Flow oriented linear dichroism to probe protein orientation in membrane environments

Rodger, Alison; Rajendra, Jascindra; Marrington, Rachel; Ardhammar, Malin; Nordén, Bengt; Hirst, Jonathan D.; Gilbert, Andrew T. B.; Dafforn, Timothy R.; Halsall, David; Woolhead, Cheryl A.; Robinson, Colin; Pinheiro, Teresa J. T.; Kazlauskaite, Jurate; Seymour, Mark; Pérez, Niuvis Pérez; Hannon, Michael J.

doi:10.1039/b205080n

Cited by 68 publications

(88 citation statements)

References 19 publications

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“…LD Measurements of f210 Fibrils under Flow-LD had been used to investigate the orientation of absorbing chromophores within elongated molecules (23)(24)(25)(26)(27)(28). Although chiral compounds generate CD signals, oriented compounds either intrinsically or during the measurements often exhibit LD signals.…”

Section: Resultsmentioning

confidence: 99%

“…where A is the absorption of the fibrils, S is the orientation factor that defines the efficiency of the fibril orientation (S ϭ 1 and 0 for perfect and random orientations, respectively), and ␣ is the angle that the transition moment makes with the orientation axis (23)(24)(25)(26)(27)(28). The reduced LD spectrum indicated a dominant peak at 198.5 nm with LD r ϭ Ϫ0.28 (Fig.…”

Section: Orientation Of Functional Groups In Fibrils-mentioning

confidence: 99%

“…S2). The chromophores at 198 and 216 nm were assigned to a net amide -* transition moment and net n-* transition moment of carbonyl groups of the backbone, respectively (24,25,(27)(28)(29). For each peptide bond, the electric dipole transition moment of the amide -* transition ( -*) is directed approximately along the NO direction, whereas the magnetic dipole transition moment of the amide n-* transition (m nϪ *) is directed along the carbonyl bond (Fig.…”

Section: Orientation Of Functional Groups In Fibrils-mentioning

confidence: 99%

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Flow-induced Alignment of Amyloid Protofilaments Revealed by Linear Dichroism

Adachi

Yamaguchi

Yagi

et al. 2007

Journal of Biological Chemistry

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Amyloid fibrils underlying various serious amyloidoses including Alzheimer and prion diseases form characteristic deposits in which linear fibrils with an unbranched and rigid morphology associate laterally or radially, e.g. radial senile amyloid plaques of amyloid ␤. To clarify the formation of these high order amyloid deposits, studying the rheology is important. A 22-residue K3 peptide fragment of ␤ 2 -microglobulin, a protein responsible for dialysis-related amyloidosis, forms long and homogeneous protofilament-like fibrils in 20% (v/v) 2,2,2-trifluoroethanol and 10 mM HCl (pH ϳ2). Here, using circular dichroism and linear dichroism, we observed the flow-induced alignment of fibrils. Analysis of far-and near-UV linear dichroism spectra suggested that both the net -* transition moment of the backbone carbonyl group and L b transition moment of the Tyr 26 side chain are oriented in parallel to the fibril axis, revealing the structural details of amyloid protofilaments. Moreover, the intensities of flow-induced circular dichroism or linear dichroism signals depended critically on the length and type of fibrils, suggesting that they are useful for detecting and characterizing amyloid fibrils.Although the structural features of amyloid fibrils are of urgent importance (1-3), the high molecular weight and noncrystalline assembly preclude the use of conventional methods, such as x-ray crystallography or multidimensional NMR, to acquire high resolution structural images. Recently, it has been found that amyloid fibrils are, in general, amenable to the magic angle-spinning solid-state nuclear magnetic resonance methods, providing a general view of the atomic level structure in which ␤-strands are stacked in a parallel and registered manner (4 -6). A structure revealed by x-ray diffraction of a crystalline short amyloidogenic peptide was consistent with this view (7).More recently, the mechanical characterization of individual fibrils by atomic force microscopy revealed that the insulin fibrils have a strength and stiffness comparable with that of steel and silk, respectively (8). Among various structural features, although the long and rigid morphology of amyloid fibrils might be responsible for their biological consequences, rheological details remain unknown.␤ 2 -Microglobulin (␤2-m), 4 a typical immunoglobulin domain made of 99 residues, is a target of extensive study because of its clinical importance and suitable size for examining the relationship between protein folding and amyloid formation (9 -14). Dialysis-related amyloidosis is a common and serious complication among patients on long term hemodialysis, in which amyloid fibrils of ␤2-m deposit in the synovia of the carpal tunnel (9, 15). A 22-residue K3 peptide, corresponding to Ser 20 -Lys 41 of ␤2-m forms protofilament-like fibrils in various solvents including a low concentration of 2,2,2-trifluoroethanol (16 -19). Although the efficient fibrillation of intact ␤2-m requires seeding, K3 forms fibrils spontaneously. Furthermore, K3 formed two types of fibr...

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Section: Resultsmentioning

confidence: 99%

Section: Orientation Of Functional Groups In Fibrils-mentioning

confidence: 99%

Section: Orientation Of Functional Groups In Fibrils-mentioning

confidence: 99%

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Flow-induced Alignment of Amyloid Protofilaments Revealed by Linear Dichroism

Adachi

Yamaguchi

Yagi

et al. 2007

Journal of Biological Chemistry

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“…We have achieved this by the use of a Couette flow cell which induces alignment as a result of shear flow in a liquid. Our own advances in cuvette design have only recently permitted the use of LD to examine relatively low volume (200 l) biological samples (39,40). Our initial studies of some common protein fibers, including actin, amyloid, and collagen, have allowed us for the first time to assign the signals observed to known secondary structure types (41).…”

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confidence: 99%

FtsZ Fiber Bundling Is Triggered by a Conformational Change in Bound GTP

Marrington

Small²,

Rodger

et al. 2004

Journal of Biological Chemistry

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Polymer formation by the essential FtsZ protein plays a crucial role in the cytokinesis of most prokaryotes. Lateral associations between these FtsZ polymers to form bundles or sheets are widely predicted to be extremely important for FtsZ function in vivo. We have carried out a study in vitro of FtsZ polymer formation and bundling using linear dichroism (LD) to assess structural properties of the polymers. We demonstrate proof-of-principle experiments to show that LD can be used as a technique to follow FtsZ polymerization, and we present the LD spectra of FtsZ polymers. Our subsequent examination of FtsZ polymer bundling induced by calcium reveals a substantial increase in the LD signal indicative of increased polymer length and rigidity. We also detect a specific conformational change in the guanine moiety associated with bundling, whereas the conformation and configuration of the FtsZ monomers within the polymer remain largely unchanged. We demonstrate that other divalent cations can induce this conformational change in FtsZ-bound GTP coincident with polymer bundling. Therefore, we present "flipping" of the guanine moiety in FtsZ-bound GTP as a mechanism that explains the link between reduced GTPase activity, increased polymer stability, and polymer bundling.

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“…Together with single molecule force measurements by AFM, it should be possible to use these methodologies to systematically probe the energetic characteristics of peptide-lipid interactions as a function of the chemical structure of the lipid and the peptide, in order to understand the relative importance of the non-covalent interactions that are involved. In order to probe the structure of peptide-lipid adducts, a number of spectroscopic techniques have found application, including NMR, 48 linear and circular dichroism, 49 and attenuated total reflection FTIR. 50 All of these methods may be performed on oriented bilayers, providing information on the orientation of peptides with respect to the bilayer normal, 51 as well as information concerning the 2° structure of the peptide.…”

Section: Peptide-lipid Interactionsmentioning

confidence: 99%

Peptide—Lipid Interactions: Insights and Perspectives

Sanderson

2005

ChemInform

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Publisher's copyright statement:Additional information: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. This submission was created using the RSC Article Template (DO NOT DELETE THIS TEXT) (LINE INCLUDED FOR SPACING ONLY -DO NOT DELETE THIS TEXT)As the number of membrane proteins in the Protein Data Bank increases, efforts to understand how they interact with their natural environment are increasing in importance. A number of membrane proteins crystallise with lipid molecules implicitly bound at discrete locations that are consistent with the transmembrane regions of the protein. Bioinformatics studies also point to the specific interactions of some amino acids with membrane lipids. The results of experiments using model systems are revealing how these interactions contribute to the stability of both the protein and the membrane in which it is embedded. From a different perspective, the processes involved in the binding of peptides to membrane surfaces to produce a variety of effects are being understood in ever-increasing detail. This review describes current research efforts and thinking in this area.

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Flow oriented linear dichroism to probe protein orientation in membrane environments

Cited by 68 publications

References 19 publications

Flow-induced Alignment of Amyloid Protofilaments Revealed by Linear Dichroism

Flow-induced Alignment of Amyloid Protofilaments Revealed by Linear Dichroism

FtsZ Fiber Bundling Is Triggered by a Conformational Change in Bound GTP

Peptide—Lipid Interactions: Insights and Perspectives

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