - Craig Yoshioka
- Department of Biomedical Engineering, Oregon Health & Science University, Portland Oregon 97239, United States
| | - Omar Davulcu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Michael S Chapman
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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Atomic-resolution protein structure determination by cryo-EM. Nature 2020; 587:157-161. [DOI: 10.1038/s41586-020-2833-4] [Citation(s) in RCA: 269] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/14/2020] [Indexed: 01/09/2023]
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Xie Q, Yoshioka CK, Chapman MS. Adeno-Associated Virus (AAV-DJ)-Cryo-EM Structure at 1.56 Å Resolution. Viruses 2020; 12:E1194. [PMID: 33092282 PMCID: PMC7589773 DOI: 10.3390/v12101194] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 01/12/2023] Open
Abstract
Adeno-associated virus is the leading viral vector for gene therapy. AAV-DJ is a recombinant variant developed for tropism to the liver. The AAV-DJ structure has been determined to 1.56 Å resolution through cryo-electron microscopy (cryo-EM). Only apoferritin is reported in preprints at 1.6 Å or higher resolution, and AAV-DJ nearly matches the highest resolutions ever attained through X-ray diffraction of virus crystals. However, cryo-EM has the advantage that most of the hydrogens are clear, improving the accuracy of atomic refinement, and removing ambiguity in hydrogen bond identification. Outside of secondary structures where hydrogen bonding was predictable a priori, the networks of hydrogen bonds coming from direct observation of hydrogens and acceptor atoms are quite different from those inferred even at 2.8 Å resolution. The implications for understanding viral assembly mean that cryo-EM will likely become the favored approach for high resolution structural virology.
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Affiliation(s)
- Qing Xie
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA;
| | - Craig K. Yoshioka
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA;
| | - Michael S. Chapman
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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Bradley JA, Seidler GT, Cooper G, Vos M, Hitchcock AP, Sorini AP, Schlimmer C, Nagle KP. Comparative study of the valence electronic excitations of N2 by inelastic x-ray and electron scattering. PHYSICAL REVIEW LETTERS 2010; 105:053202. [PMID: 20867914 DOI: 10.1103/physrevlett.105.053202] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 06/23/2010] [Indexed: 05/29/2023]
Abstract
Bound-state, valence electronic excitation spectra of N2 are probed by nonresonant inelastic x-ray and electron scattering. Within usual theoretical treatments, dynamical structure factors derived from the two probes should be identical. However, we find strong disagreements outside the dipole scattering limit, even at high probe energies. This suggests an unexpectedly important contribution from intramolecular multiple scattering of the probe electron from core electrons or the nucleus. These effects should grow progressively stronger as the atomic number of the target species increases.
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Affiliation(s)
- J A Bradley
- Physics Department, University of Washington, Seattle, Washington 98195, USA
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Hutt PK, Islam MM, Rabheru A, McDowell MRC. Empirical tests of the electron-atom dispersion relation. ACTA ACUST UNITED AC 2001. [DOI: 10.1088/0022-3700/9/14/014] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Byron FW, Joachain CJ. Elastic scattering of electrons and positrons by atomic hydrogen and helium at intermediate and high energies. ACTA ACUST UNITED AC 2001. [DOI: 10.1088/0022-3700/10/2/010] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Ermolaev AM, Walters HRJ. Exact second Born amplitude for elastic electron-hydrogen scattering. ACTA ACUST UNITED AC 2001. [DOI: 10.1088/0022-3700/12/24/005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Heer FJD, McDowell MRC, Wagenaar RW. Numerical study of the dispersion relation for e--H scattering. ACTA ACUST UNITED AC 2001. [DOI: 10.1088/0022-3700/10/10/023] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Tayal SS, Tripathi AN, Srivastava MK. Comments on the eikonal-Born series approach to electron-atom scattering. ACTA ACUST UNITED AC 2001. [DOI: 10.1088/0022-3700/12/5/007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Wingerden BV, Heer FJD, Weigold E, Nygaard KJ. Elastic scattering of electrons by molecular and atomic hydrogen. ACTA ACUST UNITED AC 2001. [DOI: 10.1088/0022-3700/10/7/023] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Byron FW, Joachain CJ. A third-order optical potential theory for elastic scattering of electrons and positrons by atomic hydrogen. ACTA ACUST UNITED AC 1999. [DOI: 10.1088/0022-3700/14/14/015] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Ree JVD. Electron-hydrogen scattering calculations at energies between 13.6 and 60 eV including n=3 levels. ACTA ACUST UNITED AC 1999. [DOI: 10.1088/0022-3700/15/14/016] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Wyngaarden WLV, Walters HRJ. Elastic scattering and excitation of the 1s to 2s and 1s2p transitions in atomic hydrogen by electrons to medium to high energies. ACTA ACUST UNITED AC 1999. [DOI: 10.1088/0022-3700/19/6/014] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Byron FW, Joachain CJ, Potvliege RM. Elastic and inelastic scattering of electrons and positrons by atomic hydrogen at intermediate and high energies in the unitarised eikonal-Born series method. ACTA ACUST UNITED AC 1999. [DOI: 10.1088/0022-3700/18/8/018] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Byron FW, Joachain CJ, Potvliege RM. Unitarisation of the eikonal-Born series method for electron-atom and positron-atom collisions. ACTA ACUST UNITED AC 1999. [DOI: 10.1088/0022-3700/15/21/014] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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McCarthy IE, Saha BC, Stelbovics AT. Electron-hydrogen elastic scattering in intermediate energies. ACTA ACUST UNITED AC 1999. [DOI: 10.1088/0022-3700/15/11/007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Brandsden BH, Scott T, Shingal R, Roychoudhury RK. Elastic and inelastic scattering of electrons by atomic hydrogen at intermediate energies in a coupled-channel second-order potential model. ACTA ACUST UNITED AC 1999. [DOI: 10.1088/0022-3700/15/24/017] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Scott T, Bransden BH. A second-order potential for the elastic scattering of electrons by atomic hydrogen. ACTA ACUST UNITED AC 1999. [DOI: 10.1088/0022-3700/14/13/023] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Walters HRJ. Exact second Born exchange amplitude for elastic electron-hydrogen scattering. ACTA ACUST UNITED AC 1999. [DOI: 10.1088/0022-3700/13/24/004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Warner CD, King GC, Hammond P, Slevin J. Resonance structure in elastic scattering of electrons from atomic hydrogen. ACTA ACUST UNITED AC 1999. [DOI: 10.1088/0022-3700/19/20/012] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Kingston AE, Walters HRJ. Electron scattering by atomic hydrogen: the distorted-wave second Born approximation. ACTA ACUST UNITED AC 1999. [DOI: 10.1088/0022-3700/13/23/021] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Wang YD, Callaway J, Unnikrishnan K. Differential cross sections and angular-correlation parameters for the excitation of hydrogen atoms to n=3 and n=2 states by electron impact between 16 and 100 eV. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1994; 49:1854-1865. [PMID: 9910436 DOI: 10.1103/physreva.49.1854] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Bray I, Stelbovics AT. Convergent close-coupling calculations of electron-hydrogen scattering. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1992; 46:6995-7011. [PMID: 9908034 DOI: 10.1103/physreva.46.6995] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Shyn TW, Grafe A. Angular distribution of electrons elastically scattered from hydrogen atoms. II. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1992; 46:2949-2951. [PMID: 9908456 DOI: 10.1103/physreva.46.2949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Kim YH, Fox JL, Porter HS. Densities and vibrational distribution of H3+in the Jovian auroral ionosphere. ACTA ACUST UNITED AC 1992. [DOI: 10.1029/92je00454] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Bray I, Konovalov DA, McCarthy IE. Electron scattering by atomic hydrogen: Elastic and inelastic phenomena at 13.9-200 eV. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1991; 44:5586-5598. [PMID: 9906616 DOI: 10.1103/physreva.44.5586] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Bray I, Konovalov DA, McCarthy IE. Coupled-channel optical calculation of electron-hydrogen scattering: Elastic scattering from 0.5 to 30 eV. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1991; 43:5878-5885. [PMID: 9904916 DOI: 10.1103/physreva.43.5878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Bray I, Madison DH, McCarthy IE. Coupled-channel optical calculation of electron-hydrogen scattering: The distorted-wave optical potential. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1990; 41:5916-5928. [PMID: 9902991 DOI: 10.1103/physreva.41.5916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Madison DH, Bray I, McCarthy I. Effect of second-order exchange in electron-hydrogen scattering. PHYSICAL REVIEW LETTERS 1990; 64:2265-2268. [PMID: 10041630 DOI: 10.1103/physrevlett.64.2265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Bray I, Madison DH, McCarthy IE. Full optical potential for the electron-hydrogen entrance channel. PHYSICAL REVIEW. A, GENERAL PHYSICS 1989; 40:2820-2823. [PMID: 9902485 DOI: 10.1103/physreva.40.2820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Shyn TW, Cho SY. Angular distribution of electrons elastically scattered from hydrogen atoms. PHYSICAL REVIEW. A, GENERAL PHYSICS 1989; 40:1315-1320. [PMID: 9902265 DOI: 10.1103/physreva.40.1315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Callaway J, Unnikrishnan K. Optical-potential model calculation of electron-hydrogen elastic scattering at intermediate and high energies. PHYSICAL REVIEW. A, GENERAL PHYSICS 1989; 40:1660-1663. [PMID: 9902307 DOI: 10.1103/physreva.40.1660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Callaway J. Scattering of electrons by atomic hydrogen at intermediate energies: Elastic scattering and n=2 excitation from 12 to 54 eV. PHYSICAL REVIEW. A, GENERAL PHYSICS 1985; 32:775-783. [PMID: 9896125 DOI: 10.1103/physreva.32.775] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Bransden BH, McCarthy IE, Mitroy JD, Stelbovics AT. Extended coupled-channels calculations for electron-hydrogen scattering. PHYSICAL REVIEW. A, GENERAL PHYSICS 1985; 32:166-175. [PMID: 9896037 DOI: 10.1103/physreva.32.166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Fletcher GD, Alguard MJ, Gay TJ, Hughes VW, Wainwright PF, Lubell MS, Raith W. Experimental study of spin-exchange effects in elastic and ionizing collisions of polarized electrons with polarized hydrogen atoms. PHYSICAL REVIEW. A, GENERAL PHYSICS 1985; 31:2854-2884. [PMID: 9895840 DOI: 10.1103/physreva.31.2854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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