An amino acid code for irregular and mixed protein packing.
An amino acid code for irregular and mixed protein packing.
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作者：
Joo H;Chavan AG;Fraga KJ;Tsai J
为了加深我们对蛋白质三级结构的理解，本文在分析不规则卷曲和转弯二级结构堆积以及混合二级结构之间堆积的基础上，发展了knob-socket模型。旋钮插座模型基于2个图案的重复模式简化了包装：3个残基插座用于2°结构内的包装，4个残基旋钮插座用于3°包装。对于卷曲和转角二级结构，旋钮插座允许鉴定氨基酸组成和空间三级排列之间的相关性。卷曲对三级堆积的贡献几乎与α-螺旋一样多。不规则二级结构涉及连续接触残基的3个残基团或XYZ插座。在不规则插座中，Gly、Pro、Asp和Ser受到青睐，而Cys、His、Met和Trp不受青睐。对于不规则旋钮，偏好顺序是Arg、Asp、Pro、Asn、Thr、Leu和Gly，而Cys、His、Met和Trp不是。在混合包装中，旋钮氨基酸的偏好是它们包装的插座的功能，而插座的氨基酸组成不依赖于旋钮的二级结构。具有XYZ β-折叠插座的线圈旋钮的独特图案可能潜在地起到抑制β-折叠延伸的作用。此外，分析β-折叠和混合α-螺旋/β-折叠内的链的优选交叉角确定了可用于蛋白质设计的典型堆积模式。最后，球窝模型将蛋白质三级结构的复杂性抽象为一个直观的堆积表面拓扑图。
To advance our understanding of protein tertiary structure, the development of the knob-socket model is completed in an analysis of the packing in irregular coil and turn secondary structure packing as well as between mixed secondary structure. The knob-socket model simplifies packing based on repeated patterns of 2 motifs: a 3 residue socket for packing within 2° structure and a 4 residue knob-socket for 3° packing. For coil and turn secondary structure, knob-sockets allow identification of a correlation between amino acid composition and tertiary arrangements in space. Coil contributes almost as much as α-helices to tertiary packing. Irregular secondary structure involves 3 residue cliques of consecutive contacting residues or XYZ sockets. In irregular sockets, Gly, Pro, Asp and Ser are favored, while Cys, His, Met and Trp are not. For irregular knobs, the preference order is Arg, Asp, Pro, Asn, Thr, Leu, and Gly, while Cys, His, Met and Trp are not. In mixed packing, the knob amino acid preferences are a function of the socket that they are packing into, whereas the amino acid composition of the sockets does not depend on the secondary structure of the knob. A unique motif of a coil knob with an XYZ β-sheet socket may potentially function to inhibit β-sheet extension. In addition, analysis of the preferred crossing angles for strands within a β-sheet and mixed α-helices/β-sheets identifies canonical packing patterns useful in protein design. Lastly, the knob-socket model abstracts the complexity of protein tertiary structure into an intuitive packing surface topology map.
影响因子：
2.9
作者：
Hu, Chengcheng;Koehl, Patrice;Max, Nelson
通讯作者：
Max, Nelson