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1998 | 45 | 4 |
Tytuł artykułu

Hydration of C-H groups in natural dithymidine nucleotide and its methylphosphonate analogues

Treść / Zawartość
Warianty tytułu
Języki publikacji
EN
Abstrakty
EN
In this paper we report our preliminary studies on the hydration pattern of selected C-H groups in natural thymidyl(3'-5)thymidine and its RP and SP-methylphosphonate analogues using Molecular Dynamic simulations in aqueous solutions. The methyl groups attached to the phosphorus center (P-Me) in methylphosphonate analogues are hydrated by water molecules as efficiently as the hydrophilic P=O group in the natural dithymidine nucleotide and better than the neutral P=O functions in these compounds, although the nature of the hydration is different. The C5-Me centers of the 3'-yl units seem to be better hydrated in the methylphosphonate analogues than in the natural dithymidine phosphate and than other centers of the thymine basesin methylphosphonate analogues. Due to chirality of the phosphorus center, the C5-Me group of the 5'-yl unit in the SP diastereomer coordinates more water than that in the RP diastereomer. The C6-H group in the 5'-yl unit of the SP diastereomer exhibits a specific interaction with water.
Wydawca
-
Rocznik
Tom
45
Numer
4
Opis fizyczny
p.977-985,fig.
Twórcy
autor
  • Polish Academy of Sciences, Poznan, Poland
autor
autor
Bibliografia
  • 1. Hecht, D., Tadesse. L. & Walters, L. (1992) Defining hydrophobicity: Probing the struc­ture of solute-induced hydration shells by Fou­rier Transform Infrared Spectroscopy. J. Am. Chem. Soc. 114, 4336-4339.
  • 2. Desiraju, G.R. (1996) The C-H...0 hydrogen bond. Structural implications and supramo- lecular design. Acc. Chem. Res. 29,441-449.
  • 3. Derewenda, Z.S., Lee, L. & Derewenda. U. (1995) The occurrence of C-H...0 hydrogen bonds in proteins.«/. Mol Biol 252, 248-262.
  • 4. Wang, Y. & Patel, D.J. (1994) Solution struc­ture of the d(T-C-G-A) duplex at acidic pH. A parallel-stranded helix containing C -C, GC and A-A pairs. J. MoL Biol 242, 508-526.
  • 5. Auffinger, P.. LouiseMay, S. & Westhof, E. (1996) Hydration of C-H groups in tRNA. Faraday Discuss. 103, 151-173.
  • 6. Kulinska, K., Sarzynska, J., Szabo. T. & Staw- inski, J. (1997) FTIR Study on nucleotide ana­logues. 1. Spectral characterization of dinu­cleoside methylphosphonates and dinucleo- side 5'-methylenephosphonates in solution and in solid phase. J. Biomol Struct. Dynam. 15, 119-128.
  • 7. Kulinska, K., Kulinski, T., Stawinski, J. & Laaksonen, A. (1998) Molecular dynamics computer simulation study of nucleotide ana­logues. Comparison of the hydration pattern of dithymidine phosphate with those of dithy- midine methylphoaphonate diastereomers. J. BiomoL Struct. Dynam. 15, 987-998.
  • 8. Szabo, T., Noréus, D., Norrestam, R. & Staw­iński, J. (1993) Molecular and crystal struc­ture of Sp-thymidin-3'-yl 4-thiothymidin-5'-yl methylphosphonate. Nucleic Acids Res. 21, 3921-3926.
  • 9. Weiner, S.J., Kollman, P.A., Nguyen, D.T. & Case, D.A. (1986) An all atom force field for simulation of proteins and nucleic acids. J. Comput, Chem. 7, 230-252.
  • 10. Lyubartsev, A. & Laaksonen, A. (1997) M. Dy- namix User Manual. Stockholm University.
  • ll.Saenger, W. (1984) Principles of Nucleic Acid Structure; pp. 80-81, Springer-Verlag, New York, Berlin.
Typ dokumentu
Bibliografia
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Identyfikator YADDA
bwmeta1.element.agro-article-76097e2f-456c-4415-9f73-c07dfa8632f6
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