Lins Laurence, Thomas Annick, Brasseur Robert
Centre de Biophysique Moléculaire Numérique, Faculté des Sciences Agronomiques de Gembloux, Passage des Déportés 2, 5030 Gembloux, Belgium.
Protein Sci. 2003 Jul;12(7):1406-17. doi: 10.1110/ps.0304803.
We analyzed the total, hydrophobic, and hydrophilic accessible surfaces (ASAs) of residues from a nonredundant bank of 587 3D structure proteins. In an extended fold, residues are classified into three families with respect to their hydrophobicity balance. As expected, residues lose part of their solvent-accessible surface with folding but the three groups remain. The decrease of accessibility is more pronounced for hydrophobic than hydrophilic residues. Amazingly, Lysine is the residue with the largest hydrophobic accessible surface in folded structures. Our analysis points out a clear difference between the mean (other studies) and median (this study) ASA values of hydrophobic residues, which should be taken into consideration for future investigations on a protein-accessible surface, in order to improve predictions requiring ASA values. The different secondary structures correspond to different accessibility of residues. Random coils, turns, and beta-structures (outside beta-sheets) are the most accessible folds, with an average of 30% accessibility. The helical residues are about 20% accessible, and the difference between the hydrophobic and the hydrophilic residues illustrates the amphipathy of many helices. Residues from beta-sheets are the most inaccessible to solvent (10% accessible). Hence, beta-sheets are the most appropriate structures to shield the hydrophobic parts of residues from water. We also show that there is an equal balance between the hydrophobic and the hydrophilic accessible surfaces of the 3D protein surfaces irrespective of the protein size. This results in a patchwork surface of hydrophobic and hydrophilic areas, which could be important for protein interactions and/or activity.
我们分析了来自587个非冗余3D结构蛋白质库中残基的总可及表面积（ASA）、疏水可及表面积和亲水可及表面积。在伸展构象中，残基根据其疏水性平衡被分为三类。正如预期的那样，残基在折叠时会失去部分溶剂可及表面，但这三类仍然存在。疏水残基的可及性降低比亲水残基更明显。令人惊讶的是，赖氨酸是折叠结构中疏水可及表面积最大的残基。我们的分析指出了疏水残基的平均（其他研究）和中位数（本研究）ASA值之间的明显差异，在未来关于蛋白质可及表面的研究中应考虑这一点，以便改进需要ASA值的预测。不同的二级结构对应于残基的不同可及性。无规卷曲、转角和β结构（β折叠片外）是最易接近的构象，平均可及性为30%。螺旋残基的可及性约为20%，疏水残基和亲水残基之间的差异说明了许多螺旋的两亲性。β折叠片中的残基对溶剂最不可及（可及性为10%）。因此，β折叠片是保护残基疏水部分免受水影响的最合适结构。我们还表明，无论蛋白质大小如何，3D蛋白质表面的疏水和亲水可及表面之间存在平衡。这导致了疏水和亲水区域的拼凑表面，这可能对蛋白质相互作用和/或活性很重要。
