In:
Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 109, No. 26 ( 2012-06-26)
Abstract:
Because knotting is an impediment to the efficient and reproducible folding needed to achieve the native protein structure ( 4 , 5 ), we conclude that the observed knotting patterns are due to strong positive evolutionarily selection. We believe that it is rather unlikely that knots and slipknots are merely fortuitously formed and retained structures that bring catalytic amino acids into the right positions to enable catalysis. Rather, our results suggest that it is the knotting and slipknotting, per se, that is important for the function of these proteins and may provide them with some special properties that are yet not fully understood. To shed light on the function of knots and slipknots in proteins, we investigated the extent to which the precise location and relative positions of protein portions forming knotted domains are conserved during the evolution. To do this, we searched for knots and slipknots in all sufficiently complete protein structures deposited in the Protein Data Bank. To analyze the architecture of the knotted regions, we used a mathematical approach that applies an unbiased closure method ( 1 ) to every subchain within the given protein ( 2 ). This approach permitted us to map the precise positions of knots and slipknots in the analyzed protein structures. We observed a strong conservation of knot and slipknot architectures in several families of orthologous proteins, which maintain the same function in different species. We observed, for example, that ubiquitin C-terminal hydrolases originating from Plasmodium falciparum or Homo sapiens possess very similar knotting architectures despite their evolutionary separation by more than a billion years and despite the fact that their sequences are only 28% identical ( 3 ). Fig. P1 shows a matrix presentation of the knotting architecture of these two proteins. We observed a similarly high conservation of knotting architectures within several families of proteins forming transmembrane channels. The slipknot loop in all of these families seems to strap together several transmembrane helices, which most likely stabilizes the structure of the transmembrane channel. Fig. P1. The conservation of complex knotting pattern in ubiquitin C-terminal hydrolases from H. sapiens and P. falciparum . The matrix presentation of protein knotting shows the knot type formed by subchains delimited by the corresponding amino acid residue positions indicated on the horizontal and vertical axis. Each of the complete protein chains forms a knot with five crossings, known as the 5 2 knot. Clipping a few amino acid residues from the N terminus unknots each of the proteins. Progressive truncation from the C terminus results first in a fragment that is unknotted when considered as a whole, but its shorter subchains can form 3 1 knots. To understand this matrix presentation of protein knotting, the entire polypeptide chain, unfolded for this purpose, is presented along the diagonal of the matrices. The corresponding regions of knots and slipknots are indicated. The strict conservation of the knotting pattern is obvious despite the fact that these two proteins share only 28% sequence identity. The majority of proteins fold into their native structure in such a way that their polypeptide chain remains unknotted. That is, if one would hold the two ends of the polypeptide chain and move them apart, the chain would assume an unentangled linear configuration. Some proteins, however, fold in such a way that their polypeptide chains become knotted or form slipknots. Slipknots are entanglements containing a knotted region, but if the two ends of the slipknot are pulled apart one obtains an unknotted configuration, similar to what happens with bows in shoelace knots. The function of knots and slipknots in proteins is largely unknown. In particular, it is not known whether they are essential for function or are unnecessary features acquired by chance and then preserved during the evolution. For example, the knotting of a polypeptide chain could have fortuitously brought some amino acid residues into a distance and geometry that are favorable for a particular catalytic reaction, whereas a nearly identical distance and geometry could have been equally well attained using folds that do not require protein knotting or slipknotting. By comparing the sequence and structure of proteins that serve the same role in evolutionarily distant species, such as humans and yeasts, one finds protein regions that are strongly conserved and others that are highly divergent. Strongly conserved regions are essential for function, and studying them helps us to understand the details of molecular mechanisms involved in enzymatic catalysis or binding to other molecules, such as nucleic acids.
Type of Medium:
Online Resource
ISSN:
0027-8424
,
1091-6490
DOI:
10.1073/pnas.1205918109
Language:
English
Publisher:
Proceedings of the National Academy of Sciences
Publication Date:
2012
detail.hit.zdb_id:
209104-5
detail.hit.zdb_id:
1461794-8
SSG:
11
SSG:
12
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