Dasgupta Rubin, Ganguly Himal K, Modugula E K, Basu Gautam
Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India.
Biopolymers. 2017 Jan;108(1). doi: 10.1002/bip.22919.
Helix N-capping motifs often form hydrogen bonds with terminal amide groups which otherwise would be free. Also, without an amide hydrogen, proline (trans) is over-represented at helix N-termini (N1 position) because this naturally removes the need to hydrogen bond one terminal amide. However, the preference of cisPro, vis-à-vis helix N-termini, is not known. We show that cisPro (α or PP ) often appears at the N-cap position (N0) of helices. The N-cap cisPro(α ) is associated with a six-residue sequence motif - X -X -cisPro-X -X -X - with preference for Glu/Gln at X , Phe/Tyr/Trp at X and Ser/Thr at X . The motif, formed by the fusion of a helix and a type VIa β-turn, contains a hydrogen bond between the side chain of X and the side chain/backbone of X , a α-helical hydrogen bond between X and X and stacking interaction between cisPro and an aromatic residue at X . NMR experiments on peptides containing the motif and its variants showed that local interactions associated with the motif, as found in folded proteins, were not enough to significantly tilt the cis/trans equilibrium towards cisPro. This suggests that some other evolutionary pressure must select the cisPro motif (over transPro) at helix N-termini. Database analysis showed that >C = O of the pre-cisPro(α ) residue at the helix N-cap, directed opposite to the N→C helical axis, participates in long-range interactions. We hypothesize that the cisPro(α ) motif is preferred at helix N-termini because it allows the helix to participate in long-range interactions that may be structurally and functionally important.
螺旋N端封端基序常常与原本会游离的末端酰胺基团形成氢键。此外，由于脯氨酸（反式）没有酰胺氢，它在螺旋N端（N1位置）的含量过高，因为这自然消除了与一个末端酰胺形成氢键的需求。然而，关于顺式脯氨酸相对于螺旋N端的偏好情况尚不清楚。我们发现顺式脯氨酸（α或PP）常常出现在螺旋的N端封端位置（N0）。N端封端的顺式脯氨酸（α）与一个六残基序列基序相关联——X -X -顺式脯氨酸-X -X -X -，在X位置偏好谷氨酸/谷氨酰胺，在X位置偏好苯丙氨酸/酪氨酸/色氨酸，在X位置偏好丝氨酸/苏氨酸。这个由一个螺旋和一个VIa型β转角融合形成的基序，在X的侧链与X的侧链/主链之间存在一个氢键，在X和X之间存在一个α螺旋氢键，以及顺式脯氨酸与X位置的一个芳香族残基之间存在堆积相互作用。对包含该基序及其变体的肽段进行的核磁共振实验表明，如在折叠蛋白中所发现的与该基序相关的局部相互作用，不足以显著地使顺式/反式平衡向顺式脯氨酸倾斜。这表明一定存在其他一些进化压力在螺旋N端选择了顺式脯氨酸基序（而非反式脯氨酸基序）。数据库分析表明，位于螺旋N端封端位置的前顺式脯氨酸（α）残基的>C = O，其方向与N→C螺旋轴相反，参与了长程相互作用。我们推测顺式脯氨酸（α）基序在螺旋N端更受青睐是因为它使螺旋能够参与可能在结构和功能上都很重要的长程相互作用。
