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09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Computational identification of slow conformational fluctuations in proteins
Arvind Ramanathan1, Pratul K Agarwal
1Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology, Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.
The Journal of Physical Chemistry. B
|November 14, 2009
Summary
Protein flexibility, particularly slow motions on the microsecond to millisecond timescale, is crucial for enzyme catalysis. Quasi-harmonic analysis (QHA) effectively identified these motions in ubiquitin and cyclophilin A, linking protein flexibility to function.
Area of Science:
- Biophysics
- Computational Biology
- Structural Biology
Background:
- Protein conformational flexibility is intrinsically linked to biological function.
- Slow conformational dynamics (microsecond-millisecond timescale) are increasingly recognized for their role in enzyme catalysis.
- Computational approaches offer powerful tools to investigate the structure-flexibility-function relationship in proteins.
Purpose of the Study:
- To identify and characterize microsecond timescale conformational flexibility in ubiquitin using computational methods.
- To investigate the role of slow conformational fluctuations in protein function, specifically in enzyme catalysis.
- To compare computational findings with experimental data from nuclear magnetic resonance (NMR) and X-ray crystallography.
Main Methods:
- Quasi-harmonic analysis (QHA) applied to molecular dynamics (MD) ensembles.
- Normal-mode analysis (NMA) of protein structures.
- Analysis of conformational fluctuations along reaction pathways for enzyme catalysis.
Main Results:
- The slowest 10 QHA modes captured over 78% of ubiquitin's motions from a 0.5 microsecond MD ensemble.
- Identified slow motions in ubiquitin showed high agreement (>75%) with NMR ensembles and X-ray structures.
- QHA successfully characterized conformational fluctuations coupled to cis/trans isomerization in cyclophilin A (CypA), mirroring experimental flexibility.
Conclusions:
- Slow conformational fluctuations, particularly those identified by QHA, are critical determinants of protein function.
- Ubiquitin's flexibility in specific loop regions (beta1-beta2, alpha1-beta3, beta3-beta4) is functionally relevant for protein binding.
- NMA proved less effective than QHA for capturing long timescale dynamics due to reference structure dependence.
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