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  • 1
    Publication Date: 2011-10-25
    Description: The manipulation of protein backbone structure to control interaction and function is a challenge for protein engineering. We integrated computational design with experimental selection for grafting the backbone and side chains of a two-segment HIV gp120 epitope, targeted by the cross-neutralizing antibody b12, onto an unrelated scaffold protein. The final scaffolds bound b12 with high specificity and with affinity similar to that of gp120, and crystallographic analysis of a scaffold bound to b12 revealed high structural mimicry of the gp120-b12 complex structure. The method can be generalized to design other functional proteins through backbone grafting.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Azoitei, Mihai L -- Correia, Bruno E -- Ban, Yih-En Andrew -- Carrico, Chris -- Kalyuzhniy, Oleksandr -- Chen, Lei -- Schroeter, Alexandria -- Huang, Po-Ssu -- McLellan, Jason S -- Kwong, Peter D -- Baker, David -- Strong, Roland K -- Schief, William R -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Oct 21;334(6054):373-6. doi: 10.1126/science.1209368.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22021856" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Motifs ; Amino Acid Sequence ; Antibodies, Monoclonal/chemistry/immunology/metabolism ; Antibodies, Neutralizing/*chemistry/*immunology/metabolism ; Antibody Affinity ; Antibody Specificity ; Antigens, CD4/metabolism ; Computational Biology ; Computer Simulation ; Crystallography, X-Ray ; Epitopes/immunology ; HIV Antibodies/chemistry/*immunology/metabolism ; HIV Envelope Protein gp120/*chemistry/*immunology/metabolism ; Models, Molecular ; Molecular Mimicry ; Molecular Sequence Data ; Mutagenesis ; Protein Conformation ; *Protein Engineering ; Protein Interaction Domains and Motifs ; Surface Plasmon Resonance
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2014-02-07
    Description: Vaccines prevent infectious disease largely by inducing protective neutralizing antibodies against vulnerable epitopes. Several major pathogens have resisted traditional vaccine development, although vulnerable epitopes targeted by neutralizing antibodies have been identified for several such cases. Hence, new vaccine design methods to induce epitope-specific neutralizing antibodies are needed. Here we show, with a neutralization epitope from respiratory syncytial virus, that computational protein design can generate small, thermally and conformationally stable protein scaffolds that accurately mimic the viral epitope structure and induce potent neutralizing antibodies. These scaffolds represent promising leads for the research and development of a human respiratory syncytial virus vaccine needed to protect infants, young children and the elderly. More generally, the results provide proof of principle for epitope-focused and scaffold-based vaccine design, and encourage the evaluation and further development of these strategies for a variety of other vaccine targets, including antigenically highly variable pathogens such as human immunodeficiency virus and influenza.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260937/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260937/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Correia, Bruno E -- Bates, John T -- Loomis, Rebecca J -- Baneyx, Gretchen -- Carrico, Chris -- Jardine, Joseph G -- Rupert, Peter -- Correnti, Colin -- Kalyuzhniy, Oleksandr -- Vittal, Vinayak -- Connell, Mary J -- Stevens, Eric -- Schroeter, Alexandria -- Chen, Man -- Macpherson, Skye -- Serra, Andreia M -- Adachi, Yumiko -- Holmes, Margaret A -- Li, Yuxing -- Klevit, Rachel E -- Graham, Barney S -- Wyatt, Richard T -- Baker, David -- Strong, Roland K -- Crowe, James E Jr -- Johnson, Philip R -- Schief, William R -- 1R01AI102766-01A1/AI/NIAID NIH HHS/ -- 1UM1AI100663/AI/NIAID NIH HHS/ -- 2T32GM007270/GM/NIGMS NIH HHS/ -- 5R21AI088554/AI/NIAID NIH HHS/ -- P01 AI094419/AI/NIAID NIH HHS/ -- P01AI094419/AI/NIAID NIH HHS/ -- P30 AI036214/AI/NIAID NIH HHS/ -- P30 AI045008/AI/NIAID NIH HHS/ -- P30AI36214/AI/NIAID NIH HHS/ -- R01 AI102766/AI/NIAID NIH HHS/ -- R21 AI088554/AI/NIAID NIH HHS/ -- T32 CA080416/CA/NCI NIH HHS/ -- T32 GM007270/GM/NIGMS NIH HHS/ -- T32CA080416/CA/NCI NIH HHS/ -- U54 AI 005714/AI/NIAID NIH HHS/ -- U54 AI057141/AI/NIAID NIH HHS/ -- UM1 AI100663/AI/NIAID NIH HHS/ -- Intramural NIH HHS/ -- England -- Nature. 2014 Mar 13;507(7491):201-6. doi: 10.1038/nature12966. Epub 2014 Feb 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA [2] PhD Program in Computational Biology, Instituto Gulbenkian Ciencia and Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal [3] Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA. ; The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA. ; The Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania 19104, USA. ; Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA. ; Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA. ; 1] Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA [2] Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA [3] IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA [4] Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA. ; 1] Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA [2] IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA [3] Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA. ; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA. ; 1] Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA [2]. ; 1] Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA [2] IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA [3] Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA. ; 1] The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA [2] Department of Pathology, Microbiology and Immunology, Vanderbilt Medical Center, Nashville, Tennessee 37232, USA [3] Department of Pediatrics, Vanderbilt Medical Center, Nashville, Tennessee 37232, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24499818" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Antibodies, Monoclonal/analysis/immunology ; Antibodies, Neutralizing/analysis/immunology ; Antibodies, Viral/analysis/immunology ; Antigens, Viral/chemistry/immunology ; Crystallography, X-Ray ; *Drug Design ; Enzyme-Linked Immunosorbent Assay ; Epitopes/*chemistry/*immunology ; Macaca mulatta/immunology ; Male ; Mice ; Mice, Inbred BALB C ; Models, Molecular ; Neutralization Tests ; Protein Conformation ; *Protein Stability ; Respiratory Syncytial Virus Vaccines/*chemistry/*immunology ; Respiratory Syncytial Viruses/chemistry/immunology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2017-11-11
    Description: Ectoine protects DNA from damage by ionizing radiation Ectoine protects DNA from damage by ionizing radiation, Published online: 10 November 2017; doi:10.1038/s41598-017-15512-4
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 4
    ISSN: 1434-601X
    Keywords: PACS. 14.60.Cd Electrons and positrons – 23.20.Ra Internal pair production – 25.70.Bc Elastic and quasielastic scattering – 25.70.De Coulomb excitation – 25.70.Hi Transfer reactions – 29.30.Aj Charged particle spectrometers: electric and magnetic
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract: We present new results from measurements and simulations of positron spectra, originating from 238U + 181Ta collisions at beam energies close to the Coulomb barrier. The measurements were performed using an improved experimental setup at the double-Orange spectrometer of GSI. Particular emphasis is put on the signature of positrons from Internal-Pair-Conversion (IPC) processes in the measured e+-energy spectra, following the de-excitation of electromagnetic transitions in the moving Ta-like nucleus. It is shown by Monte Carlo simulations that, for the chosen current sweeping procedure used in the present experiments, positron emission from discrete IPC transitions can lead to rather narrow line structures in the measured energy spectra. The measured positron spectra do not show evidence for line structures within the statistical accuracy achieved, although expected from the intensities of the observed γ-transitions ( E γ∼ 1250-1600 keV) and theoretical conversion coefficients. This is due to the reduced detection efficiency for IPC positrons, caused by the limited spatial and momentum acceptance of the spectrometer. A comparison with previous results, in which lines have been observed, is presented and the implications are discussed.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1434-601X
    Keywords: PACS:14.60.Cd Electrons and positrons – 23.20.Ra Internal pair production – 25.70.Bc Elastic and quasielastic scattering – 25.70.De Coulomb excitation – 25.70.Hi Transfer reaction – 29.30.Aj Charged-particle spectrometers: electric and magnetic
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract. We present the results of a Doppler-shift correction to the measured e+e−–sum-energy spectra obtained from e+e−–coincidence measurements in 238U +206Pb and 238U +181Ta collisions at beam energies close to the Coulomb barrier, using an improved experimental setup at the double-Orange spectrometer of GSI. Internal-Pair-Conversion (IPC) e+e− pairs from discrete nuclear transitions of a moving emitter have been observed following Coulomb excitation of the 1.844 MeV (E1) transition in 206Pb and neutron transfer to the 1.770 MeV (M1) transition in 207Pb. In the collision system 238U +181Ta, IPC transitions were observed from the Ta-like as well as from the U-like nuclei. In all systems the Doppler-shift corrected e+e−–sum-energy spectra show weak lines at the energies expected from the corresponding γ–ray spectra with cross sections being consistent with the measured excitation cross sections of the γ lines and the theoretically predicted IPC coefficients. No other than IPC e+e−–sum-energy lines were found in the measured spectra. The transfer cross sections show a strong dependence on the distance of closest approach (Rmin), thus signaling also a strong dependence on the bombarding energy close to the Coulomb barrier.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1434-601X
    Keywords: PACS:14.60.Cd Electrons (including positrons) – 23.20.En Angular distributions and correlation measurements – 23.20.Ra Internal pair production – 29.25.Rm Sources of radioactive nuclei – 29.30.Aj Charged-particle spectrometers: electric and magnetic
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract: We present the first energy and angle resolved measurements of e+e−-pairs emitted from heavy nuclei (Z≥ 40) at rest by internal pair conversion (IPC) of transitions with energies of less than 2 MeV as well as recent theoretical results using the DWBA method, which takes full account of relativistic effects, magnetic substates and finite size of the nucleus. The 1.76 MeV E0 transition in 90Zr (90Sr source) and the 1.77 MeV M1 transition in 207Pb (207Bi source) have been investigated experimentally using the essentially improved setup at the double-ORANGE β-spectrometer of GSI. The measurements prove the capability of the setup to cleanly identify the IPC pairs in the presence of five orders of magnitude higher β− and γ background from the same source and to yield essentially background-free sum spectra despite the large background. Using the ability of the ORANGE setup to directly determine the opening angle of the e+e−–pairs (Θe+e−), the angular correlation of the emitted pairs was measured within the range covered experimentally (40°≤Θe+e−≤ 180°). In the 90Zr case the correlation could be deduced for a wide range of energy differences E Δ of the pairs (−530 keV ≤E Δ≤ 530 keV). The 90Zr results are in good agreement with recent theory. The angular correlation deduced for the M1 transition in 207Pb is in strong disagreement with theoretical predictions derived within the Born approximation and shows almost isotropic character. This is again in agreement with the new theoretical results.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1434-601X
    Keywords: 25.70.Np
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract Subthreshold ¯p andK − and energeticπ − production was studied in Ne + NaF, Cu, Sn and Bi, and in Ni + Ni collisions with incident energies between 1.6 and 2 GeV/u. The measured cross sections indicate a dominant contribution of baryonic resonances. This is also consistent with a generalized scaling behaviour of the cross sections with the energy available in the collision and the energy necessary to produce particles as observed with Ne induced reactions. Deviations from scaling especially pronounced in the Ni-Ni system will be discussed in terms of absorption effects. The flat slope of the excitation function for ¯p production can be related to a reduced production threshold caused by a reduction of the antiproton mass in the dense and heated medium by about 100—150 MeV/c2. A similar in-medium mass reduction is also indicated forK − mesons. An increased ¯p reabsorption probability for the heavier systems is concluded from the comparison of the ¯p yields in Ne + NaF, Ne + Sn and Ni + Ni collisions.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1434-601X
    Keywords: 14.60.Cd ; 25.70.Cd ; 25.70.Ef
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract We present the results obtained from a series of ρ+ρ−-coincidence measurements in heavy-ion collisions using the double-Orangeβ-spectrometer at GSI. The collision systems U+U, U+Pb, and U+Ta were investigated at bombarding energies close to and slightly above (U+Ta) the Coulomb barrier. For all systems studied, very narrow (FWHM−20 keV) ρ+ρ− lines were observed in the sum-energy spectra, with kinetic energies ranging from ∼555 keV to ∼810 keV, superimposed on a continuous distribution mainly due to uncorrelated ρ+ρ− emission. Particularly in the U+Ta system, a pronounced sum-energy line appears at ∼634 keV, predominantly in deep-inelastic collisions. In some cases (e.g. U+Pb) the line characteristics is consistent with a two-body decay mode of an emitter which moves with the c.m. velocity of the colliding ions. However, other lines, and in particular the 634 keV line (U+Ta), exhibit a rather isotropical opening-angle distribution whereas their energy is unequally shared between positrons and electrons, thus being in clear disagreement with this scenario. In general, the data preclude an emission from the separated (moving) nuclei, and, in the latter cases, provide evidence that the e+e−-pair decay occurs in the vicinity of the Coulomb field of a third heavy (positively charged) partner having only a small transverse velocity (|v|⊥〈0.02c)
    Type of Medium: Electronic Resource
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