Christlet T H, Biswas M, Veluraja K
Department of Physics, Manonmaniam Sundaranar University, Tirunelveli 627 012, Tamil Nadu, India.
Acta Crystallogr D Biol Crystallogr. 1999 Aug;55(Pt 8):1414-20. doi: 10.1107/s0907444999006010.
An analysis of the frequency of occurrence of various residues at position X was carried out on the consensus glycosylating sequence Asn-X-Ser/Thr using the PDB three-dimensional database. 488 non-homologous proteins bearing 696 Asn-X-Ser/Thr (X not equal Pro) sequences were analysed. More than 65% of Asn residues, when they occur as part of the consensus sequence, lie on the surface of the protein, implying a potentiality for glycosylation. A deviation parameter (DP) was calculated as a measure of preferential (positive) or non-preferential (negative) selection. At the X position in the consensus-sequence segment, the amino acids Gly, Asn and Phe have statistically significant positive DP values. The high value of DP for Asn is a consequence of the preferential occurrence of homodoublets, while for Phe it may be a consequence of the stacking interaction of the aromatic ring with the glycan. Gly at the X position in the consensus glycosylating sequence may be functionally significant owing to its preference and its high percentage of occurrence in proteins. The Ramachandran (Phi,Psi) angles around Gly in the consensus sequence show clustering in the region which is disallowed for non-glycyl residues. In this region, a hydrogen bond between the side chain of Asn and the peptide backbone/side chain of Ser/Thr is possible, reflecting a positional as well as a conformational role in the consensus glycosylating sequence. For the 44 confirmed N-glycosylating sequences, an in-depth analysis of the (Psi(N), Phi(X), Psi(X), Phi(S/T)) dihedral angles, which position the side chains of Asn and Ser/Thr, shows that these can be grouped into nine conformational states. In most cases, a direct or water-mediated hydrogen bond between OD1 of Asn and OG of Ser/Thr is possible, reflecting the possible importance of this hydrogen bonding in the glycosylation process.
利用蛋白质数据银行（PDB）三维数据库，对共有糖基化序列天冬酰胺- X -丝氨酸/苏氨酸中X位置上各种残基的出现频率进行了分析。分析了含有696个天冬酰胺- X -丝氨酸/苏氨酸（X不等于脯氨酸）序列的488种非同源蛋白质。超过65%的天冬酰胺残基作为共有序列的一部分出现时，位于蛋白质表面，这意味着存在糖基化的可能性。计算了一个偏差参数（DP），作为优先（正）或非优先（负）选择的量度。在共有序列片段的X位置，甘氨酸、天冬酰胺和苯丙氨酸的氨基酸具有统计学上显著的正DP值。天冬酰胺的DP值高是同型双峰优先出现的结果，而苯丙氨酸的DP值高可能是芳香环与聚糖堆积相互作用的结果。共有糖基化序列中X位置的甘氨酸因其偏好性及其在蛋白质中出现的高百分比，可能具有功能意义。共有序列中甘氨酸周围的拉氏（φ，ψ）角在非甘氨酸残基不允许的区域呈聚集状态。在该区域，天冬酰胺侧链与丝氨酸/苏氨酸的肽主链/侧链之间可能形成氢键，这反映了在共有糖基化序列中的位置和构象作用。对于44个已确认的N -糖基化序列，对定位天冬酰胺和丝氨酸/苏氨酸侧链的（ψ（N），φ（X），ψ（X），φ（S/T））二面角进行的深入分析表明，这些二面角可分为9种构象状态。在大多数情况下，天冬酰胺的OD1与丝氨酸/苏氨酸的OG之间可能形成直接或水介导的氢键，这反映了这种氢键在糖基化过程中的可能重要性。
