Publications by authors named "Bartosz Stankiewicz"
Article Synopsis
- * Two models of a small molecule, one rigid and one flexible, are used to test the assumptions that internal and rotational motions are decoupled and that the molecule is rigid.
- * The findings suggest that the rigid model can reproduce the target RDC values, but struggles with orientation distribution, while the flexible model fails to reproduce both target RDC values and orientation distribution, highlighting challenges in studying flexible biomolecules.
A method for structure refinement of molecules based on residual dipolar coupling (RDC) data is proposed. It calculates RDC values using rotational and molecule-internal configurational sampling instead of the common refinement procedure that is based on the approximation of the nonuniform rotational distribution of the molecule by a single alignment tensor representing the average nonuniformity of this distribution. Using rotational sampling, as is occurring in the experiment leading to observable RDCs, the method stays close to the experiment.
View Article and Find Full Text PDFExploring the Effect of Enhanced Sampling on Protein Stability Prediction.
J Chem Theory Comput
April 2022
Changes in protein stability due to side-chain mutations are evaluated by alchemical free-energy calculations based on classical molecular dynamics (MD) simulations in explicit solvent using the GROMOS force field. Three proteins of different complexity with a total number of 93 single-point mutations are analyzed, and the relative free-energy differences are discussed with respect to configurational sampling and (dis)agreement with experimental data. For the smallest protein studied, a 34-residue WW domain, the starting structure dependence of the alchemical free-energy changes, is discussed in detail.
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- J-coupling values from NMR experiments are challenging to use for determining protein structures due to their sensitivity to the averaging period linked to conformational changes in torsional angles, and the complexity of the inverse Karplus relation.
- A new approach, utilizing J-coupling time-averaging local-elevation restraining MD simulation, helps address these challenges effectively.
- Applying this method to hen egg white lysozyme demonstrated that it can generate a conformational ensemble that aligns with experimental data, emphasizing the importance of averaging and overcoming local minima in torsional angles for accurate protein structure determination.
Considering the possibility of a common genetic background of vertigo and epilepsy, we genotyped an affected group of individuals with vertigo and an unaffected group, by studying 26 single-nucleotide polymorphisms (SNPs) in 14 genes which were previously reported to be of particular importance for epilepsy. Significant differences were found between the patients and the control group (χ2 = 38.3, df = 3, p = 1.
View Article and Find Full Text PDFMethodology of selecting the reference source for an active noise control system in a car.
Int J Occup Saf Ergon
August 2013
At the end of the 20th century, a significant development in digital technologies of signal processing made it possible to apply active noise control methods in new domains. A proper selection of the reference signal source is a main problem in implementing such systems. This paper presents an estimation method based on an indicator of the coherent power level.
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