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Wyświetlanie 1-10 z 59
Tytuł:
Dynamics simulation studies of solvation effect on the trans-xylomollin conformation
Autorzy:
Mahboub, R.
Tematy:
conformation
solvation
Distance Restraints
Dynamics Simulations
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Wydawca:
Przedsiębiorstwo Wydawnictw Naukowych Darwin / Scientific Publishing House DARWIN
Powiązania:
https://bibliotekanauki.pl/articles/412427.pdf  Link otwiera się w nowym oknie
Opis:
The present work describes the solvation effect on the trans-xylomollin conformation. We have studied the trans-xylomollin conformations with the distance restraints using simulation calculations. Distance Restraint Molecular Dynamic (DR-MD) and Distance Restraint Langevin Dynamic (DR-LD) simulations of the trans-xylomollin were performed with an efficient program. The geometries, interaction energies, bonds, angles, and the Van der Waals (VDW) interactions were carried out in solution and gas phases. This comparative study shows that the trans-xylomollin acquires low total energy in solution using DR-MD method and stable conformation under the AMBER field. This molecule reaches its high stable conformation state in solution environment. The solvation effect is more important with DR-MD simulations. Our results are goods and in agreement with the used force field.
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Statistical properties of a polymer chain in the environment with low concentration of nanoparticles
Autorzy:
A. Tsehay, Dessalegne
Luo, Meng-Bo
Tematy:
diffusion
conformation
polymer chain
nanoparticles
molecular dynamics
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Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Powiązania:
https://bibliotekanauki.pl/articles/1050809.pdf  Link otwiera się w nowym oknie
Opis:
We have investigated the statistical properties of polymer in the environment with low concentration of nanoparticles by using large-scale molecular dynamics simulations. The scaling law for the mean square radius of gyration was examined and simulation results for the polymer lengths 64≤N≤144 yielding a reasonably accurate value of the Flory exponent ν=0.58 at weak polymer-nanoparticle interaction ε_{PN}. Within the same range of N, the mean asphericity of the chain is independent of N. We found that the polymer behaves like a self-avoiding walk chain at small ε_{PN} and a compact sphere at large ε_{PN}. The results are attributed to the increase in the contact between polymer and nanoparticles with increasing ε_{PN}. Normal diffusions of polymer are always observed at whatever ε_{PN} and size and concentration of nanoparticles. Our result shows that the normal diffusion behavior of polymer is independent of polymer's state even though there is a phase transition from a desorbed polymer phase at small ε_{PN} to an adsorbed polymer phase at large ε_{PN}.
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Fluorescence decay time distribution analysis of cyclic enkephalin analogues; Influence of solvent and Leu configuration in position 5 on conformation
Autorzy:
Malicka, Joanna
Ganzynkowicz, Robert
Groth, Małgorzata
Czaplewski, Cezary
Karolczak, Jerzy
Liwo, Adam
Wiczk, Wiesław
Tematy:
lifetime distribution
fluorescence
energy transfer
conformation
enkephalin
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Wydawca:
Polskie Towarzystwo Biochemiczne
Powiązania:
https://bibliotekanauki.pl/articles/1044169.pdf  Link otwiera się w nowym oknie
Opis:
Lifetime distribution analysis were performed to study the influence of Leu configuration in position 5 on changes of the peptide chain of cyclic analogues of enkephalins containing a fluorescence donor and acceptor in different solvents. The configuration change of Leu5 in all the analogues of enkephalins studied which contain donor-acceptor pairs has no apparent influence on Trp lifetime distributions. In contrast, there is a significant solvent effect on the shape of lifetime distribution.
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Protein conformational changes induced by adsorption onto material surfaces: an important issue for biomedical applications of material science
Autorzy:
Ballet, T.
Boulange, L.
Brechet, Y.
Bruckert, F.
Weidenhaupt, M.
Tematy:
protein
conformation
unfolding
aggregation
material surface
nanostructure
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Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Powiązania:
https://bibliotekanauki.pl/articles/200039.pdf  Link otwiera się w nowym oknie
Opis:
Protein adsorption on solid surfaces is a widespread phenomenon of large biological and biotechnological significance. Conformational changes are likely to accompany protein adsorption, but are difficult to evidence directly. Nevertheless they have important consequences, since the partial unfolding of protein domains can expose hitherto hidden amino acids. This remodeling of the protein surface can trigger the activation of molecular complexes such as the blood coagulation cascade or the innate immune complement system. In the case of extracellular matrix, it can also change the way cells interact with the material surfaces and result in modified cell behavior. In this review, we present direct and indirect evidences that support the view that some proteins change their conformation upon adsorption. We also show that both physical and chemical methods are needed to study the extent and kinetics of protein conformational changes. In particular, AFM techniques and cryo-electron microscopy provide useful and complementary information. We then review the chemical and topological features of both proteins and material surfaces in relation with protein adsorption. Mutating key amino acids in proteins changes their stability and this is related to material-induced conformational changes, as shown for instance with insulin. In addition, combinatorial methods should provide valuable information about peptide or antibody adsorption on well-defined material surfaces. These techniques could be combined with molecular modeling methods to decipher the rules governing conformational changes associated with protein adsorption.
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Conformational destabilization of Bacillus licheniformis α-amylase induced by lysine modification and calcium depletion
Autorzy:
Tan, Cheau
Rahman, Raja
Kadir, Habsah
Tayyab, Saad
Tematy:
salt bridges
urea
BLA
calcium
lysine
stability
conformation
Pokaż więcej
Wydawca:
Polskie Towarzystwo Biochemiczne
Powiązania:
https://bibliotekanauki.pl/articles/1039896.pdf  Link otwiera się w nowym oknie
Opis:
Bacillus licheniformis α-amylase (BLA) was chemically modified using 100-fold molar excess of succinic anhydride over protein or 0.66 M potassium cyanate to obtain 42 % succinylated and 81 % carbamylated BLAs. Size and charge homogeneity of modified preparations was established by Sephacryl S-200 HR gel chromatography and polyacrylamide gel electrophoresis. Conformational alteration in these preparations was evident by the larger Stokes radii (3.40 nm for carbamylated and 3.34 nm for succinylated BLAs) compared to 2.43 nm obtained for native BLA. Urea denaturation results using mean residue ellipticity (MRE) as a probe also showed conformational destabilization based on the early start of transition as well as ΔGDH2O values obtained for both modified derivatives and Ca-depleted BLA. Decrease in ΔGDH2O value from 5,930 cal/mol (for native BLA) to 3,957 cal/mol (for succinylated BLA), 3,336 cal/mol (for carbamylated BLA) and 3,430 cal/mol for Ca-depleted BLA suggested reduced conformational stability upon modification of amino groups of BLA or depletion of calcium. Since both succinylation and carbamylation reactions abolish the positive charge on amino groups (both α- and ε- amino), the decrease in conformational stability can be ascribed to the disruption of salt bridges present in the protein which might have released the intrinsic calcium from its binding site.
Dostawca treści:
Biblioteka Nauki
Artykuł
Wyświetlanie 1-10 z 59

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