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991.
Nataša Tomášková Rastislav Varhač Gabriel Žoldák Lenka Olekšáková Dagmar Sedláková Erik Sedlák 《Journal of biological inorganic chemistry》2007,12(2):257-266
The alkaline isomerization of horse heart ferricytochrome c (cyt c) has been studied by electronic absorption spectroscopy in the presence of the Hofmeister series of anions: chloride, bromide,
rhodanide and perchlorate. The anions significantly affect the apparent pK
a value of the transition in a concentration-dependent manner according to their position in the Hofmeister series. The Soret
region of the absorption spectra is not affected by the presence of the salts and shows no significant structural perturbation
of the heme crevice. In the presence of perchlorate and rhodanide anions, the cyanide exchange rate between the bulk solvent
and the binding site is increased. These results imply higher flexibility of the protein structure in the presence of chaotropic
salts. The thermal and isothermal denaturations monitored by differential scanning calorimetry and circular dichroism, respectively,
showed a decrease in the conformational stability of cyt c in the presence of the chaotropic salts. A positive correlation between the stability, ΔG, of cyt c and the apparent pK
a values that characterize the alkaline transition indicates the presence of a thermodynamic linkage between these conformational
transitions. In addition, the rate constant of the cyanide binding and the partial molar entropies of anions negatively correlate
with the pK
a values. This indicates the important role of anion-induced solvent reorganization on the structural flexibility of cyt c in the alkaline transitions.
Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users. 相似文献
992.
《Cell reports》2023,42(5):112449
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993.
Kazumasa Sakurai Tsuyoshi KonumaMasanori Yagi Yuji Goto 《Biochimica et Biophysica Acta (BBA)/General Subjects》2009
Bovine β-lactoglobulin (βLG) has been one of the most extensively studied proteins in the history of protein science mainly because its abundance in cow's milk makes it readily available to researchers. However, compared to other textbook proteins, progress in the study of βLG has been slow because of obstacles such as a low reversibility from denaturation linked with thiol–disulfide exchange or monomer–dimer equilibrium preventing a detailed NMR analysis. Recently, the expression of various types of recombinant βLGs combined with heteronuclear NMR analysis has significantly improved understanding of the physico-chemical properties of βLG. In this review, we address several topics including pH-dependent structural dynamics, ligand binding, and the complex folding mechanism with non-native intermediates. These unique properties might be brought about by conformational frustration of the βLG structure, partly attributed to the relatively large molecular size of βLG. We expect studies with βLG to continue to reveal various important findings, difficult to obtain with small globular proteins, leading to a more comprehensive understanding of the conformation, dynamics and folding of proteins. 相似文献
994.
Summary A search algorithm, called MEDUSA, is presented which allows the determination of multiple conformations of biomolecules in solution with exchange rate constants typically between 103 and 107 s–1 on the basis of experimental high-resolution NMR data. Multiples of structures are generated which are consistent as ensembles with NMR cross-relaxation rates (NOESY, ROESY), scalar J-coupling constants, and T1p
measurements. The algorithm is applied to the cyclic decapeptide antamanide dissolved in chloroform. The characteristic radio-frequency field dependence of the T1p
relaxation rates found for the NH protons of Val1 and Phe6 can be explained by a dynamical exchange between two structures. 相似文献
995.
Conformational potential energy hypersurfaces, PES, for the terminally blocked L-Cysteine, L,L-Cystine and D,L-Cystine have been analyzed by means of molecular mechanics in combination with the programs ROSE, CICADA, PANIC and COMBINE. Low energy conformations and conformational transitions, conformational channels, have been located. Global and fragmental flexibility and conformational softness have been calculated for each conformer as well as for the entire molecule. The PES analyses were used for simulation of conformational movement based on Boltzmann probability of the points obtained on the PES. Boltzmann travelling revealed interesting correlated conformational movement where three or even more dihedral angles changed simultaneously. It could be shown that conformational behavior and flexibility were strongly influenced by the absolute configurations of the amino acids in the peptides. 相似文献
996.
O.P. Skljarov 《Journal of biological physics》1999,25(2-3):223-234
The mathematical model is offered to describe an algorithm for functioning of a speech rhythm. The duration of a speech signal is divided into the numbered sequence of durations of voice and voiceless segments. All elements of this sequence will be considered as values normalized on the maximum element. We determine this sequence of the elements as a speech rhythm. 1) The model describes a speech rhythm as the recurrent relations between elements of a rhythm. 2) The model permits use of the concept of information entropy. 3) The model explains experimental findings obtained by our research group during comparative investigation of a rhythm in normal speech and stuttering. In particular, the model explains the existence of two classes of stutterers with various rhythms of speech. 相似文献
997.
Annette Eva Langkilde 《FEBS letters》2009,583(16):2600-13459
Protein fibrillation is first and foremost a structural phenomenon. Adequate structural investigation of the central conformational individuals of the fibrillation process is however exceedingly difficult. This is due to the nature of the process, which may be described as a dynamically evolving equilibrium between a large number of structural species. These are furthermore of highly diverging sizes and present in very uneven amounts and timeframes. Different structural methods have different strengths and limitations. These, and in particular recent advances within solution analysis of the undisturbed equilibrium using small angle X-ray scattering, are reviewed here. 相似文献
998.
Ryuhei Harada 《Molecular simulation》2018,44(3):206-212
Parallel cascade selection molecular dynamics (PaCS-MD) has been proposed as a conformational sampling method for enhancing structural transitions from a given reactant to a product by repeating cycles of short-time MD simulations. In the present paper, we assessed how the time scale of a short-time MD simulation affected the computational efficiency by changing the simulation length. In conclusion, ps-order (tps) PaCS-MD simulations showed a higher computational efficiency as a total simulation time over the cycles than ns-order (tns) PaCS-MD simulations, indicating that tps might be suitable for generating structural transitions efficiently. 相似文献
999.
In this work, suitable mathematical relationships to compute isobaric heat capacities from molecular simulations in the Grand Canonical (GC) ensemble are derived and tested via Monte Carlo methods. Using atomistic classical force fields, the residual isobaric heat capacities of pure carbon dioxide (CO2) and pure methanol (MeOH) were obtained at supercritical conditions (with critical properties estimated from a finite-size scaling analysis). The total isobaric heat capacity was determined by combining the residual isobaric heat capacity obtained from molecular simulations with the ideal gas contributions obtained from experimental correlations. Isobaric heat capacities generated from both GC and Isothermal–Isobaric ensemble simulations were compared to predictions from accurate equations of state (EOS)s for CO2 and MeOH at corresponding reduced temperatures and pressures. Isobaric heat capacities calculated from both ensembles were in good agreement with those obtained from the Span and Wagner EOS for CO2 and the IUPAC EOS for MeOH. For comparable computation times, simulations run in the GC ensemble generate results with significantly lower statistical uncertainty than those run in the Isothermal–Isobaric ensemble. 相似文献
1000.
Alireza Moosavi Zenooz Reza Ranjbar Fatemeh Nikbakht Oberon Bolouri 《Preparative biochemistry & biotechnology》2017,47(6):570-577
Biodiesel production from microalgae feedstock should be performed after growth and harvesting of the cells, and the most feasible method for harvesting and dewatering of microalgae is flocculation. Flocculation modeling can be used for evaluation and prediction of its performance under different affective parameters. However, the modeling of flocculation in microalgae is not simple and has not performed yet, under all experimental conditions, mostly due to different behaviors of microalgae cells during the process under different flocculation conditions. In the current study, the modeling of microalgae flocculation is studied with different neural network architectures. Microalgae species, Chlorella sp., was flocculated with ferric chloride under different conditions and then the experimental data modeled using artificial neural network. Neural network architectures of multilayer perceptron (MLP) and radial basis function architectures, failed to predict the targets successfully, though, modeling was effective with ensemble architecture of MLP networks. Comparison between the performances of the ensemble and each individual network explains the ability of the ensemble architecture in microalgae flocculation modeling. 相似文献