An amino acid code for β-sheet packing structure.
An amino acid code for β-sheet packing structure.
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DOI：
10.1002/prot.24569
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发表时间：
2014-09
影响因子：
2.9
通讯作者：
Tsai, Jerry
中科院分区：
文献类型：
--
作者：
Joo, Hyun;Tsai, Jerry
为了了解蛋白质序列和结构之间的关系，本工作将旋钮插座模型扩展到β-Sheet包装的研究中。在一组全面的β-Sheet折叠中，残基之间的接触被用来识别堆积集团：所有相互接触的残基集合。然后根据大小和联系顺序对这些包装集团进行分类。根据这一分析，表征了描述β-Sheet包装所需的两种类型的4个残基填充团。两者都发生在相邻的两条氢键β链之间。首先，定义β-Sheet中的二级结构填充，组合Socket或XY：HG口袋由一条链上的4个残基i，i+2和另一条链上的j，j+2组成。其次，表征β-Sheet之间的三次堆积，旋钮插座XY：H+B由一个3个残基XY：H插座(一条链上有i，i+2，另一条链上有j)与一个旋钮B残基(按顺序k远的残基)填充组成。根据旋钮B残留物的堆积深度，可以发现两种类型的旋钮插座：侧链插座和主链插座。口袋和旋钮插座的氨基酸组成揭示了β-Sheet包装的序列特异性。对于β-Sheet形成，XY：HG口袋清楚地显示了氨基酸的序列特异性。对于三次填充，XY：H+B侧链和主链插座在每个位置都显示出不同的氨基酸偏好。这些关系定义了β-Sheet结构的氨基酸编码，并提供了β-Sheet包装的直观拓扑图。
To understand the relationship between protein sequence and structure, this work extends the knob-socket model in an investigation of β-sheet packing. Over a comprehensive set of β-sheet folds, the contacts between residues were used to identify packing cliques: sets of residues that all contact each other. These packing cliques were then classified based on size and contact order. From this analysis, the 2 types of 4 residue packing cliques necessary to describe β-sheet packing were characterized. Both occur between 2 adjacent hydrogen bonded β-strands. First, defining the secondary structure packing within β-sheets, the combined socket or XY:HG pocket consists of 4 residues i,i+2 on one strand and j,j+2 on the other. Second, characterizing the tertiary packing between β-sheets, the knob-socket XY:H+B consists of a 3 residue XY:H socket (i,i+2 on one strand and j on the other) packed against a knob B residue (residue k distant in sequence). Depending on the packing depth of the knob B residue, 2 types of knob-sockets are found: side-chain and main-chain sockets. The amino acid composition of the pockets and knob-sockets reveal the sequence specificity of β-sheet packing. For β-sheet formation, the XY:HG pocket clearly shows sequence specificity of amino acids. For tertiary packing, the XY:H+B side-chain and main-chain sockets exhibit distinct amino acid preferences at each position. These relationships define an amino acid code for β-sheet structure and provide an intuitive topological mapping of β-sheet packing.
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影响因子：
2.9
作者：
CHOTHIA, C;JANIN, J
通讯作者：
JANIN, J
影响因子：
5.6
作者：
Budyak, Ivan L.;Zhuravleva, Anastasia;Gierasch, Lila M.
通讯作者：
Gierasch, Lila M.
影响因子：
22.7
作者：
BRON, C;KERBOSCH, J
通讯作者：
KERBOSCH, J
影响因子：
5.7
作者：
HARPAZ, Y;GERSTEIN, M;CHOTHIA, C
通讯作者：
CHOTHIA, C
DOI：
10.1073/pnas.78.7.4146
发表时间：
1981-01-01
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES
影响因子：
--
作者：
CHOTHIA, C;JANIN, J
通讯作者：
JANIN, J