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]
Prediction tools
[edit]Experimentally predicting RSA is an expensive and time-consuming task. In recent decades, several computational methods have been introduced for RSA prediction.[7][8][9]
References
[edit]- ^ a b c d e f g h 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. arXiv:1211.4251. Bibcode:2013PLoSO...880635T. doi:10.1371/journal.pone.0080635. PMC 3836772. PMID 24278298.
- ^ a b c d Miller, S.; Janin, J.; Lesk, A. M.; Chothia, C. (1987). "Interior and surface of monomeric proteins". J. Mol. Biol. 196 (3): 641–656. doi:10.1016/0022-2836(87)90038-6. PMID 3681970.
- ^ a b c d 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 (4716): 834–838. Bibcode:1985Sci...229..834R. doi:10.1126/science.4023714. PMID 4023714. S2CID 22227053.
- ^ Kabsch, W.; Sander, C. (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features". Biopolymers. 22 (12): 2577–2637. doi:10.1002/bip.360221211. PMID 6667333. S2CID 29185760.
- ^ 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 (3): 216–26. doi:10.1002/prot.340200303. PMID 7892171. S2CID 19285647. Retrieved 10 April 2015.
- ^ Kaleel, Manaz; Torrisi, Mirko; Mooney, Catherine; Pollastri, Gianluca (2019-09-01). "PaleAle 5.0: prediction of protein relative solvent accessibility by deep learning". Amino Acids. 51 (9): 1289–1296. doi:10.1007/s00726-019-02767-6. hdl:10197/11324. ISSN 1438-2199. PMID 31388850. S2CID 199469523.
- ^ Wang, Sheng; Li, Wei; Liu, Shiwang; Xu, Jinbo (2016-07-08). "RaptorX-Property: a web server for protein structure property prediction". Nucleic Acids Research. 44 (W1): W430–W435. doi:10.1093/nar/gkw306. ISSN 0305-1048. PMC 4987890. PMID 27112573.
- ^ Magnan, Christophe N.; Baldi, Pierre (2014-09-15). "SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity". Bioinformatics. 30 (18): 2592–2597. doi:10.1093/bioinformatics/btu352. ISSN 1367-4803. PMC 4215083. PMID 24860169.