Cyrus Chothia

SCOP : A structural classification of proteins database for the investigation of sequences and structures

To facilitate understanding of, and access to, the information available for protein structures, we have constructed the Structural Classification of Proteins (scop) database. This database provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structure. It also provides for each entry links to co-ordinates, images of the structure, interactive viewers, sequence data and literature references. Two search facilities are available. The homology search permits users to enter a sequence and obtain a list of any structures to which it has significant levels of sequence similarity. The key word search finds, for a word entered by the user, matches from both the text of the scop database and the headers of Brookhaven Protein Databank structure files. The database is freely accessible on World Wide Web (WWW) with an entry point to URL http: parallel scop.mrc-lmb.cam.ac.uk magnitude of scop.

The relation between the divergence of sequence and structure in proteins.

Homologous proteins have regions which retain the same general fold and regions where the folds differ. For pairs of distantly related proteins (residue identity approximately 20%), the regions with the same fold may comprise less than half of each molecule. The regions with the same general fold differ in structure by amounts that increase as the amino acid sequences diverge. The root mean square deviation in the positions of the main chain atoms, delta, is related to the fraction of mutated residues, H, by the expression: delta(A) = 0.40 e1.87H.

Structural patterns in globular proteins.

A simple diagrammatic representation has been used to show the arrangement of α helices and β sheets in 31 globular proteins, which are classified into four clearly separated classes. The observed arrangements are significantly non-random in that pieces of secondary structure adjacent in sequence along the polypeptide chain are also often in contact in three dimensions.

The nature of the accessible and buried surfaces in proteins.

The accessible surface areas have been calculated for the individual residues in 12 proteins, and for the extended chains, the secondary structures and tertiary structure of six proteins. The results include the following: 1. (1) The formation of α-helices and β-pleated sheets from an extended chain buries a greater proportion of polar surface than non-polar and gives 2 to 3 kcal/mol of hydrophobic free energy per residue. 2. (2) The surfaces buried between the secondary structures are very hydrophobic: being two-thirds non-polar and having more than half the polar part formed by groups that hydrogen bond within their own piece of secondary structure, or which are partially accessible to the solvent. 3. (3) As the six proteins increase in molecular weight they bury an increasing proportion of their non-polar surface (60 to 79%), but a constant proportion of their polar surface (75%). The implications of these results for the theory of protein structure are discussed. In the Appendix it is shown that the accessible surface area of folded proteins is simply proportional to the two-thirds power of their molecular weight.

SCOP: a Structural Classification of Proteins database

The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known proteins structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. SCOP also provides for each structure links to atomic co-ordinates, images of the structures, interactive viewers, sequence data, data on any conformational changes related to function and literature references. The database is freely accessible on the World Wide Web (WWW) with an entry point at URL http://scop.mrc-lmb.cam.ac.uk/scop/

Data growth and its impact on the SCOP database: new developments

The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. The SCOP hierarchy comprises the following levels: Species, Protein, Family, Superfamily, Fold and Class. While keeping the original classification scheme intact, we have changed the production of SCOP in order to cope with a rapid growth of new structural data and to facilitate the discovery of new protein relationships. We describe ongoing developments and new features implemented in SCOP. A new update protocol supports batch classification of new protein structures by their detected relationships at Family and Superfamily levels in contrast to our previous sequential handling of new structural data by release date. We introduce pre-SCOP, a preview of the SCOP developmental version that enables earlier access to the information on new relationships. We also discuss the impact of worldwide Structural Genomics initiatives, which are producing new protein structures at an increasing rate, on the rates of discovery and growth of protein families and superfamilies. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop.

Hydrophobic bonding and accessible surface area in proteins.

THE hydrophobic bond is the term used by Kauzmann1 to describe the gain in free energy on the transfer of non-polar residues from an aqueous environment to the interior of proteins. This has been accepted as one of the major forces involved in the folding of proteins. The exact origin of the energy of the hydrophobic bond is controversial2, but empirical values have been derived for 10 protein residue side chains by Nozaki and Tanford3 who measured the solubility of amino acids in the organic solvents ethanol and dioxane.

Haemoglobin: the structural changes related to ligand binding and its allosteric mechanism.

Abstract The structural changes that occur on ligand binding to haemoglobin have been studied by comparison of the atomic co-ordinates of human deoxy, horse met and human carbonmonoxy haemoglobin, using computer graphics and least-squares fitting methods. The changes that occur on going from deoxy to either of the liganded forms are very similar. These include tertiary structure changes within the α1β1 dimer and a quaternary structure change in which the packing of α1β1 against α2β2 alters. On going from deoxy to liganded haemoglobin, no significant structural change occurs in the central regions of the α1β1 dimer, including the α1β1 interface and nearby helices B, C, G and H in both subunits. Movements occur in the outer parts of the dimer, where the haems, F helices and FG corners of both subunits move towards the centre of the molecule. The two haems and the two FG corners come ~2 A closer together. One important effect of the changes in both subunits is to translate the F helix across the face of the haem by ~1 A. This moves the haem-linked histidine F8 from a position that is asymmetric with respect to the porphyrin nitrogens in deoxy to a more symmetric position in liganded haemoglobin. The motion of the β haem removes the ligand-binding site from the vicinity of ValβE11, which hinders ligand binding in deoxy. The changes in tertiary structure are linked to the quaternary change through the motion of the FG corners. The C helices and FG corners of α1β1 are in contact with the FG corners and C helices of α2β2 in both quaternary structures. In the quaternary change the contacts between α1FG and β2C and between α2FG and β1C act as “flexible joints” allowing small relative motions. The same side-chains are involved in the contacts in both structures. The contacts between α1C and β2FG and between α2C and β1FG act as “switch” regions, having two different stable positions with different side-chains in contact. The change between the two positions involves a relative movement of ~6 A. The quaternary structure change to liganded haemoglobin destroys the contacts made by the C-terminal residues of each subunit in deoxy haemoglobin, and these residues rotate freely in the liganded form. These structural results, together with other work, particularly the calculations of Gelin & Karplus and of Warshel, support a description of the haemoglobin mechanism in which (1) the binding of ligand to the deoxy form is accompanied by steric strain, originating from the particular position of the F helix and of His F8 relative to the haem. (2) The strain leads to decreased stability of the deoxy quaternary structure relative to the liganded quaternary structure, so that the proportion of molecules in the high-affinity form increases as successive ligands bind. (3) The quaternary structure change to the high-affinity form induces tertiary structure changes that reposition the F helix and HisF8 relative to the haem and there is then no strain on ligand binding. In the absence of ligand the deoxy structure is favoured by the greater surface area buried between α1β1 and α2β2 in this quaternary structure. Further implications of the structural results are discussed.

How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins.

To determine how different amino acid sequences form similar protein structures, and how proteins adapt to mutations that change the volume of residues buried in their close-packed interiors, we have analysed and compared the atomic structures of nine different globins. The homology of the sequences in the two most distantly related molecules is only 16%. The principal determinants of three-dimensional structure of these proteins are the approximately 59 residues involved in helix to helix and helix to haem packings. Half of these residues are buried within the molecules. The observed variations in the sequence keep the side-chains of buried residues non-polar, but do not maintain their size: the mean variation of the volume among homologous amino acids is 56 A3. Changes in the volumes of buried residues are accompanied by changes in the geometry of the helix packings. The relative positions and orientations of homologous pairs of helices in the globins differ by rigid body shifts of up to 7 A and 30 °. In order to retain functional activity these shifts are coupled so that the geometry of the residues forming the haem pocket is very similar in all the globins. We discuss the implications of these results for the mechanism of protein evolution.

Surface, subunit interfaces and interior of oligomeric proteins.

The solvent-accessible surface area (As) of 23 oligomeric proteins is calculated using atomic co-ordinates from high-resolution and well-refined crystal structures. As is correlated with the protein molecular weight, and a power law predicts its value to within 5% on average. The accessible surface of the average oligomer is similar to that of monomeric proteins in its hydropathy and amino acid composition. The distribution of the 20 amino acid types between the protein surface and its interior is also the same as in monomers. Interfaces, i.e. surfaces involved in subunit contacts, differ from the rest of the subunit surface. They are enriched in hydrophobic side-chains, yet they contain a number of charged groups, especially from Arg residues, which are the most abundant residues at interfaces except for Leu. Buried Arg residues are involved in H-bonds between subunits. We counted H-bonds at interfaces and found that several have none, others have one H-bond per 200 A2 of interface area on average (1 A = 0.1 nm). A majority of interface H-bonds involve charged donor or acceptor groups, which should make their contribution to the free energy of dissociation significant, even when they are few. The smaller interfaces cover about 700 A2 of the subunit surface. The larger ones cover 3000 to 10,000 A2, up to 40% of the subunit surface area in catalase. The lower value corresponds to an estimate of the accessible surface area loss required for stabilizing subunit association through the hydrophobic effect alone. Oligomers with small interfaces have globular subunits with accessible surface areas similar to those of monomeric proteins. We suggest that these oligomers assemble from preformed monomers with little change in conformation. In oligomers with large interfaces, isolated subunits should be unstable given their excessively large accessible surface, and assembly is expected to require major structural changes.