Abstract
In this work we are trying to gain an insight on the molecular mechanisms of the salt effects on conformational stability of proteins with use of fully atomistic Molecular Dynamics simulations techniques. Such ‘in silico’ approach allows us to obtain quite realistic data on the time and scale resolutions that are unavailable for both ‘in vitro’ and ‘in vivo’ experimental techniques. We investigated a trialanine peptide which is the one of the simplest examples of biomolecules, bearing the essential features of proteins.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Marcus, Y.: Ion solvation. John Wiley and Sons Ltd., Chichester (1985)
Dogonadze, R.R., Kalman, A.K.E., Ulstrup, J. (eds.): The Chemical Physics of Solvation. Part A. Elsevier, Amsterdam (1985)
Dogonadze, R.R., Kalman, A.K.E., Ulstrup, J. (eds.): The Chemical Physics of Solvation. Part B. Elsevier, Amsterdam (1986)
Dogonadze, R., Kalman, E., Kornyshev, A., Ulstrup, J.: The Chemical Physics of Solvation. Part C. Elsevier, Amsterdam (1988)
Westhof, E. (ed.): Water and Biological Macromolecules. The Macmillan press Ltd., Basingstoke (1993)
Price, N.C., Dwek, R.A., Wormald, M., Ratcliffe, G.R.: Principles and problems in physical chemistry for biochemists. Oxford University Press, Oxford (2001)
Hirata, F. (ed.): Molecular theory of solvation. Kluwer Academic Publishers, Dordrecht (2003)
Goto, Y., Takahashi, N., Fink, A.L.: Mechanism of acid-induced folding of proteins. Biochemistry 29, 3480–3488 (1990)
Goto, Y., Aimoto, S.: Anion and ph-dependent conformational transition of an amphiphilic polypeptide. Journal of Molecular Biology 218, 387–396 (1991)
Goto, Y., Hagihara, Y.: Mechanism of the conformational transition of melittin. Biochemistry 31, 732–738 (1992)
Cacace, M.G., Landau, E.M., Ramsden, J.J.: The hofmeister series: salt and solvent effects on interfacial phenomena. Quarterly Reviews of Biophysics 30, 241–277 (1997)
Karlstrom, G.: On the effective interaction between an ion and a hydrophobic particle in polar solvents. a step towards an understanding of the hofmeister effect? Physical Chemistry Chemical Physics 5, 3238–3246 (2003)
Rick, S.W.: A reoptimization of the five-site water potential (TIP5P) for use with ewald sums. Journal of Chemical Physics 120, 6085–6093 (2004)
Berendsen, H.J.C., Van der Spoel, D., Van Drunen, R.: Gromacs: A message-passing parallel molecular-dynamics implementation. Computer Physics Communications 91, 43–56 (1995)
Lindahl, E., Hess, B., van der Spoel, D.: Gromacs 3.0: a package for molecular simulation and trajectory analysis. Journal of Molecular Modeling 7, 306–317 (2001)
Kaminski, G.A., Friesner, R.A., Tirado-Rives, J., Jorgensen, W.L.: Evaluation and reparametrization of the opls-aa force field for proteins via comparison with accurate quantum chemical calculations on peptides. Journal of Physical Chemistry B 105, 6474–6487 (2001)
Mahoney, M.W., Jorgensen, W.L.: A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. Journal of Chemical Physics 112, 8910–8922 (2000)
Schaftenaar, G., Noordik, J.H.: Molden: a pre- and post-processing program for molecular and electronic structures. Journal of Computer-Aided Molecular Design 14, 123–134 (2000)
Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, W.F., Dinola, A., Haak, J.R.: Molecular-dynamics with coupling to an external bath. Journal of Chemical Physics 81, 3684–3690 (1984)
Woutersen, S., Hamm, P.: Structure determination of trialanine in water using polarization sensitive two-dimensional vibrational spectroscopy. Journal of Chemical Physics B 104, 11316–11320 (2000)
Woutersen, S., Hamm, P.: Isotope-edited two-dimensional vibrational spectroscopy of trialanine in aqueous solution. Journal of Chemical Physics 114, 2727–2737 (2001)
Schweitzer-Stenner, R., Eker, F., Huang, Q., Griebenow, K.: Dihedral angles of trialanine in d2o determined by combining ftir and polarized visible raman spectroscopy. Journal of the American Chemical Society 123, 9628–9633 (2001)
Mu, Y.G., Kosov, D.S., Stock, G.: Conformational dynamics of trialanine in water. 2. comparison of amber, charmm, gromos, and opls force fields to nmr and infrared experiments. Journal of Chemical Physics B 107, 5064–5073 (2003)
Lynden-Bell, R.M., Rasaiah, J.C.: From hydrophobic to hydrophilic behaviour: A simulation study of solvation entropy and free energy of simple solutes. Journal of Chemical Physics 107, 1981–1991 (1997)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Fedorov, M.V., Schumm, S., Goodman, J.M. (2006). Solvent Effects and Conformational Stability of a Tripeptide. In: R. Berthold, M., Glen, R.C., Fischer, I. (eds) Computational Life Sciences II. CompLife 2006. Lecture Notes in Computer Science(), vol 4216. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11875741_14
Download citation
DOI: https://doi.org/10.1007/11875741_14
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-45767-1
Online ISBN: 978-3-540-45768-8
eBook Packages: Computer ScienceComputer Science (R0)