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Theoretical density functional studies of tautomeric and conformational forms of N(4)-hydroxycytosine and its 5-fluoro and 5-methyl derivatives

100%

Bakalarski G. , Lesyng B.

tom Vol. 72, nr 7S

1792-1797

Density functional (DFT) calculations at the BLYP/DNP and B3LYP/6-31G(d,p) levels were performed for amino and imino tautomers of N(4)-hydroxycytosine (HC), N(4)-hydroxy-5-fluorocytosine (5F-HC) and N(4)-hydroxy-5-methylcytosine (5Me-HC). Full optimization of the molecular skeleton and zero-point vibrational corrections computed at the B3LYP level were included in the energy analysis. THe results are compared with ab initio MBPT(2)/6-31G(d,p)//HF/6-31G(d,p) calculations [1] performed for HC and 5F-HC. THe DFT methods, and in particular the B3LYP approximatio, predict properly the higher stability of the imino tautomers, and with lower computational costs reproduce very well the energy differences obtained using the conventional ab initio methods.

Structural basis of oncogenesis caused by point mutations in the kinase domain of the MET proto-oncogene

80%

Miller M. , Zbar B. , Ginalski K. , Lesyng B.

nr 3

From experimental, structural probability distributions to the theoretical causality analysis of molecular changes

61%

Daniluk P. , Dziubiński M. , Lesyng B. , Hallay-Suszek M. , Rakowski F. , Walewski Ł.

tom Vol. 19, no. 3

257-276

A brief overview of causality analysis (CA) methods applied to MD simulations data for model biomolecular systems is presented. A CausalMD application for postprocessing of MD data was designed and implemented. MD simulations of two model systems, porphycene (ab initio MD) and HIV-1 protease (coarse-grained MD) were carried out and analyzed. Granger’s causality methodology based on a Multivariate Autoregressive (MVAR) formalism, followed by the Directed Transfer Function (DTF) analysis was applied. A novel approach based on the descriptors of local structure was also presented and prelim- inary results were reported. Casuality analyses are required for a better understanding of biomolecular functioning mechanisms. In particular, such analyses can link physics-based structural dynamics with functions inferred from molecular evolution processes. Current limitations and future developments of the presented methodologies are indicated.