Abstract
BackgroundMost signalling and regulatory proteins participate in transient protein-protein interactions during biological processes. They usually serve as key regulators of various cellular processes and are often stable in both protein-bound and unbound forms. Availability of high-resolution structures of their unbound and bound forms provides an opportunity to understand the molecular mechanisms involved. In this work, we have addressed the question “What is the nature, extent, location and functional significance of structural changes which are associated with formation of protein-protein complexes?”ResultsA database of 76 non-redundant sets of high resolution 3-D structures of protein-protein complexes, representing diverse functions, and corresponding unbound forms, has been used in this analysis. Structural changes associated with protein-protein complexation have been investigated using structural measures and Protein Blocks description. Our study highlights that significant structural rearrangement occurs on binding at the interface as well as at regions away from the interface to form a highly specific, stable and functional complex. Notably, predominantly unaltered interfaces interact mainly with interfaces undergoing substantial structural alterations, revealing the presence of at least one structural regulatory component in every complex.Interestingly, about one-half of the number of complexes, comprising largely of signalling proteins, show substantial localized structural change at surfaces away from the interface. Normal mode analysis and available information on functions on some of these complexes suggests that many of these changes are allosteric. This change is largely manifest in the proteins whose interfaces are altered upon binding, implicating structural change as the possible trigger of allosteric effect. Although large-scale studies of allostery induced by small-molecule effectors are available in literature, this is, to our knowledge, the first study indicating the prevalence of allostery induced by protein effectors.ConclusionsThe enrichment of allosteric sites in signalling proteins, whose mutations commonly lead to diseases such as cancer, provides support for the usage of allosteric modulators in combating these diseases.
Highlights
Most signalling and regulatory proteins participate in transient protein-protein interactions during biological processes
Proteins bound to other proteins undergo larger structural changes than unliganded proteins Structural change observed in different forms of a protein could be due to experimental artifacts [44], intrinsic flexibility [45] or due to a biologically important external perturbation [46], such as ligand binding or post-translational modification
To differentiate structural changes potentially related to protein-protein interactions from those which are artefacts, we compared variations occurring in the dataset of protein-protein complexes with two control datasets
Summary
Most signalling and regulatory proteins participate in transient protein-protein interactions during biological processes They usually serve as key regulators of various cellular processes and are often stable in both protein-bound and unbound forms. The effect at target site can be varied, e.g., activation of catalysis, regulation of ligand-binding, control of complex formation[9] Given their importance, several high-throughput interaction assays [14,15], such as yeast two-hybrid and tandem affinity purification, have been developed to supplement the dataset of protein-protein interactions from lowthroughput methods [16,17]. The gold standard for protein-protein interactions is usually a dataset of complexes of interacting proteins solved using X-ray crystallography [19,20,21] It is a much smaller and incomplete dataset in comparison to high-throughput protein-protein interaction datasets, it is reliable and enables mapping of interaction regions and structural changes which accompany interactions. SCOPPI [22], iPfam [23], SNAPPI-DB [24], 3D Complex [25], InterEvol [26] and ProtCID [27] are some of the available 3D structural databases of protein-protein complexes
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