Fourier Transform Infrared Spectroscopy Studies of the Secondary Structure in mt-PA6 and mt-PA6 Treated with L-Arginine, L-Asparagine, and (+)-Citrulline in Aqueous Solution

1994 ◽  
Vol 48 (9) ◽  
pp. 1150-1155
Author(s):  
J. L. Kirsch ◽  
R. E. Zimmerman ◽  
L. G. Tensmeyer
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Spectral Data ◽  
Bound Water ◽  
Buffer Solution ◽  
Absorption Region ◽  
Ir Studies ◽  
Vibrational Bands ◽  
Ft Ir ◽  
Spectroscopy Studies

FT-IR studies of the secondary structure of mt-PA6 and mt-PA6 treated with L-arginine, (+)-citrulline, and L-asparagine were carried out in aqueous buffer solution. Spectral subtraction was used to remove the interfering water bands in the amide absorption region, and the amide I absorptions were monitored to investigate changes in the secondary structure of the mt-PA6 induced by the binding of these amino acids. The spectral data showed a narrowing of the amide I absorption of mt-PA6 on treatment with L-arginine, (+)-cirrulline, and L-asparagine. Deconvolution of the amide I absorption revealed vibrational bands characteristic of β-sheet (1632 cm−1), disordered or bound water (1644 cm−1), and turns (1660 cm−1) secondary structures for the mt-PA6. Curve-fitting methods were also used to examine the changes in spectra and secondary structure of the mt-PA6 resulting from amino acid treatment. Analysis of the spectral data shows that loss in intensity of the bands near 1644 and 1660 cm−1 is responsible for the amino acid-induced narrowing of the mt-PA6 amide I absorption. In addition, the spectral data could suggest different binding interactions for L-arginine to mt-PA6 compared to the L-asparagine and (+)-citrulline.

scholarly journals The Temperature-Dependent Adsorption Behaviour of Benzene Molecules in ZSM-5 Zeolite Pores: TPD and FT-IR Spectroscopy Studies

2005 ◽  
Vol 23 (2) ◽  
pp. 95-107 ◽  
Author(s):  
Arati Sahasrabudhe ◽  
Salil Varma ◽  
Narendra M. Gupta
Keyword(s):  
Benzene Molecule ◽  
Hydroxyl Groups ◽  
Fixed Amount ◽  
Oh Groups ◽  
Ir Studies ◽  
Ft Ir ◽  
Temperature Programmed ◽  
Spectroscopy Studies ◽  
Ir Spectroscopic

Temperature-programmed desorption (TPD) and in situ Fourier-transform infrared (FT-IR) spectroscopic methods were employed to investigate the effect of loading and sample temperature on the state of benzene molecules inside the channels of NaZSM-5 zeolite. TPD profiles revealed the existence of at least three distinct states of benzene adsorption, characterized by desorption peak maxima at ca. 120°C, 170°C and 220°C, respectively. Based on the growth behaviour of these bands, it is suggested that the benzene molecules occupy sinusoidal channels, straight channels and external surfaces, in that order. A reverse trend was observed during the subsequent flushing of the sample at varying temperatures. A virtually fixed amount of benzene was occluded at these three locations, depending upon the loading. The FT-IR studies revealed that the benzene molecule exists in a compressed state in the zeolitic channels, with the molecular clusters formed in the process dispersing only at temperatures above 150°C. For initial benzene loadings of up to ca. 1.5 molecules/unit cell, the spectrum obtained showed that in the O—H stretch region the bridge-bonded OH groups and hydroxyl groups associated with the internal zeolitic channels were perturbed simultaneously. The results show that even for a loading lower than necessary for saturation, a considerable amount of benzene remains condensed at the external surface of ZSM-5 zeolite.

In Situ FT-IR Studies of Oxide and Oxynitride Sol-Gel-Derived Thin Films

1984 ◽  
Vol 32 ◽  
Author(s):  
David M. Haaland ◽  
C. Jeffrey Brinker
Keyword(s):  
Thin Film ◽  
Thin Films ◽  
High Temperature ◽  
Low Temperatures ◽  
Sol Gel ◽  
Ir Studies ◽  
Oxynitride Glass ◽  
Vibrational Bands ◽  
Ft Ir

ABSTRACTA high-temperature infrared cell was developed to study the gel-to-glass conversion of sol-gel-derived thin films. FT-IR spectra of matched thin-film borosilicate sol-gel samples were taken as the samples were heated at 100°C intervals to 700°C in either air or ammonia. The gels were converted to oxide and oxynitride glasses, respectively, by these heat treatments. The gel-to-glass conversion could be followed and compared for these two treatments by monitoring changes in the vibrational bands present in the spectra. Comparisons between the infrared spectra of NH3-treated and air-treated films heated above 500°C reveal the appearance of new B-N bonds at the expense of B-O-Si bonds for the NH3-fired films. These spectra also exhibit changes which may indicate the formation of Si-N bonds. Thus, ammonolysis reactions can result in thin-film oxynitride glass formation at relatively low temperatures.

A Study of the Amide III Band by FT-IR Spectrometry of the Secondary Structure of Albumin, Myoglobin, and γ-Globulin

1987 ◽  
Vol 41 (2) ◽  
pp. 180-184 ◽  
Author(s):  
Koichi Kaiden ◽  
Tomoko Matsui ◽  
Shigeyuki Tanaka
Keyword(s):  
Secondary Structure ◽  
Conformational Changes ◽  
Phosphate Buffer Solution ◽  
Heat Denaturation ◽  
Buffer Solution ◽  
Ir Spectrometry ◽  
Ft Ir ◽  
Α Helix ◽  
Β Lactoglobulin ◽  
Β Sheet

FT-IR spectrometry was applied to the identification of the secondary structure species of a living protein. The spectra of native myoglobin and albumin were obtained with methods using either KBr pellet or film formed on a KBr window from an aqueous solution. Pellet preparation of myoglobin and albumin caused the structure to change from α-helix to β-structure. The conformational changes that arise from heat denaturation of myoglobin, albumin, and γ-globulin were observed by the changes in the amide I, II, and III bands. The bands of the 1300, 1260, and 1235 cm−1 regions were respectively assigned to α-helix, disordered, and β-sheet structures. These band positions were substantiated by the spectra of β-lactoglobulin and α-casein. α-Helix structure probably changes to β-structure in the presence of alkali halide, and changes to disordered structure with heat denaturation in phosphate buffer solution. The secondary structure of a protein is further identified by use of the information obtained from the amide I, II, and III bands; the amide III band is especially important. Furthermore, it may be possible to characterize the species of secondary structures of proteins adsorbed on material surfaces.

Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 445-458 ◽  
Author(s):  
Nick Goldman ◽  
Jeffrey L Thorne ◽  
David T Jones
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Protein Evolution ◽  
Solvent Accessibility ◽  
Strong Association ◽  
Length Distribution ◽  
Parametric Bootstrap ◽  
Amino Acid Replacement ◽  
Physical Constraints ◽  
The Impact

Abstract Empirically derived models of amino acid replacement are employed to study the association between various physical features of proteins and evolution. The strengths of these associations are statistically evaluated by applying the models of protein evolution to 11 diverse sets of protein sequences. Parametric bootstrap tests indicate that the solvent accessibility status of a site has a particularly strong association with the process of amino acid replacement that it experiences. Significant association between secondary structure environment and the amino acid replacement process is also observed. Careful description of the length distribution of secondary structure elements and of the organization of secondary structure and solvent accessibility along a protein did not always significantly improve the fit of the evolutionary models to the data sets that were analyzed. As indicated by the strength of the association of both solvent accessibility and secondary structure with amino acid replacement, the process of protein evolution—both above and below the species level—will not be well understood until the physical constraints that affect protein evolution are identified and characterized.

scholarly journals Large-Scale Synonymous Substitutions in Cucumber Mosaic Virus RNA 3 Facilitate Amino Acid Mutations in the Coat Protein

2018 ◽  
Vol 92 (22) ◽  
Author(s):  
Tomofumi Mochizuki ◽  
Rie Ohara ◽  
Marilyn J. Roossinck
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Viral Genome ◽  
Large Scale ◽  
Viral Rna ◽  
Wild Type ◽  
Competitive Fitness ◽  
Content Type ◽  
Synonymous Substitutions ◽  
Cp Gene

ABSTRACTThe effect of large-scale synonymous substitutions in a small icosahedral, single-stranded RNA viral genome on virulence, viral titer, and protein evolution were analyzed. The coat protein (CP) gene of the Fny stain of cucumber mosaic virus (CMV) was modified. We created four CP mutants in which all the codons of nine amino acids in the 5′ or 3′ half of the CP gene were replaced by either the most frequently or the least frequently used synonymous codons in monocot plants. When the dicot host (Nicotiana benthamiana) was inoculated with these four CP mutants, viral RNA titers in uninoculated symptomatic leaves decreased, while all mutants eventually showed mosaic symptoms similar to those for the wild type. The codon adaptation index of these four CP mutants against dicot genes was similar to those of the wild-type CP gene, indicating that the reduction of viral RNA titer was due to deleterious changes of the secondary structure of RNAs 3 and 4. When two 5′ mutants were serially passaged inN. benthamiana, viral RNA titers were rapidly restored but competitive fitness remained decreased. Although no nucleic acid changes were observed in the passaged wild-type CMV, one to three amino acid changes were observed in the synonymously mutated CP of each passaged virus, which were involved in recovery of viral RNA titer of 5′ mutants. Thus, we demonstrated that deleterious effects of the large-scale synonymous substitutions in the RNA viral genome facilitated the rapid amino acid mutation(s) in the CP to restore the viral RNA titer.IMPORTANCERecently, it has been known that synonymous substitutions in RNA virus genes affect viral pathogenicity and competitive fitness by alteration of global or local RNA secondary structure of the viral genome. We confirmed that large-scale synonymous substitutions in the CP gene of CMV resulted in decreased viral RNA titer. Importantly, when viral evolution was stimulated by serial-passage inoculation, viral RNA titer was rapidly restored, concurrent with a few amino acid changes in the CP. This novel finding indicates that the deleterious effects of large-scale nucleic acid mutations on viral RNA secondary structure are readily tolerated by structural changes in the CP, demonstrating a novel part of the adaptive evolution of an RNA viral genome. In addition, our experimental system for serial inoculation of large-scale synonymous mutants could uncover a role for new amino acid residues in the viral protein that have not been observed in the wild-type virus strains.

scholarly journals Chiroptical Sensing of Amino Acid Derivatives by Host–Guest Complexation with Cyclo[6]aramide

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 4064
Author(s):  
Xuebin Wang ◽  
Jiecheng Ji ◽  
Zejiang Liu ◽  
Yimin Cai ◽  
Jialiang Tang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Density Functional ◽  
Cd Spectroscopy ◽  
Functional Theory ◽  
Chirality Transfer ◽  
Supramolecular Chirality ◽  
New Strategy ◽  
Spectroscopy Studies ◽  
Effective Component ◽  
Acid Esters

A hydrogen-bonded (H-bonded) amide macrocycle was found to serve as an effective component in the host–guest assembly for a supramolecular chirality transfer process. Circular dichroism (CD) spectroscopy studies showed that the near-planar macrocycle could produce a CD response when combined with three of the twelve L-α-amino acid esters (all cryptochiral molecules) tested as possible guests. The host–guest complexation between the macrocycle and cationic guests was explored using NMR, revealing the presence of a strong affinity involving the multi-point recognition of guests. This was further corroborated by density functional theory (DFT) calculations. The present work proposes a new strategy for amplifying the CD signals of cryptochiral molecules by means of H-bonded macrocycle-based host–guest association, and is expected to be useful in designing supramolecular chiroptical sensing materials.

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