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  • 1
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2009
    In:  Proceedings of the National Academy of Sciences Vol. 106, No. 23 ( 2009-06-09), p. 9244-9249
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 106, No. 23 ( 2009-06-09), p. 9244-9249
    Abstract: Observation and structural studies of reaction intermediates of proteins are challenging because of the mixtures of states usually present at low concentrations. Here, we use a 250 GHz gyrotron (cyclotron resonance maser) and cryogenic temperatures to perform high-frequency dynamic nuclear polarization (DNP) NMR experiments that enhance sensitivity in magic-angle spinning NMR spectra of cryo-trapped photocycle intermediates of bacteriorhodopsin (bR) by a factor of ≈90. Multidimensional spectroscopy of U- 13 C, 15 N-labeled samples resolved coexisting states and allowed chemical shift assignments in the retinylidene chromophore for several intermediates not observed previously. The correlation spectra reveal unexpected heterogeneity in dark-adapted bR, distortion in the K state, and, most importantly, 4 discrete L substates. Thermal relaxation of the mixture of L's showed that 3 of these substates revert to bR 568 and that only the 1 substate with both the strongest counterion and a fully relaxed 13- cis bond is functional. These definitive observations of functional and shunt states in the bR photocycle provide a preview of the mechanistic insights that will be accessible in membrane proteins via sensitivity-enhanced DNP NMR. These observations would have not been possible absent the signal enhancement available from DNP.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2009
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2008
    In:  Proceedings of the National Academy of Sciences Vol. 105, No. 3 ( 2008-01-22), p. 883-888
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 105, No. 3 ( 2008-01-22), p. 883-888
    Abstract: By exploiting dynamic nuclear polarization (DNP) at 90 K, we observe the first NMR spectrum of the K intermediate in the ion-motive photocycle of bacteriorhodopsin. The intermediate is identified by its reversion to the resting state of the protein in red light and by its thermal decay to the L intermediate. The 15 N chemical shift of the Schiff base in K indicates that contact has been lost with its counterion. Under these circumstances, the visible absorption of K is expected to be more red-shifted than is observed and this suggests torsion around single bonds of the retinylidene chromophore. This is in contrast to the development of a strong counterion interaction and double bond torsion in L. Thus, photon energy is stored in electrostatic modes in K and is transferred to torsional modes in L. This transfer is facilitated by the reduction in bond alternation that occurs with the initial loss of the counterion interaction, and is driven by the attraction of the Schiff base to a new counterion. Nevertheless, the process appears to be difficult, as judged by the multiple L substates, with weaker counterion interactions, that are trapped at lower temperatures. The double-bond torsion ultimately developed in the first half of the photocycle is probably responsible for enforcing vectoriality in the pump by causing a decisive switch in the connectivity of the active site once the Schiff base and its counterion are neutralized by proton transfer.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2008
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    American Association for the Advancement of Science (AAAS) ; 1991
    In:  Science Vol. 253, No. 5015 ( 1991-07-05), p. 88-88
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 253, No. 5015 ( 1991-07-05), p. 88-88
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    RVK:
    RVK:
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 1991
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
    SSG: 11
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  • 4
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2000
    In:  Proceedings of the National Academy of Sciences Vol. 97, No. 9 ( 2000-04-25), p. 4643-4648
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 97, No. 9 ( 2000-04-25), p. 4643-4648
    Abstract: The photoisomerization of the retinal in bacteriorhodopsin is selective and efficient and yields perturbation of the protein structure within femtoseconds. The stored light energy in the primary intermediate is then used for the net translocation of a proton across the membrane in the microsecond to millisecond regime. This study is aimed at identifying how the protein changes on photoisomerization by using the O-H groups of threonines as internal probes. Polarized Fourier-transform IR spectroscopy of [3- 18 O]threonine-labeled and unlabeled bacteriorhodopsin indicates that 3 of the threonines (of a total of 18) change their hydrogen bonding. One is exchangeable in D 2 O, but two are not. A comprehensive mutation study indicates that the residues involved are Thr-89, Thr-17, and Thr-121 (or Thr-90). The perturbation of only three threonine side chains suggests that the structural alteration at this stage of the photocycle is local and specific. Furthermore, the structural change of Thr-17, which is located 〉 11 Å from the retinal chromophore, implicates a specific perturbation channel in the protein that accompanies the retinal motion.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2000
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    American Association for the Advancement of Science (AAAS) ; 1974
    In:  Science Vol. 186, No. 4167 ( 1974-12-06), p. 929-932
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 186, No. 4167 ( 1974-12-06), p. 929-932
    Abstract: A kinetic model based on allosteric mechanisms of cooperativity fits the experimentally observed phosphate dependence of hemoglobin reactions. Subunit inequivalence is found to be important in analyzing hemoglobin kinetics. The observed increase in the rate of deoxygenation in the presence of organic phosphates is primarily related to the increased rate of dissociation of the second oxygen molecule.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    RVK:
    RVK:
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 1974
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
    SSG: 11
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  • 6
    Online Resource
    Online Resource
    The Royal Society ; 2015
    In:  Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences Vol. 471, No. 2181 ( 2015-09), p. 20150370-
    In: Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, The Royal Society, Vol. 471, No. 2181 ( 2015-09), p. 20150370-
    Abstract: The monotonic and non-monotonic variations of atomic properties within and between the rows of the periodic table underlie our understanding of chemistry and accounting for these variations has been a signature strength of quantum mechanics (QM). However, the computational burden of QM motivates the development of more efficient means of describing electrons and reactivity. The recently developed LEWIS • model incorporates lessons learnt from QM into a force field that includes electrons as explicit pseudo-classical particles. Here, we extend LEWIS • across the 2 p and 3 p elements, and show that it is capable of reproducing both monotonic and non-monotonic variations of chemically important atomic properties in a cost-effective manner. An indicator of the strength of the construct is the ability of pairwise potentials trained on ionization energies and the order of spin configurations to predict atomic polarizabilities. In this manner, some insights of QM are uncoupled from its onerous computational burden.
    Type of Medium: Online Resource
    ISSN: 1364-5021 , 1471-2946
    Language: English
    Publisher: The Royal Society
    Publication Date: 2015
    detail.hit.zdb_id: 209241-4
    detail.hit.zdb_id: 1460987-3
    SSG: 11
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  • 7
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 1979
    In:  Proceedings of the National Academy of Sciences Vol. 76, No. 6 ( 1979-06), p. 2740-2744
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 76, No. 6 ( 1979-06), p. 2740-2744
    Abstract: The tactoidal state in systems containing long, rod-like molecules consists of partially aligned solute molecules in equilibrium with and at a concentration not much higher than that in the conjugate isotropic phase. Under the liquid lattice model of Flory [ Proc. R. Soc. London Ser. A , (1956) 234, 73-89], as well as under other models, tactoid formation by molecules of fixed axial ratio depends on nonideality induced by excluded volumes; the process is wholly entropy driven and requires no direct interactions between rods. Many rod-like biological polymers exhibit reversible polymerization, so that axial ratio and length are not fixed. Polymerization and rod length will then not only induce nonideality, alignment, and phase separation, but will be affected by these. In this work these interrelations are treated under the model of Flory, modified to include a free energy of polymerization and to permit reversible changes in rod length. The primary conclusion is that, in contrast to the situation for fixed lengths, excluded volume-dependent nonideality alone does not suffice to induce a tactoidal phase separation. In the absence of attractions or repulsions between rods the anisotropic phase is highly concentrated. This phase only becomes tactoidal when a minimal level of repulsive interaction between rods is reached. Under this model, tactoid formation in systems such as deoxygenated hemoglobin S and tobacco mosaic virus depends on repulsive interactions or metastability or both. As a secondary result it is shown that rod length in the anisotropic phase is much greater than in the conjugate isotropic phase.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 1979
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2001
    In:  Proceedings of the National Academy of Sciences Vol. 98, No. 4 ( 2001-02-13), p. 1571-1576
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 98, No. 4 ( 2001-02-13), p. 1571-1576
    Abstract: Unidirectional proton transport in bacteriorhodopsin is enforced by the switching machinery of the active site. Threonine 89 is located in this region, with its O—H group forming a hydrogen bond with Asp-85, the acceptor for proton transfer from the Schiff base of the retinal chromophore. Previous IR spectroscopy of [3- 18 O]threonine-labeled bacteriorhodopsin showed that the hydrogen bond of the O—D group of Thr-89 in D 2 O is strengthened in the K photocycle intermediate. Here, we show that the strength and orientation of this hydrogen bond remains unchanged in the L intermediate and through the M intermediate. Furthermore, a strong interaction between Asp-85 and the O—H (O—D) group of Thr-89 in M is indicated by a shift in the C⩵O stretching vibration of the former because of 18 O substitution in the latter. Thus, the strong hydrogen bond between Asp-85 and Thr-89 in K persists through M, contrary to structural models based on x-ray crystallography of the photocycle intermediates. We propose that, upon photoisomerization of the chromophore, Thr-89 forms a tight, persistent complex with one of the side-chain oxygens of Asp-85 and is thereby precluded from participating in the switching process. On the other hand, the loss of hydrogen bonding at the other oxygen of Asp-85 in M may be related to the switching event.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2001
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
    Location Call Number Limitation Availability
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