In this work, we present a study of the interaction between human serum albumin (HSA) and acetylsalicylic acid (ASA, C9H8O4) by molecular dynamics simulations (MD). Starting from an experimentally resolved structure of the complex, we performed the extraction of the ligand by means of the application of an external force. After stabilization of the system, we quantified the force used to remove the ASA from its specific site of binding to HSA and calculated the mechanical nonequilibrium external work done during this process. We obtain a reasonable value for the upper boundary of the Gibbs free energy difference (an equilibrium thermodynamic potential) between the complexed and noncomplexed states. To achieve this goal, we used the finite sampling estimator of the average work, calculated from the Jarzynski Equality. To evaluate the effect of the solvent, we calculated the so-called “viscous work,” that is, the work done to move the aspirin in the same trajectory through the solvent in absence of the protein, so as to assess the relevance of its contribution to the total work. The results are in good agreement with the available experimental data for the albumin affinity constant for aspirin, obtained through quenching fluorescence methods. 1. Introduction Human serum albumin (HSA) is the most abundant plasma protein in the human body and plays an important role in drug transport and metabolism. Generally regarded as a nonspecific transport protein, HSA has been assigned a number of enzymatic properties [1–3]. Additionally, the enzymatic activity of HSA on different substrates and drugs has also been studied and documented. Nevertheless, the structural mechanism of this activity is yet unknown. To assess the structural basis of binding mechanisms, we evaluated the interaction between HSA and acetylsalicylic acid (ASA, C9H8O4) by means of molecular dynamics simulations (MD). Starting from an experimentally resolved structure of the complex, we extracted the ligand by means of the application of an external force, under near quasistatic conditions, thus evaluating the work involved in breaking the interactions present in the protein-ligand complex, and hence obtaining an upper boundary for the free energy of binding of the complex. We quantified the force used to remove the ASA from its specific site of binding to HSA and calculated the mechanical nonequilibrium external work done during this process. The aim of the present study is to calculate an upper boundary for the Gibbs free energy difference associated to that process, through the average work
References
[1]
F. Yang, C. Bian, L. Zhu, G. Zhao, Z. Huang, and M. Huang, “Effect of human serum albumin on drug metabolism: structural evidence of esterase activity of human serum albumin,” Journal of Structural Biology, vol. 157, no. 2, pp. 348–355, 2007.
[2]
N. Ahmed, D. Dobler, M. Dean, and P. J. Thornalley, “Peptide mapping identifies hotspot site of modification in human serum albumin by methylglyoxal involved in ligand binding and esterase activity,” Journal of Biological Chemistry, vol. 280, no. 7, pp. 5724–5732, 2005.
[3]
N. Dubois-Presle, F. Lapicque, M. H. Maurice et al., “Stereoselective esterase activity of human serum albumin toward ketoprofen glucuronide,” Molecular Pharmacology, vol. 47, no. 3, pp. 647–653, 1995.
[4]
B. Bojko, A. Su？kowska, M. Maciazek, J. Równicka, F. Njau, and W. W. Su？kowski, “Changes of serum albumin affinity for aspirin induced by fatty acid,” International Journal of Biological Macromolecules, vol. 42, no. 4, pp. 314–323, 2008.
[5]
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, “GROMACS: fast, flexible, and free,” Journal of Computational Chemistry, vol. 26, no. 16, pp. 1701–1718, 2005.
[6]
W. F. van Gunsteren, S. R. Billeter, A. A. Eising et al., Biomolecular Simulation: The GROMOS96 Manual and Userguide, Hochschuleverlag AG an der ETH Zürich, 1996.
[7]
B. Hess, H. Bekker, H. J. C. Berendsen, and J. G. E. M. Fraaije, “LINCS: a linear constraint solver for molecular simulations,” Journal of Computational Chemistry, vol. 18, no. 12, pp. 1463–1472, 1997.
[8]
S. Miyamoto and P. A. Kollman, “Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models,” Journal of Computational Chemistry, vol. 13, pp. 952–962, 1992.
[9]
W. Humphrey, A. Dalke, and K. Schulten, “VMD: Visual molecular dynamics,” Journal of Molecular Graphics, vol. 14, no. 1, pp. 33–38, 1996.
[10]
http://www.ks.uiuc.edu/Research/vmd/.
[11]
http://plasma-gate.weizmann.ac.il/Grace/.
[12]
N. Guex and M. C. Peitsch, “SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling,” Electrophoresis, vol. 18, no. 15, pp. 2714–2723, 1997.
[13]
H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma, “The missing term in effective pair potentials,” Journal of Physical Chemistry, vol. 91, no. 24, pp. 6269–6271, 1987.
[14]
S. Leekumjorn, Y. Wu, A. K. Sum, and C. Chan, “Experimental and computational studies investigating trehalose protection of HepG2 cells from palmitate-induced toxicity,” Biophysical Journal, vol. 94, no. 7, pp. 2869–2883, 2008.
[15]
D. P. Tieleman and H. J. C. Berendsen, “A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer,” Biophysical Journal, vol. 74, no. 6, pp. 2786–2801, 1998.
[16]
H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak, “Molecular dynamics with coupling to an external bath,” The Journal of Chemical Physics, vol. 81, no. 8, pp. 3684–3690, 1984.
[17]
A. A. Spector, “Fatty acid binding to plasma albumin,” Journal of Lipid Research, vol. 16, no. 3, pp. 165–179, 1975.
[18]
G. Hummer and A. Szabo, “Free energy reconstruction from nonequilibrium single-molecule pulling experiments,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 7, pp. 3658–3661, 2001.
[19]
C. Jarzynski, “Equilibrium free-energy differences from nonequilibrium measurements: a master-equation approach,” Physical Review E, vol. 56, no. 5, pp. 5018–5035, 1997.
[20]
C. Jarzynski, “Nonequilibrium equality for free energy differences,” Physical Review Letters, vol. 78, no. 14, pp. 2690–2693, 1997.
[21]
S. Park, F. Khalili-Araghi, E. Tajkhorshid, and K. Schulten, “Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality,” Journal of Chemical Physics, vol. 119, no. 6, pp. 3559–3566, 2003.
[22]
E. G. D. Cohen and M. David, “A note on the Jarzynski equality,” Journal of Statistical Mechanics, vol. 2004, Article ID P07006, 17 pages, 2004.
[23]
C. Jarzynski, “Nonequilibrium work theorem for a system strongly coupled to a thermal environment,” Journal of Statistical Mechanics, vol. 2004, Article ID P09005, 2004.
