Recognition of Interaction Interface Residues in Low-Resolution Structures of Protein Assemblies Solely from the Positions of Cα Atoms

Abstract

BackgroundThe number of available structures of large multi-protein assemblies is quite small. Such structures provide phenomenal insights on the organization, mechanism of formation and functional properties of the assembly. Hence detailed analysis of such structures is highly rewarding. However, the common problem in such analyses is the low resolution of these structures. In the recent times a number of attempts that combine low resolution cryo-EM data with higher resolution structures determined using X-ray analysis or NMR or generated using comparative modeling have been reported. Even in such attempts the best result one arrives at is the very course idea about the assembly structure in terms of trace of the Cα atoms which are modeled with modest accuracy.Methodology/Principal FindingsIn this paper first we present an objective approach to identify potentially solvent exposed and buried residues solely from the position of Cα atoms and amino acid sequence using residue type-dependent thresholds for accessible surface areas of Cα. We extend the method further to recognize potential protein-protein interface residues.Conclusion/ SignificanceOur approach to identify buried and exposed residues solely from the positions of Cα atoms resulted in an accuracy of 84%, sensitivity of 83–89% and specificity of 67–94% while recognition of interfacial residues corresponded to an accuracy of 94%, sensitivity of 70–96% and specificity of 58–94%. Interestingly, detailed analysis of cases of mismatch between recognition of interface residues from Cα positions and all-atom models suggested that, recognition of interfacial residues using Cα atoms only correspond better with intuitive notion of what is an interfacial residue. Our method should be useful in the objective analysis of structures of protein assemblies when positions of only Cα positions are available as, for example, in the cases of integration of cryo-EM data and high resolution structures of the components of the assembly.

Protein-Protein Interactions in Clathrin Vesicular Assembly: Radial Distribution of Evolutionary Constraints in Interfaces

“…We have developed a method which can recognize the protein-protein interaction interfaces solely from Cα positions in low resolution structures of big assemblies such as CCV [28]. However, prior to applying this method, in order to circumvent the second problem mentioned above, we identified near neighbors for every chain in the complex structures using distance criterion; if the distance between two Cα residues from different chains is less than or equal to 5 Å then the chains possessing the residues are termed as near neighbors.…”

Prediction of protein-protein interactions in dengue virus coat proteins guided by low resolution cryoEM structures

“…In the present study, low resolution structures of dengue viruses have been subjected to the analysis described in our earlier paper [ 10 ] to predict the protein-protein interaction interface residues in E and M coat proteins. The interface residues in these low resolution structures were inferred from the Cα coordinates only using the protocol as mentioned in "Methods" section.…”

“…Hence, one gets only a course idea about the regions participating in these changing protein-protein interactions. We have developed an objective and automatic method that can recognize/predict protein-protein interaction residues with high sensitivity and accuracy, given the low resolution structures with positions of Cα atoms only [ 10 ]. In the present study, using the above mentioned method, we have predicted the residues on both the coat proteins that seemed likely to participate in protein-protein interactions in different phases of the life cycle of dengue virus.…”

Predictive and Experimental Approaches for Elucidating Protein–Protein Interactions and Quaternary Structures

“…Ning Gao and co-workers used a hybrid method combining structural information, chemical cross-linking proximity mapping followed by mass spectrometry (CX-MS) and cryo-EM for the modelling of five assembly factors in the ITS2 region of the pre-60S ribosome [ 83 ]. Residue-level details of PPI of dengue virus coat proteins was predicted using Cα atom positions from low-resolution cryo-EM structures [ 84 , 85 ].…”