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Nature of structural inhomogeneities on folding a helix and their influence on spectral measurements.

ABSTRACT: Extensive conformational sampling and calculations of vibrational coupling provide a quantitative basis for the structurally inhomogeneous spectra of the amide unit in aqueous solutions containing folded and unfolded state distributions of helices. Replica exchange molecular dynamics simulations of the capped helical peptide, AA(AAKAA)(3)AAY, is carried out over a range of temperatures, where the system populates the folded and unfolded states. This sampling defines a set of ensembles that characterizes the conformational variability for configurations identified by their fraction of helical content. The effects of hydrogen bonding, both internal and external (with water), and the coupling between amide-I modes are computed as a function of temperature and helical content. End-to-end distance and coupling distributions are also computed. The solvent H-bonding, which is present at all temperatures, shifts the amide-I band toward lower frequency compared with the unsolvated band. Upon thermal denaturation of the peptide, the amide-I band shifts to higher frequency because the increase in solvent H-bonding fails to compensate for the loss in internal (helical) H-bonds. The loss of uniformity of the mode coupling along the helix at higher temperatures accounts for the well-known thermal broadening of the amide IR spectrum. The calculated inhomogeneities of segments of the peptide predict experimental properties of isotope-edited helices.

SUBMITTER: Gnanakaran S

PROVIDER: S-EPMC438958 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:To describe the association between pattern electroretinogram (PERG) amplitude and spectral domain-optical coherence tomography (SD-OCT) macular thickness, retinal nerve fibre layer (RNFL) thickness and optic disc topography measurements.Both eyes (n = 132) of 66 glaucoma patients (mean age = 67.9 years) enrolled in the University of California, San Diego, CA, USA, Diagnostic Innovations in Glaucoma Study (DIGS) were included. Eyes were tested with PERG (Glaid PERGLA, Lace Elettronica, Pisa, Italy), RTVue SD-OCT (Optovue Inc., Fremont, CA, USA) GCC, and NHM4 protocols on the same day. Of the 66 enrolled patients, 43 had glaucoma defined by repeated abnormal standard automated perimetry (SAP) results in at least one eye and 23 were glaucoma suspects defined by a glaucomatous-appearing optic disc by physicians' examination in at least one eye and normal SAP results in both eyes. Associations (R(2)) were determined between PERG amplitude (μV) and SD-OCT macular ganglion cell complex (GCC) thickness (μm), macular thickness (μm), macular outer retinal thickness (macular thickness minus GCC thickness) (μm), RNFL thickness (μm), neuroretinal rim area (mm(2)), and rim volume (mm(3)).PERG amplitude was significantly associated with GCC thickness (R(2) = 0.179, P < 0.001), RNFL thickness (R(2) = 0.174, P < 0.001), and macular thickness (R(2) = 0.095, P<0.001). R(2) associations with other parameters were not significant (all P > 0.624). Significant associations remained for GCC and average RNFL thickness when age and intraocular pressure at the time of testing were included in multivariate models (both P ≤ 0.030).PERG amplitude is significantly (but weakly) associated with macular GCC thickness, RNFL thickness, and macular thickness. The lack of association between PERG amplitude and macular outer retinal thickness supports previous results, possibly suggesting that that the PERG is driven primarily by retinal ganglion cell (inner retinal) responses.

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Nature of structural inhomogeneities on folding a helix and their influence on spectral measurements.

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