Abstract
Helices are one of the most common and were among the earliest recognized secondary structure elements in proteins. The assignment of helices in a protein underlies the analysis of its structure and function. Though the mathematical expression for a helical curve is simple, no previous assignment programs have used a genuine helical curve as a model for helix assignment. In this paper we present a two-step assignment algorithm. The first step searches for a series of bona fide helical curves each one best fits the coordinates of four successive backbone Cα atoms. The second step uses the best fit helical curves as input to make helix assignment. The application to the protein structures in the PDB (protein data bank) proves that the algorithm is able to assign accurately not only regular α-helix but also 310 and π helices as well as their left-handed versions. One salient feature of the algorithm is that the assigned helices are structurally more uniform than those by the previous programs. The structural uniformity should be useful for protein structure classification and prediction while the accurate assignment of a helix to a particular type underlies structure-function relationship in proteins.
Highlights
Helices were proposed as the main secondary structure elements for proteins in 1951 [1] through model building using low-resolution X-ray diffraction data well before atomic coordinates could be determined from high-resolution data [2, 3]
In this paper we present a two-step algorithm that follows the division of the assignment problem into two separate problems: a minimization problem and a restraint satisfaction problem
The accurately assigned helices and the helix clusters as well as the common structural features shared by all the helices in a cluster should be useful for protein structure classification and prediction as well as secondary structure prediction while the accurate assignment of a helix to a particular type should provide a basis for the discovery of structure-function relationship in proteins
Summary
Helices were proposed as the main secondary structure elements for proteins in 1951 [1] through model building using low-resolution X-ray diffraction data well before atomic coordinates could be determined from high-resolution data [2, 3]. As is evident from the helix model, the hydrogen bonding interaction between an amino (NH) group and a carbonyl (CO) group plays a decisive role in helix stability. The early recognition of the importance of hydrogen bonding interaction greatly affects our understanding of helices in proteins. As a consequence of the characteristic hydrogen bonding pattern and van der Waals repulsion, the backbone φ and ψ angles of a helix residue lie in two well-separated regions with the larger one corresponding to the right-handed helices while the much smaller one the lefthanded ones. For the same reasons there exist no large variations in the derived geometrical
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