Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach
Abstract
We proposed a computational protocol of simulating the T-jump peptide unfolding experiments and the related transient IR and two-dimensional IR (2DIR) spectra based on the Markov state model (MSM) and nonlinear exciton propagation (NEP) methods. MSMs partition the conformation space into a set of nonoverlapping metastable states, and we can calculate spectra signal for each of these states using the NEP method. Thus the overall spectroscopic observable for a given system is simply the sum of spectra of different metastable states weighted by their populations. We show that results from MSMs constructed from a large number of simulations have a much better agreement with the equilibrium experimental 2DIR spectra compared to that generated from straightforward MD simulations starting from the folded state. This indicates that a sufficient sampling of important relevant conformational states is critical for calculating the accurate spectroscopic observables. MSMs are also capable of simulating the unfolding relaxation dynamics upon the temperature jump. The agreement of the simulation using MSMs and NEP with the experiment not only provides a justification for our protocol, but also provides the physical insight of the underlying spectroscopic observables. The protocol we developed has the potential to be extended to simulate a wide range of fast triggering plus optical detection experiments for biomolecules.
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Using exciton methods, MSMs illuminated the processes giving rise to temperature-jump infrared (IR) and 2DIR data, providing physical insight into the observed spectroscopic signatures of distinct states in the trpzip2 peptide and an α/β fragment of NTL9.
“Using exciton methods, MSMs were able to illuminate the processes giving rise to temperature-jump infrared (IR) and 2DIR data, providing physical insight into the observed spectroscopic signatures of distinct states in the trpzip2 peptide [72] and an α/β fragment of NTL9 [73].”
From Markov state models of biomolecular conformational dynamics (2014) · cites this paper as [72]
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- Authors
- Zhuang, W., Cui, R. Z., Silva, D.-A., & Huang, X.
- Affiliations
- Dalian Institute of Chemical Physics (CN)
- Hong Kong University of Science and Technology (HK)
- Corresponding author
- Zhuang, Wei
- Huang, Xuhui
- Venue
- The Journal of Physical Chemistry B
- Publisher
- American Chemical Society (ACS)
- Published
- 2011-03-09
- Volume
- 115
- Issue
- 18
- Pages
- 5415-5424
- ISSN
- 1520-5207 (ISSN-L)
- 1520-6106
- OpenAlex
- W2053923359
- Cited by
- 70
- References
- 94
- Citations by year
- 2024: 2 · 2023: 5 · 2022: 2 · 2021: 4 · 2020: 1 · 2019: 1 · 2018: 3 · 2017: 5 · 2016: 9 · 2015: 11 · 2014: 7 · 2013: 11 · 2012: 8
- FWCI
- 3.51
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- The Journal of Physical Chemistry B (publishedVersion)
- PubMed (publishedVersion)
- Dalian Institute of Chemical Physics, CAS Institutional Repository (submittedVersion)
- Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
- Funders
- National Natural Science Foundation of China (21003117, 21033008)
- Hong Kong University of Science and Technology
- National Institutes of Health
- Dalian Institute of Chemical Physics
- National Institute of General Medical Sciences (R01GM062868)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Spectroscopy and Quantum Chemical Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Spectroscopy Techniques in Biomedical and Chemical Research
- Keywords
- peptide unfolding, time-resolved infrared spectroscopy, Markov state models, metastable states, conformational sampling
- MeSH terms
- Markov Chains, Proteins, Spectrophotometry, Infrared, Time Factors, Protein Structure, Secondary, Molecular Dynamics Simulation, Protein Unfolding
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