Practical Guide to Homology Modeling: Difference between revisions
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== Are parts (or all) of the query protein intrinsically disordered? == | == Are parts (or all) of the query protein intrinsically disordered? == | ||
Attempts to determine structure for intrinsically disordered protein will be futile. Therefore, before considering homology modeling or crystallization experiments, it is important to predict whether portions of the query protein are likely to be intrinsically disordered. | |||
Although fold is required for the function of most proteins, some proteins are [[Intrinsic Disorder|intrinsically disordered]] (natively unstructured) and do not fold, at least by themselves. Often, intrinsically disordered protein transitions to an ordered state when it binds to a folded partner protein. However some proteins remain disordered while performing their functions. | Although fold is required for the function of most proteins, some proteins are [[Intrinsic Disorder|intrinsically disordered]] (natively unstructured) and do not fold, at least by themselves. Often, intrinsically disordered protein transitions to an ordered state when it binds to a folded partner protein. However some proteins remain disordered while performing their functions. | ||
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*Partially folded: The tumor suppressor protein p53 (length 393; e.g. [http://mobidb.bio.unipd.it/entries/P04637 P04637, P53_HUMAN]) is intrinsically disordered at both the N and C termini. There are many crystallographic structures for the folded mid-region (~200 residues), which lack coordinates for 90-some residues at the N terminus, and 90-some at the C terminus. Some solution NMR structures of the N terminus illustrate the disorder (e.g. 2ly4). | *Partially folded: The tumor suppressor protein p53 (length 393; e.g. [http://mobidb.bio.unipd.it/entries/P04637 P04637, P53_HUMAN]) is intrinsically disordered at both the N and C termini. There are many crystallographic structures for the folded mid-region (~200 residues), which lack coordinates for 90-some residues at the N terminus, and 90-some at the C terminus. Some solution NMR structures of the N terminus illustrate the disorder (e.g. 2ly4). | ||
*Unfolded: Caldesmon from chicken gizzard (length 771; [http://mobidb.bio.unipd.it/entries/P12957 P12957, CALD1_CHICK]) has no crystal structures, and is predicted to be disordered for essentially its full length. | *Unfolded: Caldesmon from chicken gizzard (length 771; [http://mobidb.bio.unipd.it/entries/P12957 P12957, CALD1_CHICK]) has no crystal structures, and is predicted to be disordered for essentially its full length. | ||
== References == | == References == | ||
<references/> | <references/> | ||
