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For the gels prepared at low φ, much loss of the solvent in deswelling causes large decrease of the gel volume, which is expected to result in supercoiling, i.e. to make conformation of the network chains more compact relative to random-coil.
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Energy minimization was carried out for all compounds using CHARMm force field to make stable conformation of protein with an energy gradient of 0.01 kcal/mol/A°.
The tg rotamer is rarely observed, because repulsive interactions make this conformation energetically unfavorable in comparison to gt and gg.
Aptamers could fold into more compact structures, which strongly affects the electrophoretic mobility of the conjugate on the gel and then make the conformation study rather difficult.
The formation of G-quadruplexes in telomeric DNA and the subsequent inhibition of telomerase make these conformations important as anti-cancer targets, and the drugs that help to form or stabilize them candidates for chemotherapeutic agents [ 135, 136].
This makes computational conformation prediction an attractive alternative method, either by itself or coupled together with NMR [1].
But the docking of Rh2 makes the conformation of CYP3A4 to change, including the position of a key residue Ser119 that leads to a decrease in catalytic activity.
The docking simulations were performed using the Simulated Annealing (SA) algorithm, which makes its conformation exploration using the Monte Carlo approach.
It is possible that the DN substitution might fix a closed structure by making the conformation of the Imp-βKetRE34 less prone to be open.
Interactions between [AgL]+ and [Ni(mnt)2]2− groups also occur in compound 4 with a much shorter AgNi distance of 2.7213 7) Å, while silver atoms and the NiS4 plane in compound 4 make a chair conformation with AgS distances of about 2.8 Å.
While changes in the conformation make proteins vulnerable to aggregation and degradation, little is known about synaptic chaperones which counteract these processes.
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