Dinasaurus
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I am reading that some large proteins of over 200 amino acids in length, form globular structures known as domains which are structurally independent from the rest of the protein, what is meant by this structural independence?

My first impression is that it's not attached to the rest but I don't think that makes sense, can anyone explain?
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Gerry-Atricks
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(Original post by Dinasaurus)
I am reading that some large proteins of over 200 amino acids in length, form globular structures known as domains which are structurally independent from the rest of the protein, what is meant by this structural independence?

My first impression is that it's not attached to the rest but I don't think that makes sense, can anyone explain?
A protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural domains. One domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. Domains vary in length from between about 25 amino acids up to 500 amino acids in length[

This wiki suggests that they are used as building blocks and so may recombine and be connected so are not distinct.
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OxFossil
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The concept isn't easy to define precisely, but the idea is that a domain is a chunk of protein structure that turns up in several different proteins and has a distinctive set of properties. They may also exist as a stable, recognisable entity without further amino acids chains etc attached to them, and tend to fold themselves into their characteristic form spontaneously, independent of the configuration of the rest of the protein.

Functionally, the key point is that this enables them to retain their essential function (for example, binding a specific chemical groups) in a range of different contexts. In effect, they function as "building blocks" that can be assembled in a number of different combinations to make a protein that can perform the particular combination of functions that is needed.

They make a lot of sense from an evolutionary point of view - if you need a new enzyme to perform a novel kind of DNA transcription, rather than evolve the whole thing from scratch, you can start with a mutation of an existing enzyme that contains the "zinc finger" domain (a domain which binds to DNA). And sure enough, the "zinc finger" domain pops up in a number of enzymes involved in binding to DNA during transcription.

Does that make sense?
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Dinasaurus
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(Original post by OxFossil)
The concept isn't easy to define precisely, but the idea is that a domain is a chunk of protein structure that turns up in several different proteins and has a distinctive set of properties. They may also exist as a stable, recognisable entity without further amino acids chains etc attached to them, and tend to fold themselves into their characteristic form spontaneously, independent of the configuration of the rest of the protein.

Functionally, the key point is that this enables them to retain their essential function (for example, binding a specific chemical groups) in a range of different contexts. In effect, they function as "building blocks" that can be assembled in a number of different combinations to make a protein that can perform the particular combination of functions that is needed.

They make a lot of sense from an evolutionary point of view - if you need a new enzyme to perform a novel kind of DNA transcription, rather than evolve the whole thing from scratch, you can start with a mutation of an existing enzyme that contains the "zinc finger" domain (a domain which binds to DNA). And sure enough, the "zinc finger" domain pops up in a number of enzymes involved in binding to DNA during transcription.

Does that make sense?
Oh I see. Like if you were to use a gene analogy, proteins are different species and domains are different genes. Same genes can show up in different species to code for common traits.
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OxFossil
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(Original post by Dinasaurus)
Oh I see. Like if you were to use a gene analogy, proteins are different species and domains are different genes. Same genes can show up in different species to code for common traits.
Yes, that's not a bad analogy. If you know the hox genes? They tend to be highly conserved, but are used in cunningly different ways or at different times to bring about different results. Although protein domains do the work, rather than direct it!
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