Abstract
Serum C-reactive protein (CRP) is used as a marker of inflammation in several diseases including autoimmune disease and cardiovascular disease. CRP, a member of the pentraxin family, is comprised of five identical subunits. CRP has diverse ligand-binding properties which depend upon different structural states of CRP. However, little is known about the molecular dynamics and interaction properties of CRP. In this study, we used SAPS, SCRATCH protein predictor, PDBsum, ConSurf, ProtScale, Drawhca, ASAView, SCide and SRide server and performed comprehensive analyses of molecular dynamics, protein–protein and residue–residue interactions of CRP. We used 1GNH.pdb file for the crystal structure of human CRP which generated two pentamers (ABCDE and FGHIJ). The number of residues involved in residue–residue interactions between A–B, B–C, C–D, D–E, F–G, G–H, H–I, I–J, A–E and F–J subunits were 12, 11, 10, 11, 12, 11, 10, 11, 10 and 10, respectively. Fifteen antiparallel β sheets were involved in β-sheet topology, and five β hairpins were involved in forming the secondary structure. Analysis of hydrophobic segment distribution revealed deviations in surface hydrophobicity at different cavities present in CRP. Approximately 33 % of all residues were involved in the stabilization centers. We show that the bioinformatics tools can provide a rapid method to predict molecular dynamics and interaction properties of CRP. Our prediction of molecular dynamics and interaction properties of CRP combined with the modeling data based on the known 3D structure of CRP is helpful in designing stable forms of CRP mutants for structure–function studies of CRP and may facilitate in silico drug design for therapeutic targeting of CRP.
Similar content being viewed by others
References
Agrawal, A., Singh, P. P., Bottazzi, B., Garlanda, C., & Mantovani, A. (2009). Pattern recognition by pentraxins. Advances in Experimental Medicine and Biology, 653, 98–116.
Agrawal, A., Hammond, D. J., Jr, & Singh, S. K. (2010). Atherosclerosis-related functions of C-reactive protein. Cardiovascular & Hematological Disorders: Drug Targets, 10, 235–240.
Pepys, M. B., Dash, A. C., Fletcher, T. C., Richardson, N., Munn, E. A., et al. (1978). Analogues in other mammals and in fish of human plasma proteins C-reactive protein and amyloid P component. Nature, 273, 168–177.
Kushner, I., Rzewnicki, D., & Samols, D. (2006). What does minor elevation of C-reactive protein signify? American Journal of Medicine, 119(166), e17–e28.
Ridker, P. M., Cushman, M., Stampfer, M. J., Tracy, R. P., & Hennekens, C. H. (1997). Inflammation, aspirin, and the risk of cardiovascular disease in apparently healthy men. The New England Journal of Medicine, 336, 973–979.
Shrive, A. K., Cheetham, G. M., Holden, D., Myles, D. A., Turnell, W. G., et al. (1996). Three dimensional structure of human C-reactive protein. Nature Structural Biology, 3, 346–354.
Thompson, D., Pepys, M. B., & Wood, S. P. (1999). The physiological structure of human C-reactive protein and its complex with phosphocholine. Structure, 7, 169–177.
Volanakis, J. E., & Kaplan, M. H. (1971). Specificity of C-reactive protein for choline phosphate residues of pneumococcal C-polysaccharide. Proceedings of the Society for Experimental Biology and Medicine, 136, 612–614.
Singh, S. K., Hammond, D. J., Jr, Beeler, B. W., & Agrawal, A. (2009). The binding of C-reactive protein, in the presence of phosphoethanolamine, to low-density lipoproteins is due to phosphoethanolamine-generated acidic pH. Clinica Chimica Acta, 409, 143–144.
Hammond, D. J., Jr, Singh, S. K., Thompson, J. A., Beeler, B. W., Rusiñol, A. E., et al. (2010). Identification of acidic pH-dependent ligands of pentameric C-reactive protein. Journal of Biological Chemistry, 285, 36235–36244.
Singh, S. K., Thirumalai, A., Hammond, D. J., Jr, Pangburn, M. K., Mishra, V. K., et al. (2012). Exposing a hidden functional site of C-reactive protein by site-directed mutagenesis. Journal of Biological Chemistry, 287, 3550–3558.
Potempa, L. A., Siegel, J. N., Fiedel, B. A., Potempa, R. T., & Gewurz, H. (1987). Expression, detection and assay of a neoantigen (Neo-CRP) associated with a free, human C-reactive protein subunit. Molecular Immunology, 24, 531–541.
Verma, S., Szmitko, P. E., & Yeh, E. T. (2004). C-reactive protein, structure affects function. Circulation, 109, 1914–1917.
Ji, S. R., Wu, Y., Potempa, L. A., Qiu, Q., & Zhao, J. (2006). Interactions of C-reactive protein with low-density lipoproteins, implications for an active role of modified C-reactive protein in atherosclerosis. International Journal of Biochemistry & Cell Biology, 38, 648–661.
Ji, S. R., Wu, Y., Zhu, L., Potempa, L. A., Sheng, F. L., et al. (2007). Cell membranes and liposomes dissociate C-reactive protein (CRP) to form a new, biologically active structural intermediate, mCRP(m). Journal of Federation of American Societies for Experimental Biology, 21, 284–294.
Boncler, M., & Watała, C. (2009). Regulation of cell function by isoforms of C-reactive protein, a comparative analysis. Acta Biochimica Polonica, 56, 17–31.
Eisenhardt, S. U., Habersberger, J., Murphy, A., Chen, Y. C., Woollard, K. J., et al. (2009). Dissociation of pentameric to monomeric C-reactive protein on activated platelets localizes inflammation to atherosclerotic plaques. Circulation Research, 105, 128–137.
Pepys, M. B., Hirschfield, G. M., Tennent, G. A., Gallimore, J. R., Kahan, M. C., et al. (2006). Targeting C-reactive protein for the treatment of cardiovascular disease. Nature, 440, 1217–1221.
Tokuriki, N., Stricher, F., Serrano, L., & Tawfik, D. S. (2008). How protein stability and new functions trade off. PLoS Computational Biology, 4, e1000002.
Shoichet, B. K., Baase, W. A., Kuroki, R., & Matthews, B. W. (1995). A relationship between protein stability and protein function. Proceedings of the National Academy of Sciences of the United States of America, 92, 452–456.
Gutierrez, H., Castillo, A., Monzon, J., & Urrutia, A. O. (2011). Protein amino acid composition, a genomic signature of encephalization in mammals. PLoS ONE, 6, e27261.
Marques, J. R., da Fonseca, R. R., Drury, B., & Melo, A. (2010). Amino acid patterns around disulfide bonds. International Journal of Molecular Sciences, 11, 4673–4686.
Bhattacharyya, R., Pal, D., & Chakrabarti, P. (2004). Disulfide bonds, their stereospecific environment and conservation in protein structures. Protein Engineering, Design & Selection, 17, 795–808.
Hogg, P. J. (2003). Disulfide bonds as switches for protein function. Trends in Biochemical Sciences, 28, 210–214.
Klink, T. A., Woycechowsky, K. J., Taylor, K. M., & Raines, R. T. (2000). Contribution of disulfide bonds to the conformational stability and catalytic activity of ribonuclease A. European Journal of Biochemistry, 267, 566–572.
Sardiu, M. E., Cheung, M. S., & Yi-Kuo, Y. (2007). Cysteine-cysteine contact preference leads to target-focusing in protein folding. Journal of Biophysics, 93, 938–951.
Wedemeyer, W. J., Welker, E., Narayan, M., & Scheraga, H. A. (2000). Disulfide bonds and protein folding. Biochemistry, 39, 4208–4216.
Kamat, A. P., & Lesk, A. M. (2007). Contact patterns between helices and strands of sheet define protein folding patterns. Proteins, 66, 869–876.
Chikalov, I., Yao, P., Moshkov, M., & Latombe, J. C. (2011). Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories. BMC Bioinformatics, 12(Suppl 1), S34.
Manning, J. R., Jefferson, E. R., & Barton, G. J. (2008). The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. BMC Bioinformatics, 9, 51.
Chakraborty, C., Agoramoorthy, G., & Hsu, M. J. (2011). Exploring the evolutionary relationship of insulin receptor substrate family using computational biology. PLoS ONE, 6, e16580.
Higurashi, M., Ishida, T., & Kinoshita, K. (2008). Identification of transient hub proteins and the possible structural basis for their multiple interactions. Protein Science, 17, 72–78.
Chakraborty, C., Roy, S. S., Hsu, M. J., & Agoramoorthy, G. (2011). Landscape mapping of functional proteins in insulin signal transduction and insulin resistance, a network-based protein–protein interaction analysis. PLoS ONE, 6, e16388.
Privalov, P. L. (1979). Stability of proteins, small globular proteins. Advances in Protein Chemistry, 33, 167–241.
Baldwin, R. L. (1986). Temperature dependence of the hydrophobic interaction in protein folding. Proceedings of the National Academy of Sciences of the United States of America, 83, 8069–8072.
Dill, K. A. (1990). Dominant forces in protein folding. Biochemistry, 29, 7133–7155.
Stigter, D., & Dill, K. A. (1990). Charge effects on folded and unfolded proteins. Biochemistry, 29, 1262–1271.
Andjelković, U., Theisgen, S., Scheidt, H. A., Petković, M., Huster, D., et al. (2012). The thermal stability of the external invertase isoforms from Saccharomyces cerevisiae correlates with the surface charge density. Biochimie, 94, 510–515.
Simon, Á., Dosztányi, Z., Magyar, C., Szirtes, G., Rajnavölgyi, É., et al. (2001). Stabilization centers and protein stability. Theoretical Chemistry Accounts, Theory, Computation, and Modeling, 106, 121–127.
Dosztányi, Z., Fiser, A., & Simon, I. (1997). Stabilization centers in proteins, identification, characterization and predictions. Journal of Molecular Cell Biology, 272, 597–612.
Gilis, D., & Rooman, M. (1997). Predicting protein stability changes upon mutation using database-derived potentials, solvent accessibility determines the importance of local versus non-local interactions along the sequence. Journal of Molecular Cell Biology, 272, 276–290.
Sayers, E. W., Barrett, T., Benson, D. A., Bolton, E., Bryant, S. H., et al. (2011). Database resources of the national center for biotechnology information. Nucleic Acids Research, 39, D38–D51.
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., et al. (2000). The protein data bank. Nucleic Acids Research, 28, 235–242.
Brendel, V., Bucher, P., Nourbakhsh, I., Blaisdell, B. E., & Karlin, S. (1992). Methods and algorithms for statistical analysis of protein sequences. Proceedings of the National Academy of Sciences of the United States of America, 89, 2002–2006.
Cheng, J., Randall, A. Z., Sweredoski, M. J., & Baldi, P. (2005). SCRATCH, a protein structure and structural feature prediction server. Nucleic Acids Research, 33, W72–W76.
Laskowski, R. A. (2001). PDBsum, summaries and analyses of PDB structures. Nucleic Acids Research, 29, 221–222.
Laskowski, R. A., Chistyakov, V. V., & Thornton, J. M. (2005). PDBsum more, new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Research, 33, D266–D268.
Laskowski, R. A. (2009). PDBsum new things. Nucleic Acids Research, 37, D355–D359.
Hutchinson, E. G., & Thornton, J. M. (1990). HERA, a program to draw schematic diagrams of protein secondary structures. Proteins, 8, 203–212.
Ashkenazy, H., Erez, E., Martz, E., Pupko, T., & Ben-Tal, N. (2010). ConSurf 2010, calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Research, 38, W529–W533.
Roseman, M. A. (1988). Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds. Journal of Molecular Biology, 200, 513–522.
Callebaut, I., Labesse, G., Durand, P., Poupon, A., Canard, L., et al. (1997). Deciphering protein sequence information through hydrophobic cluster analysis (HCA), current status and perspectives. Cellular and Molecular Life Sciences, 53, 621–645.
Shrake, A., & Rupley, J. A. (1973). Environment and exposure to solvent of protein atoms, Lysozyme and insulin. Journal of Molecular Biology, 79, 351–371.
Ahmad, S., Gromiha, M., Fawareh, H., & Sarai, A. (2004). ASAView, database and tool for solvent accessibility representation in proteins. BMC Bioinformatics, 5, 51.
Glaser, F., Pupko, T., Paz, I., Bell, R. E., Bechor-Shental, D., et al. (2003). ConSurf, identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics, 19, 163–164.
Dosztányi, Z. S., Magyar, C. S., Tusnády, G. E., & Simon, I. (2003). SCide, identification of stabilization centers in proteins. Bioinformatics, 19, 899–900.
Magyar, C., Gromiha, M. M., Pujadas, G., Tusnády, G. E., & Simon, I. (2005). SRide, a server for identifying stabilizing residues in proteins. Nucleic Acids Research, 33, W303–W305.
Gromiha, M. M., Pujadas, G., Magyar, C., Selvaraj, S., & Simon, I. (2004). Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation. Proteins, 55, 316–329.
Wang, M. Y., Ji, S. R., Bai, C. J., El Kebir, D., Li, H. Y., et al. (2011). A redox switch in C-reactive protein modulates activation of endothelial cells. Journal of Federation of American Societies for Experimental Biology, 25, 3186–3196.
Ji, S. R., Ma, L., Bai, C. J., Shi, J. M., Li, H. Y., et al. (2009). Monomeric C-reactive protein activates endothelial cells via interaction with lipid raft micro-domains. Journal of Federation of American Societies for Experimental Biology, 23, 1806–1816.
Chemel, B. R., Bonner, L. A., Watts, V. J., & Nichols, D. E. (2012). Ligand-specific roles for transmembrane 5 serine residues in the binding and efficacy of dopamine D(1) receptor catechol agonists. Molecular Pharmacology, 81, 729–738.
Ma, B., Elkayam, T., Wolfson, H., & Nussinov, R. (2003). Protein-protein interactions, structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proceedings of the National Academy of Sciences of the United States of America, 100, 5772–5777.
Kumar, S. V., Ravunny, R. K., & Chakraborty, C. (2011). Conserved domains, conserved residues, and surface cavities of C-reactive protein (CRP). Applied Biochemistry and Biotechnology, 165, 497–505.
Khreiss, T., Jozsef, L., Hossain, S., Chan, J. S., Potempa, L. A., et al. (2002). Loss of pentameric symmetry of C-reactive protein is associated with delayed apoptosis of human neutrophils. The Journal of Biological Chemistry, 277, 40775–40781.
Emsley, J., White, H. E., O’Hara, B. P., Oliva, G., Srinivasan, N., et al. (1994). Structure of pentameric human serum amyloid P component. Nature, 367, 338–345.
Politi, R., & Harries, D. (2010). Enthalpically driven peptide stabilization by protective osmolytes. Chemical Communications (Cambridge, England), 46, 6449–6451.
Srinivasan, N., White, H. E., Emsley, J., Wood, S. P., Pepys, M. B., et al. (1994). Comparative analyses of pentraxins, implications for protomer assembly and ligand binding. Structure, 2, 1017–1027.
Politi, R., & Harries, D. (2011). Unraveling the molecular mechanism of enthalpy driven peptide folding by polyol osmolytes. Journal of Chemical Theory and Computation, 7, 3816–3828.
Bourgeas, R., Basse, M.-J., Morelli, X., & Roche, P. (2010). Atomic analysis of protein–protein interfaces with known inhibitors, the 2P2I database. PLoS ONE, 5, e9598.
Munson, M., Balasubramanian, S., Fleming, K. G., Nagi, A. D., O’Brien, R., et al. (1996). What makes a protein a protein? Hydrophobic core designs that specify stability and structural properties. Protein Science, 5, 1584–1593.
Dill, K. A., Bromberg, S., Yue, K., Fiebig, K. M., Yee, D. P., et al. (1995). Principles of protein folding, a perspective from simple exact models. Protein Science, 4, 561–602.
Giovambattista, N., Lopez, C. F., Rossky, P. J., & Debenedetti, P. G. (2008). Hydrophobicity of protein surfaces: Separating geometry from chemistry. Proceedings of the National Academy of Sciences of the United States of America, 105, 2274–2279.
Ponnuswamy, P. K. (1993). Hydrophobic characteristics of folded proteins. Progress in Biophysics and Molecular Biology, 59, 57–103.
Agrawal, A., Simpson, M. J., Black, S., Carey, M. P., & Samols, D. (2002). A C-reactive protein mutant that does not bind to phosphocholine and pneumococcal C-polysaccharide. Journal of Immunology, 169, 3217–3222.
Black, S., Agrawal, A., & Samols, D. (2003). The phosphocholine and the polycation-binding sites on rabbit C-reactive protein are structurally and functionally distinct. Molecular Immunology, 39, 1045–1054.
Bang, R., Marnell, L., Mold, C., Stein, M. P., Clos, K. T., et al. (2005). Analysis of binding sites in human C-reactive protein for Fc{gamma}RI, Fc{gamma}RIIA, and C1q by site-directed mutagenesis. The Journal of Biological Chemistry, 280, 25095–25102.
Yue, C. C., Muller-Greven, J., Dailey, P., Lozanski, G., Anderson, V., & Macintyre, S. (1996). Identification of a C-reactive protein binding site in two hepatic carboxylesterases capable of retaining C-reactive protein within the endoplasmic reticulum. The Journal of Biological Chemistry, 271, 22245–22250.
Black, S., Kushner, I., & Samols, D. (2004). C-reactive protein. The Journal of Biological Chemistry, 279, 48487–48490.
Gaboriaud, C., Juanhuix, J., Gruez, A., Lacroix, M., & Darnault, C. (2003). The crystal structure of the globular head of complement protein C1q provides a basis for its versatile recognition properties. The Journal of Biological Chemistry, 278, 46974–46982.
Stigter, D., Alonso, D. O., & Dill, K. A. (1991). Protein stability, electrostatics and compact denatured states. Proceedings of the National Academy of Sciences of the United States of America, 88, 4176–4180.
Abkevich, V. I., Gutin, A. M., & Shakhnovich, E. I. (1995). Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. The Journal of Biological Chemistry, 252, 460–471.
Mirny, L. A., & Shakhnovich, E. (1996). How to drive a protein folding potential? A new approach to an old problem. The Journal of Biological Chemistry, 264, 1164–1179.
Bahar, I., & Jernigan, R. L. (1997). Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. The Journal of Biological Chemistry, 266, 195–214.
Dosztányi, Z., Fiser, A., & Simon, I. (1997). Stabilization centers in proteins, identification, characterization and predictions. The Journal of Biological Chemistry, 272, 597–612.
Ponnuswamy, P. K., & Gromiha, M. M. (1994). On the conformational stability of folded proteins. Journal of Theoretical Biology, 166, 63–74.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Chakraborty, C., Agrawal, A. Computational Analysis of C-Reactive Protein for Assessment of Molecular Dynamics and Interaction Properties. Cell Biochem Biophys 67, 645–656 (2013). https://doi.org/10.1007/s12013-013-9553-4
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12013-013-9553-4