Newell Nicholas E
Independent Scientist, Reading, MA 01867, United States.
Bioinformatics. 2024 Dec 26;41(1). doi: 10.1093/bioinformatics/btae741.
Beta turns are the most common type of secondary structure in proteins after alpha helices and beta sheets and play many key structural and functional roles. Turn backbone (BB) geometry has been classified at multiple levels of precision, but the current picture of side chain (SC) structure and interaction in turns is incomplete, because the distribution of SC conformations associated with each sequence motif has commonly been represented only by a static image of a single, typical structure for each turn BB geometry, and only motifs which specify a single amino acid (e.g. aspartic acid at turn position 1) have been systematically investigated. Furthermore, no general evaluation has been made of the SC interactions between turns and their BB neighborhoods. Finally, the visualization and comparison of the wide range of turn conformations has been hampered by the almost exclusive characterization of turn structure in BB dihedral-angle (Ramachandran) space.
This work introduces MapTurns, a web server for motif maps, which employ a turn-local Euclidean-space coordinate system and a global turn alignment to comprehensively map the distributions of BB and SC structure and H-bonding associated with sequence motifs in beta turns and their local BB contexts. Maps characterize many new SC motifs, provide detailed rationalizations of sequence preferences, and support mutational analysis and the general study of SC interactions, and they should prove useful in applications such as protein design.
MapTurns is available at www.betaturn.com. Sample code is available at: https://github.com/nenewell/MapTurns/tree/main.
β转角是蛋白质中仅次于α螺旋和β折叠的最常见二级结构类型，发挥着许多关键的结构和功能作用。转角主链（BB）几何结构已在多个精度级别上进行了分类，但目前关于转角侧链（SC）结构和相互作用的情况并不完整，因为与每个序列基序相关的SC构象分布通常仅由每个转角BB几何结构的单个典型结构的静态图像表示，并且仅对指定单个氨基酸的基序（例如转角位置1处的天冬氨酸）进行了系统研究。此外，尚未对转角与其BB邻域之间的SC相互作用进行全面评估。最后，由于几乎完全在BB二面角（拉氏）空间中表征转角结构，阻碍了对广泛转角构象的可视化和比较。
这项工作引入了MapTurns，一个用于基序图谱的网络服务器，它采用转角局部欧几里得空间坐标系和全局转角比对，以全面绘制与β转角及其局部BB环境中的序列基序相关的BB和SC结构以及氢键的分布。图谱表征了许多新的SC基序，提供了序列偏好的详细解释，并支持突变分析和SC相互作用的一般研究，它们在蛋白质设计等应用中应该会很有用。
MapTurns可在www.betaturn.com上获取。示例代码可在：https://github.com/nenewell/MapTurns/tree/main获取。
