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

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.

[1]  R. Deslauriers,et al.  Conformational mobility of the pyrrolidine ring of proline in peptides and peptide hormones as manifest in carbon 13 spin-lattice relaxation times. , 1974, The Journal of biological chemistry.

[2]  D. DeTar,et al.  CONFORMATIONS OF PROLINE , 1977 .

[3]  T. Burjanadze,et al.  Hydroxyproline content and location in relation to collagen thermal stability , 1979, Biopolymers.

[4]  J. T. Gerig,et al.  Molecular dynamics of collagen side chains in hard and soft tissues. A multinuclear magnetic resonance study. , 1987, Biochemistry.

[5]  C. Giessner-Prettre,et al.  Ab initio quantum mechanical calculations of the variation of the 1H and 13C nuclear magnetic shielding constants in proline as a function of the angle psi. , 1987, European journal of biochemistry.

[6]  H. Saito,et al.  A 13C NMR study on collagens in the solid state: hydration/dehydration-induced conformational change of collagen and detection of internal motions. , 1992, Journal of biochemistry.

[7]  I. Ando,et al.  Side-chain conformation of poly(l-proline) form II in the crystalline state as studied by high-resolution solid-state 13C NMR spectroscopy , 1994 .

[8]  B D Sykes,et al.  1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects , 1995, Journal of biomolecular NMR.

[9]  K. Mayo,et al.  13C multiplet nuclear magnetic resonance relaxation-derived ring puckering and backbone dynamics in proline-containing glycine-based peptides. , 1995, Biophysical journal.

[10]  J. Ramshaw,et al.  Gly-X-Y tripeptide frequencies in collagen: a context for host-guest triple-helical peptides. , 1998, Journal of structural biology.

[11]  Richard W. Farndale,et al.  Structural Basis of Collagen Recognition by Integrin α2β1 , 2000, Cell.

[12]  R. Berisio,et al.  Structural bases of collagen stabilization induced by proline hydroxylation. , 2001, Biopolymers.

[13]  Dirk Labudde,et al.  A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics , 2002, Journal of biomolecular NMR.

[14]  M. Goh,et al.  A statistically derived parameterization for the collagen triple‐helix , 2002, Protein science : a publication of the Protein Society.

[15]  R. Berisio,et al.  Crystal structure of the collagen triple helix model [(Pro‐Pro‐Gly)10]3 , 2002, Protein science : a publication of the Protein Society.

[16]  O. Jardetzky,et al.  Investigation of the neighboring residue effects on protein chemical shifts. , 2002, Journal of the American Chemical Society.

[17]  Ronald T Raines,et al.  Stereoelectronic effects on collagen stability: the dichotomy of 4-fluoroproline diastereomers. , 2003, Journal of the American Chemical Society.

[18]  D. Huster,et al.  Dynamics of the biopolymers in articular cartilage studied by magic angle spinning NMR , 2004 .

[19]  Keiichi Noguchi,et al.  Crystal structures of collagen model peptides with Pro‐Hyp‐Gly repeating sequence at 1.26 Å resolution: Implications for proline ring puckering , 2004, Biopolymers.

[20]  Ronald T Raines,et al.  Stereoelectronic and steric effects in the collagen triple helix: toward a code for strand association. , 2005, Journal of the American Chemical Society.

[21]  Julius Jellinek,et al.  Energy Landscapes: With Applications to Clusters, Biomolecules and Glasses , 2005 .

[22]  Teri E. Klein,et al.  A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen‐like peptides , 2005, J. Comput. Chem..

[23]  J. Myllyharju Intracellular Post-Translational Modifications of Collagens , 2005 .

[24]  K. Dill,et al.  The flexibility in the proline ring couples to the protein backbone , 2005, Protein science : a publication of the Protein Society.

[25]  P. Bouř,et al.  Demonstration of the ring conformation in polyproline by the Raman optical activity. , 2006, Journal of the American Chemical Society.

[26]  Ronald T. Raines,et al.  Reciprocity of steric and stereoelectronic effects in the collagen triple helix. , 2006, Journal of the American Chemical Society.

[27]  T. Irving,et al.  On the packing structure of collagen: response to Okuyama et al.'s comment on Microfibrillar structure of type I collagen in situ , 2009 .

[28]  R. Wierenga,et al.  The planar conformation of a strained proline ring: A QM/MM study , 2006, Proteins.

[29]  R. Podgornik Energy Landscapes: Applications to Clusters, Biomolecules and Glasses (Cambridge Molecular Science) , 2007 .

[30]  A. Aliev,et al.  Conformational analysis of L-prolines in water. , 2007, The journal of physical chemistry. B.

[31]  K. Kar,et al.  Triple-helical peptides: an approach to collagen conformation, stability, and self-association. , 2008, Biopolymers.

[32]  S. Krane,et al.  The importance of proline residues in the structure, stability and susceptibility to proteolytic degradation of collagens , 2008, Amino Acids.

[33]  R. Raines,et al.  4-chloroprolines: synthesis, conformational analysis, and effect on the collagen triple helix. , 2008, Biopolymers.

[34]  Takako Sasaki,et al.  Structural basis of sequence-specific collagen recognition by SPARC , 2008, Proceedings of the National Academy of Sciences.

[35]  R. Raines,et al.  Stereoelectronic and steric effects in side chains preorganize a protein main chain , 2009, Proceedings of the National Academy of Sciences.

[36]  Ronald T Raines,et al.  Collagen structure and stability. , 2009, Annual review of biochemistry.

[37]  K. Okuyama,et al.  Crystal structure of (Pro-Pro-Gly)9 at 1.1 A resolution , 2011 .

[38]  E. Huizinga,et al.  Implications for collagen I chain registry from the structure of the collagen von Willebrand factor A3 domain complex , 2012, Proceedings of the National Academy of Sciences.

[39]  Keita Miyama,et al.  Crystal structure of (Gly-Pro-Hyp)(9) : implications for the collagen molecular model. , 2012, Biopolymers.

[40]  Y. Kang,et al.  Crystal structure of the collagen triple helix model [{PRO-HYP(R)-GLY}4-{HYP(S)-Pro-GLY}2-{PRO-HYP(R)-GLY}4]3 , 2012 .