|
|
Bioinformation. 2008; 2(10): 422–427. Published online 2008 July 14. | PMCID: PMC2561160 |
Copyright © 2008 Biomedical Informatics Publishing Group Structural segments and residue propensities in protein-RNA interfaces: Comparison with protein-protein and protein-DNA complexes Sumit Biswas,1 Mainak Guharoy,1 and Pinak Chakrabarti1* 1Department of Biochemistry and Bioinformatics Centre, Bose Institute, Kolkata 700054, India Received May 23, 2008; Revised June 19, 2008; Accepted July 7, 2008. This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium,
for non-commercial purposes, provided the original author and source are credited. The interface of a protein molecule that is involved in binding another protein, DNA or RNA has been characterized in terms of the number of unique secondary structural segments (SSSs),
made up of stretches of helix, strand and non-regular (NR) regions. On average 10-11 segments define the protein interface in protein-protein (PP) and protein-DNA (PD) complexes, while the
number is higher (14) for protein-RNA (PR) complexes. While the length of helical segments in PP interaction increases with the interface area, this is not the case in PD and PR complexes.
The propensities of residues to occur in the three types of secondary structural elements (SSEs) in the interface relative to the corresponding elements in the protein tertiary structures
have been calculated. Arg, Lys, Asn, Tyr, His and Gln are preferred residues in PR complexes; in addition, Ser and Thr are also favoured in PD interfaces. Keywords: protein-protein interactions, protein-DNA interactions, protein-RNA interactions, binding interface, protein secondary structure PP - protein-protein, PD - protein-DNA, PR - protein-RNA, SSE - secondary structural element, SSS - secondary structural segment Characterization of protein-protein (PP), protein-DNA (PD) and protein-RNA (PR) interactions is essential for understanding the mechanisms of biological processes on a molecular level. Interactions
are highly specific and any distortion may be deleterious to the cellular function. Various experimental techniques have been employed to identify the interactions [ 1], with X-ray crystallography and NMR
spectroscopy providing the most detailed view. The atomic coordinates of the complexes stored in the Protein Data Bank (PDB) [ 2] have been analyzed to derive information on the physicochemical features of
the interface formed between the two components. PP interactions [ 3- 5] have attracted the maximum attention. These can vary in strength – some are obligatory (permanent), as can be seen in the formation of
the quaternary structures, while others are non-obligatory, in which the individual protomers exist independently in the stable form [ 6], but the time scale of interaction can vary widely from ~10 -3 to 10 3s
(transient to stable complexes, exemplified by electron transfer in redox proteins and antigen-antibody complexes, respectively). Studies in PD interactions have aimed at unravelling of the sequence specificity
of nucleotide recognition [ 7- 11]. In comparison PR interactions have been relatively fewer in number as data have been scarce till only recently [ 12- 14]. Most of the complexes contain double-stranded DNA and
the RNA is usually single stranded, though in a few cases depending on the sequence and length, it may fold into stem-loop structures including double helical segments. Akin to the non-obligatory PP complexes,
PD and PR complexes are mostly transient, forming only when the protein encounters the nucleic acid, and exhibit a wide range of stability and lifetimes. With increase in our understanding of protein structure
and interactions attempts are now geared towards synthetic biology for designing receptors for proteins and nucleic acids [ 15]. In this connection it is important to know what types of secondary structures are
used in the interface and the residue usage vis-à-vis the rest of the protein structure. In this article these features are derived for PD and PR interfaces and compared to those observed in PP complexes [ 16]. The list of 128 protein-DNA complexes used has been given in [ 11]. A search of PDB [ 2] (August, 2007) yielded 381 hits for the query “protein-RNA complex”. The list of entries was culled using PISCES [ 17], such
that the maximum percentage identity was 25% and the resolution not worse than 3.0 Å. The minimum chain length for the protein part was kept at 40 and for RNA, at least 3 bases. For this non-redundant dataset of
50 protein-RNA complexes, the information on the biologically relevant assembly was obtained from the Nucleic Acid Database (NDB) [ 18] (since many PDB files have coordinates only for the crystallographic asymmetric unit,
which may just contain a part of the whole molecule). The protein secondary structural elements (SSEs) were assigned using DSSP [ 19]. Only three types of SSEs were considered. All helices (with DSSP notations ‘H’ and ‘G’) were included irrespective of their type, ‘E’
and ‘B’ constituted strands; turns (‘T’ and ‘S’) and the unclassified residues (with assignment ‘ ’) together formed the nonregular (NR) region. Based on the presence of interface residues in distinct SSEs along the chain,
the interface can be split into secondary structural segments (SSS) - a segment is specified by the span between the two extreme locations of the interface residues on that SSE (with or without intervening non-interface residues)
[ 16]. The propensity (P i) SSE of a residue i to occur in a given secondary structural element (SSE) was calculated by the following formula (1) under supplementary material. Basic RNA-binding module and the interface area Among the 50 RNA-binding proteins (Table 1, supplementary material) many are multimeric, each having distinct recognition sites which are structurally equivalent. Any one of them can be assumed to be the basic unit that gets
repeated. We define this basic unit as one RNA-binding module (akin to what we have done for protein-DNA complexes [ 11]). The basic RNA-binding module that has been constructed can be repeated (by the application of simple symmetry
operators) to generate the complete biological assembly. Thus for a homodimeric molecule (such as 1ooa), only one subunit interacting with the RNA was considered. In some other cases with more than two identical protein-RNA units
(as in 2gic, where five identical protein chains bind symmetrically to five individual RNA strands), only one protein chain complexed with one RNA was considered. A considerable number (5) of the complexes in the dataset are coat
proteins or nucleocapsids of viruses and bacteriophages. Basically, these are huge complexes (eg., 2fz2) formed by the application of a number of symmetry operators to a simple protein-RNA unit. For such complexes too, one subunit
of the protein with one strand of the RNA was considered. 42 of the 50 complexes had the protein monomer binding to single-stranded RNA, and the rest to double-stranded RNA. The interface area is given by the sum of the accessible surface area of the two isolated components minus that of the complex. This is the area that gets buried between the two components, which usually contribute almost equally
[ 4, 5]. The average interface area in PR complexes is comparable to that observed in PD and PP complexes (Table 2 under supplementary material), though there is a larger variation around the mean. This is expected as the length of
RNA located in the interface varies considerably (range: 3 to 37) among the different structures. Secondary structural segments in the interface Data presented in Table 2 (see supplementary material) indicate that there is not much distinction between the numbers of SSSs present in PP and PD interfaces, even when the value is normalized for a fixed size (1000 Å 2) of the
interface. However, both these numbers are higher for PR interfaces. When the three SSSs (helix, strand and NR) are considered individually, the numbers are comparatively higher for PR than those in PD and PP interfaces. In contrast,
the average lengths of the SSSs remain more or less the same in the three categories. Variation of SSS length with interface size The majority of the PP complexes have an interface with an area of 1600±400 Å 2 that has been termed as the standard size [ 4]. The variation of the segment lengths as a function of the interface size has also been addressed [ 16].
It was found that the average length of helix is doubled from ~4 when the area increases ten-fold from 500 Å 2; however, such changes were not observed for strand and NR segments. In comparison, in PD complexes (), a variation
in the length of helical segments is not seen (the last bin is based on just single interface and is not considered) and a rather uniform length of 5.1-5.8 residues is observed, corresponding to ~1.5 turn of an α-helix interacting with
the major groove of DNA. Interfaces have been classified as helical when the number of helical residues in the interface is more than 40% [ 16]. Considering strand and NR segments, in contrast to PP complexes, there are changes in PD
complexes - the strand length decreases by about two fold and that of NR increases to the same extent. In PR complexes (), the length distribution, irrespective of segment type, is fairly uniform over the range of 500 to 3000 Å 2;
but below 500 Å 2, the helical segments that are part of the interface contribute only two residues. Secondary structure preferences of interface residues Calculation of the propensities of residues to occur in a SSE in the PP interface relative to the same element in the overall protein tertiary structure indicated that Arg and the aromatic residues are observed more in all interface
SSEs [ 16]. In PD complexes (), propensities > 1.5 are observed for the basic residues (Arg, Lys and His). Residues with hydroxyl groups (especially Ser and Thr) also have higher values. Residues with amide side-chains, Asn in particular,
is found more in PD interfaces. Of the aromatic residues, Phe is less abundant. Gly, which is underrepresented in interface SSEs in PP complexes, is found more in PD complexes. It may be noted that unlike the PP complexes, the hydrophobic residues
are unfavoured in PD interfaces, which are more polar in nature [ 7, 8, 11]. In PR complexes the highest propensities are observed in Arg, Asn and Lys (). Tyr, His and Gln are also preferred, but Ser and Thr, unlike in PD complexes, are
not as favoured. Of interest is the fact that Asp, which is known to have a high propensity to be located in strands that form β-sheet across PP interfaces [ 16], is also highly represented in strands in PR interfaces. This is in sharp contrast
to the protein-DNA interfaces where Asp is poorly represented. Met located in NR segments is also preferred in PR complexes. A non-redundant dataset of PR complexes has been created. This and a similar dataset of PD complexes [ 11] have been analyzed in terms of SSSs that constitute the protein part of the interface. PP complexes can bury a larger surface area by the
use of longer helical segments [ 16]. However, in PR complexes the SSS length is rather invariant (), but their number tends to increase regularly with the interface size (). At any given size of the interface, the number of segments
in PR complexes is usually more than that in PP complexes. In PD complexes the helices are of uniform length, but the strands get shorter with the concomitant increase in the length of NR, as the size of the interface increases. Relative to the tertiary
structure the interface SSEs are depleted in Ala, Val, Ile and Leu in all types of complexes - interestingly these are the residues that have high α-helix or β-sheet propensities [ 20]. Compared to PP interfaces, aromatic residues are less favoured at
the binding sites of nucleic acids. Preferred residues in PR complexes are Arg, Lys, Asn, Tyr, His and Gln; PD interfaces are also enriched in Ser and Thr. One feature that is common to both PP and PR interfaces is the presence of Asp in interface strands.
The residue usage in a SSE in the interface relative to that in the overall tertiary structure would be useful in the design of structural motifs capable of interacting with another protein or nucleic acid. 1. Shoemaker BA, Panchenko AR. Plos Comp Biol. 2007;3:337. [PubMed] 2. Berman HM, et al. Nucleic Acids Res. 2000;28:235. [PubMed] 3. Jones S, Thornton JM. Proc Natl Acad Sci USA. 1996;93:13. [PubMed] 4. Lo Conte L. J Mol Biol. 1999;285:2177. [PubMed] 5. Chakrabarti P, Janin J. Proteins. 2002;47:334. [PubMed] 6. Nooren M, Thornton JM. EMBO J. 2003;22:3486. [PubMed] 7. Nadassy K, et al. Biochemistry. 1999;38:1999. [PubMed] 8. Jones S, et al. J Mol Biol. 1999;287:877. [PubMed] 9. Luscombe NM, et al. Genome Biol. 2000;1:001.1. [PubMed] 10. Sarai A, Kono H. Annu Rev Biophys Biomol Struct. 2005;34:379. [PubMed] 11. Biswas S, et al. Proteins. 2008 [PubMed] 12. Jones S, et al. Nucleic Acids Res. 2001;29:943. [PubMed] 13. Treger M, Westhof E. J Mol Recogn. 2001;14:199. [PubMed] 14. Ellis JJ, et al. Nuc Acids Res. 2007;66:903. [PubMed] 15. Endy D. Nature. 2005;438:449. [PubMed] 16. Guharoy M, Chakrabarti P. Bioinformatics. 2007;23:1909. [PubMed] 17. Wang G, Dunbrack RL. Bioinformatics. 2003;19:1589. [PubMed] 18. Berman HM, et al. Biophys J. 1992;63:751. [PubMed] 19. Kabsch W, Sander C. Biopolymers. 1983;22:2577. [PubMed] 20. Chakrabarti P, Pal D. Prog Biophys Mol Biol. 2001;76:1. [PubMed]
|
This article has been 
