Analyses on clustering of the conserved residues at protein-RNA interfaces and its application in binding site identification

Abstract

Background: The maintenance of protein structural stability requires the cooperativity among spatially neighboring residues. Previous studies have shown that conserved residues tend to occur clustered together within enzyme active sites and protein-protein/DNA interfaces. It is possible that conserved residues form one or more local clusters in protein tertiary structures as it can facilitate the formation of functional motifs. In this work, we systematically investigate the spatial distributions of conserved residues as well as hot spot ones within protein-RNA interfaces. Results: The analysis of 191 polypeptide chains from 160 complexes shows the polypeptides interacting with tRNAs evolve relatively rapidly. A statistical analysis of residues in different regions shows that the interface residues are often more conserved, while the most conserved ones are those occurring at protein interiors which maintain the stability of folded polypeptide chains. Additionally, we found that 77.8% of the interfaces have the conserved residues clustered within the entire interface regions. Appling the clustering characteristics to the identification of the real interface, there are 31.1% of cases where the real interfaces are ranked in top 10% of 1000 randomly generated surface patches. In the conserved clusters, the preferred residues are the hydrophobic (Leu, Ile, Met), aromatic (Tyr, Phe, Trp) and interestingly only one positively charged Arg residues. For the hot spot residues, 51.5% of them are situated in the conserved residue clusters, and they are largely consistent with the preferred residue types in the conserved clusters. Conclusions: The protein-RNA interface residues are often more conserved than non-interface surface ones. The conserved interface residues occur more spatially clustered relative to the entire interface residues. The high consistence of hot spot residue types and the preferred residue types in the conserved clusters has important implications for the experimental alanine scanning mutagenesis study. This work deepens the understanding of the residual organization at protein-RNA interface and is of potential applications in the identification of binding site and hot spot residues.

Clustering of Aromatic Residues in Prion-like Domains Can Tune the Formation, State, and Organization of Biomolecular Condensates

“…To identify sequences with well-clustered aromatic residues and motivated by Yang et al, we applied a metric that computes the average inverse distance among aromatic residues, which we term aromatic clustering (Figure 2C; see Methods). 106 Of relevance to our application, this parameter is robust in the limit of small fractions of aromatic with the fraction of aromatic or aliphatic residues (x-axis). Among those of X. laevis PLDs, the clustering score Velo1 PLD (black diamond) is higher than all but one, and among those of the PLDs from PhaseSepDB, the clustering score is higher than all but two.…”

The formation of a fuzzy complex in the negative arm regulates the robustness of the circadian clock

“…We measured clustering of particular residue classes (e.g., positive, negative, and aromatic residues) within FRQ's sequence by calculating the average inverse weighted distance (IWD). The IWD is defined as: where S is the set of target residue positions, Si is the i-th element of S, NS is the number of items in S, and Npairs is the number of pairwise combinations between elements of S (Schueler-Furman and Baker, 2003;Yang et al, 2020). The IWD was then compared to the IWD calculated from 10,000 randomly shuffled FRQ sequences to assess significance as IWD values above the 95 percentile, and following the approach presented in (Cohan et al, 2021) we calculated a residue class specific Z-score to allow comparisons across orthologs that differ in length and amino acid composition.…”

SNB‐PSSM: A spatial neighbor‐based PSSM used for protein–RNA binding site prediction

“…This tendency holds true for protein–protein/nucleic acid interactions 11,12 . The higher packing density of conserved residues at interfaces and within enzyme active sites may suggest their cooperativity in function exertion 10 . That the conserved residues form one or more localized clusters within interfaces or tertiary structures will facilitate the formation of some “functional motifs.” Thus, based on the above, we think the PSSM profile encoded in a form of spatial neighbors can better reflect the evolutionary characteristics of interface conserved residues than that encoded in a form of sequence neighbors.…”

“…Tang et al utilized sequence and structure characteristics encoded in a structural window to predict RNA‐binding residues 9 . Studies have shown the conserved interface residues often occur clustered together in tertiary structures 10 . This tendency holds true for protein–protein/nucleic acid interactions 11,12 .…”