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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching
Chia-Han Chu1, Wei-Cheng Lo, Hsin-Wei Wang
1Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China.
Plos One
|October 27, 2010
Summary
This study introduces a new method to detect three-dimensional domain swapping (DS) in proteins using angle-distance images. The novel approach accurately identifies DS relationships, even with low sequence identity, aiding protein structure analysis.
Area of Science:
- Structural Biology
- Bioinformatics
- Computational Biology
Background:
- Three-dimensional domain swapping (DS) is a protein oligomerization mechanism with implications in evolution, disease, and biomaterials.
- Existing bioinformatics tools are inadequate for detecting DS due to significant conformational changes between monomeric and oligomeric forms.
- A lack of comprehensive datasets hinders the study of DS.
Purpose of the Study:
- To develop a novel and effective bioinformatics method for detecting three-dimensional domain swapping (DS) in proteins.
- To address the limitations of conventional structural comparison methods in identifying DS.
- To create a web-based tool for DS detection to facilitate large-scale studies.
Main Methods:
- Utilized angle-distance (A-D) image transformations of secondary structural elements (SSEs) to represent protein structures.
- Developed a matching algorithm to identify corresponding SSE pairs within A-D images.
- Designed a novel DS score based on A-D image analysis for classifying structural similarities and detecting DS relationships.
Main Results:
- The proposed DS detection method achieved a Matthews correlation coefficient (MCC) and sensitivity over 0.81, even for proteins with <10% sequence identity.
- The method demonstrated high performance with an average alignment percentage of 90% and RMSD of 1.8Å for 1,211 DS-related protein pairs.
- Hinge loop determination quality was comparable to manual inspection, and structural alignment performance remained stable for homologous proteins with low sequence identity.
Conclusions:
- The novel A-D image-based method provides a robust and accurate approach for detecting three-dimensional domain swapping.
- The developed web-based tool facilitates the identification of DS relationships, supporting further research and applications.
- This method is expected to stimulate extensive investigations into DS and its related biological and material science applications.
