Fig 2 - uploaded by Benjamin Bulheller
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Electronic transitions of the amide group in the far-UV region. The molecular orbitals shown are the bonding, nonbonding and antibonding p orbitals (p b , p nb and p*) and two lone pairs on the oxygen atom (n and n 0 ).
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Circular dichroism (CD) is an important technique in the structural characterisation of proteins, and especially for secondary structure determination. The CD of proteins can be calculated from first principles using the so-called matrix method, with an accuracy which is almost quantitative for helical proteins. Thus, for proteins of unknown struct...
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Context 1
... coil structures, all induce bands of distinc- tive shapes and magnitudes in the far-ultraviolet (Fig. 1). 42 For example, in an a-helix, an intense positive band at 190 nm and a negative band at 208 nm arise from the exciton splitting of electronic transitions from the amide non-bonding p orbi- tal, p nb , to the anti-bonding p orbital, p*, (Fig. 2). A negative band is located at about 220 nm, arising from the electronic transition from an oxygen lone pair orbital, n, to the p* orbital (Fig. 2). Other motifs give other spectroscopic shapes and ...
Context 2
... positive band at 190 nm and a negative band at 208 nm arise from the exciton splitting of electronic transitions from the amide non-bonding p orbi- tal, p nb , to the anti-bonding p orbital, p*, (Fig. 2). A negative band is located at about 220 nm, arising from the electronic transition from an oxygen lone pair orbital, n, to the p* orbital (Fig. 2). Other motifs give other spectroscopic shapes and ...
Citations
... Circular dichroism spectra following UV irradiation are exhibited in Fig. 6(a). CD spectra with minima at 208 and 222 nm are characteristic of BSA, a protein with α-helices [38]. Table 2 shows secondary structure fractions. ...
... This yields a CD profile; that is, a set of values for the rotational strength for each electronic transition as a function of the wavelength l, qðlÞ. 72 The methodology for the theoretical calculation of a CD spectrum is implemented in the DichroCalc software. 72,73 Resolving PMO solution conformations ...
... 72 The methodology for the theoretical calculation of a CD spectrum is implemented in the DichroCalc software. 72,73 Resolving PMO solution conformations ...
Elucidating the structure-function relationships for therapeutic RNA mimicking phosphorodiamidate morpholino oligonucleotides (PMOs) is challenging due to the lack of information about their structures. While PMOs have been approved by the US Food and Drug Administration for treatment of Duchenne muscular dystrophy, no structural information on these unique, charge-neutral, and stable molecules is available. We performed circular dichroism and solution viscosity measurements combined with molecular dynamics simulations and machine learning to resolve solution structures of 22-mer, 25-mer, and 30-mer length PMOs. The PMO conformational dynamics are defined by the competition between non-polar nucleobases and uncharged phosphorodiamidate groups for shielding from solvent exposure. PMO molecules form non-canonical, partially helical, stable folded structures with a small 1.4- to 1.7-nm radius of gyration, low count of three to six base pairs and six to nine base stacks, characterized by −34 to −51 kcal/mol free energy, −57 to −103 kcal/mol enthalpy, and −23 to −53 kcal/mol entropy for folding. The 4.5- to 6.2-cm3/g intrinsic viscosity and Huggins constant of 4.5–9.9 are indicative of extended and aggregating systems. The results obtained highlight the importance of the conformational ensemble view of PMO solution structures, thermodynamic stability of their non-canonical structures, and concentration-dependent viscosity properties. These principles form a paradigm to understand the structure-properties-function relationship for therapeutic PMOs to advance the design of new RNA-mimic-based drugs.
... available via a web-interface [22], which allows the nonexpert simply to upload a Protein Data Bank file with the coordinates of a protein structure and to compute the CD spectrum. The theoretical background and related developments have been summarised elsewhere [11,23] and the approach has been used, sometimes in conjunction with molecular dynamics simulations, to study a diverse range of systems, e.g. glycosylated antimicrobial peptides [24], SARS-CoV-2 proteins [25] and chymotrypsin adsorbed on silica [26]. ...
Circular dichroism (CD) spectroscopy is a powerful technique employed to study the structure of biomolecules. More accurate calculation of CD from first principles will aid both computational and experimental studies of protein structure and dynamics. We apply a diabatisation scheme to improve the description of nearest neighbour interactions between two electronic transitions (nπ* and πnbπ*) localised on each individual peptide bond (amide group) in a protein. These interactions are incorporated into DichroCalc, an exciton-based computational method to calculate CD, and yield improvements over the standard DichroCalc parameter set, particularly for calculation of CD for important secondary structural elements such as an α helix.
... Linear optical spectroscopy is a crucial analytical tool in biology, chemistry, materials science, molecular physics, and various other disciplines. It provides information about, e.g., the dipole strengths and orientations, 1-3 energy landscape, 4-7 exciton structure, 8,9 and stoichiometry 10 in pigment aggregates. In principle, all the information contained in an experimental spectrum could be extracted by comparison with exact simulations. ...
The accuracy of approximate methods for calculating linear optical spectra depends on many variables. In this study, we fix most of these parameters to typical values found in photosynthetic light-harvesting complexes of plants and determine the accuracy of approximate spectra with respect to exact calculation as a function of the energy gap and interpigment coupling in a pigment dimer. We use a spectral density with the first eight intramolecular modes of chlorophyll a and include inhomogeneous disorder for the calculation of spectra. We compare the accuracy of absorption, linear dichroism, and circular dichroism spectra calculated using the Full Cumulant Expansion (FCE), coherent time-dependent Redfield (ctR), and time-independent Redfield and modified Redfield methods. As a reference we use spectra calculated with the Exact Stochastic Path Integral Evaluation method. We find the FCE method to be the most accurate for the calculation of all spectra. The ctR method performs well for the qualitative calculation of absorption and linear dichroism spectra when pigments are moderately coupled (∼15 cm ⁻¹ ), but ctR spectra may differ significantly from exact spectra when strong interpigment coupling (>100 cm ⁻¹ ) is present. The dependence of the quality of Redfield and modified Redfield spectra on molecular parameters is similar, and these methods almost always perform worse than ctR, especially when the interpigment coupling is strong or the excitonic energy gap is small (for a given coupling). The accuracy of approximate spectra is not affected by resonance with intramolecular modes for typical system-bath coupling and disorder values found in plant light-harvesting complexes.
... Linear optical spectroscopy is a crucial analytical tool in biology, chemistry, materials science, molecular physics, and various other disciplines. It provides information about, i.a., the dipole strengths and orientations 1-3 , energy landscape 4-7 , exciton structure 8,9 , and stoichiometry 10 in pigment aggregates. In principle, all the information contained in an experimental spectrum could be extracted by comparison with exact simulations. ...
The accuracy of approximate methods for calculating linear optical spectra depends on many variables. In this study, we fix most of these parameters to typical values found in photosynthetic light-harvesting complexes of plants and determine the accuracy of approximate spectra with respect to exact calculation as a function of the energy gap and interpigment coupling in a pigment dimer. We use a spectral density with the first eight intramolecular modes of chlorophyll a and include inhomogeneous disorder for the calculation of spectra. We compare the accuracy of absorption, linear dichroism, and circular dichroism spectra calculated using the Full Cumulant Expansion (FCE), coherent time-dependent Redfield (ctR), and time-independent Redfield and modified Redfield methods. As a reference we use spectra calculated with the Exact Stochastic Path Integral Evaluation method. We find the FCE method to be the most accurate for the calculation of all spectra. The ctR method performs well for the qualitative calculation of absorption and linear dichroism spectra when pigments are moderately coupled ($\sim 15\text{ cm}^{-1}$), but ctR spectra may differ significantly from exact spectra when strong interpigment coupling ($\sim 100\text{ cm}^{-1}$) is present. The dependence of the quality of Redfield and modified Redfield spectra on molecular parameters is similar, and these methods almost always perform worse than ctR, especially when the interpigment coupling is strong or the excitonic energy gap is small (for a given coupling). The accuracy of approximate spectra is not affected by resonance between the excitonic energy gap and intramolecular modes when realistic inhomogeneous disorder is included.
... Anisotropy property is an important feature of some structures and materials. It is a phenomenon of absorption of the light polarized along the perpendicular and parallel directions with respect to a specific orientation axis [1][2][3]. The anisotropy from the optical aspect can be detected and analyzed by the linear dichroism (LD) effect [1][2][3]. ...
... It is a phenomenon of absorption of the light polarized along the perpendicular and parallel directions with respect to a specific orientation axis [1][2][3]. The anisotropy from the optical aspect can be detected and analyzed by the linear dichroism (LD) effect [1][2][3]. This optical method can exhibit the LD effect modes of a particular object accurately. ...
... However, some problems still need to be solved with the optical detection method, such as enhancing some weak signals and adjusting of these signals. The most popular method to enhance these weak signals, such as the weak signals of circular dichroism, the Fano effect [3][4][5][6][7], Raman, and the fluorescence effect [8][9][10], is the plasmon enhancement method. The plasmon enhancement methods utilize the surface plasmon (SP) to enhance the near electric field for improving the interaction between incident light and the media [7,8]. ...
Anisotropy is an important property used for characterizing objects. It is always analyzed by the conventional optical method. However, the conventional optical method, which used parameters changes for enhancing and adjusting the signals, is ineffective and inconvenient. In this study, a new on-chip electrical approach to characterize the anisotropy of the object was proposed. This approach utilized the electrical signal, photocurrent, to characterize the anisotropy features of the material. This near-field sensing approach can easily tune/enhance the anisotropy signals compared to the conventional far-field optical technique. As a simple and good example, a metal-grating structure was used. To describe the anisotropy property of the object, an electrical anisotropy, η, was introduced. The simulated results demonstrated that the proposed method is as accurate as the conventional optical method. Moreover, the electrical method is also more effective and flexible in adjusting and tuning the anisotropy signals. The most significant enhanced η mode was improved from 26.08% to 92.48%. This work hopefully will inspire more research into the development/integration of the on-chip sensing devices that serve next-generation sensors for biomolecular, chemical, and temperature-sensitive anisotropy materials.
... They used both the side-to-side and end-to-end geometry for detecting sensitivity (Wang et al. 2010). Shimada (2013) Also, the structural properties of optical and biosystems like proteins have been studied using polarized light spectroscopy techniques (Bulheller et al. 2007). ...
In this paper, we, theoretically, study the optical activity of a linear chain of 40 nm sized in diameter alloy spherical nanoparticles in the presence of a static external magnetic field illuminated by the electromagnetic field of left/right circular polarization in different angles of incidence. Regarding the subwavelength particle size, the coupled dipole method is employed to study the absorption cross section and magnetic circular dichroism (MCD) of the one-dimensional chain. The circular dichroism spectrum reveals that by increasing the Fe percentage in the alloy NPs, the peak intensity of the MCD signal decreases, and the spectrum broadens on the contrary. The refractive index sensitivity of MCD signals is investigated, either. It is shown that MCD signals are more sensitive than plasmonic signals to the refractive index variation. It is shown that the increment in the Fe atomic percentage results in more sensitive signals, as well. As an estimate, the calculations show more than 50% enhancement in the sensitivity of MCD signals of alloy Au0.85Fe0.15\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${Au}_{{0.85}}{Fe}_{{0.15}}$$\end{document} in comparison to plasmonic signals of gold NPs.
... Each light absorption causes a change in the light intensity and consequently in the amplitude of the incident wave. When a chiral substance absorbs left-and right-circularly polarized light to different extents, different amplitudes of the circularly polarized waves result, and the superimposed light is no longer linear but elliptically polarized light [48,72,73,75]. ...
... In addition to chiral carbon atoms, optically active chromophores in asymmetric molecular structures such as α-helix, β-sheet can also possess optical activity. Therefore, CD spectroscopy is widely used to analyze the structures of biomolecules such as proteins and DNA [75,76]. In proteins, the peptide bonds are the absorbing group. ...
... The CD spectra of all samples in Figure 3 showed positive maxima at 190 nm and negative bands at approximately 208 and 220 nm. The CD bands in Figure 3 were attributed to electronic transitions of a peptide bond in the far UV region [75]. In this spectral region, the amides within the secondary structure components of a protein strongly absorb circularly polarized light and exhibit different numbers of electronic transitions for a given wavelength. ...
In complex foods, bioactive secondary plant metabolites (SPM) can bind to food proteins. Especially when being covalently bound, such modifications can alter the structure and, thus, the functional and biological properties of the proteins. Additionally, the bioactivity of the SPM can be affected as well. Consequently, knowledge of the influence of chemical modifications on these properties is particularly important for food processing, food safety, and nutritional physiology. As a model, the molecular structure of conjugates between the bioactive metabolite benzyl isothiocyanate (BITC, a hydrolysis product of the glucosinolate glucotropaeolin) and the whey protein α-lactalbumin (α-LA) was investigated using circular dichroism spectroscopy, anilino-1-naphthalenesulfonic acid fluorescence, and dynamic light scattering. Free amino groups were determined before and after the BITC conjugation. Finally, mass spectrometric analysis of the BITC-α-LA protein hydrolysates was performed. As a result of the chemical modifications, a change in the secondary structure of α-LA and an increase in surface hydrophobicity and hydrodynamic radii were documented. BITC modification at the ε-amino group of certain lysine side chains inhibited tryptic hydrolysis. Furthermore, two BITC-modified amino acids were identified, located at two lysine side chains (K32 and K113) in the amino acid sequence of α-LA.
... 22 These contributions to the response were previously employed for calculating the nonlinear optical properties of molecules. 16,23,24 However, at the second order to the response there is an additional component due to square of vector potential magnitude |A| 2 in the minimal coupling description or due to magnetic field square B 2 in multipolar description. 25 Such contributions do not contribute at linear response (as they are originally quadratic) so they can be neglected for linear optical activity, however, they should be studied for nonlinear techniques, e.g. ...
Microscopic theory for the second harmonic generation in a helical molecular system is developed in the minimal coupling representation including non-local interaction effects. At the second order to the field we find a compact expression which combines dipolar, quadrupolar and magnetic contributions. A detailed derivation of the response is performed to specifically isolate the quadratic coupling terms, which we denote as the K coupling. Applying the theory to a helical macromolecule we find that the dipolar and quadrupolar contributions reflect the symmetry properties of the system and its homogeneity, while the K coupling contribution reveals inhomogeneities of the system.
... Thus, fluorescence is showing when tryptophans dip into the membrane, CD indicates when the peptide folds, which in this case is coincident with insertion [12]. CD, to a good approximation, may be deemed to be the sum of the signals of all the component parts, and there are several structure-fitting methods which can be used to give a reasonable estimate of the number of residues that are in different secondary structure motifs [32][33][34][35][36][37][38][39][40]. Most approaches select members of a reference set of protein CD spectra that most closely resemble an unknown text spectrum and then determine the secondary structure context of the unknown protein from a weighted sum of the secondary structure percentages of the best matching members of the reference spectra [36,[41][42][43][44]. ...
A range of membrane models have been developed to study components of cellular systems. Lipid vesicles or liposomes are one such artificial membrane model which mimics many properties of the biological system: they are lipid bilayers composed of one or more lipids to which other molecules can associate. Liposomes are thus ideal to study the roles of cellular lipids and their interactions with other membrane components to understand a wide range of cellular processes including membrane disruption, membrane transport and catalytic activity. Although liposomes are much simpler than cellular membranes, they are still challenging to study and a variety of complementary techniques are needed. In this review article, we consider several currently used analytical methods for spectroscopic measurements of unilamellar liposomes and their interaction with proteins and peptides. Among the variety of spectroscopic techniques seeing increasing application, we have chosen to discuss: fluorescence based techniques such as FRET (fluorescence resonance energy transfer) and FRAP (fluorescence recovery after photobleaching), that are used to identify localisation and dynamics of molecules in the membrane; circular dichroism (CD) and linear dichroism (LD) for conformational and orientation changes of proteins on membrane binding; and SERS (Surface Enhanced Raman Spectroscopy) as a rapidly developing ultrasensitive technique for site-selective molecular characterisation. The review contains brief theoretical basics of the listed techniques and recent examples of their successful applications for membrane studies.
