Abstract
An important feature of ribosomal S1 proteins is multiple copies of structural domains in bacteria, the number of which changes in a strictly limited range from one to six. For S1 proteins, little is known about the contribution of flexible regions to protein domain function. We exhaustively studied a tendency for intrinsic disorder and flexibility within and between structural domains for all available UniProt S1 sequences. Using charge–hydrophobicity plot cumulative distribution function (CH-CDF) analysis we classified 53% of S1 proteins as ordered proteins; the remaining proteins were related to molten globule state. S1 proteins are characterized by an equal ratio of regions connecting the secondary structure within and between structural domains, which indicates a similar organization of separate S1 domains and multi-domain S1 proteins. According to the FoldUnfold and IsUnstruct programs, in the multi-domain proteins, relatively short flexible or disordered regions are predominant. The lowest percentage of flexibility is in the central parts of multi-domain proteins. Our results suggest that the ratio of flexibility in the separate domains is related to their roles in the activity and functionality of S1: a more stable and compact central part in the multi-domain proteins is vital for RNA interaction, terminals domains are important for other functions.
Highlights
It is known that multi-domain proteins are frequently characterized by the occurrence of domain repeats in proteomes across the three domains of life: Bacteria, Archaea, and Eukaryotes [1,2]
We show that S1 proteins belong to a unique family, which differs in the classical sense from proteins with tandem repeats
We found that the one-domain and two-domain containing S1 proteins apparently have more stable and rigid structure
Summary
It is known that multi-domain proteins are frequently characterized by the occurrence of domain repeats in proteomes across the three domains of life: Bacteria, Archaea, and Eukaryotes [1,2]. As demonstrated in our recent paper [5], the family of polyfunctional ribosomal proteins S1 contains about 20% of all bacterial proteins, including the S1 domain. This fold could be found in different eukaryotic protein families and protein complexes in different number variations. Such multiple copies of the structure increase the affinity and/or specificity of the protein binding to nucleic acid molecules
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