Joël Janin

Conformation of amino acid side-chains in proteins☆

We have analysed the side-chain dihedral angles in 2536 residues from 19 protein structures. The distributions of x1 and x2 are compared with predictions made on the basis of simple energy calculations. The x1 distribution is trimodal; the g− position of the side-chain (trans to Hα), which is rare except in serine, the t position (trans to the amino group), and the g+ position (trans to the carbonyl group), which is preferred in all residues. Characteristic x2 distributions are observed for residues with a tetrahedral γ-carbon, for aromatic residues, and for aspartic acid/asparagine. The number of configurations actually observed is small for all types of side-chains, with 60% or more of them in only one or two configurations. We give estimates of the experimental errors on x1 and x2 (3 ° to 16 °, depending on the type of the residue), and show that the dihedral angles remain within 15 ° to 18 ° (standard deviation) from the configurations with the lowest calculated energies. The distribution of the side-chains among the permitted configurations varies slightly with the conformation of the main chain, and with the position of the residue relative to the protein surface. Configurations that are rare for exposed residues are even rarer for buried residues, suggesting that, while the folded structure puts little strain on side-chain conformations, the side-chain positions with the lowest energy in the unfolded structure are chosen preferentially during folding.

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.

Dissecting protein-protein recognition sites

The recognition sites in 70 pairwise protein–protein complexes of known three‐dimensional structure are dissected in a set of surface patches by clustering atoms at the interface. When the interface buries <2000 Å2 of protein surface, the recognition sites usually form a single patch on the surface of each component protein. In contrast, larger interfaces are generally multipatch, with at least one pair of patches that are equivalent in size to a single‐patch interface. Each recognition site, or patch within a site, contains a core made of buried interface atoms, surrounded by a rim of atoms that remain accessible to solvent in the complex. A simple geometric model reproduces the number and distribution of atoms within a patch. The rim is similar in composition to the rest of the protein surface, but the core has a distinctive amino acid composition, which may help in identifying potential protein recognition sites on single proteins of known structures. Proteins 2002;47:334–343.

CAPRI: A Critical Assessment of PRedicted Interactions

CAPRI is a communitywide experiment to assess the capacity of protein‐docking methods to predict protein–protein interactions. Nineteen groups participated in rounds 1 and 2 of CAPRI and submitted blind structure predictions for seven protein–protein complexes based on the known structure of the component proteins. The predictions were compared to the unpublished X‐ray structures of the complexes. We describe here the motivations for launching CAPRI, the rules that we applied to select targets and run the experiment, and some conclusions that can already be drawn. The results stress the need for new scoring functions and for methods handling the conformation changes that were observed in some of the target systems. CAPRI has already been a powerful drive for the community of computational biologists who development docking algorithms. We hope that this issue of Proteins will also be of interest to the community of structural biologists, which we call upon to provide new targets for future rounds of CAPRI, and to all molecular biologists who view protein–protein recognition as an essential process. Proteins 2003;52:2–9.

Protein–protein docking benchmark version 3.0

We present version 3.0 of our publicly available protein–protein docking benchmark. This update includes 40 new test cases, representing a 48% increase from Benchmark 2.0. For all of the new cases, the crystal structures of both binding partners are available. As with Benchmark 2.0, Structural Classification of Proteins (Murzin et al., J Mol Biol 1995;247:536–540) was used to remove redundant test cases. The 124 unbound‐unbound test cases in Benchmark 3.0 are classified into 88 rigid‐body cases, 19 medium‐difficulty cases, and 17 difficult cases, based on the degree of conformational change at the interface upon complex formation. In addition to providing the community with more test cases for evaluating docking methods, the expansion of Benchmark 3.0 will facilitate the development of new algorithms that require a large number of training examples. Benchmark 3.0 is available to the public at http://zlab.bu.edu/benchmark. Proteins 2008.

Silk fibroin: Structural implications of a remarkable amino acid sequence

The amino acid sequence of the heavy chain of Bombyx mori silk fibroin was derived from the gene sequence. The 5,263‐residue (391‐kDa) polypeptide chain comprises 12 low‐complexity “crystalline” domains made up of Gly–X repeats and covering 94% of the sequence; X is Ala in 65%, Ser in 23%, and Tyr in 9% of the repeats. The remainder includes a nonrepetitive 151‐residue header sequence, 11 nearly identical copies of a 43‐residue spacer sequence, and a 58‐residue C‐terminal sequence. The header sequence is homologous to the N‐terminal sequence of other fibroins with a completely different crystalline region. In Bombyx mori, each crystalline domain is made up of subdomains of ∼70 residues, which in most cases begin with repeats of the GAGAGS hexapeptide and terminate with the GAAS tetrapeptide. Within the subdomains, the Gly–X alternance is strict, which strongly supports the classic Pauling–Corey model, in which β‐sheets pack on each other in alternating layers of Gly/Gly and X/X contacts. When fitting the actual sequence to that model, we propose that each subdomain forms a β‐strand and each crystalline domain a two‐layered β‐sandwich, and we suggest that the β‐sheets may be parallel, rather than antiparallel, as has been assumed up to now. Proteins 2001;44:119–122.

A protein-protein docking benchmark.

We have developed a nonredundant benchmark for testing protein–protein docking algorithms. Currently it contains 59 test cases: 22 enzyme‐inhibitor complexes, 19 antibody‐antigen complexes, 11 other complexes, and 7 difficult test cases. Thirty‐one of the test cases, for which the unbound structures of both the receptor and ligand are available, are classified as follows: 16 enzyme‐inhibitor, 5 antibody‐antigen, 5 others, and 5 difficult. Such a centralized resource should benefit the docking community not only as a large curated test set but also as a common ground for comparing different algorithms. The benchmark is available at (http://zlab.bu.edu/∼rong/dock/benchmark.shtml). Proteins 2003;52:88–91.

Protein-protein interaction and quaternary structure.

Protein-protein recognition plays an essential role in structure and function. Specific non-covalent interactions stabilize the structure of macromolecular assemblies, exemplified in this review by oligomeric proteins and the capsids of icosahedral viruses. They also allow proteins to form complexes that have a very wide range of stability and lifetimes and are involved in all cellular processes. We present some of the structure-based computational methods that have been developed to characterize the quaternary structure of oligomeric proteins and other molecular assemblies and analyze the properties of the interfaces between the subunits. We compare the size, the chemical and amino acid compositions and the atomic packing of the subunit interfaces of protein-protein complexes, oligomeric proteins, viral capsids and protein-nucleic acid complexes. These biologically significant interfaces are generally close-packed, whereas the non-specific interfaces between molecules in protein crystals are loosely packed, an observation that gives a structural basis to specific recognition. A distinction is made within each interface between a core that contains buried atoms and a solvent accessible rim. The core and the rim differ in their amino acid composition and their conservation in evolution, and the distinction helps correlating the structural data with the results of site-directed mutagenesis and in vitro studies of self-assembly.

Protein–protein docking benchmark 2.0: An update

We present a new version of the Protein–Protein Docking Benchmark, reconstructed from the bottom up to include more complexes, particularly focusing on more unbound–unbound test cases. SCOP (Structural Classification of Proteins) was used to assess redundancy between the complexes in this version. The new benchmark consists of 72 unbound–unbound cases, with 52 rigid‐body cases, 13 medium‐difficulty cases, and 7 high‐difficulty cases with substantial conformational change. In addition, we retained 12 antibody–antigen test cases with the antibody structure in the bound form. The new benchmark provides a platform for evaluating the progress of docking methods on a wide variety of targets. The new version of the benchmark is available to the public at http://zlab.bu.edu/benchmark2. Proteins 2005;60:214–216.

Dissecting subunit interfaces in homodimeric proteins

The subunit interfaces of 122 homodimers of known three‐dimensional structure are analyzed and dissected into sets of surface patches by clustering atoms at the interface; 70 interfaces are single‐patch, the others have up to six patches, often contributed by different structural domains. The average interface buries 1,940 Å2 of the surface of each monomer, contains one or two patches burying 600–1,600 Å2, is 65% nonpolar and includes 18 hydrogen bonds. However, the range of size and of hydrophobicity is wide among the 122 interfaces. Each interface has a core made of residues with atoms buried in the dimer, surrounded by a rim of residues with atoms that remain accessible to solvent. The core, which constitutes 77% of the interface on average, has an amino acid composition that resembles the protein interior except for the presence of arginine residues, whereas the rim is more like the protein surface. These properties of the interfaces in homodimers, which are permanent assemblies, are compared to those of protein‐protein complexes where the components associate after they have independently folded. On average, subunit interfaces in homodimers are twice larger than in complexes, and much less polar due to the large fraction belonging to the core, although the amino acid compositions of the cores are similar in the two types of interfaces. Proteins 2003.