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Updated: Jun 18, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Computational exploration of the network of sequence flow between protein structures
1Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA.
Proteins
|November 10, 2009
Summary
Small protein sequence changes can cause large shifts between protein folds, aiding in discovering ancient structures and designing novel protein switches. This protein evolution insight reveals a dense network connecting various protein folds.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Biology
Background:
- Proteins undergo conformational transitions between stable folds.
- These transitions are significant for evolutionary studies and protein design.
- Understanding sequence-structure relationships is key to protein function.
Purpose of the Study:
- To investigate how minor sequence modifications induce major protein fold transitions.
- To map the network of sequence flow between protein folds.
- To explore the evolutionary implications of protein fold plasticity.
Main Methods:
- Computation of a sequence flow network using Protein Data Bank structures.
- Analysis of network density and connectivity.
- Examination of specific protein families (e.g., Cro family) and experimentally observed fold transitions.
Main Results:
- A dense network connects protein folds, with each structure linked to numerous others.
- Proteins attracting sequences from many neighbors are often enzymes with alpha/beta folds.
- Enzyme adaptability to substrates may drive the high connectivity.
- Capacity is suggested as a key factor in protein evolution.
Conclusions:
- Small sequence changes can lead to significant protein fold changes.
- The protein fold network provides insights into evolutionary pathways and protein design.
- A kinetic model for sequence transitions between folds based on stability is proposed.
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