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  • 1
    Electronic Resource
    Electronic Resource
    Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 8048-8067 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Two-dimensional adaptive umbrella sampling with the first umbrella coordinate equal to the potential energy of the system and the second umbrella coordinate equal to a function that discriminates important folded conformations from unfolded conformations is used to determine the equilibrium properties of complex biological systems. Compared to one-dimensional adaptive umbrella sampling with the potential energy as umbrella coordinate (multicanonical sampling), more reliable results can be obtained in certain cases. The method is applied to a helical peptide (RN24) with an analytical continuum solvent potential in combination with the PARAM19 force field of CHARMM. This effective potential energy function has been shown to describe the structural preferences of solvated peptides. With the two-dimensional approach and the deviation from the helical structure as the second umbrella coordinate, a converged description of the structural properties and the thermodynamics of the peptide RN24 is obtained. In particular, we find that the formation of the helix of RN24 occurs as a transition accompanied by a characteristic peak in the heat capacity. A formalism is described that uses the weighting factors obtained from a self-consistent solution of the weighted histogram analysis method equations to combine the results from a series of simulations with different biases and calculate the ensemble average of any dynamical variable as a function of the temperature without the need for extracting the density of states from the simulations. It is shown how the formalism can be used to calculate thermodynamic properties of the system. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.480139
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  • 2
    Electronic Resource
    Electronic Resource
    Direct activation of human TRPC6 and TRPC3 channels by diacylglycerol (1999)
    [s.l.] : Macmillan Magazines Ltd.
    Nature 397 (1999), S. 259-263 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Eukaryotic cells respond to many hormones and neurotransmitters with increased activity of the enzyme phospholipase C and a subsequent rise in the concentration of intracellular free calcium ([Ca2+]i). The increase in [Ca2+]i occurs ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/16711
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  • 3
    Electronic Resource
    Electronic Resource
    Nomothetic and Idiographic Methodology in Psychiatry — A historical-philosophical analysis (1999)
    Springer
    Medicine, health care and philosophy 2 (1999), S. 265-274 
    Details
    ISSN: 1572-8633
    Keywords: epistemology ; history ; idiographic ; individual ; natural sciences ; nomothetic ; psychology ; psychopathology ; science of general laws ; science of specific events
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine , Philosophy
    Notes: Abstract The purpose of this article is to demonstrate the epistemic position of psychiatry between the science of general laws in relation to frequently encountered generality and the science of specific events which is directed towards the particular. In this respect the development of the dichotomy of nomothetic and idiographic methodology from its generally forgotten neo-Kantian origins (Windelband, Rickert, Natorp, Bauch, Münch, Hessen, Münsterberg) is delineated within the context of a historical-philosophical analysis and then its incorporation into psychology and psychopathology (Stern, Binswanger, Kronfeld, Jaspers) is reconstructed. In the course of this analysis and also in the discussion of the currently accepted theories of analytical philosophy (Stegmüller) and critical rationalism (Popper) it becomes clear that, in spite of widespread current opinions to the contrary, individualizing concept formation is an indispensable element in the methodological inventory of psychiatric science.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1009973828786
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  • 4
    Electronic Resource
    Electronic Resource
    Sympathisches Nervensystem und Schmerz (1998)
    Springer
    Der Anaesthesist 47 (1998), S. 2-3 
    Details
    ISSN: 1432-055X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001010050516
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  • 5
    Electronic Resource
    Electronic Resource
    Solution conformations of structured peptides: continuum electrostatics versus distance-dependent dielectric functions (1999)
    Springer
    Theoretical chemistry accounts 101 (1999), S. 194-204 
    Details
    ISSN: 1432-2234
    Keywords: Key words: Helical peptide ; β-Hairpin ; Random coil ; Umbrella sampling ; Multicanonical sampling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. To compare different implicit solvent potentials, the folding thermodynamics of the helical peptide RN24 and the β-hairpin peptide BH8 are studied by molecular dynamics simulation with adaptive umbrella sampling. As the potential energy functions, the analytical continuum solvent (ACS) potential and three simplified variants, termed EPSR1, EPSR4, and EPSR10, are used. The ACS potential is a combination of the standard CHARMM force field for the internal energy (bonds, angles, dihedrals) and the van der Waals energy with the analytical continuum electrostatic (ACE) potential and a non-polar solvation potential. The EPSR potentials differ from the ACS potential by the use of Coulomb's law with a distance-dependent dielectric function to calculate the electrostatic energy. With the ACS potential, quantitative agreement with experiment is obtained for the helix propensity (RN24: 62% calculated vs 50–60% experiment) and the β-hairpin propensity (BH8: 33% calculated vs 19–37% experiment) of the peptides. During the simulations with the EPSR potentials, no significant formation of secondary structure is observed. It is shown that the preference for coil conformations over conformations with secondary structure by the EPSR potentials is due to an overestimation of the energy of salt bridge formation, independent of the magnitude of the Coulomb energy relative to the other energy terms. Possible improvements of the distance-dependent dielectric functions which may permit their application to the simulation of peptide folding, are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002140050429
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  • 6
    Electronic Resource
    Electronic Resource
    Adaptive umbrella sampling of the potential energy: modified updating procedure of the umbrella potential and application to peptide folding (1999)
    Springer
    Theoretical chemistry accounts 101 (1999), S. 62-66 
    Details
    ISSN: 1432-2234
    Keywords: Key words: Adaptive umbrella sampling ; Multicanonical sampling ; Helical peptide ; β-hairpin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. Adaptive umbrella sampling of the potential energy is used as a search method to determine the structures and thermodynamics of peptides in solution. It leads to uniform sampling of the potential energy, so as to combine sampling of low-energy conformations that dominate the properties of the system at room temperature with sampling of high-energy conformations that are important for transitions between different minima. A modification of the procedure for updating the umbrella potential is introduced to increase the number of transitions between folded and unfolded conformations. The method does not depend on assumptions about the geometry of the native state. Two peptides with 12 and 13 residues, respectively, are studied using the CHARMM polar-hydrogen energy function and the analytical continuum solvent potential for treatment of solvation. In the original adaptive umbrella sampling simulations of the two peptides, two and six transitions occur between folded and unfolded conformations, respectively, over a simulation time of 10 ns. The modification increases the number of transitions to 6 and 12, respectively, in the same simulation time. The precision of estimates of the average effective energy of the system as a function of temperature and of the contributions to the average effective energy of folded conformations obtained with the adaptive methods is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002140050407
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  • 7
    Electronic Resource
    Electronic Resource
    General effect of photosynthetic electron transport inhibitors on translation precludes their use for investigating regulation of D1 biosynthesis in Synechococcus sp. strain PCC 7942 (1999)
    Springer
    Photosynthesis research 62 (1999), S. 261-271 
    Details
    ISSN: 1573-5079
    Keywords: cyanobacteria ; light-regulated genes ; photosynthetic electron transport ; psbA ; translation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Both light itself and excitation pressure have been implicated as the environmental signal that stimulates interchange of the two forms of the D1 protein of photosystem II (PS II) in Synechococcus sp. strain PCC 7942. We sought an explanation for conflicting reports regarding the role of photosynthetic electron transport in regulation of psbA expression and D1 interchange. Inhibitors that block at different points in the photosynthetic electron transport chain were administered and the effect on expression of psbAII, which encodes the high-light-induced form II of D1, was examined by measuring changes in transcript levels and in the activities of reporter enzymes. Both 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), an inhibitor of PSII, and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB), an inhibitor of the cytochrome b6/f complex, prevented high-light-induced increase in β-galactosidase activity from a psbAII::lacZ gene fusion when added at a concentration that completely inhibits photosynthetic electron transport (1 μM). The same effect was observed for luciferase activity from transcriptional and translational fusions of psbAII to the luxAB genes from Vibrio harveyi. DCMU (1 μM) arrested luciferase expression at low-light levels – thus eliminating the high light response – whereas a sublethal concentration (50 nM), which reduces electron transport by 50%, had intermediate effects on psbAII-driven luciferase activity. However, psbAII transcript levels, monitored by northern blot analysis, were not altered by electron transport inhibitors, either at low-light intensity or following a high-light exposure. The suppressive effect of DCMU on expression of reporter enzymes was not restricted to the high-light response of psbAII-driven reporter systems, but was also observed using an isopropyl-(-d)-thiogalactopyranoside (IPTG)-inducible trc promoter fused to luxAB. This construct only marginally responded to IPTG addition when DCMU was present. Thus, blocking electron transport in Synechococcus affects the translation machinery in a general way, and the use of electron transport inhibitors is of limited value when focusing on specific redox regulation of D1 protein synthesis or degradation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1006340423948
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  • 8
    Electronic Resource
    Electronic Resource
    Improving the accuracy of protein pKa calculations: Conformational averaging versus the average structure (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 145-158 
    Details
    ISSN: 0887-3585
    Keywords: protein titration ; molecular dynamics ; average conformation ; continuum electrostatistics ; protein dielectric constant ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Several methods for including the conformational flexibility of proteins in the calculation of titration curves are compared. The methods use the linearized Poisson-Boltzmann equation to calculate the electrostatic free energies of solvation and are applied to bovine pancreatic trypsin inhibitor (BPTI) and hen egg-white lysozyme (HEWL). An ensemble of conformations is generated by a molecular dynamics simulation of the proteins with explicit solvent. The average titration curve of the ensemble is calculated in three different ways: an average structure is used for the pKa calculation; the electrostatic interaction free energies are averaged and used for the pKa calculation; and the titration curve for each structure is calculated and the curves are averaged. The three averaging methods give very similar results and improve the pKa values to approximately the same degree. This suggests, in contrast to implications from other work, that the observed improvement of pKa values in the present studies is due not to averaging over an ensemble of structures, but rather to the generation of a single properly averaged structure for the pKa calculation. Proteins 33:145-158, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    49. Modellbasierte Präparationstechnik für disperse Systeme (1999)
    Weinheim : Wiley-Blackwell
    Chemie Ingenieur Technik - CIT 71 (1999), S. 966-967 
    Details
    ISSN: 0009-286X
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cite.330710953
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  • 10
    Electronic Resource
    Electronic Resource
    Oxidative biodegradation mechanisms of biaxially strained poly(etherurethane urea) elastomers (1995)
    Hoboken, NJ : Wiley-Blackwell
    Journal of Biomedical Materials Research 29 (1995), S. 337-347 
    Details
    ISSN: 0021-9304
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine , Technology
    Notes: As part of ongoing studies in polyurethane biostability and biodegradation, we have investigated an in vitro system to test strained poly(etherurethane urea) (PEUU). Recently, we utilized this system to reproduce in vivo stress cracking in strained Pellethane®. In this study, strained PEUU was tested to determine whether it degrades through a common mechanism with Pellethane® and to further examine the steps involved in this degradation.Biaxially strained PEUU elastomers were treated with an α2-macroglobulin (α2-Mac) protein solution followed by an oxidative H2O2/CoCl2 treatment. Characterization of the strained PEUU specimens was performed with attenuated total reflectance-Fourier transform infrared spectroscopy, scanning electron microscopy (SEM), electron spectroscopy for chemical analysis, and contact angle analysis. The results from these characterization techniques provide conclusive evidence that biodegradation of PEUU and Pellethane® occurs through a common mechanism. Chemical changes to the PEUU include cleavage of the polyether soft segments and urethane linkages, leaving the hard segment domains unaffected. SEM analysis shows that this chain cleavage leads to the development of severe pitting and cracking of the PEUU surface. In addition, the in vitro degradation accurately reproduces the in vivo degradation chemically and physically. This result verifies that the primary species responsible for biodegradation of PEUUs, in vivo, are hydroxyl and/or hydroperoxide radicals. α2-Mac pretreatment increases the rate of degradation compared to direct treatment in H2O2/CoCl2. As the PEUU soft segment chains are cleaved, the degradation products are extracted into the treatment solution or environment. Finally, a new biodegradation mechanism of PEUUs is presented that involves crosslinking of the polyether soft segments. © 1995 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jbm.820290309
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