Myoglobin-CO conformational substate dynamics: 2D vibrational echoes and MD simulations.
Abstract: Two-dimensional (2D) infrared vibrational echoes were performed on horse heart carbonmonoxymyoglobin (MbCO) in water over a range of temperatures. The A(1) and A(3) conformational substates of MbCO are found to have different dephasing rates with different temperature dependences. A frequency-frequency correlation function derived from molecular dynamics simulations on MbCO at 298 K is used to calculate the vibrational echo decay. The calculated decay shows substantial agreement with the experimentally measured decays. The 2D vibrational echo probes protein dynamics and provides an observable that can be used to test structural assignments for the MbCO conformational substates.
Publication Date: 2002-05-23 PubMed ID: 12023251PubMed Central: PMC1302116DOI: 10.1016/S0006-3495(02)75669-5Google Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
- Research Support
- U.S. Gov't
- Non-P.H.S.
- Research Support
- U.S. Gov't
- P.H.S.
Summary
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The research aimed to analyze the conformational substate dynamics of a specific protein, horse heart carbonmonoxymyoglobin (MbCO), through a combination of two-dimensional infrared vibrational echoes and molecular dynamics simulations.
Research Methodology
- The researchers applied a technique known as two-dimensional (2D) infrared vibrational echoes to study the protein horse heart carbonmonoxymyoglobin (MbCO) in water at varying temperatures. This method allows for the investigation of fastest motions of molecules, offering greater insight into their dynamic behavior.
- The focus was on two conformational substates of the protein, A(1) and A(3), which were observed to have varying dephasing rates and temperature dependencies. A conformational substate refers to different forms that a protein can take based on changes in its three-dimensional shape, which can impact its functionality.
Findings
- The researchers discovered that these two conformational substates behave differently under changes in temperature, demonstrating different “dephasing” rates. Dephasing refers to a loss of coherence as a result of interactions with the environment.
- To further investigate these behaviors, the team used a frequency-frequency correlation function derived from molecular dynamics simulations at a fixed temperature of 298 K. Correlation function refers to the statistical relationship between two or more random variables or observed data values.
- The simulated decay, calculated with the use of the correlation function, exhibited substantial similarities with the experimental decays observed in the 2D vibrational echo experiments. This suggests that the simulation method used could accurately represent the real-world dynamics of the protein.
Implications of the Study
- The study’s findings enable a better understanding of protein dynamics, specifically their conformational changes in response to environmental factors like temperature.
- Moreover, it offers insights on how to effectively use 2D vibrational echoes and molecular dynamics simulations in studying protein dynamics. As the data derived from simulations demonstrated high consistency with experimental outcomes, these methods prove valuable in exploring protein dynamics.
- Lastly, such research enhances knowledge on how to test structural assignments for protein conformational substates using observables that can be produced from 2D vibrational echo experiments.
Cite This Article
APA
Merchant KA, Thompson DE, Xu QH, Williams RB, Loring RF, Fayer MD.
(2002).
Myoglobin-CO conformational substate dynamics: 2D vibrational echoes and MD simulations.
Biophys J, 82(6), 3277-3288.
https://doi.org/10.1016/S0006-3495(02)75669-5 Publication
Researcher Affiliations
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
MeSH Terms
- Animals
- Biophysical Phenomena
- Biophysics
- Horses
- Myoglobin / chemistry
- Protein Conformation
- Spectrophotometry, Infrared
- Thermodynamics
Grant Funding
- IR01-GM61137 / NIGMS NIH HHS
References
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Citations
This article has been cited 22 times.- Tumbic GW, Hossan MY, Thielges MC. Protein Dynamics by Two-Dimensional Infrared Spectroscopy.. Annu Rev Anal Chem (Palo Alto Calif) 2021 Jul 27;14(1):299-321.
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