Makings of a brittle bone: Unexpected lessons from a low protein diet study of a mouse OI model.

Glycine substitutions in type I collagen appear to cause osteogenesis imperfecta (OI) by disrupting folding of the triple helix, the structure of which requires Gly in every third position. It is less clear, however, whether the resulting bone malformations and fragility are caused by effects of intracellular accumulation of misfolded collagen on differentiation and function of osteoblasts, effects of secreted misfolded collagen on the function of bone matrix, or both. Here we describe a study originally conceived for testing how reducing intracellular accumulation of misfolded collagen would affect mice with a Gly610 to Cys substitution in the triple helical region of the α2(I) chain. To stimulate degradation of misfolded collagen by autophagy, we utilized a low protein diet. The diet had beneficial effects on osteoblast differentiation and bone matrix mineralization, but also affected bone modeling and suppressed overall animal growth. Our more important observations, however, were not related to the diet. They revealed how altered osteoblast function and deficient bone formation by each cell caused by the G610C mutation combined with increased osteoblastogenesis might make the bone more brittle, all of which are common OI features. In G610C mice, increased bone formation surface compensated for reduced mineral apposition rate, resulting in normal cortical area and thickness at the cost of altering cortical modeling process, retaining woven bone, and reducing the ability of bone to absorb energy through plastic deformation. Reduced collagen and increased mineral density in extracellular matrix of lamellar bone compounded the problem, further reducing bone toughness. The latter observations might have particularly important implications for understanding OI pathophysiology and designing more effective therapeutic interventions.

Zebrafish Collagen Type I: Molecular and Biochemical Characterization of the Major Structural Protein in Bone and Skin.

Over the last years the zebrafish imposed itself as a powerful model to study skeletal diseases, but a limit to its use is the poor characterization of collagen type I, the most abundant protein in bone and skin. In tetrapods collagen type I is a trimer mainly composed of two α1 chains and one α2 chain, encoded by COL1A1 and COL1A2 genes, respectively. In contrast, in zebrafish three type I collagen genes exist, col1a1a, col1a1b and col1a2 coding for α1(I), α3(I) and α2(I) chains. During embryonic and larval development the three collagen type I genes showed a similar spatio-temporal expression pattern, indicating their co-regulation and interdependence at these stages. In both embryonic and adult tissues, the presence of the three α(I) chains was demonstrated, although in embryos α1(I) was present in two distinct glycosylated states, suggesting a developmental-specific collagen composition. Even though in adult bone, skin and scales equal amounts of α1(I), α3(I) and α2(I) chains are present, the presented data suggest a tissue-specific stoichiometry and/or post-translational modification status for collagen type I. In conclusion, this data will be useful to properly interpret results and insights gained from zebrafish models of skeletal diseases.

Deficiency of CRTAP in non-lethal recessive osteogenesis imperfecta reduces collagen deposition into matrix.

Deficiency of any component of the ER-resident collagen prolyl 3-hydroxylation complex causes recessive osteogenesis imperfecta (OI). The complex modifies the α1(I)Pro986 residue and contains cartilage-associated protein (CRTAP), prolyl 3-hydroxylase 1 (P3H1) and cyclophilin B (CyPB). Fibroblasts normally secrete about 10% of CRTAP. Most CRTAP mutations cause a null allele and lethal type VII OI. We identified a 7-year-old Egyptian boy with non-lethal type VII OI and investigated the effects of his null CRTAP mutation on collagen biochemistry, the prolyl 3-hydroxylation complex, and collagen in extracellular matrix. The proband is homozygous for an insertion/deletion in CRTAP (c.118_133del16insTACCC). His dermal fibroblasts synthesize fully overmodified type I collagen, and 3-hydroxylate only 5% of α1(I)Pro986. CRTAP transcripts are 10% of control. CRTAP protein is absent from proband cells, with residual P3H1 and normal CyPB levels. Dermal collagen fibril diameters are significantly increased. By immunofluorescence of long-term cultures, we identified a severe deficiency (10-15% of control) of collagen deposited in extracellular matrix, with disorganization of the minimal fibrillar network. Quantitative pulse-chase experiments corroborate deficiency of matrix deposition, rather than increased matrix turnover. We conclude that defects of extracellular matrix, as well as intracellular defects in collagen modification, contribute to the pathology of type VII OI.

Signatures of DNA flexibility, interactions and sequence-related structural variations in classical X-ray diffraction patterns.

The theory of X-ray diffraction from ideal, rigid helices allowed Watson and Crick to unravel the DNA structure, thereby elucidating functions encoded in it. Yet, as we know now, the DNA double helix is neither ideal nor rigid. Its structure varies with the base pair sequence. Its flexibility leads to thermal fluctuations and allows molecules to adapt their structure to optimize their intermolecular interactions. In addition to the double helix symmetry revealed by Watson and Crick, classical X-ray diffraction patterns of DNA contain information about the flexibility, interactions and sequence-related variations encoded within the helical structure. To extract this information, we have developed a new diffraction theory that accounts for these effects. We show how double helix non-ideality and fluctuations broaden the diffraction peaks. Meridional intensity profiles of the peaks at the first three helical layer lines reveal information about structural adaptation and intermolecular interactions. The meridional width of the fifth layer line peaks is inversely proportional to the helical coherence length that characterizes sequence-related and thermal variations in the double helix structure. Analysis of measured fiber diffraction patterns based on this theory yields important parameters that control DNA structure, packing and function.

Undulations enhance the effect of helical structure on DNA interactions.

During the past decade, theory and experiments have provided clear evidence that specific helical patterns of charged groups and adsorbed (condensed) counterions on the DNA surface are responsible for many important features of DNA-DNA interactions in hydrated aggregates. The effects of helical structure on DNA-DNA interactions result from a preferential juxtaposition of the negatively charged sugar phosphate backbone with counterions bound within the grooves of the opposing molecule. Analysis of X-ray diffraction experiments confirmed the mutual alignment of parallel molecules in hydrated aggregates required for such juxtaposition. However, it remained unclear how this alignment and molecular interactions might be affected by intrinsic and thermal fluctuations, which cause structural deviations away from an ideal double helical conformation. We previously argued that the torsional flexibility of DNA allows the molecules to adapt their structure to accommodate a more electrostatically favorable alignment between molecules, partially compensating disruptive fluctuation effects. In the present work, we develop a more comprehensive theory, incorporating also stretching and bending fluctuations of DNA. We found the effects of stretching to be qualitatively and quantitatively similar to those of twisting fluctuations. However, this theory predicts more dramatic and surprising effects of bending. Undulations of DNA in hydrated aggregates strongly amplify rather than weaken the helical structure effects. They enhance the structural adaptation, leading to better alignment of neighboring molecules and pushing the geometry of the DNA backbone closer to that of an ideal helix. These predictions are supported by a quantitative comparison of the calculated and measured osmotic pressures in DNA.

Fluctuations and interactions of semi-flexible polyelectrolytes in columnar assemblies.

We have developed a statistical theory for columnar aggregates of semi-flexible polyelectrolytes. The applicability of previous, simplified theories was limited to polyelectrolytes with unrealistically high effective charge and, hence, with strongly suppressed thermal undulations. To avoid this problem, we utilized more consistent approximations for short-range image-charge forces and steric confinement, resulting in new predictions for polyelectrolytes with more practically important, lower effective linear charge densities. In the present paper, we focus on aggregates of wormlike chains with uniform surface charge density, although the same basic ideas may also be applied to structured polyelectrolytes. We find that undulations effectively extend the range of electrostatic interactions between polyelectrolytes upon decreasing aggregate density, in qualitative agreement with previous theories. However, in contrast to previous theories, we demonstrate that steric confinement provides the dominant rather than a negligible contribution at higher aggregate densities and significant quantitative corrections at lower densities, resulting in osmotic pressure isotherms that drastically differ from previous predictions.

Torsional deformation of double helix in interaction and aggregation of DNA.

We incorporate sequence-dependent twisting between adjacent base pairs and torsional elasticity of double helix into the theory of DNA-DNA interaction. The results show that pairing and counterion-induced-aggregation of nonhomologous DNA are accompanied by considerable torsional deformation. The deformation tunes negatively charged phosphate strands and positively charged grooves on opposing molecules to stay "in register", substantially reducing nonideality of the helical structure of DNA. Its cost, however, makes interaction between nonhomologous DNA less energetically favorable. In particular, interaction between double helical DNA may result in sequence homology recognition and selective pairing of homologous fragments containing more than 100-200 base pairs. We also find a weak, but potentially measurable, increase in the expected counterion concentration required for aggregation of nonhomologous DNA and slightly higher solubility of such DNA above the critical concentration.

Type I collagen is thermally unstable at body temperature.

Measured by ultra-slow scanning calorimetry and isothermal circular dichroism, human lung collagen monomers denature at 37 degrees C within a couple of days. Their unfolding rate decreases exponentially at lower temperature, but complete unfolding is observed even below 36 degrees C. Refolding of full-length, native collagen triple helices does occur, but only below 30 degrees C. Thus, contrary to the widely held belief, the energetically preferred conformation of the main protein of bone and skin in physiological solution is a random coil rather than a triple helix. These observations suggest that once secreted from cells collagen helices would begin to unfold. We argue that initial microunfolding of their least stable domains would trigger self-assembly of fibers where the helices are protected from complete unfolding. Our data support an earlier hypothesis that in fibers collagen helices may melt and refold locally when needed, giving fibers their strength and elasticity. Apparently, Nature adjusts collagen hydroxyproline content to ensure that the melting temperature of triple helical monomers is several degrees below rather than above body temperature.

Osteogenesis imperfecta murine: interaction between type I collagen homotrimers.

Types I, II, and III collagens are believed to have evolved from the same homotrimer ancestor and they have substantial sequence homology, but type I molecules are alpha1(I)(2)alpha2(I) heterotrimers, unlike homotrimeric types II and III. It is believed that the alpha2(I) chain first appeared in lower vertebrates and that it plays a particularly important role in bone formation. For instance, spontaneous mutations resulting in non- functional alpha2 chains and formation of type I homotrimers cause severe bone pathology (osteogenesis imperfecta) in humans and in animals. However, the exact role of the alpha2 chain is not known. Here, we report measurements of intermolecular forces between collagen helices in native and reconstituted fibers composed of type I homotrimers, heterotrimers and their mix. For comparison, we report forces between type II homotrimers in reconstituted fibers. In agreement with previous studies, we find that the absence of the alpha2 chain reduces temperature-favored attraction between collagen helices, either because of the difference in amino acid sequence of the alpha1 and alpha2 chains or because of more extensive post-translational modification of homotrimers. We find that forces between helices in fibers from type I (as well as type II) homotrimers are not sensitive to pH between pH 6 and 7.5, in contrast to type I heterotrimers. Apparently, the effect of pH is related to extra histidine residues present on alpha2 chains but not on alpha1 chains. Finally, our measurements indicate that the alpha2 chain is responsible for binding some soluble compound(s), possibly glycosaminoglycans, whose displacement results, e.g., in the loss of tendon crystallinity. The ability of the alpha2 chain to bind non-collagen matrix components may be particularly important for bone matrix formation and mineralization.

Sequence recognition in the pairing of DNA duplexes.

Pairing of DNA fragments with homologous sequences occurs in gene shuffling, DNA repair, and other vital processes. While chemical individuality of base pairs is hidden inside the double helix, x ray and NMR revealed sequence-dependent modulation of the structure of DNA backbone. Here we show that the resulting modulation of the DNA surface charge pattern enables duplexes longer than approximately 50 base pairs to recognize sequence homology electrostatically at a distance of up to several water layers. This may explain the local recognition observed in pairing of homologous chromosomes and the observed length dependence of homologous recombination.

Electrostatic interaction between long, rigid helical macromolecules at all interaxial angles.

We derive formulas for the electrostatic interaction between two long, rigid macromolecules that may have arbitrary surface charge patterns and cross at an arbitrary interaxial angle. We calculate the dependence of the interaction energy on the interaxial angle, on the separation, and on the precise alignment of the charge pattern on one molecule with respect to the other. We focus in particular on molecules with helical charge patterns. We report an exact, explicit expression for the energy of interaction between net-neutral helices in a nonpolar medium as well as an approximate result for charged helices immersed in an electrolyte solution. The latter result becomes exact in the asymptotic limit of large separations. Molecular chirality of helices manifests itself in a torque that tends to twist helices in a certain direction out of parallel alignment and that has a nontrivial behavior at small interaxial angles. We illustrate the theory with the calculation of the torque between layers of idealized, DNA-like double helices in cholesteric aggregates. We propose a mechanism of the observed cholesteric-to-columnar phase transition and suggest an explanation for the observed macroscopic (0.4-5 microm) pitch of the cholesteric phase of B-DNA.

Twist in chiral interaction between biological helices.

Using an exact solution for the pair interaction potential, we show that long, rigid, chiral molecules with helical surface charge patterns have a preferential interaxial angle approximately sqrt[RH]/L, where L is the length of the molecules, R is the closest distance between their axes, and H is the helical pitch. Estimates based on this formula suggest a solution for the puzzle of small interaxial angles in alpha-helix bundles and in cholesteric phases of DNA.

Does the triple helical domain of type I collagen encode molecular recognition and fiber assembly while telopeptides serve as catalytic domains? Effect of proteolytic cleavage on fibrillogenesis and on collagen-collagen interaction in fibers.

Over the last several decades, it has been established that proteolytic removal of short, non-helical terminal peptides (telopeptides) from type I collagen significantly alters the kinetics of in vitro fibrillogenesis. However, it has also been observed that the protein is still capable of forming fibers even after complete removal of telopeptides. This study focuses on the characterization of this fibrillogenesis competency of collagen. We have combined traditional kinetic and thermodynamic assays of fibrillogenesis efficacy with direct measurements of interaction between collagen molecules in fibers by osmotic stress and x-ray diffraction. We found that telopeptide cleavage by pepsin or by up to 20 h of Pronase treatment altered fiber assembly kinetics, but the same fraction of the protein still assembled into fibers. Small-angle x-ray diffraction showed that these fibers have normal, native-like D-stagger. Force measurements indicated that collagen-collagen interactions in fibers were not affected by either pepsin or Pronase treatment. In contrast, prolonged (>20 h) Pronase treatment resulted in cleavage of the triple helical domain as indicated by SDS-polyacrylamide gel electrophoresis. The triple-helix cleavage correlated with the observed decrease in the fraction of protein capable of forming fibers and with the measured loss of attraction between helices in fibers. These data suggest that telopeptides play a catalytic role, whereas the information necessary for proper molecular recognition and fiber assembly is encoded in the triple helical domain of collagen.

Electrostatic interaction between helical macromolecules in dense aggregates: an impetus for DNA poly- and meso-morphism.

DNA exhibits a surprising multiplicity of structures when it is packed into dense aggregates. It undergoes various polymorphous transitions (e.g., from the B to A form) and mesomorphous transformations (from hexagonal to orthorhombic or monoclinic packing, changes in the mutual alignment of nearest neighbors, etc). In this report we show that such phenomena may have their origin in the specific helical symmetry of the charge distribution on DNA surface. Electrostatic interaction between neighboring DNA molecules exhibits strong dependence on the patterns of molecular surface groups and adsorbed counter-ions. As a result, it is affected by such structural parameters as the helical pitch, groove width, the number of base pairs per helical turn, etc. We derive expressions which relate the energy of electrostatic interaction with these parameters and with the packing variables characterizing the axial and azimuthal alignment between neighboring macromolecules. We show, in particular, that the structural changes upon the B-to-A transition reduce the electrostatic energy by approximately kcal/mol per base pair, at a random adsorption of counter ions. Ion binding into the narrow groove weakens or inverts this effect, stabilizing B-DNA, as it is presumably the case in Li+-DNA assemblies. The packing symmetry and molecular alignment in DNA aggregates are shown to be affected by the patterns of ion binding.

Symmetry laws for interaction between helical macromolecules.

The power of symmetry laws is applied in many scientific areas from elementary particle physics to structural biology. The structures of many biological helices, including DNA, were resolved with the use of pertinent symmetry constraints. It was not recognized, however, that similar constraints determine cardinal features of helix-helix interactions vital for many recognition and assembly reactions in living cells. We now formulate such symmetry-determined interaction laws and apply them to explain DNA "over-winding" from 10.5 base pairs per turn in solution to 10 in hydrated fibers, counterion specificity in DNA condensation, and forces observed over the last 15 A of separation between DNA, collagen, and four-stranded guanosine helices.

Sugars and polyols inhibit fibrillogenesis of type I collagen by disrupting hydrogen-bonded water bridges between the helices.

To better understand the mechanism of collagen fibrillogenesis, we studied how various sugars and polyols affect the formation and stability of collagen fibers. We combined traditional fiber assembly assays with direct measurement of the interaction between collagen triple helices in fibers by osmotic stress and X-ray diffraction. We found that the effects of sugars and polyols were highly specific with respect to small structural differences between these solutes. For example, 1,2-propane diol only weakly inhibited the fiber assembly and practically did not affect the interaction between collagen helices in fibers. At the same concentration, 1,3-propane diol eliminated the attraction between collagen helices and strongly suppressed fibrillogenesis. The two diols have the same atomic composition and differ only by the position of one of their hydroxyls. Still, their ability to inhibit fiber assembly differs by more than an order of magnitude, as judged by protein solubility. We argue that this is because collagen fibrillogenesis requires formation of hydrogen-bonded water clusters bridging recognition sites on the opposing helices. The ability of various sugars and polyols to inhibit the fiber assembly and to destabilize existing fibers is determined by how efficiently these solutes can compete with water for crucial hydrogen bonds and, thus, disrupt the water bridges. The effect of a sugar or a polyol appears to be strongly dependent on the specific stereochemistry of the solute hydroxyls that defines the preferred hydrogen-bonding pattern of the solute.

Raman spectral evidence for hydration forces between collagen triple helices.

Hydration forces are thought to result from the energetic cost of water rearrangement near macromolecular surfaces. Raman spectra, collected on the same collagen samples on which these forces were measured, reveal a continuous change in water hydrogen-bonding structure as a function of separation between collagen triple helices. The varying spectral parameters track the force-distance curve. The energetic cost of water "restructuring," estimated from the spectra, is consistent with the measured energy of intermolecular interaction. These correlations support the idea that the change in water structure underlies the exponentially varying forces seen in this system at least over the 13-18-A range of interaxial separations.

Solvent hydrogen-bond network in protein self-assembly: solvation of collagen triple helices in nonaqueous solvents.

Forces between type I collagen triple helices are studied in solvents of varying hydrogen-bonding ability. The swelling of collagen fibers in reconstituted films is controlled by the concentration of soluble polymers that are excluded from the fibers and that compete osmotically with collagen for available solvent. The interaxial spacing between the triple helices as a function of the polymer concentration is measured by x-ray diffraction. Exponential-like changes in the spacing with increasing osmotic stress, qualitatively similar to the forces previously found in aqueous solution, are also seen in formamide and ethylene glycol. These are solvents that, like water, are capable of forming three-dimensional hydrogen-bond networks. In solvents that either cannot form a network or have a greatly impaired ability to form a hydrogen-bonded network, strikingly different behavior is observed. A hard-wall repulsion is seen with collagen solvated by ethanol, 2-propanol, and N,N-dimethylformamide. The spacing between helices hardly changes with increasing polymer concentration until the stress exceeds some threshold where removal of the solvent becomes energetically favorable. No solvation of collagen is observed in dimethoxyethane. In solvents with an intermediate ability to form hydrogen-bonded networks, methanol, 2-methoxyethanol, or N-methylformamide, the change in spacing with polymer concentration is intermediate between exponential-like and hard-wall. These results provide direct evidence that the exponential repulsion observed between collagen helices at 0-8-A surface separations in water is due to the energetic cost associated with perturbing the hydrogen-bonded network of solvent molecules between the collagen surfaces.

Measured effects of diacylglycerol on structural and elastic properties of phospholipid membranes.

Diacylglycerol, a biological membrane second messenger, is a strong perturber of phospholipid planar bilayers. It converts multibilayers to the reverse hexagonal phase (HII), composed of highly curved monolayers. We have used x-ray diffraction and osmotic stress of the HII phase to measure structural dimensions, spontaneous curvature, and bending moduli of dioleoylphosphatidylethanolamine (DOPE) monolayers doped with increasing amounts of dioleoylglycerol (DOG). The diameter of the HII phase cylinders equilibrated in excess water decreases significantly with increasing DOG content. Remarkably, however, all structural dimensions at any specific water/lipid ratio that is less than full hydration are insensitive to DOG. By plotting structural parameters of the HII phase with changing water content in a newly defined coordinate system, we show that the elastic deformation of the lipid monolayers can be described as bending around a pivotal plane of constant area. This dividing surface includes 30% of the lipid volume independent of the DOG content (polar heads and a small fraction of hydrocarbon chains). As the mole fraction of DOG increases to 0.3, the radius of spontaneous curvature defined for the pivotal surface decreases from 29 A to 19 A, and the bending modulus increases from approximately 11 to 14 (+/-0.5) kT. We derive the conversion factors and estimate the spontaneous curvatures and bending moduli for the neutral surface which, unlike the pivotal plane parameters, are intrinsic properties that apply to other deformations and geometries. The spontaneous curvature of the neutral surface differs from that of the pivotal plane by less than 10%, but the difference in the bending moduli is up to 40%. Our estimate shows that the neutral surface bending modulus is approximately 9kT and practically does not depend on the DOG content.