Journal article
Coupled protein-ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks.
- Cazade PA Department of Chemistry, University of Basel, Klingelbergstrasse 80 4056 Basel, Switzerland.
- Berezovska G Department of Chemistry, University of Basel, Klingelbergstrasse 80 4056 Basel, Switzerland.
- Meuwly M Department of Chemistry, University of Basel, Klingelbergstrasse 80 4056 Basel, Switzerland; Department of Chemistry, Brown University, Providence/RI, USA. Electronic address: m.meuwly@unibas.ch.
- 2014-09-17
Published in:
- Biochimica et biophysica acta. - 2015
Ligand dynamics
Network
Truncated hemoglobin
Algorithms
Cluster Analysis
Hemoglobins, Abnormal
Kinetics
Ligands
Molecular Dynamics Simulation
Monte Carlo Method
Motion
Oxygen
Oxyhemoglobins
Protein Binding
Protein Conformation
Structure-Activity Relationship
Truncated Hemoglobins
English
BACKGROUND
The nature of ligand motion in proteins is difficult to characterize directly using experiment. Specifically, it is unclear to what degree these motions are coupled.
METHODS
All-atom simulations are used to sample ligand motion in truncated Hemoglobin N. A transition network analysis including ligand- and protein-degrees of freedom is used to analyze the microscopic dynamics.
RESULTS
Clustering of two different subsets of MD trajectories highlights the importance of a diverse and exhaustive description to define the macrostates for a ligand-migration network. Monte Carlo simulations on the transition matrices from one particular clustering are able to faithfully capture the atomistic simulations. Contrary to clustering by ligand positions only, including a protein degree of freedom yields considerably improved coarse grained dynamics. Analysis with and without imposing detailed balance agree closely which suggests that the underlying atomistic simulations are converged with respect to sampling transitions between neighboring sites.
CONCLUSIONS
Protein and ligand dynamics are not independent from each other and ligand migration through globular proteins is not passive diffusion.
GENERAL SIGNIFICANCE
Transition network analysis is a powerful tool to analyze and characterize the microscopic dynamics in complex systems. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
The nature of ligand motion in proteins is difficult to characterize directly using experiment. Specifically, it is unclear to what degree these motions are coupled.
METHODS
All-atom simulations are used to sample ligand motion in truncated Hemoglobin N. A transition network analysis including ligand- and protein-degrees of freedom is used to analyze the microscopic dynamics.
RESULTS
Clustering of two different subsets of MD trajectories highlights the importance of a diverse and exhaustive description to define the macrostates for a ligand-migration network. Monte Carlo simulations on the transition matrices from one particular clustering are able to faithfully capture the atomistic simulations. Contrary to clustering by ligand positions only, including a protein degree of freedom yields considerably improved coarse grained dynamics. Analysis with and without imposing detailed balance agree closely which suggests that the underlying atomistic simulations are converged with respect to sampling transitions between neighboring sites.
CONCLUSIONS
Protein and ligand dynamics are not independent from each other and ligand migration through globular proteins is not passive diffusion.
GENERAL SIGNIFICANCE
Transition network analysis is a powerful tool to analyze and characterize the microscopic dynamics in complex systems. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
- Language
-
- English
- Open access status
- closed
- Identifiers
-
- DOI 10.1016/j.bbagen.2014.09.008
- PMID 25224733
- Persistent URL
- https://sonar.ch/global/documents/232034
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