Communication: Quantitative multi-site frequency maps for amide I vibrational spectroscopy

Reppert, Mike; Tokmakoff, Andrei

doi:10.1063/1.4928637

Cited by 30 publications

(59 citation statements)

References 23 publications

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“…29,30,38 The 1F map is the newest generation of our single-point field models trained to a library of dipeptide fragments. 25,32 It differs from our previous 1F map (Ref. 25 ) in the use of modified Glycine charges and TIP3P water model charges (rather than SPC/E) as described in Ref.…”

Section: Methodsmentioning

confidence: 95%

“…25 ) in the use of modified Glycine charges and TIP3P water model charges (rather than SPC/E) as described in Ref. 32 See Supporting Information for further details. Note that with the exception of the GROMOS53a6 calculations, CHARMM27 atomic charges were applied in all spectroscopic calculations (i.e.…”

Section: Methodsmentioning

confidence: 99%

“…17,25,28–32 By parameterizing electrostatic frequency shift coefficients directly against experimental data, Amide I vibrational frequencies may be predicted within an accuracy of a few cm −1 for both short dipeptide fragments 25 and isotope labels embedded within larger proteins 17,32 . Although these models are expected to improve further, the predictability of Amide I spectra has reached a point where the method can be seriously evaluated as a tool to probe disordered peptide ensembles.…”

Section: Introductionmentioning

confidence: 99%

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Refining Disordered Peptide Ensembles with Computational Amide I Spectroscopy: Application to Elastin-Like Peptides

et al. 2016

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The characterization of intrinsically disordered protein (IDP) ensembles is complicated both by inherent heterogeneity and by the fact that many common experimental techniques function poorly when applied to IDPs. For this reason, the development of alternative structural tools for probing IDP ensembles has attracted considerable attention. Here we describe our recent work in developing experimental and computational tools for characterizing IDP ensembles using Amide I (backbone carbonyl stretch) vibrational spectroscopy. In this approach, the infrared (IR) absorption frequencies of isotope-labeled amide bonds probe their local electrostatic environments and structures. Empirical frequency maps allow us to use this spectroscopic data as a direct experimental test of atomistic structural models. We apply these methods to a family of short elastin-like peptides (ELPs), fragments of the elastin protein based around the Pro-Gly turn motif characteristic of the elastomeric segments of the full protein. Using a maximum entropy analysis of experimental spectra on the basis of predicted spectra from molecular dynamics (MD) ensembles, we find that peptides with Ala or Val sidechains preceding the Pro-Gly turn unit exhibit a stronger tendency toward extended structures than do Gly-Pro-Gly motifs, suggesting an important role for steric interactions in tuning the molecular properties of elastin.

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Section: Methodsmentioning

confidence: 95%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Refining Disordered Peptide Ensembles with Computational Amide I Spectroscopy: Application to Elastin-Like Peptides

et al. 2016

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“…49,56,57 In a recent paper, 78 a benchmark study using linear absorption and 2DIR for full proteins was performed. That study focused on the Gromos-54a7 and Amber99SB-ILDN force fields.…”

mentioning

confidence: 99%

“…The time-dependent Hamiltonian accounting for the amide I vibrations is constructed for numerous snapshots along the trajectory. This is achieved by using mappings that relate the electrostatic environment predicted by the force field with the local mode vibrational frequencies, 33,44,48,48,49,51,57,[63][64][65][66][67][68][69][70] and couplings. 66,[71][72][73][74] This information is then converted to linear absorption and 2DIR spectra using response function based calculations.…”

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confidence: 99%

Assessing Spectral Simulation Protocols for the Amide I Band of Proteins

Cunha

Bondarenko

Jansen

2016

J. Chem. Theory Comput.

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We present a benchmark study of spectral simulation protocols for the amide I band of proteins. The amide I band is widely used in infrared spectroscopy of proteins due to the large signal intensity, high sensitivity to hydrogen bonding, and secondary structural motifs. This band has, thus, proven valuable in many studies of protein structure-function relationships. We benchmark spectral simulation protocols using two common force fields in combination with several electrostatic mappings and coupling models. The results are validated against experimental linear absorption and two-dimensional infrared spectroscopy for three well-studied proteins. We find two-dimensional infrared spectroscopy to be much more sensitive to the simulation protocol than linear absorption and report on the best simulation protocols. The findings demonstrate that there is still room for ideas to improve the existing models for the amide I band of proteins.

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Simulation of the T-jump triggered unfolding and thermal unfolding vibrational spectroscopy related to polypeptides conformation fluctuation

Cheng

Chen

et al. 2017

Sci. China Chem.

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Communication: Quantitative multi-site frequency maps for amide I vibrational spectroscopy

Abstract: Isotope-enriched protein standards for computational amide I spectroscopy

Cited by 30 publications

References 23 publications

Refining Disordered Peptide Ensembles with Computational Amide I Spectroscopy: Application to Elastin-Like Peptides

Refining Disordered Peptide Ensembles with Computational Amide I Spectroscopy: Application to Elastin-Like Peptides

Assessing Spectral Simulation Protocols for the Amide I Band of Proteins

Simulation of the T-jump triggered unfolding and thermal unfolding vibrational spectroscopy related to polypeptides conformation fluctuation

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