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1

Usefulness of spectroscopy for biomedical engineering

Olsztyńska-Janus S., Szymborska K., Komorowska M., Lipiński J.

Acta of Bioengineering and Biomechanics

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2008

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Vol. 10, nr 3

45-49

EN

Modifications of phenylalanine amino acid after its exposure to near-infrared (NIR) radiation have been investigated using ATRFTIR (Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy). The process of amino acid aggregation after its exposure to NIR has been observed. A possible mechanism of amino acid dimer formation has been proposed with the help of theoretical calculations of quantum mechanics (MP2 and B3LYP/6–31 G* level) using the GAUSSIAN 03 package. The usefulness of spectroscopy for biomedical engineering is discussed. ATR-FTIR appears to be a powerful tool for measuring tissue damage in aqueous environments.

2

The ligand database server

Broniatowska E, Stępień O., Roterman I.

Bio-Algorithms and Med-Systems

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2006

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Vol. 2, no. 4

21--24

EN

The new database (library) of all smal molecules - ligands creating complexes with protein molecules deposited in the Protein Data Bank is provided. The library contains complete Chemical information for all ligands making possible calculations for the complex; e.g. the ground state electronic structure and partial charges, both calculated by quantum-chemical methods and non-bonding parameters. These properties of ligand molecule are important for computer simulation of protein-ligand interactions. The ligand library can be useful in designing the biochemical experiments such as identification of possible ligands for proteins or drug design in the sense of similarity search to natural ligand for potential competitive inhibitors. The server is freely available via website: www.bioinformatics.cm-uj.krakow.pl/ligands.

PL

Artykuł przedstawia nową bazę danych (bibliotekę) zawierającą ligandy - molekuły tworzące naturalne kompleksy z białkami, zebranymi w bazie Protein Data Bank (PDB). Prezentowana biblioteka zawiera pełną charakterystykę liganda, niezbędną w symulacjach komputerowych kompleksów białko-ligand, np.: ładunki cząstkowe, parametry niewiążące van der Waalsa oraz parametry potencjału torsyjnego. Informacje zawarte w bazie mogą być również wykorzystane w opracowywaniu biochemicznych eksperymentów, takich jak identyfikacja możliwych ligandów białek czy projektowanie leków, przez podobieństwo do naturalnych ligandów, jako potencjalnych inhibitorów kompetycyjnych. Baza jest dostępna na stronie internetowej: www.bioinforma-tics.cm-uj.krakow.pl/ligands.

3

Parametrization of 2-thiouracil and 4-thiouracil in CHARMM all-atom empirical force field

Sarzyńska J., Kuliński T.

Computational Methods in Science and Technology

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2005

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Vol. 11, nr 1

49-55

EN

A new set of force field parameters complementing the CHARMM27 all atom empirical force field for nucleic acids was developed for 2-thiouracil and 4-thiouracil, two naturally modified RNA bases. The new parameters allow for molecular modeling and molecular dynamics simulations of RNA containing 2-thiouracil and 4-thiouracil.

4

Computational study of substrate isotope effect probes of transition state structure for acetylcholinesterase catalysis

Sikorski R., Malany S., Seravalli J., Quinn D.

Nukleonika

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2002

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Vol. 47,suppl.1

9-12

EN

Secondary isotope effects for carbonyl addition reactions of methyl thioacetate, acetone and acetaldehyde have been calculated by ab initio quantum mechanical methods in an effort to interpret measured beta-deuterium isotope effects on acetylcholinesterase- catalyzed hydrolysis of acetylthiocholine. The calculated beta-deuterium isotope effect for equilibrium addition of methanol to methyl thioacetate is D3Keq = 0.965, and the corresponding effect for addition of methoxide ion to methyl thioacetate wherein three waters are hydrogen bonded to the carbonyl oxyanion is D3Keq = 1.086. Neither of these calculated isotope effects is as inverse as the experimental beta-deuterium isotope effect for acetylcholinesterase-catalyzed hydrolysis of acetylthiocholine, D3kE = 0.90š0.03. Structural comparisons show that the water-solvated methoxide adduct of methyl thioacetate is more expanded than is the neutral methanol addition adduct, and suggest that the degree to which the isotope effect is inverse (i.e. less than) is inversely correlated to the degree of expansion of the adduct. A similar correlation of beta-deuterium and beta-deuterium secondary isotope effects with the degree of expansion of the adducts is found for equilibrium additions of methanol and methoxide ion to acetaldehyde. These computational results suggest that the markedly inverse beta-deuterium isotope effect for the acetylcholinesterase reaction arises from enzymic compression of the transition state.

5

Matrix isolation and DFT quantum mechanical studies of vibrational spectra of uracil and its methylated derivatives

Szczepaniak K., Person W.B., Leszczynski J., Kwiatkowski J. S.

Polish Journal of Chemistry

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1998

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Vol. 72, nr 2

402-420

EN

The infrared spectra of uracil and its derivatives in the carbonyl region are strikingly complex, and extremely sensitive to substitution, particularly at ring nitrogen. In this work the infrared spectra of uracil, 1,3-di-deuterouracil, 1-methyluracil, 3-methyluracil and 1,3-dimethyluracil are studied experimentally by low temperature (12 K) matrix isolation infrared spectroscopic techniques, and theoretically by DFT/B3LYP/6-31G(d,p) quantum mechanical methods. Particular attention is focused on the carbonyl region and on the mechanical coupling of the C2=O and C4=O stretching vibrations with each other, with the N1H and N3H bending motions, and with other motions. It is shown that this coupling plays a crucial role in determining the frequencies and intersities of the normal modes that determine the spectral patterns in the infrared spectrum in the carbonyl region. The extreme sensitivity of the frequencies, intersities and spectral pattern in the carbonyl region to isotopic substitution and methylation (and to the intermolecular interactions, particularly hydrogen bonding) is attributed, to a large extent, to changes in this coupling. The DFT calculation appear to give quite accurate values for the force constants and allow separation of simple mass effects and chemical substituent effects on the coupling. Fermi resonance in the carbonyl region is an important factor contributing to the observed complexity of this spectral region. Examination of this effect making use of the visualization of normal modes of vibration provides rules for when it may be expected to be important.