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Review
. 2016 Jun 15;44(3):937-43.
doi: 10.1042/BST20160053.

Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure modelling

Antonina Andreeva  1
Affiliations
Review

Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure modelling

Antonina Andreeva. Biochem Soc Trans. .

Abstract

The Structural Classification of Proteins (SCOP) database has facilitated the development of many tools and algorithms and it has been successfully used in protein structure prediction and large-scale genome annotations. During the development of SCOP, numerous exceptions were found to topological rules, along with complex evolutionary scenarios and peculiarities in proteins including the ability to fold into alternative structures. This article reviews cases of structural variations observed for individual proteins and among groups of homologues, knowledge of which is essential for protein structure modelling.

Keywords: Structural Classification of Proteins (SCOP); homology modelling; metamorphic proteins; protein structure evolution.

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Figures

Figure 1
Figure 1. Conformational transitions in proteins
Side by side comparison of alternative conformers of: (A) α-apical domain of the thermosome: I) isolated domain (PDB 1ASS), II) domain from the closed thermosome (PDB 1A6E); the region that undergoes a secondary structural transition from α to β is indicated with a black arrow and coloured in orange in the secondary structure plot; (B) Mad2: I) O-Mad2 (PDB 1DUJ), II) I-Mad2 (PDB 3GMH, chain B), III) C-Mad2 (PDB 3GMH, chain E); the regions that undergo a structural change and a β-to-α transition are coloured in light blue and in orange respectively; (C) apolipoprotein A: I) lipid-free form (PDB 2A01), II) lipid-bound form (PDB 2MSD); (D) RfaH: I) closed form (PDB 2OUG), II) open form (PDB 2LCL). The secondary structure plots refer only to portions of each structure that are shown in particular colours (e.g. green in (A), grey in (B), blue in (C), red in (D)). All figures were prepared using Pymol (http://www.pymol.org).
Figure 2
Figure 2. Evolution of protein structures
(A) Superposition of Sm-proteins. Structures are shown in ribbon and coloured as follows: in yellow – Sm D1 (PDB 1B34, chain A), in green – Sm D2 (PDB 4PJO, chain D), in blue – Sm D3 (PDB 1D3B, chain A), in red – Sm B (PDB 1D3B, chain B), in black – Sm F (PDB 1N9R, chain A). A sequence logo showing the degree of amino acid conservation derived from the structure-based sequence alignment is shown below. (B) Side by side comparison of the structures of two Cro-proteins. I) Pfl6 (PDB 2PIJ) and II) Xfaso1 (PDB 3BD1); BLASTP pair-wise sequence alignment with 45% identity over 55 residues and one 5 residue gap; (C) fold decay event in the glutamate synthase central domain; the FMN-binding domain is shown in purple (PDB 1OFD, chain A, residues 840–1210) and the central domain in blue (PDB 1OFD, chain A, residues 490–735); structurally equivalent regions are shown in cartoon and the rest in ribbon. (D) Large insertion in an α-helix in the structures of two nonspecific endonucleases. I) Nuclease A from Anabaena sp. (PDB 1ZM8); II) Nuclease A from Streptococcus agalactiae (PDB 4QH0).
Figure 3
Figure 3. Examples of proteins with unusual topologies
(A) Loop crossing in the structure of DinI (PDB 1GHH); (B) trefoil knot in the MJ0366 structure (PDB 2EFV); (C) left-handed β–α–β connection in the structure of a protein with unknown function shew_3726 (PDB 2GPI); a black arrow indicates the location of the unusual topological feature; a schematic drawing of each feature is shown next to each structure for clarity, (D) structure of the hexadeca-haem cytochrome Hmc that does not possess a compact hydrophobic core (PDB 1GWS); (E) high contact order structure of DinB protein (PDB 2F22).
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