Browse
Submit Data
Databases
API
Help

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Electrostatic frequency shifts in amide I vibrational spectra: direct parameterization against experiment.

ABSTRACT: The interpretation of protein amide I infrared spectra has been greatly assisted by the observation that the vibrational frequency of a peptide unit reports on its local electrostatic environment. However, the interpretation of spectra remains largely qualitative due to a lack of direct quantitative connections between computational models and experimental data. Here, we present an empirical parameterization of an electrostatic amide I frequency map derived from the infrared absorption spectra of 28 dipeptides. The observed frequency shifts are analyzed in terms of the local electrostatic potential, field, and field gradient, evaluated at sites near the amide bond in molecular dynamics simulations. We find that the frequency shifts observed in experiment correlate very well with the electric field in the direction of the C=O bond evaluated at the position of the amide oxygen atom. A linear best-fit mapping between observed frequencies and electric field yield sample standard deviations of 2.8 and 3.7 cm(-1) for the CHARMM27 and OPLS-AA force fields, respectively, and maximum deviations (within our data set) of 9 cm(-1). These results are discussed in the broader context of amide I vibrational models and the effort to produce quantitative agreement between simulated and experimental absorption spectra.

SUBMITTER: Reppert M

PROVIDER: S-EPMC3631266 | biostudies-other | 2013 Apr

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Decomposition of vibrational shifts of nitriles into electrostatic and hydrogen-bonding effects.

Project description:Infrared (IR) band shifts of isolated vibrational transitions can serve as quantitative and directional probes of local electrostatic fields, due to the vibrational Stark effect. However, departures from the Stark model can arise when the probe participates in specific, chemical interactions, such as direct hydrogen bonding. We present a method to identify and correct for these departures based on comparison of (13)C NMR chemical shifts and IR frequencies each calibrated in turn by a solvatochromic model. We demonstrate how the tandem use of these experimental observables can be applied to a thiocyanate-modified protein, ketosteroid isomerase, and show, by comparison to structural models, that changes in electrostatic field can be measured within the complex protein environment even in the background of direct hydrogen bonding to the probe.

| S-EPMC2943212 | biostudies-literature

Vibrational frequency shifts and relaxation rates for a selected vibrational mode in cytochrome C.

Project description:The vibrational energy relaxation of a selected vibrational mode in cytochrome c--a C-D stretch in the terminal methyl group of Met80--has been studied using equilibrium molecular dynamics simulation and normal mode analysis methods. As demonstrated in the pioneering work of Romesberg and co-workers, isotopic labeling of the C-H (to C-D) stretch in alkyl side chains shifts the stretching frequency to the transparent region of the protein's density of states, making it an effective and versatile probe of protein structure and dynamics. Molecular dynamics trajectories of solvated cytochrome c were run at 300 K, and vibrational population relaxation times were estimated using the classical Landau-Teller-Zwanzig model and a number of semiclassical theories of resonant and two-phonon vibrational relaxation processes. The C-D stretch vibrational population relaxation time is estimated to be T(1) = 14-40 ps; the relatively close agreement between various semiclassical estimates of T(1) lends support to the applicability of those expressions. Normal mode calculations were used to identify the dominant coupling between the protein and C-D oscillator. All bath modes strongly coupled to the C-D stretch are in close proximity. Angle bending modes in the terminal methyl group of Met80 appear to be the most likely acceptor modes defining the mechanism of population relaxation of the C-D vibration.

| S-EPMC1303319 | biostudies-literature

Development and validation of transferable amide I vibrational frequency maps for peptides.

Project description:Infrared (IR) spectroscopy of the amide I band has been widely utilized for the analysis of peptides and proteins. Theoretical modeling of IR spectra of proteins requires an accurate and efficient description of the amide I frequencies. In this paper, amide I frequency maps for protein backbone and side chain groups are developed from experimental spectra and vibrational lifetimes of N-methylacetamide and acetamide in different solvents. The frequency maps, along with established nearest-neighbor frequency shift and coupling schemes, are then applied to a variety of peptides in aqueous solution and reproduce experimental spectra well. The frequency maps are designed to be transferable to different environments; therefore, they can be used for heterogeneous systems, such as membrane proteins.

| S-EPMC3274961 | biostudies-literature

Understanding Chemical versus Electrostatic Shifts in X-ray Photoelectron Spectra of Organic Self-Assembled Monolayers.

Project description:The focus of the present article is on understanding the insight that X-ray photoelectron spectroscopy (XPS) measurements can provide when studying self-assembled monolayers. Comparing density functional theory calculations to experimental data on deliberately chosen model systems, we show that both the chemical environment and electrostatic effects arising from a superposition of molecular dipoles influence the measured core-level binding energies to a significant degree. The crucial role of the often overlooked electrostatic effects in polar self-assembled monolayers (SAMs) is unambiguously demonstrated by changing the dipole density through varying the SAM coverage. As a consequence of this effect, care has to be taken when extracting chemical information from the XP spectra of ordered organic adsorbate layers. Our results, furthermore, imply that XPS is a powerful tool for probing local variations in the electrostatic energy in nanoscopic systems, especially in SAMs.

| S-EPMC4761973 | biostudies-literature

Amide I vibrational mode suppression in surface (SERS) and tip (TERS) enhanced Raman spectra of protein specimens.

Project description:Surface- and tip-enhanced Raman spectroscopy (SERS and TERS) are modern spectroscopic techniques, which are becoming widely used and show a great potential for the structural characterisation of biological systems. Strong enhancement of the Raman signal through localised surface plasmon resonance enables chemical detection at the single-molecule scale. Enhanced Raman spectra collected from biological specimens, such as peptides, proteins or microorganisms, were often observed to lack the amide I band, which is commonly used as a marker for the interpretation of the secondary protein structure. The cause of this phenomenon was unclear for many decades. In this work, we investigated this phenomenon for native insulin and insulin fibrils using both TERS and SERS and compared these spectra to the spectra of well-defined homo peptides. The results indicate that the appearance of the amide I Raman band does not correlate with the protein aggregation state, but is instead determined by the size of the amino acid side chain. For short model peptides, the absence of the amide I band in TERS and SERS spectra correlates with the presence of a bulky side chain. Homo-glycine and -alanine, which are peptides with small side chain groups (H and CH(3), respectively), exhibited an intense amide I band in almost 100% of the acquired spectra. Peptides with bulky side chains, such as tyrosine and tryptophan, exhibited the amide I band in 70% and 31% of the acquired spectra, respectively.

| S-EPMC3586543 | biostudies-literature

Empirical maps for the calculation of amide I vibrational spectra of proteins from classical molecular dynamics simulations.

Project description:New sets of parameters (maps) for calculating amide I vibrational spectra for proteins through a vibrational exciton model are proposed. The maps are calculated as a function of electric field and van der Waals forces on the atoms of peptide bonds, taking into account the full interaction between peptide bonds and the surrounding environment. The maps are designed to be employed using data obtained from standard all-atom molecular simulations without any additional constraints on the system. Six proteins representing a wide range of sizes and secondary structure complexity were chosen as a test set. Spectra calculated for these proteins reproduce experimental data both qualitatively and quantitatively. The proposed maps lead to spectra that capture the weak second peak observed in proteins containing ?-sheets, allowing for clear distinction between ?-helical and ?-sheet proteins. While the parametrization is specific to the CHARMM force field, the methodology presented can be readily applied to any empirical force field.

| S-EPMC4317051 | biostudies-literature

Detection of chiral sum frequency generation vibrational spectra of proteins and peptides at interfaces in situ.

Project description:In this work, we demonstrate the feasibility to collect off-electronic resonance chiral sum frequency generation (SFG) vibrational spectra from interfacial proteins and peptides at the solid/liquid interface in situ. It is difficult to directly detect a chiral SFG vibrational spectrum from interfacial fibrinogen molecules. By adopting an interference enhancement method, such a chiral SFG vibrational spectrum can be deduced from interference spectra between the normal achiral spectrum and the chiral spectrum. We found that the chiral SFG vibrational spectrum of interfacial fibrinogen was mainly contributed by the beta-sheet structure. For a beta-sheet peptide tachyplesin I, which may be quite ordered at the solid/liquid interface, chiral SFG vibrational spectra can be collected directly. We believe that these chiral signals are mainly contributed by electric dipole contributions, which can dominate the chiroptical responses of uniaxial systems. For the first time, to our knowledge, this work indicates that the off-electronic resonance SFG technique is sensitive enough to collect chiral SFG vibrational spectra of interfacial proteins and peptides, providing more structural information to elucidate interfacial protein and peptide structures.

| S-EPMC555967 | biostudies-literature

Solvent-induced infrared frequency shifts in aromatic nitriles are quantitatively described by the vibrational Stark effect.

Project description:The physical properties of solvents strongly affect the spectra of dissolved solutes, and this phenomenon can be exploited to gain insight into the solvent-solute interaction. The large solvatochromic shifts observed for many dye molecules in polar solvents are due to variations in the solvent reaction field, and these shifts are widely used to estimate the change in the dye's dipole moment upon photoexcitation, which is typically on the order of ?1-10 D. In contrast, the change in dipole moment for vibrational transitions is approximately 2 orders of magnitude smaller. Nonetheless, vibrational chromophores display significant solvatochromism, and the relative contributions of specific chemical interactions and electrostatic interactions are debated, complicating the interpretation of vibrational frequency shifts in complex systems such as proteins. Here we present a series of substituted benzonitriles that display widely varying degrees of vibrational solvatochromism. In most cases, this variation can be quantitatively described by the experimentally determined Stark tuning rate, coupled with a simple Onsager-like model of solvation, reinforcing the view that vibrational frequency shifts are largely caused by electrostatic interactions. In addition, we discuss specific cases where continuum solvation models fail to predict solvatochromic shifts, revealing the necessity for more advanced theoretical models that capture local aspects of solute-solvent interactions.

| S-EPMC3404211 | biostudies-literature

Predicting Nuclear Resonance Vibrational Spectra of [Fe(OEP)(NO)].

Project description:Nuclear Resonance Vibrational Spectroscopy (NRVS) is a sensitive vibrational probe for biologically important heme complexes. The exquisite sensitivity of the NRVS data to the electronic structure provides detailed insights into the nature of these interesting compounds, but requires highly accurate computational methods for the mode assignments. To determine the best combinations of density functionals and basis sets, a series of benchmark DFT calculations on the previously characterized complex [Fe(OEP)NO] (OEP(2-)=octaethylporphyrinatio dianion) were performed. A test set of 21 methodology combinations including 8 functionals (BP86, mPWPW91, B3LYP, PBE1PBE, M062X, M06L, LC-BP86 and ?B97X-D) and 5 basis set (VTZ, TZVP, Lanl2DZ for iron and 6-31G*, 6-31+G* for other atoms) was carried out to calculate electronic structures and vibrational frequencies. We also implemented the conversion of frequency calculations into orientation-selective mode composition factors (e(2)), which can used to simulate the Vibrational Density Of States (VDOS) using Gaussian normal distribution functions. These use a series of user-friendly scripts for their application to NRVS. The structures as well as the isotropic and anisotropic NRVS of [Fe(OEP)NO] obtained with the M06L functional with a variety of basis sets are found to best reproduce the available experimental data, followed by B3LYP/LanL2DZ calculations. Other density functionals and basis sets do not produce the same level of accuracy. The noticeably worse agreement between theory and experiment for the out-plane NRVS compared with the excellent performance of the M06L functional for the in-plane prediction is attributed to deficiencies of the physical model rather than the computational methodology.

| S-EPMC3507453 | biostudies-literature

An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra.

Project description:Computational chemistry has become a central tool in spectroscopic studies in most of chemical science. The quality of a calculated vibrational spectrum is commonly expressed as the deviation of the peak position from the experimental reference. With the increasing application of vibrational spectroscopy to complex (biological) systems, this is likely not sustainable. Here we present a quality measure for theoretical vibrational spectra based on matching the spectra to a reference database with the help of correlation coefficients. This approach can easily be applied to large sets of data and complex spectra without easily identifiable peak positions. We demonstrate this on a database of infrared spectra of 670 compounds using six different theoretical (DFT and force field) methods. Most importantly, it is intuitively understandable by both theoreticians and experimentalists.

| S-EPMC7467738 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data