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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity
Márton Münz1, Rune Lyngsø, Jotun Hein
1Structural Bioinformatics and Computational Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
BMC Bioinformatics
|April 20, 2010
Summary
This study introduces a novel method to align proteins based on their dynamics, not just structure. This approach reveals conserved protein dynamics and their relationship to sequence and structure.
Area of Science:
- Biophysics
- Computational Biology
- Structural Biology
Background:
- Protein dynamics are crucial for function and are evolutionarily constrained.
- Comparing protein dynamics is essential for understanding sequence and structure effects.
- Traditional methods rely on sequence or structural alignment, which can be limiting.
Purpose of the Study:
- To develop and validate a new methodology for comparative molecular dynamics.
- To enable protein alignment based solely on dynamic motions.
- To quantify dynamic similarity between proteins without prior alignment.
Main Methods:
- Developed a novel dynamics-based alignment method.
- Applied the method to 10 PDZ domains.
- Quantified dynamic similarity and compared it with structural similarity (Dali).
Main Results:
- Successfully aligned proteins based on dynamics.
- Identified evolutionarily conserved patterns in protein backbone dynamics.
- Found high correlation between dynamic and structural similarity.
Conclusions:
- Protein dynamics can be aligned and quantified without prior sequence or structural information.
- Sequence plays a refined role in protein dynamics beyond dictating the overall fold.
- The proposed method is generally applicable for comparative molecular dynamics studies.
