Abstract
A comparative study of the conformation dynamics of the human alpha-fetoprotein fragment LDSYQCT and heptapeptides derived from it by point substitutions has revealed a significant influence of electrostatic interactions on the set of preferred conformations and dynamics of amino acid residues when the peptides with blocked termini are examined at ɛ = 1. Peptide flexibility rises when the termini are left free (charged). At ɛ = 10 or 80, the set of probable conformations for all residues expands to much the same extent, i.e., at higher permittivity of the medium the dynamic effects of amino acid changes are leveled off.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Abbreviations
- A:
-
alanine
- C:
-
cysteine
- D:
-
aspartic acid
- E:
-
glutamic acid
- F:
-
phenylalanine
- G:
-
glycine
- H:
-
histidine
- I:
-
isoleucine
- K:
-
lysine
- L:
-
leucine
- M:
-
methionine
- N:
-
asparagine
- P:
-
proline
- Q:
-
glutamine
- R:
-
arginine
- S:
-
serine
- T:
-
threonine
- V:
-
valine
- W:
-
tryptophan
- Y:
-
tyrosine
References
K. V. Shaitan, M. G. Mikhailyuk, K. M. Leont’ev, et al., Biofizika 48, 210 (2003).
K. V. Shaitan, M. G. Mikhailyuk, K. M. Leont’ev, et al., Biofizika 47, 411 (2002).
K. V. Shaitan, A. K. Vasil’ev, S. A. Saraikin, and M. G. Mikhailyuk, Biofizika 44, 668 (1999).
W. D. Cornell, P. Cieplak, C. Bayly, et al., J. Am., Chem. Soc. 117, 5179 (1995).
J. Ponder and D. Case, Adv. Protein Chem. 66, 27 (2003).
H. Gohlke, C. Kiel, and D. A. Case, J. Mol. Biol. 330(4), 891 (2003).
E. M. Popov, The Protein Problem (Nauka, Moscow, 1997), Vol. 3 [in Russian].
M. B. Murray, D. K. Tadaki, S. R. Campion, et al., Protein engineering. 11(11), 1041 (1998).
D. A. Engler, R. S. Campion, M. R. Hauser, et al., J. Biol. Chem. 267, 2271 (1992).
B. Rizzuti, L. Sportelli, and R. Guzzi, Biophys. Chem. 94(1–2), 107 (2001).
Q. Cheng, D. R. Benson, M. Rivera, and K. Kuczera, Biopolimers (in press).
G. I. Abelev, Adv. Cancer Res. 14, 295 (1971).
Yu. S. Tatarinov, Human alpha-fetoprotein. 30 years from basic research to clinical application. (Moscow, 1994).
A. A. Terentiev and N. T. Moldogazieva, Biokhimiya 71, 157 (2006).
A. N. Kazimirski, J. M. Salmasi, A. A. Terentiev, et al., Tumor Biol. 21,Suppl. 1, 37 (2000).
D. A. Case, T. E. Cheatham III, T. Darden, et al., J. Comput. Chem. 26, 1668 (2005).
N. T. Moldogazieva, A. A. Terentiev, A. N. Kazimirski, Yu. M. Antonov, and K. V. Shaitan, Biokhimiya 72, 655 (2007).
G. M. Lipkind, S. F. Arkhipova, and E. M. Popov, Izv. AN SSSR Ser. Khim. 2, 313 (1970).
J. Kyte and R. F. Doolittle, J. Mol. Biol. 157(1), 105 (1982).
C. Chothia, Nature 254, 344 (1975).
D. A. Pearlman, D. A. Case, J. W. Caldwell, et al., Amber 4.0 (University of California, San Francisco, 1991).
H.V. Westerhoff and K. van Dam, Thermodynamics and Control of Biological Free-energy Transduction (Elsevier, Amsterdam, 1987; Mir, Moscow, 1992).
V. L. Golo and K. V. Shaitan, Biofizika 47, 611 (2002).
A. S. Lemak and N. K. Balabaev, Molec. Simulation 15, 223 (1995).
A. S. Lemak and N. K. Balabaev, J. Comput. Chem. 17, 1685 (1996).
G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, J. Mol. Biol. 7, 75 (1963).
V. E. Bychkova, R. H. Pain, and O. B. Ptitsyn, FEBS Letts. 238, 231 (1988).
N. T. Moldogazieva, A. A. Terentiev, and K. V. Shaitan, Biomed. Khim. 51, 127 (2005).
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text © N.T. Moldogazieva, K.V. Shaitan, K.B. Tereshkina, Yu.M. Antonov, A.A. Terentiev, 2007, published in Biofizika, 2007, Vol. 52, No. 4, pp. 611–624.
Rights and permissions
About this article
Cite this article
Moldogazieva, N.T., Shaitan, K.V., Tereshkina, K.B. et al. Molecular dynamics of human alpha-fetoprotein fragment LDSYQCT and its analogs at different dielectric constants. BIOPHYSICS 52, 365–374 (2007). https://doi.org/10.1134/S0006350907040021
Received:
Issue Date:
DOI: https://doi.org/10.1134/S0006350907040021