Disulfide Bond Analysis
What are disulfide bonds
Protein disulfide bonds are the links between the sulfur atoms of two cysteine amino acids. This motif is also called a cystine residue. All life forms, from viruses to mammals, make this bond.
How they form
Disulfide bonds are formed in proteins as they mature in the cell [1]. This maturation mostly occurs in the endoplasmic reticulum and mitochondrial inter-membrane space in eukaryotic cells [2] and in the periplasmic space in bacteria [3]. The formation of disulfide bonds is assisted by the oxidoreductases. The active-site(s) of these enzymes contain a reactive dithiol/disulfide that undergoes cycles of oxidation/reduction with disulfides or dithiols in the protein substrate resulting in reduction, formation or interchange of disulfide bonds in the maturing protein [4].
Their evolution
The cysteine content of proteins has increased as proteins have evolved [5,6]. Moreover, cysteines involved in disulfide bonds are significantly more conserved than cysteines not involved in disulfide bonds [7]. They are even more conserved than tryptophans, which is the most conserved amino acid. Over all eukaryotic species, > 90% of disulfide bonds are conserved once acquired [7]. There is also a positive correlation between the rate of disulfide bond acquisition and organismal complexity [7]. The faster rate of accrual of disulfide bonds in complex organisms is in accordance with the greater diversity and sophistication of protein function in these species.
Types of disulfide bonds
Disulfide bonds perform either a structural or functional role [8]. Most disulfide bonds are structural and assist protein folding and stabilize the tertiary and quaternary structure. A proportion of disulfide bonds serve a functional role in the mature protein. There are two types of functional disulfide: the catalytic and allosteric bonds. The catalytic bonds are found at the active sites of the oxidoreductases [4]. The allosteric disulfide bonds control the function of the protein in which they reside by mediating a change when they are reduced or oxidized [9,10]. Allosteric control is defined as a change in one site, the allosteric site, that influences another site by exploiting the protein's flexibility [11]. By definition, therefore, cleavage or formation of an allosteric disulfide bond influences another site in the protein. The influence at the other site can manifest as new ligand binding, for example [12]. The redox state of the allosteric disulfides are controlled by catalytic disulfides of the oxidoreductases [8].
Disulfide bond configurations
Disulfide bond geometry is described in terms of the five chi (χ) angles that make up the cystine residue (see figure at right). By convention, there are three fundamental types of disulfide bonds based on the sign of the central three (χ2, χ3 and χ2’) torsional angles [13,14]. These are the spirals, hooks or staples. The disulfides are further characterised as right- or left-handed according to whether the sulfur-sulfur bond angle (χ3) is positive or negative, respectively. There are 20 possible disulfide bond configurations when all five bond angles of the cystine are taken into account [9]. The –LHSpiral configuration accounts for about one quarter of disulfide bonds. Nearly all the catalytic bonds are +/–RHHook's, while the –RHStaple is the most common configuration of the known allosteric disulfides [15,16]. A common aspect of the allosteric bonds identified to date is that they link beta-strands or beta-loops [8].
Disulfide bond analysis tool
Below is our software tool for analysing disulfide bonds [17]. Different geometric measures, secondary structural information and solvent accessibility values of the disulfide bonds are provided. Any structure from the PDB can be analysed by entering its PDB identifier. Alternatively, custom PDB files may be uploaded. The analysis can be downloaded as an Excel 97-2003 spreadsheet.
The analysis of the disulfides from all of the PDB, both X-ray and NMR structures (about 85,000 bonds currently), can be directly downloaded. This analysis will be updated every month.
disulfide_analysis_19_Apr_2012.zip
This web service also provides a remote API for accessing the analysis software. An example of how to do this is below:
where the PDB ID 1cdj may be replaced with any PDB ID in the RCSB Protein Data Bank.
For detailed documentation/tutorial of how to use the Disulfide Bond Analysis tool click here.
References
1. Depuydt M, Messens J, Collet JF. How proteins form disulfide bonds. Antioxid Redox Signal. 2011;15(1):49-66.
2. Braakman I, Bulleid NJ. Protein folding and modification in the mammalian endoplasmic reticulum. Annu Rev Biochem. 2011;80:71-99.
3. Nakamoto H, Bardwell JC. Catalysis of disulfide bond formation and isomerization in the Escherichia coli periplasm. Biochim Biophys Acta. 2004;1694(1-3):111-119.
4. Berndt C, Lillig CH, Holmgren A. Thioredoxins and glutaredoxins as facilitators of protein folding. Biochim Biophys Acta. 2008;1783(4):641-650.
5. Brooks DJ, Fresco JR, Lesk AM, Singh M. Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code. Mol Biol Evol. 2002;19(10):1645-1655.
6. Jordan IK, Kondrashov FA, Adzhubei IA, et al. A universal trend of amino acid gain and loss in protein evolution. Nature. 2005;433(7026):633-638.
7. Wong JWH, Ho SYW, Hogg PJ. Disulfide bond acquisition through eukaryotic protein evolution. Mol Biol Evol. 2011;28:327-334.
8. Azimi I, Wong JW, Hogg PJ. Control of mature protein function by allosteric disulfide bonds. Antioxid Redox Signal. 2010;14(1):113-126.
9. Schmidt B, Ho L, Hogg PJ. Allosteric disulfide bonds. Biochemistry. 2006;45(24):7429-7433.
10. Schmidt B, Hogg PJ. Search for allosteric disulfide bonds in NMR structures. BMC Struct Biol. 2007;7:49.
11. Monod J, Wyman J, Changeux JP. On the nature of allosteric transitions: a plausible model. J Mol Biol. 1965;12:88-118.
12. Ganderton T, Wong JWH, Schroeder C, Hogg PJ. Lateral self-association of von Willebrand Factor involves the Cys2431-Cys2453 disulfide/dithiol in the C2 domain. Blood. 2011;118:5312-5318.
13. Richardson J, Richardson D. Prediction of protein structure and the principles of protein conformation. New York: Plenum Press; 1989.
14. Harrison PM, Sternberg MJ. The disulphide beta-cross: from cystine geometry and clustering to classification of small disulphide-rich protein folds. J Mol Biol. 1996;264(3):603-623.
15. Matthias LJ, Azimi I, Tabrett CA, Hogg PJ. Reduced monomeric CD4 is the preferred receptor for HIV. J Biol Chem. 2010;285(52):40793-40799.
16. Azimi I, Matthias LJ, Center RJ, Wong JW, Hogg PJ. Disulfide bond that constrains the HIV-1 gp120 V3 domain is cleaved by thioredoxin. J Biol Chem. 2010;285(51):40072-40080.
17. Wong JW, Hogg PJ. Analysis of disulfide bonds in protein structures. J Thromb Haemost. 2010;8:2345. |  |