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  • 1
    Publication Date: 2013-04-05
    Description: Current human immunodeficiency virus-1 (HIV-1) vaccines elicit strain-specific neutralizing antibodies. However, cross-reactive neutralizing antibodies arise in approximately 20% of HIV-1-infected individuals, and details of their generation could provide a blueprint for effective vaccination. Here we report the isolation, evolution and structure of a broadly neutralizing antibody from an African donor followed from the time of infection. The mature antibody, CH103, neutralized approximately 55% of HIV-1 isolates, and its co-crystal structure with the HIV-1 envelope protein gp120 revealed a new loop-based mechanism of CD4-binding-site recognition. Virus and antibody gene sequencing revealed concomitant virus evolution and antibody maturation. Notably, the unmutated common ancestor of the CH103 lineage avidly bound the transmitted/founder HIV-1 envelope glycoprotein, and evolution of antibody neutralization breadth was preceded by extensive viral diversification in and near the CH103 epitope. These data determine the viral and antibody evolution leading to induction of a lineage of HIV-1 broadly neutralizing antibodies, and provide insights into strategies to elicit similar antibodies by vaccination.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3637846/" 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/PMC3637846/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liao, Hua-Xin -- Lynch, Rebecca -- Zhou, Tongqing -- Gao, Feng -- Alam, S Munir -- Boyd, Scott D -- Fire, Andrew Z -- Roskin, Krishna M -- Schramm, Chaim A -- Zhang, Zhenhai -- Zhu, Jiang -- Shapiro, Lawrence -- NISC Comparative Sequencing Program -- Mullikin, James C -- Gnanakaran, S -- Hraber, Peter -- Wiehe, Kevin -- Kelsoe, Garnett -- Yang, Guang -- Xia, Shi-Mao -- Montefiori, David C -- Parks, Robert -- Lloyd, Krissey E -- Scearce, Richard M -- Soderberg, Kelly A -- Cohen, Myron -- Kamanga, Gift -- Louder, Mark K -- Tran, Lillian M -- Chen, Yue -- Cai, Fangping -- Chen, Sheri -- Moquin, Stephanie -- Du, Xiulian -- Joyce, M Gordon -- Srivatsan, Sanjay -- Zhang, Baoshan -- Zheng, Anqi -- Shaw, George M -- Hahn, Beatrice H -- Kepler, Thomas B -- Korber, Bette T M -- Kwong, Peter D -- Mascola, John R -- Haynes, Barton F -- AI067854/AI/NIAID NIH HHS/ -- AI100645/AI/NIAID NIH HHS/ -- P30 AI050410/AI/NIAID NIH HHS/ -- UM1 AI100645/AI/NIAID NIH HHS/ -- Intramural NIH HHS/ -- England -- Nature. 2013 Apr 25;496(7446):469-76. doi: 10.1038/nature12053. Epub 2013 Apr 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Duke University Human Vaccine Institute, Departments of Medicine and Immunology, Duke University School of Medicine, Durham, North Carolina 27710, USA. hliao@duke.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23552890" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines/immunology ; Africa ; Amino Acid Sequence ; Antibodies, Monoclonal/chemistry/genetics/immunology ; Antibodies, Neutralizing/*chemistry/genetics/*immunology ; Antigens, CD4/chemistry/immunology ; Cell Lineage ; Cells, Cultured ; Clone Cells/cytology ; Cross Reactions/immunology ; Crystallography, X-Ray ; Epitopes/chemistry/immunology ; *Evolution, Molecular ; HIV Antibodies/*chemistry/genetics/*immunology ; HIV Envelope Protein gp120/chemistry/genetics/immunology/metabolism ; HIV-1/*chemistry/classification/*immunology ; Humans ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Neutralization Tests ; Phylogeny ; Protein Structure, Tertiary
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2016-01-23
    Description: Major histocompatibility complex E (MHC-E) is a highly conserved, ubiquitously expressed, nonclassical MHC class Ib molecule with limited polymorphism that is primarily involved in the regulation of natural killer (NK) cells. We found that vaccinating rhesus macaques with rhesus cytomegalovirus vectors in which genes Rh157.5 and Rh157.4 are deleted results in MHC-E-restricted presentation of highly varied peptide epitopes to CD8alphabeta(+) T cells, at ~4 distinct epitopes per 100 amino acids in all tested antigens. Computational structural analysis revealed that MHC-E provides heterogeneous chemical environments for diverse side-chain interactions within a stable, open binding groove. Because MHC-E is up-regulated to evade NK cell activity in cells infected with HIV, simian immunodeficiency virus, and other persistent viruses, MHC-E-restricted CD8(+) T cell responses have the potential to exploit pathogen immune-evasion adaptations, a capability that might endow these unconventional responses with superior efficacy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769032/" 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/PMC4769032/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hansen, Scott G -- Wu, Helen L -- Burwitz, Benjamin J -- Hughes, Colette M -- Hammond, Katherine B -- Ventura, Abigail B -- Reed, Jason S -- Gilbride, Roxanne M -- Ainslie, Emily -- Morrow, David W -- Ford, Julia C -- Selseth, Andrea N -- Pathak, Reesab -- Malouli, Daniel -- Legasse, Alfred W -- Axthelm, Michael K -- Nelson, Jay A -- Gillespie, Geraldine M -- Walters, Lucy C -- Brackenridge, Simon -- Sharpe, Hannah R -- Lopez, Cesar A -- Fruh, Klaus -- Korber, Bette T -- McMichael, Andrew J -- Gnanakaran, S -- Sacha, Jonah B -- Picker, Louis J -- HHSN272201100013C/AI/NIAID NIH HHS/ -- HHSN272201100013C/PHS HHS/ -- P01 AI094417/AI/NIAID NIH HHS/ -- P01-AI094417/AI/NIAID NIH HHS/ -- P50-GM065794/GM/NIGMS NIH HHS/ -- P51 OD011092/OD/NIH HHS/ -- P51-OD011092/OD/NIH HHS/ -- R01 AI059457/AI/NIAID NIH HHS/ -- R01 AI095113/AI/NIAID NIH HHS/ -- R01 AI117802/AI/NIAID NIH HHS/ -- R01 DE021291/DE/NIDCR NIH HHS/ -- R01-AI059457/AI/NIAID NIH HHS/ -- R01-AI095113/AI/NIAID NIH HHS/ -- R01-AI117802/AI/NIAID NIH HHS/ -- R01-DE021291/DE/NIDCR NIH HHS/ -- R37 AI054292/AI/NIAID NIH HHS/ -- R37-AI054292/AI/NIAID NIH HHS/ -- U24 OD010850/OD/NIH HHS/ -- U24-OD010850/OD/NIH HHS/ -- UM1 AI100645/AI/NIAID NIH HHS/ -- UM1-AI100645-01/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2016 Feb 12;351(6274):714-20. doi: 10.1126/science.aac9475. Epub 2016 Jan 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA. ; Nuffield Department of Medicine, University of Oxford, Oxford OX37FZ, UK. ; Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. ; Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. The New Mexico Consortium, Los Alamos, NM 87545, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26797147" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigen Presentation ; Antigenic Variation ; CD8-Positive T-Lymphocytes/*immunology ; Cytomegalovirus/genetics/*immunology ; Epitopes, T-Lymphocyte/chemistry/*immunology ; Genetic Vectors/genetics/immunology ; Histocompatibility Antigens Class I/chemistry/*immunology ; Host-Pathogen Interactions/immunology ; Immune Evasion ; Killer Cells, Natural/immunology ; Macaca mulatta ; Protein Structure, Secondary ; Simian Immunodeficiency Virus/*immunology ; Vaccination
    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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  • 3
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2011-09-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korber, Bette -- Gnanakaran, S -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1589-90. doi: 10.1126/science.1211919.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Theoretical Biology and Biophysics, T6, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. btk@lanl.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21921189" target="_blank"〉PubMed〈/a〉
    Keywords: *AIDS Vaccines ; Antibodies, Neutralizing/chemistry/*immunology/metabolism ; Antibody Affinity ; Antigens, CD4/chemistry/immunology/metabolism ; Binding Sites ; Binding Sites, Antibody ; Complementarity Determining Regions/genetics ; Crystallography, X-Ray ; Epitopes ; Genes, Immunoglobulin Heavy Chain ; HIV Antibodies/chemistry/*immunology/metabolism ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology ; Humans ; Models, Molecular ; Molecular Mimicry ; Protein Conformation
    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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  • 4
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 106 (1997), S. 3485-3493 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The reaction dynamics of ClO− in water following femtosecond ultraviolet photolysis is investigated by measuring time-resolved absorption and anisotropy. Ab initio calculations show that light absorption induces charge shifting from the O− atom to the Cl atom. Molecular dynamics simulations predict that the charge shift is followed by the destruction of the solvent structure around the O atom and its formation around newly formed negative charge on the Cl atom. An ultrafast (∼60 fs) transient absorption change is observed and likely corresponds to the inertial part of the destruction of the solvent structure around the newly formed neutral O atom of the excited state OCl−. The early time anisotropy of −0.13±0.05 decays on the 230 fs time scale and is attributed to the dissociation along a new reaction path toward Cl+O− that is seen independently through the evaluation of the spectrum of Cl. The remaining anisotropy decays within 6 ps due to rotational diffusion of the ion. Probe wavelength dependence of the longer time dynamics (1.3–7 ps) is proposed to be the vibrational relaxation of the vibrationally hot ground state of ClO−, the generation of which can be described as electron transfer from the excited state OCl− to the ground state ClO−. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 3486-3496 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: When HgI2 is photodissociated, it produces a vibrationally hot ground state HgI molecule. Pugliano et al. have reported a T1 time of ∼3 ps for dipolar HgI in ethanol [J. Chem. Phys. 103, 6498 (1995)]. We have carried out equilibrium molecular dynamics simulation for the above system to calculate the T1 time theoretically and to understand the nature of solvent forces giving rise to the relaxation. The solvent friction on the vibrational coordinate was calculated for dipolar and nonpolar HgI. The vibrational decay rate obtained from the simulation is in quantitative agreement with the experimentally determined value. The dissipation of excess vibrational energy in HgI is mainly facilitated by the Lennard-Jones force fluctuations. The structure and nature of the solvent molecules giving rise to these interactions are discussed in detail. The effects of anharmonicity, the similarity between the friction spectra and the optical Kerr spectra and the validity of the Landau–Teller formula are discussed. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The vibrational population dynamics of HgI fragments in ethanol solution, resulting from the 320 nm photolysis of HgI2, are examined both experimentally and by a simulation. The experiments reveal an HgI population distribution which rapidly relaxes toward equilibrium. At the earliest times, the HgI exhibits vibrational coherent wave-packet motion that dephases with a time constant of ca. 1 ps. These data are used to gain insight into the character of the solvated potential energy curves. The population relaxation was adequately reproduced by master equations which were formulated to incorporate the HgI anharmonicity and a solvent frequency dependent friction. This treatment characterizes the spontaneous vibrational relaxation timescale for the n″=1→0 transition to be ca. 3 ps, and is used to identify the relaxation rate constants for all other HgI level pairs. The simulations estimate that the initial excess energy of HgI is centered at n″(approximately-equal-to)10 which corresponds to a total excess energy of ca. 1050 cm−1. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Fluorescence excitation, dispersed fluorescence, and picosecond time-resolved fluorescence spectroscopies have been used to study the dimeric molecule 9,9'-bifluorenyl, isolated under supersonic jet conditions. The excitation spectrum reveals a splitting in several principal resonances of the S0→S1 excitation spectrum, which can be attributed to electronic coupling between the two fluorenyl moieties. The splitting, which for different vibronic transitions correlates with Franck–Condon factors, is consistent with an exciton model that includes higher electronic states. The splitting is reasonably well reproduced by a multipole interaction potential. Calculations have verified that the electron exchange coupling is small. Furthermore, the relative intensities of the resonances allow an estimate of the equilibrium geometry, suggesting that the molecular long axes have an angular displacement of 60°–70°, consistent with the geometry found by x-ray diffraction. A most interesting feature of this species is that it is weakly fluorescent in fluid solution, which has been attributed to activated conformational barrier crossing of the excited molecule. In contrast, the fluorescence quantum efficiency of the isolated molecule can be close to unity, the lifetime ranging from 18 to 20 ns at vibrational energies 〈1400 cm−1. Above this region, the fluorescence decay time decreases steadily, to ≈2 ns by 2550 cm−1, indicating the onset of a nonradiative relaxation channel. Since the molecule was also seen to exhibit vibrational relaxation at low energies (i.e., ≤400 cm−1), the relaxation dynamics observed above 1400 cm−1 reflect the existence of a conformational potential energy barrier in the isolated molecule.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 0022-2313
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 0022-2313
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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