Physics: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: [math]\displaystyle{ \text{RSA} = \text{ASA} / \text{MaxASA} }[/math] [1]
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 [math]\displaystyle{ {\AA}^2 }[/math].
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 [math]\displaystyle{ \phi=-120^\circ }[/math] and [math]\displaystyle{ \psi=140^\circ }[/math].[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 [math]\displaystyle{ \phi=-50^\circ }[/math] and [math]\displaystyle{ \psi=-45^\circ }[/math]. 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.Cite error: Closing </ref> missing for <ref> tag
Prediction tools
Experimentally predicting RSA is an expensive and time-consuming task. In recent decades, several computational methods have been introduced for RSA prediction.[5][6][7]
References
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 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. PMID 24278298. Bibcode: 2013PLoSO...880635T.
- ↑ 2.0 2.1 2.2 2.3 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.
- ↑ 3.0 3.1 3.2 3.3 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. doi:10.1126/science.4023714. PMID 4023714. Bibcode: 1985Sci...229..834R.
- ↑ 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.
- ↑ Kaleel, Manaz; Torrisi, Mirko; Mooney, Catherine; Pollastri, Gianluca (2019-09-01). "PaleAle 5.0: prediction of protein relative solvent accessibility by deep learning" (in en). Amino Acids 51 (9): 1289–1296. doi:10.1007/s00726-019-02767-6. ISSN 1438-2199. PMID 31388850.
- ↑ Wang, Sheng; Li, Wei; Liu, Shiwang; Xu, Jinbo (2016-07-08). "RaptorX-Property: a web server for protein structure property prediction" (in en). Nucleic Acids Research 44 (W1): W430–W435. doi:10.1093/nar/gkw306. ISSN 0305-1048. 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" (in en). Bioinformatics 30 (18): 2592–2597. doi:10.1093/bioinformatics/btu352. ISSN 1367-4803. PMID 24860169.
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