Vibrational spectroscopic characteristics of secondary structure polypeptides in liquid water: constrained MD simulation studies

Using the constrained MD simulation method in combination with quantum chemistry calculation, Hessian matrix reconstruction, and fragmentation approximation methods, we established a computational scheme for numerical simulations of amide I IR absorption, vibrational circular dichroism (VCD), and 2D IR photon echo spectra of peptides in solution. Six different secondary structure peptides, i.e., alpha-helix, 3(10)-helix, pi-helix, antiparallel and parallel beta-sheets, and polyproline II (P(II)), are considered, and the vibrational characteristic features in their linear and nonlinear spectra in the amide I band region are discussed. Isotope-labeling effects on IR and VCD spectra are notable only for alpha- and pi-helical peptides due to the strong vibrational couplings between two nearest neighboring amide I local oscillators. The amplitudes of difference 2D IR spectra are shown to be strongly dependent on both the extent of mode delocalization and the relative orientation of local mode transition dipoles determined by secondary structure.     

Vibrational and chiroptical spectroscopic characterization of γ‐turn model cyclic tetrapeptides containing two β‐Ala residues

The optical spectroscopic characterization of γ‐turns in solution is uncertain and their distinction from β‐turns is often difficult. This work reports systematic ECD and vibrational circular dichroism (VCD) spectroscopic studies on γ‐turn model cyclic tetrapeptides cyclo(Ala‐β‐Ala‐Pro‐β‐Ala) ( 1 ), cyclo(Pro‐β‐Ala‐Pro‐β‐Ala) ( 2 ) and cyclo(Ala‐β‐Ala‐Ala‐β‐Ala) ( 3 ). Conformational analysis performed at the 6‐31G(d)/B3LYP level of theory using an adequate PCM solvent model predicted one predominant conformer for 1‐3 , featuring two inverse γ‐turns. The ECD spectra in ACN of 1 and 2 are characterized by a negative n→π* band near 230 nm and a positive π→π* band below 200 nm with a long wavelength shoulder. The ECD spectra in TFE of 1‐3 show similar spectra with blue‐shifted bands. The VCD spectra in ACN‐d₃ of 1 and 2 show a +/?/+/? amide I sign pattern resulting from four uncoupled vibrations in the case of 1 and a sequence of two positive couplets in the case of 2 . A ?/+/+/? amide I VCD pattern was measured for 3 in TFE‐d₂. All three peptides give a positive couplet or couplet‐like feature (+/?) in the amide II region. VCD spectroscopy, in agreement with theoretical calculations revealed that low frequency amide I vibrations (at ～1630 cm^?1 or below) are indicative of a C₇ H‐bonded inverse γ‐turns with Pro in position 2, while γ‐turns encompassing Ala absorb at higher frequency (above 1645 cm^?1). Chirality, 2010. © 2010 Wiley‐Liss, Inc.     

Structural analysis of some soluble elastins by means of FT‐IR and 2D IR correlation spectroscopy

Fourier transform infrared (FT‐IR) spectroscopy combined with 2D correlation spectroscopy has been used to offer some information about stability and structure of some soluble elastins. Temperature has been chosen as the perturbation to monitor the infrared behavior of various soluble elastins, namely, α‐elastin p, α‐elastin, and k‐elastin. In the 3800–2700 cm^?1 region, the H‐containing groups were analyzed. The bonded hydroxyls are found to decrease prior to the NH‐related hydrogen bonds and also to the conformational reorganization of hydrocarbon chains. The transition temperatures were evaluated and they were found to agree with those obtained from DSC data. The FTIR spectra and their 2nd derivatives denote that α‐ elastins exhibited amide‐I, ‐II and ‐III bands at 1656, 1539 and 1236 cm^?1, respectively, while in k‐elastin these bands were found at 1652 cm^?1 for amide I, 1540 cm^?1 for amide II and 1248 cm^?1 for amide III. The macroscopic IR finger‐print method, which combines: general IR spectra, secondary derivative spectra, and 2D‐IR correlation spectra, is useful to discriminate different elastins. Thus using the differences of the position and intensity of the bands from “fingerprint region” of studied elastins, which include the peaks assigned to C?O, C? C groups from α‐helix, β‐turn, and the peaks assigned to the amide groups, it is possible to identify and discriminate elastins from each others. Furthermore, the pattern of 2D‐IR correlation spectra under thermal perturbation, allow their direct identification and discrimination. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 1072–1084, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Characterization of β-bend ribbon spiral forming peptides using electronic and vibrational CD

Terminally blocked (L-Pro-Aib)_n and Aib-(L-Pro-Aib)_n sequential oligopeptides are known to form right-handed β-bend ribbon spirals under a variety of experimental conditions. Here we describe the results of a complete CD and ir characterization of this subtype of 3₁₀-helical structure. The electronic CD spectra were obtained in solvents of different polarity in the 260-180 nm region. The vibrational CD and Fourier transform ir (FTIR) spectra were measured in deuterochloroform solution in the amide I and amide II (1750-1500 cm^?1) regions. The critical chain length for full development of the β-bend ribbon spiral structure is found to be five to six residues. Spectral effects related to concentration-induced stabilization of the structures of the longer peptides were seen in the resolution-enhanced FTIR spectra. Comparison to previous studies of (Aib)_n and (Pro)_n oligomers indicate that the low frequency of the amide I mode is due to the interaction of secondary and tertiary amide bonds and not to a strong difference in conformation from a regular 3₁₀-helix. © 1995 John Wiley & Sons, Inc.     

Four-wave mixing signals from β-carotene and its n = 15 homologue

The third-order nonlinear optical responses of β-carotene and its homologue having a conjugation-double bond n = 15 have been investigated using sub-20 fs ultra-short optical pulses in order to clarify the dissipation processes of excess energy. Using the four-wave mixing spectroscopy, we observed a clear coherent oscillation with a period of a few tens of femtoseconds. The spectral density of these molecules was estimated that allowed the theoretical linear and nonlinear optical signals to be directly compared with the experimental data. Calculations based on the Brownian oscillator model were performed under the impulsive excitation limit. We show that the memory of the vibronic coherence generated upon the excitation into the S₂ state is lost via the relaxation process including the S₁ state. The vibronic decoherence lifetime of the system was estimated to be 1 ps, which is about 5 times larger than the life time of the S₂ state (∼150 fs) determined in previous studies. The role of coherence and the efficient energy transfer in the light-harvesting antenna complexes are discussed.     

VCD Robustness of the Amide‐I and Amide‐II Vibrational Modes of Small Peptide Models

The rotational strengths and the robustness values of amide‐I and amide‐II vibrational modes of For(AA)_nNHMe (where AA is Val, Asn, Asp, or Cys, n = 1–5 for Val and Asn; n = 1 for Asp and Cys) model peptides with α‐helix and β‐sheet backbone conformations were computed by density functional methods. The robustness results verify empirical rules drawn from experiments and from computed rotational strengths linking amide‐I and amide‐II patterns in the vibrational circular dichroism (VCD) spectra of peptides with their backbone structures. For peptides with at least three residues (n ≥ 3) these characteristic patterns from coupled amide vibrational modes have robust signatures. For shorter peptide models many vibrational modes are nonrobust, and the robust modes can be dependent on the residues or on their side chain conformations in addition to backbone conformations. These robust VCD bands, however, provide information for the detailed structural analysis of these smaller systems. Chirality 27:625–634, 2015 © 2015 Wiley Periodicals, Inc.     

Atomistic Modeling of IR Action Spectra Under Circularly Polarized Electromagnetic Fields: Toward Action VCD Spectra

The nonlinear response and dissociation propensity of an isolated chiral molecule, camphor, to a circularly polarized infrared laser pulse was simulated by molecular dynamics as a function of the excitation wavelength. The results indicate similarities with linear absorption spectra, but also differences that are ascribable to dynamical anharmonic effects. Comparing the responses between left‐ and right‐circularly polarized pulses in terms of dissociation probabilities, or equivalently between R‐ and S‐camphor to a similarly polarized pulse, we find significant differences for the fingerprint C = O amide mode, with a sensitivity that could be sufficient to possibly enable vibrational circular dichroism as an action technique for probing molecular chirality and absolute conformations in the gas phase. Chirality 27:253–261, 2015. © 2015 Wiley Periodicals, Inc.     

Spectroscopic study on structure of horseradish peroxidase in water and dimethyl sulfoxide mixture

The structure of horseradish peroxidase (HRP) in phosphate buffered saline (PBS)/dimethyl sulfoxide (DMSO) mixed solvents at different compositions is investigated by IR, electronic absorption, and fluorescence spectroscopies. The fluorescence spectra and the amide I spectra of ferric HRP [HRP(Fe3+)] show that overall structural changes are relatively small up to 60% DMSO. Although the amide I band of HRP(Fe3+) shows a gradual change in the secondary structure and a decrease in the contents of a helices, its fluorescence spectra indicate that the distance between the heme and Trp173 is almost constant. In contrast, the changes in the positions of the Soret bands for resting HRP(Fe3+) and catalytic intermediates (compounds I and II) and the IR spectra at the C-O stretching vibration mode of carbonyl ferrous HRP [HRP(Fe2+)-CO] show that the microenvironment in the distal heme pocket is altered, even with low DMSO contents. The large reduction of the catalytic activity of HRP even at low DMSO contents can be attributed to the structural transition in the distal heme pocket. In PBS/DMSO mixtures containing more than 70 vol % DMSO, HRP undergoes large structural changes, including a large loss of the secondary structure and a dissociation of the heme from the apoprotein. The presence of the components of the amide I band that can be assigned to strongly hydrogen bonding amide C=O groups at 1616 and 1684 cm(-1) suggests that the denatured HRP may aggregate through strong hydrogen bonds.     

Stereoelectronic Properties of N-acetyl-α,β-dehydroamino acid N′-methylamides

Summary α,β-Dehydroamino acids are useful peptide modifiers. However, their stereoelectronic properties still remain insufficiently recognized. Based on FTIR experiments in the range ofv _s(N-H), AI, AII andv _s(C^α=C^β) and ab initio calculations with B3LYP/6–31G*, we studied the solution conformational preferences and the amide electron density perturbation of Ac-ΔXaa-NHMe, where ΔXaa=ΔAla, (E)-ΔAbu, (Z)-ΔAbu, (Z)-ΔLeu, (Z)-ΔPhe and ΔVal. Each of these dehydroamides adopts a C₅ structure, which in Ac-ΔAla-NHMe is fully extended and accompanied by the strong C₅ hydrogen bond. Interaction with bond C^α=C^β lessens the amidic resonance within the flanking amide groups. TheN-terminal C=O bond is noticeably shorter, both amide bonds are longer than the corresponding bonds in the saturated entities and the N-terminal amide system is distorted. Ac-ΔAla-NHMe constitutes an exception. ItsC-terminal amide bond is shorter than the standard one and both amide systems are ideally planar. Ac-(E)-ΔAbu-NHMe shares stereoelectronic features with both Ac-ΔAla-NHMe and (Z)-dehydroamides.     

Vibrational analysis of peptides,polypeptides, and proteins. II. β-Poly(L-alanine) and β-poly(L-alanylglycine)

The normal vibration frequencies of poly(L -alanine) and poly(L -alanylglycine) in the antiparallel chain-pleated sheet structure have been calculated, using the force field for polyglycine I from the previous paper (Biopolymers 15 , 2439–2464) plus additional force constants for the methyl group. The agreement with observed ir and Raman bands is very good. This substantiates the excellent transferability of the force field, since polyglycine I was shown to have a rippled-sheet structure. The amide I and amide II mode splittings are very well accounted for by transition dipole coupling, showing that subtle structural differences are sensitively manifested through this mechanism.     

Vibrational circular dichroism in amino acids and peptides. 7. Amide stretching vibrations in polypeptides

Vibrational circular dichroism (VCD) spectra for the principal amide stretching vibrations, amide A (N? H stretch) and amide I (predominantly C?O stretch), are presented and analyzed for a variety of polypeptides dissolved in chloroform, as well as for two examples in D₂O. Our results for poly(γ-benzyl-L -glutamate) confirm the first and only previous report of VCD in polypeptides carried out by Singh and Keiderling [(1981) Biopolymers 20 , 237–240]. Collectively, our spectra show that the sense of the bisignate VCD in these two regions depends on the sense of α-helicity and not on the absolute configuration of the constituent amino acids. This conclusion is established by obtaining VCD for the two polypeptides, poly(β-benzyl-L -asparate) and poly(im-benzyl-L -histidine), that form left-handed as opposed to right-handed α-helices. A new amide band having significant VCD intensity owing to its Fermi resonance interaction with the N? H stretching mode has been identified as a weak shoulder on the low-frequency side of the amide A band near 3200 cm^?1 and is assigned as a combination band of the amide I and amide II vibrations. VCD spectra of polypeptides in D₂O solution, although weak, have been successfully measured in the amide I region, where spectra appear to be more complicated due to the presence of solvated and internally hydrogen-bonded amide groups. Strong monosignate contributions to the VCD in the amide A and amide I regions for some of the polypeptides indicate coupling of an electronic nature between these two regions and is deduced by an application of the concept of local sum rules of rotational strength. It appears that a detailed understanding of the VCD obtained for polypeptides will not only be diagnostic of secondary structure, but also of more subtle structural and vibrational effects that give rise to local, intrinsic chirality in the amide vibrations.     

Determination of solid-state fungal growth by Fourier transform infrared-photoacoustic spectroscopy

Abstract Photoacoustic spectroscopy (PAS) does not require optically transparent samples and is, therefore, well suited for analysis of solid-state samples. Fourier transform infrared (FTIR)-PAS of solid materials containing protein exhibited strong absorption in the amide I and amide II regions of the IR spectrum. Growth of a filamentous fungus, Phanerochaete chrysosporium , on cellulose discs was quantitatively determined by monitoring amide I absorption with FTIR-PAS.     

Temperature dependence of amino acid side chain IR absorptions in the amide I' region

Amide I' IR spectra are widely used for studies of structural changes in peptides and proteins as a function of temperature. Temperature dependent absorptions of amino acid side‐chains that overlap the amide I' may significantly complicate the structural analyses. While the side‐chain IR spectra have been investigated previously, thus far their dependence on temperature has not been reported. Here we present the study of the changes in the IR spectra with temperature for side‐chain groups of aspartate, glutamate, asparagine, glutamine, arginine, and tyrosine in the amide I' region (in D₂O). Band fitting analysis was employed to extract the temperature dependence of the individual spectral parameters, such as peak frequency, integrated intensity, band width, and shape. As expected, the side‐chain IR bands exhibit significant changes with temperature. The majority of the spectral parameters, particularly the frequency and intensity, show linear dependence on temperature, but the direction and magnitude vary depending on the particular side‐chain group. The exception is arginine, which exhibits a distinctly nonlinear frequency shift with temperature for its asymmetric CN₃H₅⁺ bending signal, although a linear fit can account for this change to within ~1/3 cm^‐1. The applicability of the determined spectral parameters for estimations of temperature‐dependent side‐chain absorptions in peptides and proteins are discussed. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 536–548, 2014.     

Experimental evidence for the role of buried polar groups in determining the reduction potential of metalloproteins: the S79P variant of Chromatium vinosum HiPIP

 The amide group between residues 78 and 79 of Chromatium vinosum high-potential iron-sulfur protein (HiPIP) is in close proximity to the Fe₄S₄ cluster of this protein and interacts via a hydrogen bond with Sγ of Cys77, one of the cluster ligands. The reduction potential of the S79P variant was 104±3 mV lower than that of the recombinant wild-type (rcWT) HiPIP (5 mM phosphate, 100 mM NaCl, pH 7, 293 K), principally due to a decrease in the enthalpic term which favors the reduction of the rcWT protein. Analysis of the variant protein by NMR spectroscopy indicated that the substitution has little effect on the structure of the HiPIP or on the electron distribution in the oxidized cluster. Potential energy calculations indicate that the difference in reduction potential between rcWT and S79P variant HiPIPs is due to the different electrostatic properties of amide 79 in these two proteins. These results suggest that the influence of amide group 79 on the reduction potential of C. vinosum HiPIP is a manifestation of a general electrostatic effect rather than a specific interaction. More generally, these results provide experimental evidence for the importance of buried polar groups in determining the reduction potentials of metalloproteins. Received: 26 April 1999 / Accepted: 24 August 1999     

ACE gene polymorphism and cardiac structure in patients with insulin resistance

Aims: Angiotensin-converting enzyme (ACE) is a key enzyme in the production of angiotensin II, thus may participate in the modulation of cardiac growth. The aim of our study is to analyze the ACE gene I/D polymorphisms in patients with insulin resistance (IR) and to evaluate its relationship to left ventricular mass and functions. Methods: Eighteen subjects (13 female and 5 male, mean age 39.8 ± 14) with IR were enrolled in the present study. Twenty-three healthy people without IR were recruited as the control group. ACE amplification of DNA was performed by polymerase chain reaction methodology. Fasting glucose and insulin, postprandial glucose, homeostasis model assessment (HOMA-IR) and HOMA-beta, lipid profile, anthropometric measurements were assessed. Left ventricular structure and functions were measured by echocardiography. Results: Distribution of I/D polymorphism of the ACE gene in the study group was as follows: genotype II–0%, ID–38.9%, DD–61.1% of patients. Distribution of individual genotypes was similar in patients with and without IR. No significant difference was found between genotype groups in terms of anthropometric measurements and metabolic parameters and blood pressure. Echocardiography showed no significant changes in left ventricular structure and functions in patients with IR. Conclusions: We considered that in patients with IR, there is no relationship between I/D polymorphism of the ACE gene and LVH.     

Enzymatic Preparation of Aromatic Ethylamines from Aromatic L-Amino Acids

The characteristic mode for the herbicidal action of 2-amino-3-chloro-1,4-naphthoquinone (ACN) was investigated by using autotrophic green microalgae (Scenedesmus acutus). The effects of ACN on the growth, chlorophyll content, protoporphyrin-IX accumulation, and ethane production in Scenedesmus cells were measured in comparison with three reference herbicides, i.e., ioxynil, dinoseb, and chlorophthalim. ACN appeared to have a different mechanism for action from these three herbicides. S. acutus cells grown with ACN produced ethane, but the mechanism for its production is considered to have been different from that of chlorophthalim. ACN may inhibit porphyrin biosynthesis at a different stage from that by chlorophthalim.     

Vibrational 13C-cross-polarization/magic angle spinning NMR spectroscopic and thermal characterization of poly(alanine-glycine) as model for silk I Bombyx mori fibroin

This study focuses on the conformational characterization of poly(alanine-glycine) II (pAG II) as a model for a Bombyx mori fibroin silk I structure. Raman, IR, and 13C-cross-polarization/magic angle spinning NMR spectra of pAG II are discussed in comparison with those of the crystalline fraction of B. mori silk fibroin (chymotryptic precipitate, Cp) with a silk I (silk I-Cp) structure. The spectral data give evidence that silk I-Cp and the synthetic copolypeptide pAG II have similar conformations. Moreover, the spectral findings reveal that silk I-Cp is more crystalline than pAG II; consequently, the latter contains a larger amount of the random coil conformation. Differential scanning calorimetry measurements confirm this result. N-Deuteration experiments on pAG II allow us to attribute the Raman component at 1320 cm(-1) to the amide III mode of a beta-turn type II conformation, thus confirming the results of those who propose a repeated beta-turn type II structure for silk I. The analysis of the Raman spectra in the nuNH region confirms that the silk I structure is characterized by the presence of different types of H-bonding arrangements, in agreement with the above model.     

Optimal deep brain stimulation of the subthalamic nucleus—a computational study

Deep brain stimulation (DBS) of the subthalamic nucleus, typically with periodic, high frequency pulse trains, has proven to be an effective treatment for the motor symptoms of Parkinson’s disease (PD). Here, we use a biophysically-based model of spiking cells in the basal ganglia (Terman et al., Journal of Neuroscience, 22, 2963–2976, 2002; Rubin and Terman, Journal of Computational Neuroscience, 16, 211–235, 2004) to provide computational evidence that alternative temporal patterns of DBS inputs might be equally effective as the standard high-frequency waveforms, but require lower amplitudes. Within this model, DBS performance is assessed in two ways. First, we determine the extent to which DBS causes Gpi (globus pallidus pars interna) synaptic outputs, which are burstlike and synchronized in the unstimulated Parkinsonian state, to cease their pathological modulation of simulated thalamocortical cells. Second, we evaluate how DBS affects the GPi cells’ auto- and cross-correlograms. In both cases, a nonlinear closed-loop learning algorithm identifies effective DBS inputs that are optimized to have minimal strength. The network dynamics that result differ from the regular, entrained firing which some previous studies have associated with conventional high-frequency DBS. This type of optimized solution is also found with heterogeneity in both the intrinsic network dynamics and the strength of DBS inputs received at various cells. Such alternative DBS inputs could potentially be identified, guided by the model-free learning algorithm, in experimental or eventual clinical settings. Action Editor: Steven J. Schiff Xiao-Jiang Feng and Eric Shea-Brown contributed equally to this work.     

Dihedral angles of tripeptides in solution directly determined by polarized Raman and FTIR spectroscopy

The amide I mode of the peptide linkage is highly delocalized in peptides and protein segments due to through-bond and through-space vibrationally coupling between adjacent peptide groups. J. Phys. Chem. B. 104:11316-11320) used coherent femtosecond infrared (IR) spectroscopy to determine the excitonic coupling energy and the orientational angle between the transition dipole moments of the interacting amide I modes of cationic tri-alanine in D(2)O. Recently, the same parameters were determined for all protonation states of tri-alanine by analyzing the amide I bands in the respective IR and isotropic Raman spectra (. J. Am. Chem. Soc. 119:1720-1726.). In both studies, the dihedral angles phi and psi were then obtained by utilizing the orientational dependence of the coupling energy obtained from ab initio calculations on tri-glycine in vacuo (. J. Raman Spectrosc. 29:81-86) to obtain an extended 3(1) helix-like structure for the tripeptide. In the present paper, a novel algorithm for the analysis of excitonic coupling between amide I modes is presented, which is based on the approach by Schweitzer-Stenner et al. but avoids the problematic use of results from ab initio calculations. Instead, the dihedral angles are directly determined from infrared and visible polarized Raman spectra. First, the interaction energy and the corresponding degree of wave-function mixing were obtained from the amide I profile in the isotropic Raman spectrum. Second, the depolarization ratios and the amide I profiles in the anisotropic Raman and IR-absorption spectra were used to determine the orientational angle between the peptide planes and the transition dipole moments, respectively. Finally, these two geometric parameters were utilized to determine the dihedral angles phi and psi between the interacting peptide groups. Stable extended conformations with dihedral angles in the beta-sheet region were obtained for all protonation states of tri-alanine, namely phi(+) = -126 degrees, psi(+) = 178 degrees; phi(+/-) = -110 degrees, psi(+/-) = 155 degrees; and phi(-) = -127 degrees, psi(-) = 165 degrees for the cationic, zwitterionic, and anionic state, respectively. These values reflect an extended beta-helix structure. Tri-glycine was found to be much more heterogeneous in that different extended conformers coexist in the cationic and zwitterionic state, which yield a noncoincidence between isotropic and anisotropic Raman scattering. Our study introduces vibrational spectroscopy as a suitable tool for the structure analysis of peptides in solution and tripeptides as suitable model systems for investigating the role of local interactions in determining the propensity of peptide segments for distinct secondary structure motifs.     

Synthesis and structural study of a fully protected α-C-galactosyl model dipeptide

Summary The synthesis of three N-alkyl-6,7-dideoxy-1,2:3,4-di-O-isopropylidene-7-[(alkyl-carbonyl)amino]-L-glycero-α-D-galacto-octopyranuronamides6a-c, analogous model dipeptides containing two amide groups connected to the α-carbon bearing the fully protected galactose as a side chain, has been realized with the aim of determining the conformational influence of the galactosyl moiety on the peptide backbone. Molecular modeing of6a, X-ray crystallography of6c and IR and NMR experiments on6a-c in organic solvents show that the carbohydrate ring assumes a twist boat conformation. In non-polar organic solvents, the NH of the left amide group interacts with one ketal oxygen of the galactosyl group.