Abstract
Proteins in the living cell can interact with a wide variety of solutes, ranging from ions, peptides, other proteins, DNA to membranes. Charged groups play a major role and solution conditions such as pH and ionic strength can modulate the interactions significantly. Describing these systems in a statistical mechanical framework involves thousands of pair-interactions and therefore a certain amount of coarse graining is often required. We here present a conceptually simple “mesoscopic” protein model where the detailed charge distribution and surface topology is well preserved. Monte Carlo simulations based on this model can be used to accurately reproduce second virial coeffients, pH titration curves and binding constants 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
Lund, M., Jönsson, B.: A mesoscopic model for protein-protein interactions in solution. Biophys. J. 85, 2940–2947 (2003)
Hill, T.L.: An Introduction to Statistical Thermodynamics. Dover Publications Inc., New York (1986)
Debye, P., Huckel, E.: Z. Physik 24, 185 (1923)
Guldbrand, L., Jönsson, B., Wennerström, H., Linse, P.: Electric double layer forces. a monte carlo study. J. Chem. Phys. 80, 2221 (1984)
Israelachvili, J.N.: Intermolecular and Surface Forces, 2nd edn. Academic Press, London (1992)
Warshel, A., Russel, S.T., Churg, A.K.: Macroscopic models for studies of electrostatic interactions in proteins: Limitations and applicability. Proc. Natl. Acad. Sci. 81, 4785–4789 (1984)
Kesvatera, T., Jönsson, B., Thulin, E., Linse, S.: Binding of ca2+ to calbindin d9k: Structural stability and function at high salt concentration. Biochemistry 33, 14170–14176 (1994)
Demchuk, E., Wade, C.: Improving the continuum dielectric approach to calculating pk a ’s of ionizable groups in proteins. J. Phys. Chem. 100, 17373–17387 (1996)
Kesvatera, T., Jönsson, B., Thulin, E., Linse, S.: Measurement and modelling of sequence-specific pK a values of calbindin D9k . J. Mol. Biol. 259, 828 (1996)
Penfold, R., Warwicker, J., Jönsson, B.: Electrostatic models for calcium binding proteins. J. Phys. Chem. B 102, 8599–8610 (1998)
Kesvatera, T., Jönsson, B., Thulin, E., Linse, S.: Ionization behaviour of acidic residues in calbindin d9k . Proteins 37, 106–115 (1999)
Metropolis, N.A., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A., Teller, E.: Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087–1097 (1953)
Frenkel, D., Smit, B.: Understanding Molecular Simulation. Academic Press, London (1996)
Tanford, C., Hauenstein, J.D.: Hydrogen ion equilibria of ribonuclease. J. Am. Chem. Soc. 78, 5287–5291 (1956)
Ullner, M., Jönsson, B., Söderberg, B., Peterson, C.: A Monte Carlo study of titrating polyelectrolytes. J. Chem. Phys. 104, 3048–3057 (1996)
Lund, M., Jönsson, B.: On the charge regulation of proteins. Biochemistry 44(15), 5722–5727 (2005)
Bratko, D., Striolo, A., Wu, J.Z., Blanch, H.W., Prausnitz, J.M.: Orientation-averaged pair potentials between dipolar proteins or colloids. J. Phys. Chem. 106, 2714–2720 (2002)
Bode, W., Wei, A.Z., Huber, R., Meyer, E., Travis, J., Neumann, S.: X-ray crystal structure of the complex of human leukocyte elastase (pmn elestase) and the third domain of the turkey ovomucoid inhibitor. EMBO 5, 2453 (1986)
Havranek, J.J., Harbury, P.B.: Tanford-kirkwood electrostatics for protein modeling. Proc. Natl. Acad. Sci. 96, 11145–11150 (1999)
Shaller, W., Robertson, A.D.: ph, ionic strength, and temperature dependences of ionization equilibria for the carboxyl groups in turkey ovomucoid thirs domain. Biochemistry 34, 4714–4723 (1995)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Lund, M. (2007). Coarse Graining Biomolecular Systems. In: Kågström, B., Elmroth, E., Dongarra, J., Waśniewski, J. (eds) Applied Parallel Computing. State of the Art in Scientific Computing. PARA 2006. Lecture Notes in Computer Science, vol 4699. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-75755-9_9
Download citation
DOI: https://doi.org/10.1007/978-3-540-75755-9_9
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-75754-2
Online ISBN: 978-3-540-75755-9
eBook Packages: Computer ScienceComputer Science (R0)