Abstract:
:alpha-helices are the most common secondary structures in observed proteins. However, they are not always found in ideal helical conformation and they often exhibit structural distortions. Quantification of these irregularities become essential in understanding the packing of helices and therefore, their role in the functional characteristics of the protein. The backbone torsions phi, psi are of limited utility in this endeavor, because distorted helices often maintain the backbone geometry. The local compensatory effects are responsible for the preservation of the entire hydrogen bond network of the helical stretch. Earlier descriptions of helical linearity and curvature rest mostly on approximation, thus motivating the search for a better method for understanding and quantifying helical irregularities. We developed a method which involves the rotation and superposition of identical repeating units of the protein by the quaternion method. The set of parameters derived from the rotation-superposition algorithm helps in identifying the bends and kinks which are not necessarily induced by unusual amino acids like proline. The quantification of irregularities of observed helices might lead to a better understanding of their packing interactions.
journal_name
Int J Biol Macromoljournal_title
International journal of biological macromoleculesauthors
Geetha Vdoi
10.1016/0141-8130(96)01106-3subject
Has Abstractpub_date
1996-08-01 00:00:00pages
81-9issue
2eissn
0141-8130issn
1879-0003pii
0141813096011063journal_volume
19pub_type
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