A computational investigation of the interaction of the collagen molecule with hydroxyapatite

This thesis presents the results of computer simulation studies of the interaction of the predominant molecules in the collagen protein with the hydroxyapatite mineral. Using a combination of computational techniques, quantum-mechanical methods based on the density functional theory (DFT) and molecular dynamics simulations based on interatomic potentials, we have investigated the interface between the collagen protein and the apatite mineral. First we have employed electronic structure techniques (DFT) to study a range of different binding modes of the amino acids glycine, proline and hydroxyproline, which are major constituents of the collagen I protein, at two important hydroxyapatite surfaces, (0001) and (0110) . We have performed full geometry optimizations of the hydroxyapatite surface with adsorbed amino acid molecules to obtain the optimum substrate/adsorbate structures and interaction energies. We have also used DFT to investigate the binding of a series of representative peptides containing hydrophobic side groups (proline), uncharged polar side groups (glycine and hydroxyproline), and charged polar side groups (lysine and hydroxylysine) to the hydroxyapatite (0001) and (0110) surfaces. This selection of adsorbates has given us the opportunity to study separately the interactions of the carboxylic acid and amine functional groups, as well as the effect of hydroxylation and the charges of the side group, on the strength of interaction with the surfaces. We have also investigated the same systems in an aqueous environment using classical molecular dynamics simulation, where we have calculated the energies and geometries of adsorption of the peptide at the surfaces of hydroxyapatite in competition with pre-adsorbed water. Finally, we have studied the onset of nucleation of the hydroxyapatite mineral at an entire collagen molecule in aqueous solution

Proline provides site-specific flexibility for in vivo collagen.

Fibrillar collagens have mechanical and biological roles, providing tissues with both tensile strength and cell binding sites which allow molecular interactions with cell-surface receptors such as integrins. A key question is: how do collagens allow tissue flexibility whilst maintaining well-defined ligand binding sites? Here we show that proline residues in collagen glycine-proline-hydroxyproline (Gly-Pro-Hyp) triplets provide local conformational flexibility, which in turn confers well-defined, low energy molecular compression-extension and bending, by employing two-dimensional 13C-13C correlation NMR spectroscopy on 13C-labelled intact ex vivo bone and in vitro osteoblast extracellular matrix. We also find that the positions of Gly-Pro-Hyp triplets are highly conserved between animal species, and are spatially clustered in the currently-accepted model of molecular ordering in collagen type I fibrils. We propose that the Gly-Pro-Hyp triplets in fibrillar collagens provide fibril "expansion joints" to maintain molecular ordering within the fibril, thereby preserving the structural integrity of ligand binding sites.BBSRC, EPSRC, Raymond and Beverly Sackler Fund for Physics of Medicine, Wellcome Trust, ER

Computational studies of protein posttranslational modification : glycosylation of oligoproline and collagen peptides

xvi, 238 leaves : ill. ; 29 cmGlycosylation is the most complex posttranslational modification of proteins and has consequences on protein structure and function. In particular, the hydroxyproline (Hyp) rich glycoproteins (HRGPs) of plants are heavily glycosylated. On the other hand, glycosylation has not been observed in animal collagen despite the high occurrence of Hyp residues. This thesis uses computational chemistry to provide molecular level information about the structural effects of Hyp glycosylation to help understand the biological implications of the modification and explain the lack of glycosylation in animals. Initially, the nature of the glycosidic linkage between Hyp and galactose was determined. The theoretical results were validated by comparing to the recent experimental data, which helped understand other experimental observations. Subsequently, contiguous and non-contiguous glycosylation of a nonaproline oligopeptide was considered, which revealed that contiguous glycosylation increases the stability of the all trans polyproline II (PPII) conformation, while non-contiguous glycosylation leads to loss of PPII content. Sophisticated modeling suggested that this difference arises since peptide–solvent interactions stabilize the PPII conformation in the contiguously glycosylated peptide, while sugar–peptide backbone interactions that stabilize the cis conformations of some residues are stronger in the non-contiguously glycosylated peptide. Finally, the effects of Hyp glycosylation on the collagen triple helix were assessed, where it was determined that glycosylation makes the monomeric state more stable and hence hinders triple helix formation, which agrees with experimental results and highlights that the synergy between computation and experiments is necessary to understand complex glycosylation in nature

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.The authors acknowledge BBSRC grant number BB/G021392/1 (MJD, DGR), EPSRC DTA studentship and Doctoral Prize (WYC), British Heart Foundation RG/09/003/27122 and PG/08/011/24416 (RWF, DB, DAS), Wellcome Trust 094470/Z/10/Z (RWF, DB, DAS), ERC and EPSRC (DJW).This is the final version of the article. It first appeared from NPG via http://dx.doi.org/10.1038/srep1255

Interface Property of Collagen and Hydroxyapatite in Bone and Developing Bioinspired Materials

Bone at the nanoscale consists of type I collagen and hydroxyapatite (HAP). Type I collagen and HAP [Ca10(PO4)6(OH)2] are responsible for most of the structural integrity of bone. Collagen fibrils contain HAP platelets of varying size dispersed between the collagen. We investigate heterotrimeric collagen interaction with HAP using Steering Molecular Dynamics to obtain the force-displacement relation as the collagen is undergoing shearing and peeling on the surface of HAP. Results indicate that the collagen requires 40% less force to separate form the HAP surface under peeling, when compared to shear loading conditions. In both shearing and peeling, the number of collagen-water hydrogen bonds increases by approximately 100% before rupture. We developed an HAP inspired structure and 3D printed it using ABS plastic. This bio-inspired material could have several potential applications in engineering and medicine

Interface Property of Collagen and Hydroxyapatite in Bone and Developing Bioinspired Materials

Bone at the nanoscale consists of type I collagen and hydroxyapatite (HAP). Type I collagen and HAP [Ca10(PO4)6(OH)2] are responsible for most of the structural integrity of bone. Collagen fibrils contain HAP platelets of varying size dispersed between the collagen. We investigate heterotrimeric collagen interaction with HAP using Steering Molecular Dynamics to obtain the force-displacement relation as the collagen is undergoing shearing and peeling on the surface of HAP. Results indicate that the collagen requires 40% less force to separate form the HAP surface under peeling, when compared to shear loading conditions. In both shearing and peeling, the number of collagen-water hydrogen bonds increases by approximately 100% before rupture. We developed an HAP inspired structure and 3D printed it using ABS plastic. This bio-inspired material could have several potential applications in engineering and medicine

Mechanics of mineralized collagen fibrils upon transient loads

Collagen is a key structural protein in the human body, which undergoes mineralization during the formation of hard tissues. Earlier studies have described the mechanical behavior of bone at different scales highlighting material features across hierarchical structures. Here we present a study that aims to understand the mechanical properties of mineralized collagen fibrils upon tensile/compressive transient loads, investigating how the kinetic energy propagates and it is dissipated at the molecular scale, thus filling a gap of knowledge in this area. These specific features are the mechanisms that Nature has developed to passively dissipate stress and prevent structural failures. In addition to the mechanical properties of the mineralized fibrils, we observe distinct nanomechanical behaviors for the two regions (i.e., overlap and gap) of the D-period to highlight the effect of the mineralization. We notice decreasing trends for both wave speeds and Young s moduli over input velocity with a marked strengthening effect in the gap region due to the accumulation of the hydroxyapatite. In contrast, the dissipative behavior is not affected by either loading conditions or the mineral percentage, showing a stronger dampening effect upon faster inputs compatible to the bone behavior at the macroscale. Our results improve the understanding of mineralized collagen composites unveiling the energy dissipative behavior of such materials. This impacts, besides the physiology, the design and characterization of new bioinspired composites for replacement devices (e.g., prostheses for sound transmission or conduction) and for optimized structures able to bear transient loads, e.g., impact, fatigue, in structural applications

Mechanics of collagen-hydroxyapatite model nanocomposites

Bone is a hierarchical biological composite made of a mineral component (hydroxyapatite crystals) and anorganic part (collagen molecules). Small-scale deformation phenomena that occur in bone are thought tohave a significant influence on the large scale behavior of this material. However, the nanoscale behaviorof collagen–hydroxyapatite composites is still relatively poorly understood. Here we present a molec-ular dynamics study of a bone model nanocomposite that consist of a simple sandwich structure ofcollagen and hydroxyapatite, exposed to shear-dominated loading. We assess how the geometry of thecomposite enhances the strength, stiffness and capacity to dissipate mechanical energy. We find that H-bonds between collagen and hydroxyapatite play an important role in increasing the resistance againstcatastrophic failure by increasing the fracture energy through a stick-slip mechanism

Molecular mechanics of mineralized collagen fibrils in bone

Bone is a natural composite of collagen protein and the mineral hydroxyapatite. The structure of bone is known to be important to its load-bearing characteristics, but relatively little is known about this structure or the mechanism that govern deformation at the molecular scale. Here we perform full-atomistic calculations of the three-dimensional molecular structure of a mineralized collagen protein matrix to try to better understand its mechanical characteristics under tensile loading at various mineral densities. We find that as the mineral density increases, the tensile modulus of the network increases monotonically and well beyond that of pure collagen fibrils. Our results suggest that the mineral crystals within this network bears up to four times the stress of the collagen fibrils, whereas the collagen is predominantly responsible for the material’s deformation response. These findings reveal the mechanism by which bone is able to achieve superior energy dissipation and fracture resistance characteristics beyond its individual constituents.United States. Office of Naval Research (N000141010562)United States. Army Research Office (W991NF-09-1-0541)United States. Army Research Office (W911NF-10-1-0127)National Science Foundation (U.S.) (CMMI-0642545

Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics.

We propose a new approach for force field optimisations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use (13) C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius-type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force-field parameters against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimisation. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. © Proteins 2013;. © 2013 Wiley Periodicals, Inc