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A dissection of specific and non-specific protein-protein interfaces.
TLDR
A residue propensity score and a hydrophobic interaction score are developed to assess preferences seen in the chemical and amino acid compositions of the different types of interfaces, and indexes are derived to evaluate the atomic packing, which is found to be less compact at non-specific than at specific interfaces. Expand
Dissecting protein–protein recognition sites
TLDR
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 by reproducing the number and distribution of atoms within a patch. Expand
Crystallographic structure of the nitrogenase iron protein from Azotobacter vinelandii.
TLDR
The crystal structure of the nitrogenase Fe-protein from Azotobacter vinelandii has been determined and it appears that interactions between the nucleotide and cluster sites must be indirectly coupled by allosteric changes occurring at the subunit interface. Expand
Dissecting subunit interfaces in homodimeric proteins
TLDR
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. Expand
Cis peptide bonds in proteins: residues involved, their conformations, interactions and locations.
TLDR
A comparison of cis peptides containing proline and non-proline residues show differences in conformation, location in the secondary structure and in relation to the centre of the molecule, and relative accessibilities of residues, which has led to a reclassification of turns mediated by cis peptide bonds. Expand
Stereospecific interactions of proline residues in protein structures and complexes.
TLDR
It is shown that specific interactions involving the pyrrolidine ring atoms also contribute to its location in a given secondary structure and its binding to another molecule. Expand
Quantifying the accessible surface area of protein residues in their local environment.
TLDR
The equation provides a method to estimate the ASA of a protein molecule and the average relative accessibilities of different residues, the latter being inversely correlated with hydrophobicity values. Expand
Protein–protein interaction and quaternary structure
TLDR
This review compares 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 and analyzes the properties of the interfaces between the subunits. Expand
Hydration of protein–protein interfaces
TLDR
Water‐mediated polar interactions are as abundant at the interfaces as direct protein–protein hydrogen bonds, and they may contribute to the stability of the assembly. Expand
CH-π hydrogen bonds in biological macromolecules.
TLDR
The present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Expand
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