Relative accessible surface area
Relative accessible surface area or relative solvent accessibility (RSA) of a protein residue is a measure of residue solvent exposure. It can be calculated by formula:
where ASA is the solvent accessible surface area and MaxASA is the maximum possible solvent accessible surface area for the residue.[1] Both ASA and MaxASA are commonly measured in .
To measure the relative solvent accessibility of the residue side-chain only, one usually takes MaxASA values that have been obtained from Gly-X-Gly tripeptides, where X is the residue of interest. Several MaxASA scales have been published[1][2][3] and are commonly used (see Table).
Residue | Tien et al. 2013 (theor.)[1] | Tien et al. 2013 (emp.)[1] | Miller et al. 1987[2] | Rose et al. 1985[3] |
---|---|---|---|---|
Alanine | 129.0 | 121.0 | 113.0 | 118.1 |
Arginine | 274.0 | 265.0 | 241.0 | 256.0 |
Asparagine | 195.0 | 187.0 | 158.0 | 165.5 |
Aspartate | 193.0 | 187.0 | 151.0 | 158.7 |
Cysteine | 167.0 | 148.0 | 140.0 | 146.1 |
Glutamate | 223.0 | 214.0 | 183.0 | 186.2 |
Glutamine | 225.0 | 214.0 | 189.0 | 193.2 |
Glycine | 104.0 | 97.0 | 85.0 | 88.1 |
Histidine | 224.0 | 216.0 | 194.0 | 202.5 |
Isoleucine | 197.0 | 195.0 | 182.0 | 181.0 |
Leucine | 201.0 | 191.0 | 180.0 | 193.1 |
Lysine | 236.0 | 230.0 | 211.0 | 225.8 |
Methionine | 224.0 | 203.0 | 204.0 | 203.4 |
Phenylalanine | 240.0 | 228.0 | 218.0 | 222.8 |
Proline | 159.0 | 154.0 | 143.0 | 146.8 |
Serine | 155.0 | 143.0 | 122.0 | 129.8 |
Threonine | 172.0 | 163.0 | 146.0 | 152.5 |
Tryptophan | 285.0 | 264.0 | 259.0 | 266.3 |
Tyrosine | 263.0 | 255.0 | 229.0 | 236.8 |
Valine | 174.0 | 165.0 | 160.0 | 164.5 |
In this table, the more recently published MaxASA values (from Tien et al. 2013[1]) are systematically larger than the older values (from Miller et al. 1987[2] or Rose et al. 1985[3]). This discrepancy can be traced back to the conformation in which the Gly-X-Gly tripeptides are evaluated to calculate MaxASA. The earlier works used the extended conformation, with backbone angles of and .[2][3] However, Tien et al. 2013[1] demonstrated that tripeptides in extended conformation fall among the least-exposed conformations. The largest ASA values are consistently observed in alpha helices, with backbone angles around and . Tien et al. 2013 recommend to use their theoretical MaxASA values (2nd column in Table), as they were obtained from a systematic enumeration of all possible conformations and likely represent a true upper bound to observable ASA.[1]
ASA and hence RSA values are generally calculated from a protein structure, for example with the software DSSP.[4] However, there is also an extensive literature attempting to predict RSA values from sequence data, using machine-learning approaches.[5] [6]
References
- 1 2 3 4 5 6 7 8 Tien, M. Z.; Meyer, A. G.; Sydykova, D. K.; Spielman, S. J.; Wilke, C. O. (2013). "Maximum allowed solvent accessibilites of residues in proteins". PLoS ONE. 8 (11): e80635. doi:10.1371/journal.pone.0080635.
- 1 2 3 4 Miller, S.; Janin, J.; Lesk, A. M.; Chothia, C. (1987). "Interior and surface of monomeric proteins". J. Mol. Biol. 196: 641–656.
- 1 2 3 4 Rose, G. D.; Geselowitz, A. R.; Lesser, G. J.; Lee, R. H.; Zehfus, M. H. (1985). "Hydrophobicity of amino acid residues in globular proteins". Science. 229: 834–838.
- ↑ Kabsch, W.; Sander, C. (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features". Biopolymers. 22: 2577–2637.
- ↑ Hyunsoo, Kim; Haesun, Park (2003). "Prediction of Protein Relative Solvent Accessibility with Support Vector Machines and Long-range Interaction 3D Local Descriptor" (PDF). Retrieved 10 April 2015.
- ↑ Rost, Burkhard; Sander, Chris (1994). "Conservation and prediction of solvent accessibility in protein families". Proteins. 20: 218. doi:10.1002/prot.340200303. PMID 7892171. Retrieved 10 April 2015.