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  • 1
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    The role of solvent viscosity in the dynamics of protein conformational changes (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-06-26
    Description: Nanosecond lasers were used to measure the rate of conformational changes in myoglobin after ligand dissociation at ambient temperatures. At low solvent viscosities the rate is independent of viscosity, but at high viscosities it depends on approximately the inverse first power of the viscosity. Kramers theory for unimolecular rate processes can be used to explain this result if the friction term is modified to include protein as well as solvent friction. The theory and experiment suggest that the dominant factor in markedly reducing the rate of conformational changes in myoglobin at low temperatures (less than 200 K) is the very high viscosity (greater than 10(7) centipoise) of the glycerol-water solvent. That is, at low temperatures conformational substates may not be "frozen" so much as "stuck."〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ansari, A -- Jones, C M -- Henry, E R -- Hofrichter, J -- Eaton, W A -- New York, N.Y. -- Science. 1992 Jun 26;256(5065):1796-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1615323" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Monoxide ; Hot Temperature ; Lasers ; Myoglobin/*chemistry ; Protein Conformation ; Solvents/*adverse effects ; Spectrophotometry, Atomic ; Viscosity
    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
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    Single-molecule fluorescence experiments determine protein folding transition path times (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-01
    Description: The transition path is the tiny fraction of an equilibrium molecular trajectory when a transition occurs as the free-energy barrier between two states is crossed. It is a single-molecule property that contains all the mechanistic information on how a process occurs. As a step toward observing transition paths in protein folding, we determined the average transition-path time for a fast- and a slow-folding protein from a photon-by-photon analysis of fluorescence trajectories in single-molecule Forster resonance energy transfer experiments. Whereas the folding rate coefficients differ by a factor of 10,000, the transition-path times differ by a factor of less than 5, which shows that a fast- and a slow-folding protein take almost the same time to fold when folding actually happens. A very simple model based on energy landscape theory can explain this result.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878298/" 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/PMC3878298/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chung, Hoi Sung -- McHale, Kevin -- Louis, John M -- Eaton, William A -- Z99 DK999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 24;335(6071):981-4. doi: 10.1126/science.1215768.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, MD 20892-0520, USA. chunghoi@niddk.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22363011" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry ; Carrier Proteins/*chemistry ; Fluorescence Resonance Energy Transfer ; Kinetics ; Likelihood Functions ; Models, Molecular ; Molecular Sequence Data ; Photons ; Protein Conformation ; *Protein Folding ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Thermodynamics
    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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    Single-molecule measurement of protein folding kinetics (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-30
    Description: In order to investigate the behavior of single molecules under conditions far from equilibrium, we have coupled a microfabricated laminar-flow mixer to a confocal optical system. This combination enables time-resolved measurement of Forster resonance energy transfer after an abrupt change in solution conditions. Observations of a small protein show the evolution of the intramolecular distance distribution as folding progresses. This technique can expose subpopulations, such as unfolded protein under conditions favoring the native structure, that would be obscured in equilibrium experiments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lipman, Everett A -- Schuler, Benjamin -- Bakajin, Olgica -- Eaton, William A -- New York, N.Y. -- Science. 2003 Aug 29;301(5637):1233-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Building 5, Room 104, National Institutes of Health, Bethesda, MD 20892-0520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947198" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry ; Cold Temperature ; Diffusion ; Energy Transfer ; Fluorescence ; Fluorescence Resonance Energy Transfer ; Kinetics ; Models, Molecular ; Protein Conformation ; Protein Denaturation ; *Protein Folding ; Thermodynamics ; Thermotoga maritima/*chemistry
    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
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    The biophysics of sickle cell hydroxyurea therapy (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-05-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eaton, W A -- Hofrichter, J -- New York, N.Y. -- Science. 1995 May 26;268(5214):1142-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7539154" target="_blank"〉PubMed〈/a〉
    Keywords: Anemia, Sickle Cell/blood/*drug therapy ; Biopolymers/metabolism ; Fetal Hemoglobin/*biosynthesis/drug effects ; Hemoglobin, Sickle/*metabolism ; Humans ; Hydroxyurea/*therapeutic use
    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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  • 5
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    Nanosecond crystallographic snapshots of protein structural changes (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-12-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eaton, W A -- Henry, E R -- Hofrichter, J -- New York, N.Y. -- Science. 1996 Dec 6;274(5293):1631-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA. eaton@helix.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8984630" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Monoxide/chemistry/metabolism ; Computer Simulation ; Crystallography, X-Ray/*methods ; Heme/chemistry ; Ligands ; Models, Molecular ; Myoglobin/*chemistry/metabolism ; Photolysis ; *Protein Conformation ; Time Factors
    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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  • 6
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    Protein reaction kinetics in a room-temperature glass (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-08-18
    Description: Protein reaction kinetics in aqueous solution at room temperature are often simplified by the thermal averaging of conformational substates. These substates exhibit widely varying reaction rates that are usually exposed by trapping in a glass at low temperature. Here, it is shown that the solvent viscosity, rather than the low temperature, is primarily responsible for the trapping. This was demonstrated by placement of myoglobin in a glass at room temperature and subsequent observation of inhomogeneous reaction kinetics. The high solvent viscosity slowed the rate of crossing the energy barriers that separated the substates and also suppressed any change in the average protein conformation after ligand dissociation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hagen, S J -- Hofrichter, J -- Eaton, W A -- New York, N.Y. -- Science. 1995 Aug 18;269(5226):959-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institutes of Health, Bethesda, MD 20892-0520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7638618" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carbon Monoxide/*chemistry/metabolism ; Glass ; Kinetics ; Ligands ; Myoglobin/*chemistry/metabolism ; Photolysis ; Protein Conformation ; Spectrum Analysis ; Temperature ; Trehalose ; Viscosity
    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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  • 7
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    Optical triggers of protein folding (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-10-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chan, C K -- Hofrichter, J -- Eaton, W A -- New York, N.Y. -- Science. 1996 Oct 25;274(5287):628-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8928010" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Monoxide/chemistry ; Cytochrome c Group/*chemistry ; Electrons ; Light ; Oxidation-Reduction ; Photochemistry ; Protein Denaturation ; *Protein Folding ; Spectrometry, Fluorescence
    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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  • 8
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    Structural origin of slow diffusion in protein folding (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-09-26
    Description: Experimental, theoretical, and computational studies of small proteins suggest that interresidue contacts not present in the folded structure play little or no role in the self-assembly mechanism. Non-native contacts can, however, influence folding kinetics by introducing additional local minima that slow diffusion over the global free-energy barrier between folded and unfolded states. Here, we combine single-molecule fluorescence with all-atom molecular dynamics simulations to discover the structural origin for the slow diffusion that markedly decreases the folding rate for a designed alpha-helical protein. Our experimental determination of transition path times and our analysis of the simulations point to non-native salt bridges between helices as the source, which provides a quantitative glimpse of how specific intramolecular interactions influence protein folding rates by altering dynamics and not activation free energies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chung, Hoi Sung -- Piana-Agostinetti, Stefano -- Shaw, David E -- Eaton, William A -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2015 Sep 25;349(6255):1504-10. doi: 10.1126/science.aab1369.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA. chunghoi@niddk.nih.gov stefano.piana-agostinetti@DEShawResearch.com david.shaw@DEShawResearch.com eaton@helix.nih.gov. ; D. E. Shaw Research, New York, NY 10036, USA. chunghoi@niddk.nih.gov stefano.piana-agostinetti@DEShawResearch.com david.shaw@DEShawResearch.com eaton@helix.nih.gov. ; D. E. Shaw Research, New York, NY 10036, USA. Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. chunghoi@niddk.nih.gov stefano.piana-agostinetti@DEShawResearch.com david.shaw@DEShawResearch.com eaton@helix.nih.gov.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26404828" target="_blank"〉PubMed〈/a〉
    Keywords: Diffusion ; Entropy ; Hydrogen-Ion Concentration ; Kinetics ; *Models, Chemical ; Molecular Dynamics Simulation ; *Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry
    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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  • 9
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    Delay time of hemoglobin S polymerization prevents most cells from sickling in vivo (1987)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1987-07-31
    Description: A laser photolysis technique has been developed to assess the quantitative significance of the delay time of hemoglobin S gelation to the pathophysiology of sickle cell disease. Changes in the saturation of hemoglobin S with carbon monoxide produced by varying the intensity of a photolytic laser beam were used to simulate changes in the saturation of oxyhemoglobin S produced by variations in oxygen pressure. The presence of polymer at steady-state saturation with carbon monoxide was determined by measurement of the kinetics of gelation after complete photodissociation. The kinetics are a very sensitive probe for polymer since small amounts of polymerized hemoglobin increase the rate of nucleation sufficiently to eliminate the delay period. First, the equilibrium gelation properties of partially photodissociated carbonmonoxyhemoglobin S were shown to be the same as partially oxygenated hemoglobin S, and the method was then used to determine the effect of saturation on the formation and disappearance of polymers in individual sickle cells. The saturation at which polymers first formed upon deoxygenation was much lower than the saturation at which polymers disappeared upon reoxygenation. The results indicate that at venous saturations with oxygen, gelation takes place in most cells at equilibrium, but is prevented from occurring in vivo because the delay times are sufficiently long that most cells return to the lungs and are reoxygenated before polymerization has begun.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mozzarelli, A -- Hofrichter, J -- Eaton, W A -- New York, N.Y. -- Science. 1987 Jul 31;237(4814):500-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3603036" target="_blank"〉PubMed〈/a〉
    Keywords: Anemia, Sickle Cell/*blood ; Biopolymers ; Carbon Monoxide/blood ; Erythrocytes, Abnormal/*metabolism ; Gels ; Hemoglobin, Sickle/*metabolism ; Humans ; Kinetics ; Lasers ; Light ; Oxygen/blood ; Photolysis ; Scattering, Radiation ; Spectrophotometry
    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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