Thermal conformational transformation of tropocollagen. I. Calorimetric study

Effects of heat in heated solution of tropocollagens of different origins were calorimetrically studied. It was found that denaturation enthalpy and entropy of different tropocollagens increase with increasing imino acid content and thermostability. It is shown that the value and dependence of denaturational enthalpy and entropy on the denaturation temperature for tropocollagens with different imino acid contents are inconsistent with the assumption that the native structure of tropocollagen is stabilized only by intramolecular hydrogen bonds. A supposition is made that the regular water structure near the macromolecule plays an essential role in stabilizing the structure. From the character of tropocollagen melting curves in salt-free solution it is found that the tropocollagen macromolecule is linearly heterogeneous. It is shown that the complex pattern of thermal absorption observed in tropocollagen salt, solution is connected with pre-denaturational conformational transformation when approaching conditions close to the physiological.     

The precipitation of toroidal collagen fibrils

The morphology of aggregates of calf-skin tropocollagen, precipitated by continuous injection into neutral phosphate buffers at 35 degrees , has been studied by electron microscopy. Although most of the collagen is precipitated as normal native fibrils, a small proportion forms closed toroidal structures having the usual native band-interband pattern. Theoretical considerations, based on elastic energies in a general microfibril model, predict that the toroids should have a simple super-helical structure, and this is not inconsistent with the observations. From the theoretical energies it was possible to estimate a crude lower limit of 3kcal./mole for the free energy of association of the tropocollagen macromolecules.     

Accounting for thermodynamic non-ideality in the Guinier region of small-angle scattering data of proteins

Hydrodynamic studies of the solution properties of proteins and other biological macromolecules are often hard to interpret when the sample is present at a reasonably concentrated solution. The reason for this is that solutions exhibit deviations from ideal behaviour which is manifested as thermodynamic non-ideality. The range of concentrations at which this behaviour typically is exhibited is as low as 1–2 mg/ml, well within the range of concentrations used for their analysis by techniques such as small-angle scattering. Here we discuss thermodynamic non-ideality used previously used in the context of light scattering and sedimentation equilibrium analytical ultracentrifugation and apply it to the Guinier region of small-angle scattering data. The results show that there is a complementarity between the radially averaged structure factor derived from small-angle X-ray scattering/small-angle neutron scattering studies and the second virial coefficient derived from sedimentation equilibrium analytical ultracentrifugation experiments.     

Structural basis of eye lens transparency: light scattering by concentrated solutions of bovine alpha-crystallin proteins.

Short range order of the crystallins does account for the transparency of the eye lens. To explain the solution structure of this highly concentrated protein solution on a quantitative basis, the hydrodynamic structure and the interparticle interactions of the proteins have to be known. For that purpose, the light scattering of concentrated solutions of alpha-crystallin has been studied. Starting from the detailed knowledge of the solution parameters of alpha-crystallin in diluted solutions, the structure of concentrated solutions up to 360 mg/ml has been studied using light scattering. Our results indicate that subtle changes in the macromolecular structure such as optical anisotropy or structural asymmetry for part of the alpha-crystallins, which results in solute light-scattering heterogeneity, can dramatically increase the light scattering by the alpha-crystallins and cause solution opacity.     

Observations on the different substrate behavior of tropocollagen molecules in solution and intermolecularly cross-linked tropocollagen within insoluble polymeric collagen fibrils.

Bacterial collagenase was used to compare the extent of digestion of tropocollagen monomers in solution and in reconstituted fibrils with that of tropocollagen molecules intermolecularly cross-linked within insoluble polymeric collagen fibrils obtained from mature tendons at given time-intervals. The extent of digestion of tropocollagen monomers in solution was directly proportional to the enzyme concentration (a range of enzyme substrate molar ratios 1:200 to 1:10 was used). The extent of digestion of polymeric collagen was followed by measuring the solubilization of fluorescent peptides from fluorescent-labelled insoluble polymeric collagen fibrils. The extent of digestion of tropocollagen within polymeric collagen was linear over a very small range of enzyme concentrations, when the enzyme/substrate ratio in the reaction mixture was less than 1:400 on a molecular basis. The behavior of tropocollagen in the form of reconstituted collagen fibrils, which had been matured at 37 degrees C for 8 weeks, was intermediate between the behaviour of solutions of tropocollagen and insoluble polymeric collagen fibrils. The significance of the results is discussed in terms of the structure of polymeric collagen fibrils and the protection against enzymic attack provided by tropocollagen molecules on the circumference of the fibril. The results suggest that assays of collagenase activities based on tropocollagen as substrate cannot be directly related to the ability of these enzymes to degrade mature insoluble collagen fibrils.     

Thermodynamics and the structure of biological macromolecules. Rozhinkes mit mandeln

In this review, I will discuss the role of thermodynamics in both the determination and evaluation of the structure of biological macromolecules. The presentation relates to the historical context, state-of-the-art and projection into the future. Fundamental features relate to the effect of charge, exemplified in the study of synthetic and natural polyelectrolytes. Hydrogen bonding and water structure constitute basic aspects of the medium in which biological reactions occur. Viscosity is a classical tool to determine the shape and size of biological macromolecules. The thermodynamic analysis of multicomponent systems is essential fo the correct understanding of the behavior of biological macromolecules in solution and for the evaluation of results from powerful experimental techniques such as ultracentrifugation, light, X-ray and neutron scattering. The hydration, shape and flexibility of DNA have been studied, as well as structural transitions in nucleosomes and chromatin. A particularly rewarding field of activity is the study of unusual structural features of enzymes isolated from the extreme halophilic bacteria of the Dead Sea, which have adapted to saturated concentrations of salt. Future studies in various laboratories will concentrate on nucleic-acid--protein interactions and on the so-called 'crowding effect', distinguishing the behavior in bacteria, or other cells, from simple test-tube experiments.     

Light scattering and fluorescence by small particles having internal structure.

We consider two related, yet distinct queries: 1. How does the internal morphology of a small particle affect the elastic light scattering signals? We have devised an algorithm, presently accurate for particles comparable only to small biological spheres (diameter less than 1 micron), which suggests that light scattering is sensitive to internal morphology only in the backward directions. Accordingly, observations should be obtained in these directions when probing for internal morphology. 2. How are fluorescent signals affected when the active molecules are variously distributed within small particles? One cannot assume that the fluorescent signals are simply proportional to the number of active molecules contained in the particle because there may also be a dependence upon the geometrical and optical properties of the particle and upon the particular spatial distribution of these molecules within the particle. Indeed, even the measured emission spectrum may be affected by such morphological features. Here, too, these calculations are mainly restricted to small particles (diameter less than 1 micron) in which the fluorescent molecules are isotropic and immobile. Under these conditions the effects are quite dramatic. These effects should be considered in quantitative procedures which utilize fluorescence for determining the concentration of specific molecules in small particles such as biological cells. They may provide a clue for discriminating among cells which differ morphologically or in which the spatial distribution of the fluorescent moiety differs. These effects may be minimized by utilizing a light source which is polarized perpendicularly to the scattering plane.     

Effect of ionic strength on the diffusion coefficient of chondroitin sulfate and heparin measured by quasielastic light scattering

The normal modes for a mixture of charged macromolecules and electrolyte solution are calculated. We derive a generalized Debye relaxation time and the apparent diffusion coefficient of the macroion, which is shown to increase from its Stokes value, obtained in excess of added salt, with decreasing ionic strength. We test our result with experimental data for macromolecules with different charge densities: heparin and chondroitin sulfate. Besides, we show for this latter molecule that while the diffusion coefficient is increased, the scattered intensity is decreased but not by the same factor. Our results are compared with other theories developed in quasielastic light scattering.     

Quasi-elastic light scattering of Artemia ribosomes sedimented in a CsCl density gradient

It is impossible to measure the diffusion coefficient of macromolecules directly and accurately by quasi—elastic light scattering, when aggregates cannot be eliminated from the solutions to be investigated. Nevertheless, a simple method can be applied to overcome this problem in many cases. Aggregates are separated from the monomeric macromolecules by rate-zonal sedimentation in a CsCl density gradient in a transparent centrifugation tube; the monomers are then located by laser light scattering intensity measurements; photon correlation spectroscopy of the scattered light finally yields their diffusion coefficient. The viscosity of aqueous CsCl solutions at different temperatures and concentrations allows a good separation by centrifugation and a low uncertainty in the reduction of the measured diffusion coefficient to standard conditions.The application of the method to eukaryotic large ribosomal subunits is described as an example.     

Dynamic light scattering of biopolymers and biocolloids.

Widespread applications of dynamic light scattering techniques to the study of macromolecular Brownian motion have yielded not only a valuable store of factual information concerning solution conformations and conformational changes, but have also provided an important window through which to view the dynamics of internal modes of motion. These techniques have coincided with a resurgence of interest in the solution physical chemistry of macromolecules, including hydrodynamic properties, and the profound effect of intermolecular interactions on both the disposition and dynamics of macromolecules in solution.     

Entropic elasticity controls nanomechanics of single tropocollagen molecules

We report molecular modeling of stretching single molecules of tropocollagen, the building block of collagen fibrils and fibers that provide mechanical support in connective tissues. For small deformation, we observe a dominance of entropic elasticity. At larger deformation, we find a transition to energetic elasticity, which is characterized by first stretching and breaking of hydrogen bonds, followed by deformation of covalent bonds in the protein backbone, eventually leading to molecular fracture. Our force-displacement curves at small forces show excellent quantitative agreement with optical tweezer experiments. Our model predicts a persistence length xi(p) approximately 16 nm, confirming experimental results suggesting that tropocollagen molecules are very flexible elastic entities. We demonstrate that assembly of single tropocollagen molecules into fibrils significantly decreases their bending flexibility, leading to decreased contributions of entropic effects during deformation. The molecular simulation results are used to develop a simple continuum model capable of describing an entire deformation range of tropocollagen molecules. Our molecular model is capable of describing different regimes of elastic and permanent deformation, without relying on empirical parameters, including a transition from entropic to energetic elasticity.     

The radius of gyration of native and reductively methylated myosin subfragment-1 from neutron scattering.

Reductive methylation of nearly all lysine groups of myosin subfragment-1 (S1) was required for crystallization and solution of its structure at atomic resolution. Possible effects of such methylation on the radius of gyration of chicken skeletal muscle myosin S1 have been investigated by using small-angle neutron scattering. In addition, we have investigated the effect of MgADP.Vi, which is thought to produce an analog of the S1.ADP.Pi state, on the S1 radius of gyration. We find that although methylation of S1, with or without SO42- ion addition, does not significantly alter the structure, addition of ADP plus vanadate does decrease the radius of gyration significantly. The S1 crystal structure predicts a radius of gyration close to that measured here by neutron scattering. These results suggest that the overall shape by crystallography resembles nucleotide-free S1 in solution. In order to estimate the effect of residues missing from the crystal structure, the structure of missing loops was estimated by secondary-structure prediction methods. Calculations using the complete crystal structure show that a simple closure of the nucleotide cleft by a rigid-body torsional rotation of residues (172-180 to 670) around an axis running along the base of the cleft alone does not produce changes as large as seen here and in x-ray scattering results. On the other hand, a rigid body rotation of either the light-chain binding domain (767 to 843 plus light chains) or of a portion of 20-kDa peptide plus this domain (706 to 843 plus light chains) is more readily capable of producing such changes.     

Characterization and hydrodynamic behaviour of modified gelatin: I. Light scattering and viscometry studies

Commercial samples of gelatin modified by succinylation and currently used as plasma substitutes and fractionated samples obtained by diafiltration have been studied by viscometry, light scattering and osmometry. Viscometric results show that the aqueous medium containing potassium phosphate (0.1 ) and NaCl (0.12 ) at pH 3.3 behaves nearly like a theta solvent (a=0.48) for these modified gelatins. The Stockmayer-Fixman diagram reveals a negative slope attributed to a swelling of the macromolecules which decreases as the molecular weight _w increases. The Stokes radius R_H determined by quasielastic light scattering is independent of the pH of the medium in a range 7-3.3. The conformation of gelatins in solution has been characterized through the ratio _G· _H⁻¹, the radius of gyration _G being determined by viscometry. This ratio decreases as the molecular weight increases. The low molecular weight fractions have a more compact structure than the Gaussian chains in theta conditions. For high molecuar weight fractions, the values of _G· _H⁻¹ tend to those of an hard sphere.     

C-phycocyanin hydration water dynamics in the presence of trehalose: an incoherent elastic neutron scattering study at different energy resolutions

We present a study of C-phycocyanin hydration water dynamics in the presence of trehalose by incoherent elastic neutron scattering. By combining data from two backscattering spectrometers with a 10-fold difference in energy resolution we extract a scattering law S(Q,omega) from the Q-dependence of the elastic intensities without sampling the quasielastic range. The hydration water is described by two dynamically different populations--one diffusing inside a sphere and the other diffusing quasifreely--with a population ratio that depends on temperature. The scattering law derived describes the experimental data from both instruments excellently over a large temperature range (235-320 K). The effective diffusion coefficient extracted is reduced by a factor of 10-15 with respect to bulk water at corresponding temperatures. Our approach demonstrates the benefits and the efficiency of using different energy resolutions in incoherent elastic neutron scattering over a large angular range for the study of biological macromolecules and hydration water.     

Scaling analysis of the concentration dependence on elasticity of agarose gel

Since the critical exponent of the elastic modulus is related to the spatial dimension and the critical exponent of the correlation length, depending on the characteristics of elasticity, we experimentally evaluated both the elastic modulus of a sol-gel transition system and also the correlation length. We could determine the correlation length of agarose gel by the dynamic light scattering method; it was well described by the power law as a function of the deviation from the sol-gel transition point. Three scaling laws between the critical exponent of the correlation length (v) and that of the elastic shear modulus (t) were compared, and the critical exponent of the elastic modulus was described by the equation of de Gennes expression (t=1+v(d-2), where d is the spatial dimension). This result suggests that agarose fibers are stiff enough to show scalar elasticity.     

Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution

A self-contained presentation of the main concepts and methods for interpretation of X-ray and neutron-scattering patterns of biological macromolecules in solution, including a reminder of the basics of X-ray and neutron scattering and a brief overview of relevant aspects of modern instrumentation, is given. For monodisperse solutions the experimental data yield the scattering intensity of the macromolecules, which depends on the contrast between the solvent and the particles as well as on their shape and internal scattering density fluctuations, and the structure factor, which is related to the interactions between macromolecules. After a brief analysis of the information content of the scattering intensity, the two main approaches for modelling the shape and/or structure of macromolecules and the global minimization schemes used in the calculations are presented. The first approach is based, in its more advanced version, on the spherical harmonics approximation and relies on few parameters, whereas the second one uses bead models with thousands of parameters. Extensions of bead modelling can be used to model domain structure and missing parts in high-resolution structures. Methods for computing the scattering patterns from atomic models including the contribution of the hydration shell are discussed and examples are given, which also illustrate that significant differences sometimes exist between crystal and solution structures. These differences are in some cases explainable in terms of rigid-body motions of parts of the structures. Results of two extensive studies--on ribosomes and on the allosteric protein aspartate transcarbamoylase--illustrate the application of the various methods. The unique bridge between equilibrium structures and thermodynamic or kinetic aspects provided by scattering techniques is illustrated by modelling of intermolecular interactions, including crystallization, based on an analysis of the structure factor and recent time-resolved work on assembly and protein folding.     

Dynamic light scattering: a practical guide and applications in biomedical sciences

Dynamic light scattering (DLS), also known as photon correlation spectroscopy (PCS), is a very powerful tool for studying the diffusion behaviour of macromolecules in solution. The diffusion coefficient, and hence the hydrodynamic radii calculated from it, depends on the size and shape of macromolecules. In this review, we provide evidence of the usefulness of DLS to study the homogeneity of proteins, nucleic acids, and complexes of protein–protein or protein–nucleic acid preparations, as well as to study protein–small molecule interactions. Further, we provide examples of DLS’s application both as a complementary method to analytical ultracentrifugation studies and as a screening tool to validate solution scattering models using determined hydrodynamic radii.     

Multichain aggregates in dilute solutions of associating polyelectrolyte keeping a constant size at the increase in the chain length of individual macromolecules

Multichain aggregates together with individual macromolecules were detected by light scattering in dilute aqueous solutions of chitosan and of its hydrophobic derivatives bearing 4 mol % of n-dodecyl side groups. It was demonstrated that the size of aggregates and their aggregation numbers increase at the introduction of hydrophobic side groups into polymer chains. The key result concerns the effect of the chain length of individual macromolecules on the aggregation behavior. It was shown that for both unmodified and hydrophobically modified (HM) chitosan, the size of aggregates is independent of the length of single chains, which may result from the electrostatic nature of the stabilization of aggregates. At the same time, the number of macromolecules in one aggregate increases significantly with decreasing length of single chains to provide a sufficient number of associating groups to stabilize the aggregate. The analysis of the light scattering data together with TEM results suggests that the aggregates of chitosan and HM chitosan represent spherical hydrogel particles with denser core and looser shell covered with dangling chains.     

Vesicle formation by amphiphilic 10-alkyl-3-methyl isoalloxazine in aqueous medium.

The synthetic 10-alkyl isoalloxazines have been found to form vesicles in aqueous and binary solvent systems and confirmed by UV-visible, fluorescence,transmission electron microscopy and quasi elastic light scattering experiments. The mean external diameters of vesicles have been calculated for isoalloxazine with different carbon atom chain at position 10 by transmission electron microscopy and quasi elastic laser light scattering. The gel to liquid phase transition of liposomes measured by differential scanning calorimetry shows reproducible endothermic peak which lies well in the range of typical aqueous vesicles.     

Molecular self-assembling and the fluorescence enhancement in morin-Al3+-cetyltrimethylammonium bromide-protein system

Fluorescence enhancement effect of the morin-Al3+-cetyltrimethylammonium bromide (CTAB)-bovine serum albumin (BSA) system is reported here and the interaction mechanism is studied using fluorescence, resonance light scattering (RLS), absorption spectroscopy, Far-UV circular dichroism (CD) spectrum and small angle X-ray scattering (SAXS) measurement. It is considered that protein can bind with Al3+, morin and CTAB through self-assembling function with electrostatic attraction, hydrogen bond, hydrophobic interaction and Vander Waal force etc, and forms a supermolecular association with multilayer structure, in which morin-Al3+ is clamped between BSA and CTAB. In this system, the fluorescence enhancement of morin originates from both intermolecular energy transfer between BSA and morin, and the hydrophobic microenvironment provided by BSA and CTAB. Whereas Al3+ plays a key role for the enhancement of energy transfer efficiency because it provides an efficient channel for the energy transfer between BSA and morin.