Removal of spectral noise in the quantitation of protein structure through infrared band decomposition

Echabe, Izaskun; Encinar, José Antonio; Arrondo, José Luis R.

doi:10.1002/(sici)1520-6343(1997)3:6<469::aid-bspy6>3.0.co;2-w

Cited by 28 publications

(38 citation statements)

References 11 publications

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“…Buffer contribution was subtracted from the individual spectra and spectral noise was reduced as described previously (29). The protein secondary structure was estimated from 600 scans of IR spectra by decomposition of the amide IЈ band into its spectral components (29). For temperature-dependent studies, the samples were submitted to heating cycles at each at the indicated temperatures.…”

Section: Methodsmentioning

confidence: 89%

“…Routinely, infrared spectra were taken in triplicate from different KcsA samples in a Bruker IF66s instrument equipped with a DTGS detector. Buffer contribution was subtracted from the individual spectra and spectral noise was reduced as described previously (29). The protein secondary structure was estimated from 600 scans of IR spectra by decomposition of the amide IЈ band into its spectral components (29).…”

Section: Methodsmentioning

confidence: 99%

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Effects of Conducting and Blocking Ions on the Structure and Stability of the Potassium Channel KcsA

Renart

Barrera

Molina

et al. 2006

Journal of Biological Chemistry

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This article reports on the interaction of conducting (K ؉ ) and blocking (Na ؉ ) monovalent metal ions with detergent-solubilized and lipid-reconstituted forms of the K ؉ channel KcsA. Monitoring of the protein intrinsic fluorescence reveals that the two ions bind competitively to KcsA with distinct affinities (dissociation constants for the KcsA⅐K ؉ and KcsA⅐Na ؉ complexes of ϳ8 and 190 mM, respectively) and induce different conformations of the ion-bound protein. The differences in binding affinity as well as the higher K ؉ concentration bathing the intracellular mouth of the channel, through which the cations gain access to the protein binding sites, should favor that only KcsA⅐K ؉ complexes are formed under physiological-like conditions. Nevertheless, despite such prediction, it was also found that concentrations of Na ؉ well below its dissociation constant and even in the presence of higher K ؉ concentrations, cause a remarkable decrease in the protein thermal stability and facilitate thermal dissociation into subunits of the tetrameric KcsA, as concluded from the temperature dependence of the protein infrared spectra and from gel electrophoresis, respectively. These latter observations cannot be explained based on the occupancy of the binding sites from above and suggest that there must be additional ion binding sites, whose occupancy could not be detected by fluorescence and in which the affinity for Na ؉ must be higher or at least similar to that of K ؉ . Moreover, cation binding as reported by means of fluorescence does not suffice to explain the large differences in free energy of stabilization involved in the formation of the KcsA⅐Na ؉ and KcsA⅐K ؉ complexes, which for the most part should arise from synergistic effects of the ion-mediated intersubunit interactions.

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Section: Methodsmentioning

confidence: 89%

Section: Methodsmentioning

confidence: 99%

Effects of Conducting and Blocking Ions on the Structure and Stability of the Potassium Channel KcsA

Renart

Barrera

Molina

et al. 2006

Journal of Biological Chemistry

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“…In all cases, the differences among the three experiments were lower than 5%. The error in estimation of the percentage of secondary structure depends mainly on the removal of spectral noise, and it was estimated to be 2% (20). For the measurement of the tyrosine ring vibration wave number, an exponential baseline was subtracted.…”

Section: Methodsmentioning

confidence: 99%

Molecular View by Fourier Transform Infrared Spectroscopy of the Relationship between Lactocin 705 and Membranes: Speculations on Antimicrobial Mechanism

Castellano

Vignolo

Farı́as

et al. 2007

Appl Environ Microbiol

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Lactocin 705 is a bacteriocin whose activity depends upon the complementation of two peptides, termed Lac705␣ and Lac705␤. Neither Lac705␣ nor Lac705␤ displayed bacteriocin activity by itself when the growth of sensitive cells was monitored. To obtain molecular insights into the lactocin 705 mechanism of action, Fourier transform infrared spectroscopy was used to investigate the interactions of each peptide (Lac705␣ and Lac705␤) with dipalmitoylphosphatidylcholine liposomal membranes. Both peptides show the ability to interact with the zwitterionic membrane but at different bilayer levels. While Lac705␣ interacts with the interfacial region inducing dehydration, Lac705␤ peptide interacts with only the hydrophobic core. This paper presents the first experimental evidence that supports the hypothesis that Lac705␣ and Lac705␤ peptides could form a transmembrane oligomer. From the obtained results, a mechanism of action of lactocin 705 on membrane systems is proposed. The component Lac705␣ could induce the dehydration of the bilayer interfacial region, and the Lac705␤ peptide could insert in the hydrophobic region of the membrane where the peptide has adequate conditions to achieve the oligomerization.In the last decade, there has been a growing interest in biopreservation through the use of microorganisms and/or their metabolites to prevent food spoilage and to extend the shelf life of foods (7,34,42). Lactic acid bacteria (LAB) are of particular interest as biopreservative organisms. The preserving effects of these organisms are due to the production of antimicrobial substances, including hydrogen peroxide, organic acid, and bacteriocins (16,36). Bacteriocins are ribosomally synthetized antimicrobial peptides active against closely related bacteria. The major classes of bacteriocins produced by LAB include: lantibiotics, small heat-stable peptides, large heat-labile proteins, and complex proteins. Most of the bacteriocins produced by LAB belong to class II, which can be subdivided into Listeria-active peptides (IIa), two-peptide bacteriocins (IIb), sec-dependent bacteriocins (IIc), and bacteriocins that do not belong to the other subgroups (IId) (27). The potential application of LAB bacteriocins as food preservatives requires an in-depth knowledge of how they exert their bactericidal effects. Many bacteriocins appear to elicit their lethal effects by permeabilizing the cell membrane of target organisms, in certain cases by targeting intermediates of cell wall biosynthesis (10, 44) or possibly proteins of the sugar phosphotransferase systems (24, 39). The meat isolate Lactobacillus curvatus CRL705 (formerly identified as Lactobacillus casei CRL705) produces lactocin 705, a small antimicrobial substance that belongs to the class IIb bacteriocins, whose activities depend upon the complementation of two peptides, termed Lac705␣ (GMSGYIQGIPDFLKGYLHGISAANKHK KGRLGY; pI ϭ 9.87) and Lac705␤ (GFWGGLGYIAGRVG AAYGHAQASANNHHSPING; pI ϭ 8.61) (17, 18). Lactocin 705 exerted an inhibitory effect on the indicator strain Lactobac...

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“…Spectra smoothing was carried out applying the maximum entropy method, assuming that noise and band shape follow a normal distribution. The minimum bandwidth was set to 12 cm Ϫ1 (8). The signal/noise ratio of the processed spectra was better than 11000:1.…”

Section: Fig 1 Sequence Alignmentmentioning

confidence: 99%

“…Protein secondary structure was quantified by band deconvolution of the amide I band (8,12). The number and position (wave number) of the bands were taken from the deconvoluted spectra; the bandwidth was estimated from the derived spectra; and the height band taken from raw spectra (13).…”

Section: Fig 1 Sequence Alignmentmentioning

confidence: 99%

Human p8 Is a HMG-I/Y-like Protein with DNA Binding Activity Enhanced by Phosphorylation

Encinar¹,

Mallo²,

Mizyrycki³

et al. 2001

Journal of Biological Chemistry

117

147

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We have studied the biochemical features, the conformational preferences in solution, and the DNA binding properties of human p8 (hp8), a nucleoprotein whose expression is affected during acute pancreatitis. Biochemical studies show that hp8 has properties of the high mobility group proteins, HMG-I/Y. Structural studies have been carried out by using circular dichroism (near-and far-ultraviolet), Fourier transform infrared, and NMR spectroscopies. All the biophysical probes indicate that hp8 is monomeric (up to 1 mM concentration) and partially unfolded in solution. The protein seems to bind DNA weakly, as shown by electrophoretic gel shift studies. On the other hand, hp8 is a substrate for protein kinase A (PKA). The phosphorylated hp8 (PKAhp8) has a higher content of secondary structure than the nonphosphorylated protein, as concluded by Fourier transform infrared studies. PKAhp8 binds DNA strongly, as shown by the changes in circular dichroism spectra, and gel shift analysis. Thus, although there is not a high sequence homology with HMG

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Removal of spectral noise in the quantitation of protein structure through infrared band decomposition

Cited by 28 publications

References 11 publications

Effects of Conducting and Blocking Ions on the Structure and Stability of the Potassium Channel KcsA

Effects of Conducting and Blocking Ions on the Structure and Stability of the Potassium Channel KcsA

Molecular View by Fourier Transform Infrared Spectroscopy of the Relationship between Lactocin 705 and Membranes: Speculations on Antimicrobial Mechanism

Human p8 Is a HMG-I/Y-like Protein with DNA Binding Activity Enhanced by Phosphorylation

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