Can alpha helix act as a hinge region in a protein structure or only random coils/loops can act or form the hinge region?
As far as I know helices are relatively sturdy and stabilized by H-bonds and salt bridges. Flexibility comes from random coil- and loop regions. However in some crystal structures you may find slightly bent helices, but I´m in doubt that this is enough for a hinge.
Cheers.
Thanks Alexander, however, when i was using a hinge prediction tool, Stone Hinge, it suggested residues which part of an alpha helix as hinge residues. This is where i was a little confused.
Although rare it is possible to have bends in helices for example PufX as determined by NMR and Pufx in RC-LH1 dimers as observed by X-ray structure determination. There are probably many examples.
Miroslav you first mention its rare but towards the end you say there are many examples... so it is rare in what aspect?
Moreover, if there are such bends in helices.. can they be flexible enough to allow significant rotation of a domain?
Sorry Manan. I meant to say that they are rare in comparison to the 100,000 structures in the PDB database. So ,maybe a few hundred could be present..
For example in a quick look I found Shin et al. BMC Microbiology 2013, 13 26 Glutamate 83 and arginine 85 of helix H3 bend are key residues for FtsZ polymerization, GTPase activity and cellular viability of Escherichia coli lateral mutations affect FtsZ polymerization and E. coli viability
@Manan "if there are such bends in helices can they be flexible enough to allow significant rotation of a domain"
Bends, as in deviations from ideal geometry without breaking the secondary structure, are not that uncommon but will not allow significant rotation.
Local unwinding is also common, but in this case it would be more accurate to call it two helices seperated by a very short turn. For an example, see the structure below
https://www.researchgate.net/publication/258129983_PDB_2L86_Amidated_human_IAPP_in_SDS_at_pH_7_3?ev=prf_pub
Data PDB 2L86 Amidated human IAPP in SDS at pH 7_3
Another example would be the coiled coil stator domains of the rotary ATPase (vatpase). The helical structure gives strength to resist the large torque generated in rotation, whilst the hinge region at the top of the coil and a disordered region in the middle allows it to have some flexibility which is used to store energy. Lot ra et all, structure 2012.
The case i am talking about is a single helix and not a coiled coil form. The residues of this single helix tend to vary among bacterial species and most often glutamate, Isoleucine, Lysine and Arginine. When i analysed the Helix geometry using HELANAL, the residue(s) were reported to form a bend. Can a bend in a helix act as hinge
Hi Manan, Hinge prediction softwares are not to be relied blindly. The merely give you propensities of particular regions or residues to be a part of a hinge. I agree with Alexander that formation of hinges by helices is uncommon.
As Jeffrey said before, a helix is not a hinge; A helix is characterised by a range of values in the Ramachandran plot that, in principle, do not allow significant deformation of a relatively straight structure. If I understood well HELANAL analysed the geometry of an input structure, and reported some residues as part of hinge?, then it just might be that phy/psi values were off the tolerance for a canonical helix, but once again, if it's a helix, it's not significantly bent, otherwise the hydrogen bond pattern is lost.
Yes, it can! Compare calmodulin with Ca2+ Ions (PDB entry 1exr) and without Ca2+ ions (PDB entry 1cfd).
There is a long central helix. Dissociation of Ca2+ ions causes conformational changes for at least 6 residues in the central helix, loosing the helical folding: a putative hinge region!
As is the case with Ca2+ bound and apo calmodulin... if the central helix loses its helical fold and /or if it attains a curved geometry would it not affect its H-bonding pattern. Moreover if it would act as a putative hinge which would require to be flexible.. would not the conformational change affect the H-bonding patter. The pattern im seeing in the protein of my interest is the the geometry of the helix remains curved in apo as well bound formed and yet it appears to show significant fluctuations in ENM/NMA simulations which i reconfirmed using HELANAL and other hinge predicting tools..
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