Vibrational Coupling between Helices Influences the Amide I Infrared Absorption of Proteins: Application to Bacteriorhodopsin and Rhodopsin

Karjalainen, Eeva-Liisa; Barth, Andreas

doi:10.1021/jp300329k

Cited by 23 publications

(27 citation statements)

References 73 publications

(194 reference statements)

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“…The α-helical band absorption maxima for GlpG changes significantly between 10 and 40 minutes - from 1651 to 1661 cm −1 . This 10 cm −1 frequency up-shift is indicative of α-helical bundle formation 32 , 40 implying tertiary structure folding of the polypeptide into its polytopic form. All signatures for α-helices and β-structure regions remained but increased in intensity until approximately five hours, where little change in intensity was observed.…”

Section: Resultsmentioning

confidence: 95%

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Structure formation during translocon-unassisted co-translational membrane protein folding

Harris¹,

Reading²,

Ataka

et al. 2017

Sci Rep

105

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Correctly folded membrane proteins underlie a plethora of cellular processes, but little is known about how they fold. Knowledge of folding mechanisms centres on reversible folding of chemically denatured membrane proteins. However, this cannot replicate the unidirectional elongation of the protein chain during co-translational folding in the cell, where insertion is assisted by translocase apparatus. We show that a lipid membrane (devoid of translocase components) is sufficient for successful co-translational folding of two bacterial α-helical membrane proteins, DsbB and GlpG. Folding is spontaneous, thermodynamically driven, and the yield depends on lipid composition. Time-resolving structure formation during co-translational folding revealed different secondary and tertiary structure folding pathways for GlpG and DsbB that correlated with membrane interfacial and biological transmembrane amino acid hydrophobicity scales. Attempts to refold DsbB and GlpG from chemically denatured states into lipid membranes resulted in extensive aggregation. Co-translational insertion and folding is thus spontaneous and minimises aggregation whilst maximising correct folding.

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Section: Resultsmentioning

confidence: 95%

“…The observed frequency up-shifts can be explained by different inter-helical coupling among helices, which can significantly influence the amide I absorption of proteins 40 . The frequency up-shift may also be due to the influence of different membrane lipid order, lateral pressure profile and curvature on inter-helical coupling within TMs.…”

Section: Resultsmentioning

confidence: 99%

Structure formation during translocon-unassisted co-translational membrane protein folding

Harris¹,

Reading²,

Ataka

et al. 2017

Sci Rep

105

View full text Add to dashboard Cite

show abstract

“…The latter frequency is characteristic for polytopic α-helical proteins. The frequency up-shift of 6 cm -1 has been explained by vibrational coupling among helices when α-helical bundles form [ 39 , 40 ].…”

Section: Resultsmentioning

confidence: 99%

In-Situ Observation of Membrane Protein Folding during Cell-Free Expression

et al. 2016

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Proper insertion, folding and assembly of functional proteins in biological membranes are key processes to warrant activity of a living cell. Here, we present a novel approach to trace folding and insertion of a nascent membrane protein leaving the ribosome and penetrating the bilayer. Surface Enhanced IR Absorption Spectroscopy selectively monitored insertion and folding of membrane proteins during cell-free expression in a label-free and non-invasive manner. Protein synthesis was performed in an optical cell containing a prism covered with a thin gold film with nanodiscs on top, providing an artificial lipid bilayer for folding. In a pilot experiment, the folding pathway of bacteriorhodopsin via various secondary and tertiary structures was visualized. Thus, a methodology is established with which the folding reaction of other more complex membrane proteins can be observed during protein biosynthesis (in situ and in operando) at molecular resolution.

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“…One of the most significant, practical advantages for a detailed structural analysis is that the amide I band is sensitive to more than the mere secondary structure. Other structural parameters can alter the amide I spectrum, such as solvent exposure [6,7], local deformations [2,8], size [2], and structural organization [9,10,11,12,13] of the individual secondary structure elements. These phenomena increase the inherent information content, but complicate spectral interpretation.…”

Section: Introductionmentioning

confidence: 99%

Simultaneous Fitting of Absorption Spectra and Their Second Derivatives for an Improved Analysis of Protein Infrared Spectra

Baldassarre

Eremina

et al. 2015

Molecules

Self Cite

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Infrared spectroscopy is a powerful tool in protein science due to its sensitivity to changes in secondary structure or conformation. In order to take advantage of the full power of infrared spectroscopy in structural studies of proteins, complex band contours, such as the amide I band, have to be decomposed into their main component bands, a process referred to as curve fitting. In this paper, we report on an improved curve fitting approach in which absorption spectra and second derivative spectra are fitted simultaneously. Our approach, which we name co-fitting, leads to a more reliable modelling of the experimental data because it uses more spectral information than the standard approach of fitting only the absorption spectrum. It also avoids that the fitting routine becomes trapped in local minima. We have tested the proposed approach using infrared absorption spectra of three mixed α/β proteins with different degrees of spectral overlap in the amide I region: ribonuclease A, pyruvate kinase, and aconitase.

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Vibrational Coupling between Helices Influences the Amide I Infrared Absorption of Proteins: Application to Bacteriorhodopsin and Rhodopsin

Cited by 23 publications

References 73 publications

Structure formation during translocon-unassisted co-translational membrane protein folding

Structure formation during translocon-unassisted co-translational membrane protein folding

In-Situ Observation of Membrane Protein Folding during Cell-Free Expression

Simultaneous Fitting of Absorption Spectra and Their Second Derivatives for an Improved Analysis of Protein Infrared Spectra

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