Watching hydrogen-bond dynamics in a β-turn by transient two-dimensional infrared spectroscopy

Kolano, Christoph; Helbing, Jan; Koziński, M.; Sander, Wolfram; Hamm, Peter

doi:10.1038/nature05352

Cited by 318 publications

(370 citation statements)

References 27 publications

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“…It enables the characterization of the mechanical response of protein at the nanometer scale (Sotomayor and Schulten 2007;Best et al 2003). Moreover, two-dimensional infrared (2D IR) spectroscopy, which maps vibrational coupling between molecular groups, can be used to probe protein folding and unfolding dynamics with picosecond time resolution (Golonzka et al 2001;Hunt 2009;Kolano et al 2006;Ganim et al 2008). Hydrogen-exchange mass-spectrometry can track the formation of secondary structures during folding by measuring how easily protons (H ?…”

Section: Introductionmentioning

confidence: 99%

Molecular dynamics simulation exploration of unfolding and refolding of a ten-amino acid miniprotein

Zhao

Cheng

2011

Amino Acids

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Steered molecular dynamics simulations are performed to explore the unfolding and refolding processes of CLN025, a 10-residue beta-hairpin. In unfolding process, when CLN025 is pulled along the termini, the forceextension curve goes back and forth between negative and positive values not long after the beginning of simulation. That is so different from what happens in other peptides, where force is positive most of the time. The abnormal phenomenon indicates that electrostatic interaction between the charged termini plays an important role in the stability of the beta-hairpin. In the refolding process, the collapse to beta-hairpin-like conformations is very fast, within only 3.6 ns, which is driven by hydrophobic interactions at the termini, as the hydrophobic cluster involves aromatic rings of Tyr1, Tyr2, Trp9, and Tyr10. Our simulations improve the understanding on the structure and function of this type of miniprotein and will be helpful to further investigate the unfolding and refolding of more complex proteins.

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Section: Introductionmentioning

confidence: 99%

Molecular dynamics simulation exploration of unfolding and refolding of a ten-amino acid miniprotein

Zhao

Cheng

2011

Amino Acids

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“…1,2 The unique value of IR spectroscopy becomes more transparent with the rapid development of various multidimensional techniques in recent years. [3][4][5][6][7] For condensed phase applications, however, the interpretation of IR spectra is not always straightforward, which highlights the importance of developing effective computational techniques that can compute linear and nonlinear IR spectra in complex molecular systems.…”

Section: Introductionmentioning

confidence: 99%

The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding

Cui

2007

The Journal of Chemical Physics

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The vibrational spectra of protonated water clusters: A benchmark for selfconsistent-charge density-functional tight binding AbstractProton transfers are involved in many chemical processes in solution and in biological systems. Although water molecules have been known to transiently facilitate proton transfers, the possibility that water molecules may serve as the "storage site" for proton in biological systems has only been raised in recent years. To characterize the structural and possibly the dynamic nature of these protonated water clusters, it is important to use effective computational techniques to properly interpret experimental spectroscopic measurements of condensed phase systems. Bearing this goal in mind, we systematically benchmark the self-consistent-charge density-functional tight-binding �SCC-DFTB� method for the description of vibrational spectra of protonated water clusters in the gas phase, which became available only recently with infrared multiphoton photodissociation and infrared predissociation spectroscopic experiments. It is found that SCC-DFTB qualitatively reproduces the important features in the vibrational spectra of protonated water clusters, especially concerning the characteristic signatures of clusters of various sizes. In agreement with recent ab initio molecular dynamics studies, it is found that dynamical effects play an important role in determining the vibrational properties of these water clusters. Considering computational efficiency, these benchmark calculations suggest that the SCC-DFTB/molecular mechanical approach can be an effective tool for probing the structural and dynamic features of protonated water molecules in biomolecular systems. The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding Proton transfers are involved in many chemical processes in solution and in biological systems. Although water molecules have been known to transiently facilitate proton transfers, the possibility that water molecules may serve as the "storage site" for proton in biological systems has only been raised in recent years. To characterize the structural and possibly the dynamic nature of these protonated water clusters, it is important to use effective computational techniques to properly interpret experimental spectroscopic measurements of condensed phase systems. Bearing this goal in mind, we systematically benchmark the self-consistent-charge density-functional tight-binding ͑SCC-DFTB͒ method for the description of vibrational spectra of protonated water clusters in the gas phase, which became available only recently with infrared multiphoton photodissociation and infrared predissociation spectroscopic experiments. It is found that SCC-DFTB qualitatively reproduces the important features in the vibrational spectra of protonated water clusters, especially concerning the characteristic signatures of clusters of various sizes. In agreement with recent ab initio molecular dynamics studies, it is found that dynamic...

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“…[35][36][37][38] for reviews). Examples include studies of the folding/unfolding of small peptides after the photoreaction of an artificially incorporated molecular group [6, 39,40] or after a temperature jump [9,10].…”

Section: Advancing the Sensitivitymentioning

confidence: 99%

Fast infrared spectroscopy of protein dynamics: advancing sensitivity and selectivity

Koziol

Johnson

Stucki-Buchli

et al. 2015

Current Opinion in Structural Biology

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2D-IR spectroscopy has matured to a powerful technique to study the structure and dynamics of peptides, but its extension to larger proteins is still in its infancy, the major limitations being sensitivity and selectivity. Site-selective information requires measuring single vibrational probes at sub-millimolar concentrations where most proteins are still stable, which is a severe challenge for conventional (FT)IR spectroscopy. Besides its ultrafast time-resolution, a so far largely underappreciated potential of 2D-IR spectroscopy lies in its sensitivity gain. The present paper sets the goals and outlines strategies how to use that sensitivity gain together with properly designed vibrational labels to make IR spectroscopy a versatile tool to study a wide class of proteins. Abstract Abstract: 2D-IR spectroscopy has matured to a powerful technique to study the structure

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Watching hydrogen-bond dynamics in a β-turn by transient two-dimensional infrared spectroscopy

Cited by 318 publications

References 27 publications

Molecular dynamics simulation exploration of unfolding and refolding of a ten-amino acid miniprotein

Molecular dynamics simulation exploration of unfolding and refolding of a ten-amino acid miniprotein

The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding

Fast infrared spectroscopy of protein dynamics: advancing sensitivity and selectivity

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