Assessing Spectral Simulation Protocols for the Amide I Band of Proteins

Cunha, Ana V.; Bondarenko, Anna S.; Jansen, Thomas L. C.

doi:10.1021/acs.jctc.6b00420

Cited by 43 publications

(59 citation statements)

References 116 publications

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“…This vibrational Hamiltonian mapping was demonstrated to work well in combination with the OPLS-AA force field in a recent benchmark study for proteins. 26 …”

Section: Theoretical Methodsmentioning

confidence: 99%

Interplay between Hydrogen Bonding and Vibrational Coupling in Liquid N-Methylacetamide

Cunha

Salamatova

Bloem

et al. 2017

J. Phys. Chem. Lett.

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Intrinsically disordered proteins play an important role in biology, and unraveling their labile structure presents a vital challenge. However, the dynamical structure of such proteins thwarts their study by standard techniques such as X-ray diffraction and NMR spectroscopy. Here, we use a neat liquid composed of N-methylacetamide molecules as a model system to elucidate dynamical and structural properties similar to those one can expect to see in intrinsically disordered proteins. To examine the structural dynamics in the neat liquid, we combine molecular dynamics, response-function-based spectral simulations, and two-dimensional polarization-resolved infrared spectroscopy in the amide I (CO stretch) region. The two-dimensional spectra reveal a delicate interplay between hydrogen bonding and intermolecular vibrational coupling effects, observed through a fast anisotropy decay. The present study constitutes a general platform for understanding the structure and dynamics of highly disordered proteins.

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“…This vibrational Hamiltonian mapping was demonstrated to work well in combination with the OPLS-AA force field in a recent benchmark study for proteins. 26 …”

Section: Theoretical Methodsmentioning

confidence: 99%

Interplay between Hydrogen Bonding and Vibrational Coupling in Liquid N-Methylacetamide

Cunha

Salamatova

Bloem

et al. 2017

J. Phys. Chem. Lett.

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“…Before PAA treatment, the type I collagen matrix revealed characteristic collagen‐related amide I, II, and III bands at 1,200–1,700 cm −1 . Compared with the baseline collagen spectrum, a minor shift in the amide I peak was observed, probably because of newly formed hydrogen bonds (Figs ). A series of collagen wagging vibration bands was detected at amide II, amide III, and between these amides (Figs ).…”

Section: Resultsmentioning

confidence: 99%

Intrafibrillar mineralization of polyacrylic acid‐bound collagen fibrils using a two‐dimensional collagen model and Portland cement‐based resins

Huang

et al. 2016

European J Oral Sciences

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The biomimetic remineralization of apatite-depleted dentin is a potential method for enhancing the durability of resin-dentin bonding. To advance this strategy from its initial proof-of-concept design, we sought to investigate the characteristics of polyacrylic acid (PAA) adsorption to desorption from type I collagen and to test the mineralization ability of PAA-bound collagen. Portland cement and β-tricalcium phosphate (β-TCP) were homogenized with a hydrophilic resin blend to produce experimental resins. The collagen fibrils reconstituted on nickel (Ni) grids were mineralized using different methods: (i) group I consisted of collagen treated with Portland cement-based resin in simulated body fluid (SBF); (ii) group II consisted of PAA-bound collagen treated with Portland cement-based resin in SBF; and (iii) group III consisted of PAA-bound collagen treated with β-TCP-doped Portland cement-based resin in deionized water. Intrafibrillar mineralization was evaluated using transmission electron microscopy. We found that a carbonyl-associated peak at pH 3.0 increased as adsorption time increased, whereas a hydrogen bond-associated peak increased as desorption time increased. The experimental resins maintained an alkaline pH and the continuous release of calcium ions. Apatite was detected within PAA-bound collagen in groups II and III. Our results suggest that PAA-bound type I collagen fibrils can be mineralized using Portland cement-based resins.

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“…Explicit solvent (e.g., water) and hetero‐atoms are thus readily (and have been) included in the calculations. The interplay between the force field used to sample conformational dynamics and models used to construct the exciton Hamiltonian is complex . Previous studies have considered CHARMM22 amongst other force fields.…”

Section: Methodsmentioning

confidence: 99%

“…They found that hydration had a significant effect on the computed IR spectra, contributing to the computed red shift of the Amide I bond of different structural components. Recently, Jansen and coworkers have benchmarked several approaches to computing the Amide I band and 2D IR of proteins from MD simulations . Up to four proteins were studied using several combinations of force fields for the MD simulations, electrostatic mappings and couplings.…”

Section: Introductionmentioning

confidence: 99%

“…Recently, Jansen and coworkers have benchmarked several approaches to computing the Amide I band and 2D IR of proteins from MD simulations. [64,65] Up to four proteins were studied using several combinations of force fields for the MD simulations, electrostatic mappings and couplings. Skinner's empirical frequency map [60] with the TDC model was reported to do well in conjunction with the OPLS-AA force field.…”

Section: Introductionmentioning

confidence: 99%

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Computing infrared spectra of proteins using the exciton model

et al. 2016

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The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are a vital complement to 2DIR experimental measurements, allowing the observed signals to be interpreted in terms of detailed structural and dynamical information. In this article, we have studied nine structurally and spectroscopically well‐characterized proteins, representing a range of structural types. We have simulated the equilibrium conformational dynamics in an explicit point charge water model. Using the resulting trajectories based on MD simulations, we have computed the one and two dimensional infrared spectra in the Amide I region, using an exciton approach, in which a local mode basis of carbonyl stretches is considered. The role of solvent in shifting the Amide I band (by 30 to 50 cm−1) is clearly evident. Similarly, the conformational dynamics contribute to the broadening of peaks in the spectrum. The inhomogeneous broadening in both the 1D and 2D spectra reflects the significant conformational diversity observed in the simulations. Through the computed 2D cross‐peak spectra, we show how different pulse schemes can provide additional information on the coupled vibrations. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

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Assessing Spectral Simulation Protocols for the Amide I Band of Proteins

Cited by 43 publications

References 116 publications

Interplay between Hydrogen Bonding and Vibrational Coupling in Liquid N-Methylacetamide

Interplay between Hydrogen Bonding and Vibrational Coupling in Liquid N-Methylacetamide

Intrafibrillar mineralization of polyacrylic acid‐bound collagen fibrils using a two‐dimensional collagen model and Portland cement‐based resins

Computing infrared spectra of proteins using the exciton model

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