ArticleProceedings of the National Academy of Sciences of the United States of America2007
Transient 2D IR spectroscopy of ubiquitin unfolding dynamics.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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51 citing papers in PubMed, 170 citations in OpenAlex.
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- A machine learning protocol for predicting structural distributions of amyloid-forming proteins from 2D IR spectra.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Multiscale theoretical study of infrared spectroscopy for the thermal denaturation process of aprotinin.Journal of molecular modeling · 2025Article
- Unlocking the unfolded structure of ubiquitin: Combining time-resolved x-ray solution scattering and molecular dynamics to generate unfolded ensembles.The Journal of chemical physics · 2024Article
- Unraveling dynamic protein structures by two-dimensional infrared spectra with a pretrained machine learning model.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Metastability of Protein Solution Structures in the Absence of a Solvent: Rugged Energy Landscape and Glass-like Behavior.Journal of the American Chemical Society · 2024Article
- Progress and Prospects in Optical Ultrafast Microscopy in the Visible Spectral Region: Transient Absorption and Two-Dimensional Microscopy.The journal of physical chemistry. C, Nanomaterials and interfaces · 2023Review
- Increasing Pump-Probe Signal toward Asymptotic Limits.The journal of physical chemistry. B · 2023Review
- Direct observation of peptide hydrogel self-assembly.Chemical science · 2022Article
- Vibrational couplings between protein and cofactor in bacterial phytochrome Agp1 revealed by 2D-IR spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Probing Denaturation of Protein A via Surface-Enhanced Infrared Absorption Spectroscopy.Biosensors · 2022Article
- AIM: A Mapping Program for Infrared Spectroscopy of Proteins.Journal of chemical theory and computation · 2022Article
- Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures.The journal of physical chemistry. B · 2021Article
- Transparent window 2D IR spectroscopy of proteins.The Journal of chemical physics · 2021Review
- Protein Dynamics by Two-Dimensional Infrared Spectroscopy.Annual review of analytical chemistry (Palo Alto, Calif.) · 2021Article
- Dynamics underlying hydroxylation selectivity of cytochrome P450cam.Biophysical journal · 2021Article
- Temperature-Jump 2D IR Spectroscopy with Intensity-Modulated CW Optical Heating.The journal of physical chemistry. B · 2020Article
- Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.Chemical reviews · 2020Review
- Uncovering the Early Stages of Domain Melting in Calmodulin with Ultrafast Temperature-Jump Infrared Spectroscopy.The journal of physical chemistry. B · 2019Article
- Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition.The journal of physical chemistry. B · 2019Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transient two-dimensional infrared (2D IR) spectroscopy is used as a probe of protein unfolding dynamics in a direct comparison of fast unfolding experiments with molecular dynamics simulations. In the experiments, the unfolding of ubiquitin is initiated by a laser temperature jump, and protein structural evolution from nanoseconds to milliseconds is probed using amide I 2D IR spectroscopy. The temperature jump prepares a subensemble near the unfolding transition state, leading to quasi-barrierless unfolding (the "burst phase") before the millisecond activated unfolding kinetics. The burst phase unfolding of ubiquitin is characterized by a loss of the coupling between vibrations of the beta-sheet, a process that manifests itself in the 2D IR spectrum as a frequency blue-shift and intensity decrease of the diagonal and cross-peaks of the sheet's two IR active modes. As the sheet unfolds, increased fluctuations and solvent exposure of the beta-sheet amide groups are also characterized by increases in homogeneous linewidth. Experimental spectra are compared with 2D IR spectra calculated from the time-evolving structures in a molecular dynamics simulation of ubiquitin unfolding. Unfolding is described as a sequential unfolding of strands in ubiquitin's beta-sheet, using two collective coordinates of the sheet: (i) the native interstrand contacts between adjacent beta-strands I and II and (ii) the remaining beta-strand contacts within the sheet. The methods used illustrate the general principles by which 2D IR spectroscopy can be used for detailed dynamical comparisons of experiment and simulation.
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