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      Hydroxyproline Ring Pucker Causes Frustration of Helix Parameters in the Collagen Triple Helix

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          Abstract

          Collagens, the most abundant proteins in mammals, are defined by their triple-helical structures and distinctive Gly-Xaa-Yaa repeating sequence, where Xaa is often proline and Yaa, hydroxyproline (Hyp/O). It is known that hydroxyproline in the Yaa position stabilises the triple helix, and that lack of proline hydroxylation in vivo leads to dysfunctional collagen extracellular matrix assembly, due to a range of factors such as a change in hydration properties. In addition, we note that in model peptides, when Yaa is unmodified proline, the Xaa proline has a strong propensity to adopt an endo ring conformation, whilst when Yaa is hydroxyproline, the Xaa proline adopts a range of endo and exo conformations. Here we use a combination of solid-state NMR spectroscopy and potential energy landscape modelling of synthetic triple-helical collagen peptides to understand this effect. We show that hydroxylation of the Yaa proline causes the Xaa proline ring conformation to become metastable, which in turn confers flexibility on the triple helix.

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          Most cited references23

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          1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects.

          In this study we report on the 1H, 13C and 15N NMR chemical shifts for the random coil state and nearest-neighbor sequence effects measured from the protected linear hexapeptide Gly-Gly-X-Y-Gly-Gly (where X and Y are any of the 20 common amino acids). We present data for a set of 40 peptides (of the possible 400) including Gly-Gly-X-Ala-Gly-Gly and Gly-Gly-X-Pro-Gly-Gly, measured under identical aqueous conditions. Because all spectra were collected under identical experimental conditions, the data from the Gly-Gly-X-Ala-Gly-Gly series provide a complete and internally consistent set of 1H, 13C and 15N random coil chemical shifts for all 20 common amino acids. In addition, studies were also conducted into nearest-neighbor effects on the random coil shift arising from a variety of X and Y positional substitutions. Comparisons between the chemical shift measurements obtained from Gly-Gly-X-Ala-Gly-Gly and Gly-Gly-X-Pro-Gly-Gly reveal significant systematic shift differences arising from the presence of proline in the peptide sequence. Similarly, measurements of the chemical shift changes occurring for both alanine and proline (i.e., the residues in the Y position) are found to depend strongly on the type of amino acid substituted into the X position. These data lend support to the hypothesis that sequence effects play a significant role in determining peptide and protein chemical shifts.
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            Gly-X-Y tripeptide frequencies in collagen: a context for host-guest triple-helical peptides.

            The collagen triple-helix consists of a repeating (Gly-X-Y)n sequence. In theory, there are more than 400 possible Gly-X-Y triplets, but analysis of sequences from fibrillar and nonfibrillar collagens shows that only a limited set of triplets are found in significant numbers, and many are never observed. The nonrandom frequency of Gly-X-Y triplets makes it practical to experimentally approach the stability of much of the collagen sequence through the study of a limited set of host-guest peptides. In these peptides, individual Gly-X-Y triplets constitute the guest, while the host consists of Gly-Pro-Hyp tripeptides. A set of host-guest peptides was designed to contain the most common nonpolar and charged triplets found in collagen. All formed stable triple-helices, with their melting temperature depending on the identity of the guest triplet. While including less than 10% of all possible triplets, the data set covers 50-60% of collagen sequences and provides a starting point for establishing a stability scale to predict the relative stability of important collagen regions, such as the matrix metalloproteinase cleavage site or binding sites. Copyright 1998 Academic Press.
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              A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics.

              The chemical shift difference (delta[13C(beta)]-delta[13C(gamma)]) is a reference-independent indicator of the Xaa-Pro peptide bond conformation. Based on a statistical analysis of the 13C chemical shifts of 1,033 prolines from 304 proteins deposited in the BioMagRes database, a software tool was created to predict the probabilities for cis or trans conformations of Xaa-Pro peptide bonds. Using this approach, the conformation at a given Xaa-Pro bond can be identified in a simple NOE-independent way immediately after obtaining its NMR resonance assignments. This will allow subsequent structure calculations to be initiated using the correct polypeptide chain conformation.
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                Author and article information

                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group
                2045-2322
                29 July 2015
                2015
                : 5
                : 12556
                Affiliations
                [1 ]Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, UK
                [2 ]Department of Biochemistry, University of Cambridge , Downing Site, Cambridge CB2 1QW, UK
                [3 ]Institute of Infection and Immunity, School of Medicine , Cardiff University, Cardiff CF14 4XN, UK
                Author notes
                [*]

                These authors contributed equally to this work.

                Article
                srep12556
                10.1038/srep12556
                4518226
                26220399
                afedff56-5d06-4e8b-a526-81a8e9248d58
                Copyright © 2015, Macmillan Publishers Limited

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 25 February 2015
                : 26 June 2015
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