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. 2012 Jan;4(1):23-34.

In silico Evaluation of Crosslinking Effects on Denaturant m(eq) values and ΔCp upon Protein Unfolding

Maryam Hamzeh-Mivehroud  1 , Ali Akbar Alizade, Monire Ahmadifar, Siavoush Dastmalchi
Affiliations

In silico Evaluation of Crosslinking Effects on Denaturant m(eq) values and ΔCp upon Protein Unfolding

Maryam Hamzeh-Mivehroud et al. Avicenna J Med Biotechnol. 2012 Jan.

Abstract

Important thermodynamic parameters including denaturant equilibrium m values (m(eq)) and heat capacity changes (ΔCp) can be predicted based on changes in Solvent Accessible Surface Area (SASA) upon unfolding. Crosslinks such as disulfide bonds influence the stability of the proteins by decreasing the entropy gain as well as reduction of SASA of unfolded state. The aim of the study was to develop mathematical models to predict the effect of crosslinks on ΔSASA and ultimately on m(eq) and ΔCp based on in silico methods. Changes of SASA upon computationally simulated unfolding were calculated for a set of 45 proteins with known m(eq) and ΔCp values and the effect of crosslinks on ΔSASA of unfolding was investigated. The results were used to predict the m(eq) of denaturation for guanidine hydrochloride and urea, as well as ΔCp for the studied proteins with overall error of 20%, 31% and 17%, respectively. The results of the current study were in close agreement with those obtained from the previous studies.

Keywords: Crosslinks; Disulfides; Protein stability; Thermodynamics.

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Figures

Figure 1
Figure 1
Dependence of A) m eq value for Gdn HCl denaturation, B) m eq value for urea denaturation, and C) heat capacity changes upon unfolding on ΔSASA for the 45 proteins shown in Table 1
Figure 2
Figure 2
Dependence of A) m eq value for GdnHCI denaturation, B) m eq value for urea denaturation, and C) heat capacity changes upon unfolding on ΔSASA after correction for the effect of crosslinks by taking out 918.5 Å 2 per crosslink for the 45 proteins in our data set (see text for further explanation)
Figure 3
Figure 3
Molecular dynamics simulation of IgG binding domain of protein G (PDB code 1PGB) solvated in 4.4 M urea in water at 500 °K for 10 ns using GROMOS-96 force field parameters. The non-protein molecules (i.e. water and urea) are not shown for the sake of clarity
Figure 4
Figure 4
Molecular dynamics simulation of lysozyme (hen egg white) (PDB code 1AKI) solvated in 4.4 M urea in water at 500 °K for 10 ns using GROMOS-96 force field parameters
See this image and copyright information in PMC

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References

    1. Uhlen M, Ponten F. Antibody-based proteomics for human tissue profiling. Mol Cell Proteomics. 2005;4(4):384–393. - PubMed
    1. Berg JM, Tymoczko JL, Stryer L. Biochemistry. 6th ed. New York: W.H. Freeman; 2006.
    1. Morris MB, Dastmalchi S, Church WB. Rhodopsin: structure, signal transduction and oligomerisation. Int J Biochem Cell Biol. 2009;41(4):721–724. - PubMed
    1. Winklhofer KF, Tatzelt J, Haass C. The two faces of protein misfolding: gain- and loss-of-function in neurodegenerative diseases. EMBO J. 2008;27(2):336–349. - PMC - PubMed
    1. Stefani M. Protein misfolding and aggregation: new examples in medicine and biology of the dark side of the protein world. Biochim Biophys Acta. 2004;1739(1):5–25. - PubMed

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