MD/DFT STUDY OF ENVIRONMENTAL EFFECTS ON 31P CHEMICAL SHIFT TENSORS IN B-DNA

PRECECHTELOVA, Jana, Petr NOVÁK, Martin KAUPP, Markéta MUNZAROVÁ a Vladimír SKLENÁŘ. MD/DFT STUDY OF ENVIRONMENTAL EFFECTS ON 31P CHEMICAL SHIFT TENSORS IN B-DNA. Materials Structure in Chemistry, Biology, Physics and Technology. Praha, 2006, roč. 13, č. 1, s. 34-34. ISSN 1211-5894.

Základní údaje

• Originální název: MD/DFT STUDY OF ENVIRONMENTAL EFFECTS ON 31P CHEMICAL SHIFT TENSORS IN B-DNA
• Název česky: MD/DFT studie vlivu prostredi na tensory 31P chemickeho stineni
• Autoři: PRECECHTELOVA, Jana (203 Česká republika), Petr NOVÁK (203 Česká republika), Martin KAUPP (276 Německo), Markéta MUNZAROVÁ (203 Česká republika) a Vladimír SKLENÁŘ (203 Česká republika, garant).
• Vydání: Materials Structure in Chemistry, Biology, Physics and Technology, Praha, 2006, 1211-5894.

Další údaje

• Originální jazyk: angličtina
• Typ výsledku: Článek v odborném periodiku
• Obor: 10403 Physical chemistry
• Stát vydavatele: Česká republika
• Utajení: není předmětem státního či obchodního tajemství
• Kód RIV: RIV/00216224:14310/06:00017640
• Organizační jednotka: Přírodovědecká fakulta
• Klíčová slova anglicky: NMR 31P DFT B-DNA
• Štítky: NMR 31P DFT B-DNA
• Příznaky: Mezinárodní význam

Anotace

31P NMR techniques have become a powerful tool to probe the conformation of the phosphodiester backbone in nucleic acids. A few years ago, a new method based on 31P chemical shift anisotropy (CSA) was suggested for constraining the orientation of the phosphate groups relative to the molecular alignment tensor. This method, though very helpful in nucleic acid (NA) structure determination, suffers from adopting an assumption that the 31P CSA tensor is uniform for all backbone phosphates in oligonucleotides. In order to check the justification of such an assumption, we have attempted to perform a combined MD/DFT study of 31P chemical shift (CS) tensors. For this purpose we tested three models differing in the size of the sugar-phosphate backbone involved. As the study requires a very precise description of environmental effects, we have also carried out a series of validation calculations to find the optimal strategy for the solvent treatment and the treatment of long-range polarization effects. The tested methodologies included an explicit solvent, the PCM-COSMO model and the charge-field perturbation approach that was used to model water molecules lying beyond the first solvation shell by explicit partial point charges. To reduce the computational costs we took the following steps: 1. the geometries were taken from the molecular dynamics simulation without reoptimizing, 2. the resolution-of-identity (RI) approximation as implemented in Turbomole5.6 was employed for the wavefunction calculations, and 3. locally dense basis sets were used in NMR calculations performed at the DFT level. The calculated 31P chemical shift tensors show a strong sensitivity to the method of the solvent treatment – the combinations of the explicit solvent with the PCM-COSMO model and the point charges, respectively, give qualitatively different chemical shift tensors. In addition, the comparison of the chemical shift tensors for the three models reveal nonintuitive trends. These results will serve as a basis for the careful choice of the appropriate methodology to calculate an average of the 31P chemical shift tensors over the molecular dynamics trajectory of the oligonucleotide d(CGCGAATTCGCG)2.

Anotace česky

31P NMR techniques have become a powerful tool to probe the conformation of the phosphodiester backbone in nucleic acids. A few years ago, a new method based on 31P chemical shift anisotropy (CSA) was suggested for constraining the orientation of the phosphate groups relative to the molecular alignment tensor. This method, though very helpful in nucleic acid (NA) structure determination, suffers from adopting an assumption that the 31P CSA tensor is uniform for all backbone phosphates in oligonucleotides. In order to check the justification of such an assumption, we have attempted to perform a combined MD/DFT study of 31P chemical shift (CS) tensors. For this purpose we tested three models differing in the size of the sugar-phosphate backbone involved. As the study requires a very precise description of environmental effects, we have also carried out a series of validation calculations to find the optimal strategy for the solvent treatment and the treatment of long-range polarization effects. The tested methodologies included an explicit solvent, the PCM-COSMO model and the charge-field perturbation approach that was used to model water molecules lying beyond the first solvation shell by explicit partial point charges. To reduce the computational costs we took the following steps: 1. the geometries were taken from the molecular dynamics simulation without reoptimizing, 2. the resolution-of-identity (RI) approximation as implemented in Turbomole5.6 was employed for the wavefunction calculations, and 3. locally dense basis sets were used in NMR calculations performed at the DFT level. The calculated 31P chemical shift tensors show a strong sensitivity to the method of the solvent treatment – the combinations of the explicit solvent with the PCM-COSMO model and the point charges, respectively, give qualitatively different chemical shift tensors. In addition, the comparison of the chemical shift tensors for the three models reveal nonintuitive trends. These results will serve as a basis for the careful choice of the appropriate methodology to calculate an average of the 31P chemical shift tensors over the molecular dynamics trajectory of the oligonucleotide d(CGCGAATTCGCG)2.

Návaznosti

• LC06030, projekt VaV: Název: Biomolekulární centrum

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum

• MSM0021622413, záměr: Název: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Proteiny v metabolismu a při interakci organismů s prostředím