Extended knobs-into-holes packing in classical and complex coiled-coil …
2003年12月1日 · Recently, we developed a program, SOCKET, to recognise knobs-into-holes packing in protein structures, which we applied to the Protein Data Bank to compile a database of coiled-coil structures. In addition to classic structures, the database reveals 4-helix bundles and larger helical assemblies.
Rosetta BundleGridSampler: 参数化生成Coiled-Coil结构 - 知乎
Coiled-Coil (α-螺旋卷曲螺旋)是蛋白质折叠或蛋白质相互识别界面中普遍存在的一种四级结构形态，通常表现为两个或以上的α-螺旋围绕着中心轴线相互缠绕并形成超螺旋。 最经典的Coiled-Coi模型是以7个氨基酸为重复基序的形式构成 (hpphppp, h=疏水氨基酸，p=极性氨基酸)，其结构特征满足knobs-into-holes (KIH) 规则。如下图，两股α螺旋相互缠绕，接触界面的氨基酸分别处于a, d, g位。 其中a,d为均为疏水氨基酸（多为I和L两种氨基酸类型），一股螺旋的a,d位氨基酸分别 …
Coiled coil - Wikipedia
The packing in a coiled-coil interface is exceptionally tight, with almost complete van der Waals contact between the side-chains of the a and d residues. This tight packing was originally predicted by Francis Crick in 1952 [5] and is referred to as Knobs into holes packing.
Socket2: a program for locating, visualizing and analyzing coiled-coil ...
2021年9月8日 · The interactions between CC helices are tight and well-defined. These are known as knobs-into-holes (KIH) interactions as first proposed by Crick (1953). A ‘knob’ is defined as a side chain that projects from one helix and packs into a …
Extended knobs-into-holes packing in classical and complex coiled-coil ...
Recently, we developed a program, SOCKET, to recognise knobs-into-holes packing in protein structures, which we applied to the Protein Data Bank to compile a database of coiled-coil structures. In addition to classic structures, the database reveals 4 …
A seven-helix coiled coil - PNAS
2006年10月17日 · The canonical knobs-into-holes packing of coiled coils confers exquisite sensitivity to the stereochemical properties of the core a and d residues. Interior packing of the side chains at the a and d positions, in fact, has been shown to …
The Structure of α-Helical Coiled Coils - ScienceDirect
2005年1月1日 · Crick called the bundle of supercoiled helices a coiled coil and referred to the regular packing of side chains as “knobs” into “holes.” The coiled coils would contain two or three parallel α-helices, supercoiled in the opposite sense of the helices.
A library of coiled-coil domains: from regular bundles to peculiar ...
2020年12月12日 · The hallmark of coiled-coil structures is a specific mode of interaction between helices, termed knobs-into-holes (Walshaw et al., 2001), in which a residue from one helix (knob) packs into a cavity formed by side-chains of residues from the opposing helix (or helices).
Applying graph theory to protein structures: an Atlas of coiled coils ...
2018年5月2日 · We have developed a Python-based API, iSOCKET, and used tools from graph theory to identify α-helical coiled coils automatically via their knobs-into-holes (KIH) interactions between partnering α helices (Crick, 1953; Walshaw and Woolfson, 2001, 2003), and to classify these into an Atlas of Coiled Coils.iSOCKET enables both expert and non ...
The Structure and Topology of α-Helical Coiled Coils
2017年1月19日 · The constituent helices of coiled coils interact via a knobs-into-holes geometry of amino-acid sidechains at their interface (Crick 1952, 1953b). In this geometry, a residue from one helix (knob) packs into a space surrounded by four sidechains of the facing helix (hole).