Vibrational circular dichroism spectroscopy of selected oligopeptide conformations

Keiderling, Timothy A.; Silva, R.A.G.D; Yoder, Gorm; Dukor, Rina K.

doi:10.1016/s0968-0896(98)00217-x

Cited by 89 publications

(99 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…That L4 shows no change in its 13 C-labeled VCD confirms it is disordered at low temperature as well. The dominant negative VCD lobe to low frequency of the IR is consistent with a coil-like conformation (27,28).…”

Section: Discussionmentioning

confidence: 69%

“…Computing IR and VCD for this form is difficult, because we do not have a defined structure. Many experiments have shown that typical polypeptide random coil spectra are similar in band shape to those obtained for a poly-L-proline II (3 1 ) helix (27,28). To provide an at least partially relevant comparison to the above helical results, we also have simulated the IR and VCD amide IЈ spectra for the Ac-A 20 -NH 2 peptide constrained to a 3 1 helical conformation (Fig.…”

Section: Band Intensities Of Labeled Residues Enhanced By Helical Envmentioning

confidence: 91%

See 1 more Smart Citation

Site-specific conformational determination in thermal unfolding studies of helical peptides using vibrational circular dichroism with isotopic substitution

Silva

Kubelka

Bouř

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

186

275

View full text Add to dashboard Cite

Understanding the detailed mechanism of protein folding requires dynamic, site-specific stereochemical information. The short time response of vibrational spectroscopies allows evaluation of the distribution of populations in rapid equilibrium as the peptide unfolds. Spectral shifts associated with isotopic labels along with local stereochemical sensitivity of vibrational circular dichroism (VCD) allow determination of the segment sequence of unfolding. For a series of alanine-rich peptides that form ␣-helices in aqueous solution, we used isotopic labeling and VCD to demonstrate that the ␣-helix noncooperatively unwinds from the ends with increasing temperature. For these blocked peptides, the C-terminal is frayed at 5°C. Ab initio level theoretical simulations of the IR and VCD band shapes are used to analyze the spectra and to confirm the conformation of the labeled components. The VCD signals associated with the labeled residues are amplified by coupling to the nonlabeled parts of the molecule. Thus small labeled segments are detectable and stereochemically defined in moderately large peptides in this report of site-specific peptide VCD conformational analysis.

show abstract

Section: Discussionmentioning

confidence: 69%

Section: Band Intensities Of Labeled Residues Enhanced By Helical Envmentioning

confidence: 91%

Site-specific conformational determination in thermal unfolding studies of helical peptides using vibrational circular dichroism with isotopic substitution

Silva

Kubelka

Bouř

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

186

275

View full text Add to dashboard Cite

show abstract

“…These observations suggest that the P II backbone conformation may occur frequently in peptides and proteins. Early CD studies (22)(23)(24)(25)(26)(27)(28)(29) of peptides and denatured proteins, and especially studies by vibrational CD (43) and Raman optical activity (44), strongly support this possibility. A new CD study of a seven-residue lysine peptide finds the P II conformation (45).…”

Section: Of Ref 31)mentioning

confidence: 99%

Polyproline II structure in a sequence of seven alanine residues

Shi

Olson

Rose

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

507

106

682

View full text Add to dashboard Cite

A sequence of seven alanine residues-too short to form an ␣-helix and whose side chains do not interact with each other-is a particularly simple model for testing the common description of denatured proteins as structureless random coils. The 3 JHN␣ coupling constants of individual alanine residues have been measured from 2 to 56°C by using isotopically labeled samples. The results display a thermal transition between different backbone conformations, which is confirmed by CD spectra. The NMR results suggest that polyproline II is the dominant conformation at 2°C and the content of ␤ strand is increased by approximately 10% at 55°C relative to that at 2°C. The polyproline II conformation is consistent with recent studies of short alanine peptides, including structure prediction by ab initio quantum mechanics and solution structures for both a blocked alanine dipeptide and an alanine tripeptide. CD and other optical spectroscopies have found structure in longer ''random coil'' peptides and have implicated polyproline II, which is a major backbone conformation in residues within loop regions of protein structures. Our result suggests that the backbone conformational entropy in alanine peptides is considerably smaller than estimated by the random coil model. New thermodynamic data confirm this suggestion: the entropy loss on alanine helix formation is only 2.2 entropy units per residue. T anford's pioneering experiments on denatured proteins in 6 M guanidinium chloride (GdmCl) (1-5) were interpreted by using the random coil model, and they anchored a widespread belief that denatured proteins are structureless chains. Tanford emphasized that 6 M GdmCl is required to eliminate all residual structure, which was detected by optical rotatory dispersion in heat-denatured proteins (6). The random coil model has been applied to modern NMR studies of backbone conformation in denatured proteins (7,8) by assuming that the backbone conformations found in protein structures, including or excluding regions of regular secondary structure, are represented with the same frequencies in denatured proteins. One might suppose, however, that the energy differences between major backbone conformations are sufficiently large to favor one conformation over others, at least in a homopeptide.We address this question by using NMR to investigate the backbone conformation as a function of temperature for a sequence of seven alanine residues in a peptide solubilized in water by two basic residues at either end of the alanine sequence. This peptide presents an appealing model system for a structureless denatured protein. It is too short to form any detectable ␣-helix in water via peptide hydrogen bonds; moreover, the OCH 3 side chain is too short to form nonpolar clusters and too inert to form other side chain interactions. To characterize the backbone conformations of this peptide, we measure system properties that are related directly to either the or the backbone angles. It is possible today to resolve and assign most backbone resonances of de...

show abstract

“…Such an opening may go on to form more extended structure, such as left-handed 3 1 -helices (or Pro II-like helices), which are major components of random coils because they are stabilized by hydrogen bonding to water (Dukor and Keiderling 1991;Keiderling et al 1999;Keiderling and Xu 2002;Shi et al 2002). These structures have been also postulated as intermediates in ␤-structure formation (McColl et al 2003).…”

Section: ␣-Helices (Closed) ␣-Helices (Open) → ␤-Strandmentioning

confidence: 99%

Effect of sodium dodecyl sulfate on folding and thermal stability of acid‐denatured cytochrome c: A spectroscopic approach

Keiderling

2004

Protein Science

102

View full text Add to dashboard Cite

The molten globule (MG) state can be an intermediate in the protein folding pathway; thus, its detailed description can help understanding protein folding. Sodium dodecyl sulfate (SDS), an anionic surfactant that is commonly used to mimic hydrophobic binding environments such as cell membranes, is known to denature some native state proteins, including horse cytochrome c (cyt c). In this article, refolding of acid denatured cyt c is studied under the influence of SDS to form MG-like states at both low concentration and above the critical micelle concentration using Fourier transform Infrared (FTIR) and ultraviolet and visible absorption as well as fluorescence and circular dichroism (CD). Thermal denaturation monitored with FTIR and CD shows distinct final high temperature states starting from MG-like states formed with different SDS/protein ratios. The results suggest that the SDS/protein ratio as well as the actual SDS (or protein) concentration affects structure and its thermal stability. Thermal denaturation monitored with CD and FTIR for cyt c at neutral pH but denatured with SDS showed that at a high SDS/protein ratio, the thermal behavior of MG-like states formed at low and neutral pH are quite similar. Based on the results obtained, the merits of two models of the protein-surfactant structure are discussed for different SDS concentrations.

show abstract

Vibrational circular dichroism spectroscopy of selected oligopeptide conformations

Cited by 89 publications

References 21 publications

Site-specific conformational determination in thermal unfolding studies of helical peptides using vibrational circular dichroism with isotopic substitution

Site-specific conformational determination in thermal unfolding studies of helical peptides using vibrational circular dichroism with isotopic substitution

Polyproline II structure in a sequence of seven alanine residues

Effect of sodium dodecyl sulfate on folding and thermal stability of acid‐denatured cytochrome c: A spectroscopic approach

Contact Info

Product

Resources

About