Abstract
A new structure classification scheme for biopolymers is introduced, which is solely based on main-chain dihedral angles. It is shown that by dividing a biopolymer into segments containing two central residues, a local classification can be performed. The method is referred to as DISICL, short for Dihedral-based Segment Identification and Classification. Compared to other popular secondary structure classification programs, DISICL is more detailed as it offers 18 distinct structural classes, which may be simplified into a classification in terms of seven more general classes. It was designed with an eye to analyzing subtle structural changes as observed in molecular dynamics simulations of biomolecular systems. Here, the DISICL algorithm is used to classify two databases of protein structures, jointly containing more than 10 million segments. The data is compared to two alternative approaches in terms of the amount of classified residues, average occurrence and length of structural elements, and pair wise matches of the classifications by the different programs. In an accompanying paper (Nagy, G.; Oostenbrink, C. Dihedral-based segment identification and classification of biopolymers II: Polynucleotides. J. Chem. Inf. Model. 2013, DOI: 10.1021/ci400542n), the analysis of polynucleotides is described and applied. Overall, DISICL represents a potentially useful tool to analyze biopolymer structures at a high level of detail.
Highlights
Biopolymers like proteins and DNA are essential building blocks of all living organisms and understanding how they fulfill their biological functions is one of the most important tasks in life sciences
We have introduced a new structure classification algorithm, DISICL, which performs the classification of short biopolymer segments based on dihedral angles within the segment
We demonstrated the potential of the algorithm by performing a large-scale classification of protein models found in the Brookhaven Protein Databank and a comparative analysis for a set of six simulation trajectories using DISICL and two already established algorithms (DSSP and STRIDE)
Summary
Biopolymers like proteins and DNA are essential building blocks of all living organisms and understanding how they fulfill their biological functions is one of the most important tasks in life sciences. We compare the abundance, average length, and agreement scores of helical structural elements of the different algorithms (3-helix, 4-helix, 5-helix of DSSP and STRIDE; 310-helix, α-helix, π-helix for DISICL; or 3-helical turns and α-helical class in the simplified library of DISICL). While this segment lacks the proper backbone hydrogen bonds with another β-strand, its linear structure is partially stabilized by side-chain interactions. Considering the details of the N-terminal part of the protein, DSSP classifies a short but stable β-sheet based on the hydrogen bonding In this region, STRIDE shows a similar but less stable sheet with an increased proportion of turns, while DISICL classifies the structure predominantly as mixture of β-caps, polyproline-like structures, and γ-turns. Visual checks confirm the hydrogen bonds as well as the extremely distorted nature of these β-strands (Figure 6D)
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