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Secondary structure assignment for conformationally irregular peptides: comparison between DSSP, STRIDE and KAKSI
1Department of Physics, North Carolina State University, Raleigh, NC 27695, United States; Center for High Performance Simulations (CHiPS), North Carolina State University, Raleigh, NC 27695, United States.
Journal of Molecular Graphics & Modelling
|November 27, 2014
Summary
Comparing protein secondary structure assignment codes reveals significant differences in disordered regions. Methods like DSSP and STRIDE show varying agreement, impacting characterization of transient structures in unfolded and intrinsically disordered proteins.
Area of Science:
- Structural Biology
- Computational Biology
- Biophysics
Background:
- Accurate protein secondary structure assignment is crucial for understanding protein function.
- Existing algorithms like DSSP and STRIDE show discrepancies in distorted or irregular protein conformations.
- Characterizing transient secondary structures in unfolded and intrinsically disordered proteins remains challenging.
Purpose of the Study:
- To investigate and quantify the differences between secondary structure assignment codes for disordered peptides.
- To evaluate the performance of DSSP, STRIDE, and KAKSI on conformationally irregular protein segments.
- To highlight challenges in secondary structure characterization for intrinsically disordered proteins.
Main Methods:
- Performed Molecular Dynamics simulations on disordered peptides: gp41659-671, polyasparagine (N18), and polyasparagine dimers.
- Analyzed simulated conformations using DSSP (hydrogen bonds), STRIDE (hydrogen bonds and dihedral angles), and KAKSI (alpha-carbon distances).
- Quantified agreement between assignments using full-sequence Segment Overlap (SOV) scores.
Main Results:
- Segment Overlap (SOV) scores varied significantly, ranging from 70% for gp41659-671 (STRIDE reference) to 49% for N18 (DSSP reference).
- Major discrepancies were observed in the assignment of turns, differentiation between alpha and 310 helices, and short parallel-sheet segments.
- The choice of secondary structure assignment code impacts the characterization of residual and transient structures.
Conclusions:
- Different secondary structure assignment algorithms exhibit notable variations, particularly for irregular peptide conformations.
- These variations pose challenges for accurately characterizing secondary structures in unfolded and intrinsically disordered proteins.
- Further refinement of secondary structure assignment methods is needed for disordered protein analysis.
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