蛋白质结构：几何、拓扑与分类原理

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"该资源是一篇关于蛋白质结构的学术文章，涵盖了蛋白质的几何形状、拓扑结构以及结构比较和分类的详细内容。作者探讨了蛋白质的重要性、基本结构原则，包括不同类型的蛋白质形状（如纤维状、球状和膜蛋白）、疏水核心、二级结构、蛋白质的堆积方式以及桶状结构和β螺旋。此外，文章还深入讨论了结构比较方法，如动态规划、基于特征的序列比对、距离矩阵匹配和几何哈希方法，以及评估结构相似性的显著性标准和蛋白质结构分类的方法。" 文章首先介绍了蛋白质的基本概念，强调了蛋白质在生物体中的重要性，如作为生命活动的执行者和遗传信息的表达者。作者通过三个类别——纤维蛋白、球状蛋白和膜蛋白，阐述了蛋白质的多样形态，并讨论了疏水核心在蛋白质稳定性中的作用。接着，介绍了蛋白质的二级结构，如α螺旋和β折叠，以及蛋白质结构中的堆积层次，包括全α、全β和α-β蛋白质。在蛋白质结构比较和分类部分，文章提出了结构比较的挑战和不同难度等级，分析了手动、半自动和基于片段的方法，以及早期和简单的比较策略。动态规划技术被用来进行序列比对，同时讨论了插入罚分和结构偏置插入罚分的概念。文章进一步探讨了无需动态规划的三维方法，如距离矩阵匹配、二级结构图匹配和几何哈希方法。此外，还详细介绍了利用结构叠加和内部特征关系的动态规划方法，以及评估显著性的各种策略，如已知结构的得分分布、随机模型和生物学意义的评分。最后，文章讨论了蛋白质结构分类的实际应用，如基因组研究，以及当前分类方法的局限性和未来展望。分类的单位、层次组织和分类问题被逐一阐述，提出了蛋白质结构分类在未来如何帮助我们理解蛋白质功能和进化的新问题。该资源为读者提供了蛋白质结构的全面概述，不仅涵盖了基础知识，还深入到高级的结构比较和分类技术，是理解蛋白质结构与功能关系的宝贵资料。

be ignored in a more detailed analysis (Eﬁmov, 1993) including recurring com-

binations of secondary structures (Eﬁmov, 1991a; Eﬁmov, 1991b; Eﬁmov, 1987)

commonly referred to as isuper-secondary structure.

2.4 Packed layers

The simplicity of having eﬀectively only two secondary structures is that there

are only three (pairwise) combinations of them that can be used to construct

proteins; so giving the three major structural classes: 1) α with α,2)α with

β and 3) β with βi (Levitt and Chothia, 1976). (For detailed analysis of each

class, see: 1) Chothia et al. (1981), Lesk and Chothia (1980); 2) Cohen et al.

(1981), Chothia and Janin (1981), Chothia and Janin (1982), and 3) Cohen et al.

(1982), With the main-chain atoms tied-up in secondary structure, a core can

be constructed using any mixture of α or β building blocks. Incorporation of a

β-sheet, however, imposes a long-range constraint across the structure. The β-

sheet has free hydrogen-bonds on its two edges, which consequently prevents the

sheet from terminating in the hydrophobic core. This divides the core into two

and, if considered more generally, imposes a layered structure onto the further

arrangement of secondary structures in the protein. (See Figure 3 for examples).

(See both Chothia and Finkelstein (1990) and Finkelstein and Ptitsyn (1987) for

further consideration of protein structure along these lines.)

2.4.1 All-α proteins

The all-α protein class is dominated by small folds, many of which form a sim-

ple bundle with helices running up then down (Figure 3(b)). The interactions

between helices are not discrete (in the way that hydrogen bonds in a β-sheet

are either there or not) which makes their classiﬁcation more diﬃcult (Lesk and

Chothia, 1980). Set against this, however, the size of the α-helix (which is gener-

ally larger than a β-strand) gives more interatomic contacts with its neighbours

(relative to the a β-strand) allowing interactions to be more clearly deﬁned. (Fig-

ure 3(b)).

2.4.2 All-β proteins

The all-β proteins are often characterised by the number of β-sheets in the struc-

tureandthenumberanddirectionofβ-strands in the sheet. This leads to a fairly

rigid classiﬁcation scheme (Richardson, 1977) which can be sensitive to the exact

deﬁnition of hydrogen-bonds and β-strands. Being less rigid than an α-helix,

the β-sheets can be relatively distorted — often with diﬀering degrees of twist

of fragmented or extra strands on the edges of the sheet. (Figure 3(a)). Various

patterns can be identiﬁed in the arrangement of the β-strands, often giving rise

to the identiﬁcation of recurring motifs (Hutchinson and Thornton, 1993).

analysis.)

A barrel can also be formed with the β-strands running in the orthogonal

direction (leaving free hydrogen-bonds on the open ends of the barrel). This

structure, however, completely dictates the course of the protein chain (as a sim-

ple helix) giving little scope for evolutionary exploitation of the fold for diﬀerent

functions. (See Chothia and Murzin (1993) for some examples). This type of

structure is associated more with structural (ﬁbrous) proteins.

2.6 Protein Topology

The path of the chain through the various layers of packed secondary structures

described above (sometimes referred to as frameworks or architectures) is referred

to as the fold of the chain. As this entails various degrees of cross-linking through

hydrogen-bonds, it is also possible to, loosely, view it from a topological perspec-

tive. This topic will be returned to in detail in Part III but, ﬁrstly, a few basic

aspects will be considered here which are relevant to the later discussions. (See

Ptitsyn and Finkelstein (1980) for a general review.) The course of the chain

through the secondary structure frameworks is largely unrestricted. Two con-

straints, however, are well observed. The strongest is that two loops cannot cross

on the same face between layers (Ptitsyn and Finkelstein, 1980)

. The source

of this constraint is a simple consequence of the bulk of the polypeptide chain:

if two loops cross, one will be buried by the other which will be energetically

unfavourable unless the buried loop can satisfy its main-chain hydrogen-bonds.

Having done this however, the loop is now probably a secondary structure and

so the rule that loops do not cross is preserved.

The second strong constraint derives from the chiral nature of the central (α)

carbon in each residue. This favours a particular (right) handedness for the α-

helix and a corresponding twist to the β-sheet which is left-handed when viewed

along the chain direction. Together, these local chiralities result in a strong

preference for connections between strands in the same sheet to be right-handed

(even when there is no α-helix involved). The few exceptions to this rule are seen

when the chain meanders to a remote part of the structure (another domain)

and the ‘context’ of the local constraint is lost (Sternberg and Thornton, 1977b)

(Figure 6). Some chiral eﬀect are also detected in the ββα and αββ arrangements

(Kajva, 1992) and in the packing of four α-helices (Weber and Salemme, 1980;

Presnell and Cohen, 1989).

2.7 Domain structure

Large hydrophobic cores are not found in globular proteins, probably because of

limitations in the folding kinetics and stability. Single compact units of more

An exception has been found in the protein with PDB code 2csmA.

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