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Copied from - Nucleic Acids Res. 2009 January; 37(Database issue): D310–D314.
ReplyDeleteFigure 1. Examples of protein domains classified by CATH according to architecture acquired by secondary structure of protein
Evolution of domain arrangement in protein
Mechanism of generating new domain combination
There are many way by which protein can form novel combinations among which gene duplication and domain arrangement is important events of acquiring new interfaces. Most of time single domain protein fused first into one gene. The physical interactions between two domains then evolve towards higher stability e.g. by allowing hydrophobic patches on
to the surfaces. After many generations, if proteins now split again, interfaces remains as recognition interface which can still mediate association of the two separated proteins. This process can also be referred as Rosetta stone method (Marcotte E. et al, 1999).
Fusion of two genes that give single, composite gene is known as fusion. And where two gene split into two component is stated as fission process. Multi-domain protein can arise by fusion processes for example fatty acid synthase complex, two polypeptide chains in yeast and mammals and in E. coli has six chains. Fusion is more common than fission, a consistent trend of Achaea, bacteria and eukaryotes (E. bornberg - bauer et al, 2004).
Copied from E. Bornberg-bauer et al., 2004
Figure-2 The Rosetta stone model (a) a Rosetta stone protein as fusion or fission of two proteins which interact with each other, and (b) as fusion of genes, to allow tighter co-regulation of both proteins
Rearrangement of domains is important for the functionality of proteins if rearrangement lead to change in geometry of interfaces (Lindqvist Y. et al., 1997). Cyclic permutation is a type of non-linear domain rearrangement wherein N-terminal fragment of one protein is similar to C-terminal fragment of other protein like in DNA methyl transferases and lectins. Existences of CP supports physical arrangement of domains are important for their functionality. Origin of CPs can be through gene followed by subsequent deletion events (Jeltsch et al, 1999), and independent gene fusion (Bujnicki J. et al, 2002).
Swap is similar to CP refers to specific domain present in reversed order. It also emphasize that functionality depends on domain order for retaining functional protein, preventing of domain order is much more important than insertions or deletions.
Figure-3. Circular permutation arising by gene duplication
Figure-4 Circular mutation by independent gene fusion
Domain preferentially lost at N-terminal than middle, Every time it does not mean that domain is physically removed instead of that domains drift in such a way that it no longer identifiable by the detection procedure. If it is missed at neighbour of same order domains, then difficult to predict whether domain functional or not. Missing domain does not have functionality but has structural importance for function of whole protein (E. bornberg - bauer et al, 2004).
3. Literature survey
3.1 Chapter 1
3.1.1 Mechanisms of evolution
Evolution cannot occur in individual, it is in population only. Population is group of interbreeding individuals of one species in a given geographic area. Population contains specific gene pool by change in gene pool evolution can be taken place.
Mutation, is a driving force of evolution, is a responsible for change in gene pool, it may create change in DNA in chromosomes, can change frequency of alleles; therefore, they are
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