Validation of protein structural models using THz spectroscopy: a promising approach to solve three-dimensional structures

Mernea, Maria; Călborean, Octavian; Grigore, Oana; Dascalu, T.; Mihăilescu, Dan

doi:10.1007/s11082-013-9872-0

Cited by 13 publications

(9 citation statements)

References 23 publications

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“…2 and 3). Earlier terahertz measurements on CytC [45][46][47][48], BSA [49,50], and other biological systems [49,[51][52][53][54]] reveal a continuously increasing featureless absorption that is usually ascribed to a glassy background due to a Debye-like quadratic growth of the vibrational density of states (VDOS) of numerous vibrations of protein molecules and water-protein complexes [49,[54][55][56][57][58][59]. Basing on our data that cover not just THz but also higher-frequency infrared range, we conclude that the terahertz absorption in EMF, CytC, and BSA is essentially nothing but the low-frequency slope of the bands centered around 48 cm −1 in EMF (Fig.…”

Section: Terahertz Absorption Bandsmentioning

confidence: 99%

Terahertz-infrared spectroscopy of Shewanella oneidensis MR-1 extracellular matrix

et al. 2018

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Employing optical spectroscopy we have performed a comparative study of the dielectric response of extracellular matrix and filaments of electrogenic bacteria Shewanella oneidensis MR-1, cytochrome c, and bovine serum albumin. Combining infrared transmission measurements on thin layers with data of the terahertz spectra, we obtain the dielectric permittivity and AC conductivity spectra of the materials in a broad frequency band from a few cm up to 7000 cm in the temperature range from 5 to 300 K. Strong absorption bands are observed in the three materials that cover the range from 10 to 300 cm and mainly determine the terahertz absorption. When cooled down to liquid helium temperatures, the bands in Shewanella oneidensis MR-1 and cytochrome c reveal a distinct fine structure. In all three materials, we identify the presence of liquid bound water in the form of librational and translational absorption bands at ≈ 200 and ≈ 600 cm, respectively. The sharp excitations seen above 1000 cm are assigned to intramolecular vibrations.

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Section: Terahertz Absorption Bandsmentioning

confidence: 99%

Terahertz-infrared spectroscopy of Shewanella oneidensis MR-1 extracellular matrix

et al. 2018

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“…The approach we used for spectra simulation based on the work of Balu et al (2008) is presented in detail in Mernea et al (2014).…”

Section: Thz Spectra Simulationsmentioning

confidence: 99%

In vitro human serum albumin glycation monitored by Terahertz spectroscopy

et al. 2015

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The nonenzymatic attachment of sugars to proteins, namely glycation, is accelerated under diabetic conditions. Monitoring the glycated human serum albumin (HSA) levels gives the short term variation of glucose concentration in diabetic patients blood. Therefore, a significant effort was made to measure glycated HSA, including by spectroscopic methods such as Raman. Here we used THz spectroscopy to monitor HSA glycation in time (over 5, 7 and 11 weeks). Different sugar types have different reactivity; therefore we also addressed the reducing sugar influence on glycation by performing in vitro HSA glycation by both glucose and fructose. Since residues protonation state influences their susceptibility for glycation, we incubated HSA with sugars at two pH values: 7 and 8. Our results show that THz absorption decreases with the incubation time of HSA with sugars. At the incubation times we considered, the most significant differences were obtained on HSA samples glycated using glucose. Differences between samples glycated by glucose and by fructose show that glycation by glucose is a slower process. At pH 7, glycation by glucose is slower than at pH 8, while glycation by fructose is slightly faster at pH 7 than at pH 8. Glycated HSA models with different degrees of glycation were built by molecular modeling. Simulated THz spectra of the models are in good agreement with the experimental data. All these show that THz spectroscopy could monitor the progression of glycation in time and that it is sensitive to reducing sugars or pH value used in the glycation process.

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Section: Introductionmentioning

confidence: 99%

“…The THz spectra of large biomolecules are linear, representing an averaging over the normal modes’ contributions [ 8 , 11 , 12 ]. This makes THz absorptions difficult to interpret, but a detailed understanding of spectra can be achieved using molecular modeling methods [ 8 , 11 , 12 ]. In the present study, the THz spectra of native ENaC and ENaC inhibited by amiloride were calculated based on molecular dynamics simulations.…”

Section: Introductionmentioning

confidence: 99%

Epithelial Sodium Channel Inhibition by Amiloride Addressed with THz Spectroscopy and Molecular Modeling

et al. 2022

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THz spectroscopy is important for the study of ion channels because it directly addresses the low frequency collective motions relevant for their function. Here we used THz spectroscopy to investigate the inhibition of the epithelial sodium channel (ENaC) by its specific blocker, amiloride. Experiments were performed on A6 cells’ suspensions, which are cells overexpressing ENaC derived from Xenopus laevis kidney. THz spectra were investigated with or without amiloride. When ENaC was inhibited by amiloride, a substantial increase in THz absorption was noticed. Molecular modeling methods were used to explain the observed spectroscopic differences. THz spectra were simulated using the structural models of ENaC and ENaC—amiloride complexes built here. The agreement between the experiment and the simulations allowed us to validate the structural models and to describe the amiloride dynamics inside the channel pore. The amiloride binding site validated using THz spectroscopy agrees with previous mutagenesis studies. Altogether, our results show that THz spectroscopy can be successfully used to discriminate between native and inhibited ENaC channels and to characterize the dynamics of channels in the presence of their specific antagonist.

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Validation of protein structural models using THz spectroscopy: a promising approach to solve three-dimensional structures

Cited by 13 publications

References 23 publications

Terahertz-infrared spectroscopy of Shewanella oneidensis MR-1 extracellular matrix

Terahertz-infrared spectroscopy of Shewanella oneidensis MR-1 extracellular matrix

In vitro human serum albumin glycation monitored by Terahertz spectroscopy

Epithelial Sodium Channel Inhibition by Amiloride Addressed with THz Spectroscopy and Molecular Modeling

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