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PubMed1998

Solution structure and dynamics of linked cell attachment modules of mouse fibronectin containing the RGD and synergy regions: comparison with the human fibronectin crystal structure.

We report the three-dimensional solution structure of the mouse fibronectin cell attachment domain consisting of the linked ninth and tenth type III modules, mFnFn3(9,10). Because the tenth module contains the RGD cell attachment sequence while the ninth contains the synergy region, mFnFn3(9,10) has the cell attachment activity of intact fibronectin. Essentially complete signal assignments and approximately 1800 distance and angle restraints were derived from multidimensional heteronuclear NMR spectra. These restraints were used with a hybrid distance geometry/simulated annealing protocol to generate an ensemble of 20 NMR structures having no distance or angle violations greater than 0.3 A or 3 degrees. Although the beta-sheet core domains of the individual modules are well-ordered structures, having backbone atom rmsd values from the mean structure of 0.51(+/-0.12) and 0.40(+/-0.07) A, respectively, the rmsd of the core atom coordinates increases to 3.63(+/-1.41) A when the core domains of both modules are used to align the coordinates. The latter result is a consequence of the fact that the relative orientation of the two modules is not highly constrained by the NMR restraints. Hence, while structures of the beta-sheet core domains of the NMR structures are very similar to the core domains of the crystal structure of hFnFn3(9,10), the ensemble of NMR structures suggests that the two modules form a less extended and more flexible structure than the fully extended rod-like crystal structure. The radius of gyration, Rg, of mFnFn3(9,10) derived from small-angle neutron scattering measurements, 20.5(+/-0.5) A, agrees with the average Rg calculated for the NMR structures, 20.4 A, and is ca 1 A less than the value of Rg calculated for the X-ray structure. The values of the rotational anisotropy, D ||/D perpendicular, derived from an analysis of 15N relaxation data, range from 1.7 to 2.1, and are significantly less than the anisotropy of 2.67 predicted by hydrodynamic modeling of the crystal coordinates. In contrast, hydrodynamic modeling of the NMR coordinates yields anisotropies in the range of 1.9 to 2.7 (average 2.4(+/-0.2)), with NMR structures bent by more than 20 degrees relative the crystal structure having calculated anisotropies in best agreement with experiment. In addition, the relaxation parameters indicate that several loops in mFnFn3(9,10), including the RGD loop, are flexible on the nanosecond to picosecond time-scale. Taken together, our results suggest that, in solution, the limited set of interactions between the mFnFn3(9,10) modules position the RGD and synergy regions to interact specifically with cell surface integrins, and at the same time permit sufficient flexibility that allows mFnFn3(9,10) to adjust for some variation in integrin structure or environment.

Amino Acid Sequence↗

PubMed2001

ATP-induced structural change of the thermosome is temperature-dependent.

Protein folding by chaperonins is powered by ATP binding and hydrolysis. ATPase activity drives the folding machine through a series of conformational rearrangements, extensively described for the group I chaperonin GroEL from Escherichia coli but still poorly understood for the group II chaperonins. The latter--archaeal thermosome and eukaryotic TRiC/CCT--function independently of a GroES-like cochaperonin and are proposed to rely on protrusions of their own apical domains for opening and closure in an ATP-controlled fashion. Here we use small-angle neutron scattering to analyze structural changes of the recombinant alpha-only and the native alphabeta-thermosome from Thermoplasma acidophilum upon their ATPase cycling in solution. We show that specific high-salt conditions, but not the presence of MgATP alone, induce formation of higher order thermosome aggregates. The mechanism of the open-closed transition of the thermosome is strongly temperature-dependent. ATP binding to the chaperonin appears to be a two-step process: at lower temperatures an open state of the ATP-thermosome is predominant, whereas heating to physiological temperatures induces its switching to a closed state. Our data reveal an analogy between the ATPase cycles of the two groups of chaperonins and enable us to put forward a model of thermosome action.

Adenosine Triphosphatases↗

PubMed1992

Influence of protein dynamics on the metal-sites of ovotransferrin.

Using the perturbed angular correlations (PAC) technique, the formation of hafnium-ovotransferrin complexes has been studied. Two binding configurations at each of the two specific binding-sites of the protein have been observed. They are characterized by well-defined electric quadrupole frequencies. Information about the dynamics of the protein was derived from temperature dependent measurements of the relaxation constant. The well-resolved spectra taken with fast BaF2-detectors allow a precise determination of the relaxation behaviour of the protein. The results are compared with the predictions from a hydrodynamic model for the reorientation of macromolecules. Thus the hydrodynamic volume of ovotransferrin and its N-terminal half-molecule were determined. The ovotransferrin volume is in agreement with a value derived for human serum transferrin from small angle neutron scattering. From experiments with immobilized protein material there is evidence for internal protein dynamics which is probed by the Hf-ion bound to the specific metal-sites.

Animals↗

PubMed1994

The growth of fractal humic acids: cluster correlation and gel formation.

The growth of humic acids, prepared by a gentle method from two different kinds of soils (I and II), has been studied using small-angle neutron scattering at an acidity corresponding to pH 5.0 and 0.10 M ionic strength (NaCl). Humic acids aggregate either to large clusters with a fractal dimension of 2.3 and an average diameter of 1720 A (I) or to clusters with an average diameter of 700 A (II). After storage for 2 days at 4 degrees C, the latter aggregates (II) formed a gel. In a step toward gelation, we observed cluster-cluster interaction from the neutron-scattering data in the form of a correlation peak. These differences in size can be explained by assuming that the smaller particles (II) are trapped into a nonequilibrium state characterized by the temperature-solvent condition. The importance of a humic acid gel network for the conservation of water and nutrients in the environment is discussed.

Gels↗

PubMed2004

Polymer-cushioned lipid bilayers in porous alumina.

Using small-angle neutron scattering (SANS) and cyclic voltammetry (CV), we show that model biological membranes can be deposited on a polymer cushion confined in highly regular porous alumina. The thicknesses of the dilute polymer cushion chemically bound to the alumina and of the supported bilayer are obtained for two polyethylene glycol cushions (PEG(5000) and PEG(20000)) and for a cushion made of chains bearing a lipid anchor at their free end (DSPE-PEG(3400)). The bilayers are studied well below and well above the chain melting temperature of the lipid mixture (DMPC/DMPE: 80/20), using a coenzyme (Ubiquinone, UQ(10)) as a redox probe for the voltammetry experiments. Analysis of the SANS form factor of the bilayers shows that the bilayer thickness can be extracted in this particular geometry. Using PEG chains grafted at a low surface density (D < 2R(g)), the thickness of the complete molecular construction is obtained by CV, which shows (after subtracting the bilayer thickness) that the polymer cushion thickness can be varied from 50 to 150 Angstroms. The values obtained with three different chain lengths, are in perfect agreement with the radius derived from the Flory theory.

Aluminum Oxide↗

PubMed1998

Conformations of kinesin: solution vs. crystal structures and interactions with microtubules.

Recently, the molecular structures of monomeric and dimeric kinesin constructs in complex with ADP have been determined by X-ray crystallography (Kull et al. 1996; Kozielski et al. 1997 a; Sack et al. 1997). The "motor" or "head" domains have almost identical conformations in the known crystal structures, yet the kinesin dimer is asymmetric: the orientation of the two heads relative to the coiled-coil formed by their neck regions is different. We used small angle solution scattering of kinesin constructs and microtubules decorated with kinesin in order to find out whether these crystal structures are of relevance for kinesin's structure under natural conditions and for its interaction with microtubules. Our preliminary results indicate that the crystal structures of monomeric and dimeric kinesin are similar to their structures in solution, though in solution the center-of-mass distance between the motor domains of the dimer could be slightly greater. The crystal structure of dimeric kinesin can be interpreted as representing two equivalent conformations. Transitions between these or very similar conformational states may occur in solution. Binding of kinesin to microtubules has conformational effects on both, the kinesin and the microtubule. Solution scattering of kinesin decorated microtubules reveals a peak in intensity that is characteristic for the B-surface lattice and that can be used to monitor the axial repeat of the microtubules under various conditions. In decoration experiments, dimeric kinesin dissociates, at least partly, leading to a stoichiometry of 1:1 (one kinesin head per tubulin dimer; Thormählen et al. 1998a) in contrast to the stoichiometry of 2:1 reported for dimeric ncd. This discrepancy is possibly due to the effect of steric hindrance between kinesin dimers on adjacent binding sites.

Animals↗

PubMed2005

Poly-Ig tandems from I-band titin share extended domain arrangements irrespective of the distinct features of their modular constituents.

The cellular function of the giant protein titin in striated muscle is a major focus of scientific attention. Particularly, its role in passive mechanics has been extensively investigated. In strong contrast, the structural details of this filament are very poorly understood. To date, only a handful of atomic models from single domain components have become available and data on poly-constructs are limited to scarce SAXS analyses. In this study, we examine the molecular parameters of poly-Ig tandems from I-band titin relevant to muscle elasticity. We revisit conservation patterns in domain and linker sequences of I-band modules and interpret these in the light of available atomic structures of Ig domains from muscle proteins. The emphasis is placed on features expected to affect inter-domain arrangements. We examine the overall conformation of a 6Ig fragment, I65-I70, from the skeletal I-band of soleus titin using SAXS and electron microscopy approaches. The possible effect of highly conserved glutamate groups at the linkers as well as the ionic strength of the medium on the overall molecular parameters of this sample is investigated. Our findings indicate that poly-Ig tandems from I-band titin tend to adopt extended arrangements with low or moderate intrinsic flexibility, independently of the specific features of linkers or component Ig domains across constitutively- and differentially-expressed tandems. Linkers do not appear to operate as free hinges so that lateral association of Ig domains must occur infrequently in samples in solution, even that inter-domain sequences of 4-5 residues length would well accommodate such geometry. It can be expected that this principle is generally applicable to all Ig-tandems from I-band titin.

Amino Acid Motifs↗

PubMed1991

Temperature and pH dependence of immunoglobulin G conformation.

Previous indirect observations have indicated that IgG may change its conformation at low or high pH and at a temperature of about 35 degrees C. By means of small angle neutron scattering a change in the value of the gyration radius of two different native IgG's was observed above 44 degrees C. No similar change was detected when the sample was previously dissolved in an acidic buffer. The acidic pretreatment caused a significant decrease in the gyration radius (Rg) value measured at 20 degrees C which was partially recovered by increasing the temperature. These observations led to the assumption that the main conformational change observed appears either in the hinge region of the molecular or in the interdomain areas separating the constant and the variable domains of the Fab parts.

Animals↗

PubMed1993

Topography of tetrahydrocannabinol in model membranes using neutron diffraction.

Small-angle neutron scattering was used to determine the intralamellar location of (-)-delta 8-tetrahydrocannabinol (delta 8-THC) in hydrated dipalmitoylphosphatidylcholine (DPPC) bilayers. Nuclear scattering density profiles were calculated from measurements on deuterium and non-deuterium-labelled inclusions (8.3% (w/w)) of delta 8-THC in DPPC multilayer samples. By comparing pairs of such nuclear density profiles, the locations of the deuterium labels were determined. Present results on the topography of delta 8-THC in membranes are compared with earlier X-ray measurements using iodine labelling. Whereas the position of the phenolic hydroxy group is similar in both types of measurement, a difference is found in the conformation of the terminal methyl groups of the cannabinoid side-chains. The X-ray measurements on dimyristoylphosphatidylcholine (DMPC) indicated that the iodine-labelled cannabinoid side-chains assume an all-trans orientation with the terminal iodine atom pointing inward into the membrane away from the tricyclic region while the neutron measurements indicate that the terminal CH3 group of delta 8-THC aligns itself at the level of the tricyclic ring system implying that the side chain exists in a more compact conformation perpendicular to the DPPC hydrocarbons. A Gaussian function analysis of the data indicates that the delta 8-THC molecule is significantly delocalized in the DPPC membrane in the liquid crystal phase. The mean location of delta 8-THC suggests that the active site on a membrane-embedded receptor protein will lie near the polar interface at the base of the phospholipid headgroups.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed1991

Lateral order in binary lipid alloys and its coupling to membrane functions.

Densitometry, Raman spectroscopy and small angle neutron scattering are employed to elucidate the miscibility behavior of lipid mixtures organized as liposomal dispersions. First, temperature-composition-phase diagrams for several binary alloys of dialkyl-lecithins differing in chain lengths by an increasing number of CH2-groups are derived. A mixture of dimyristoyllecithin and distearoyllecithin (delta CH2 = 4) shows a peritectic phase behavior with a miscibility gap in the gel state. In the fluid phase, at high enough temperatures, homogeneous mixtures of the two components are formed at all molar ratios. However, upon approaching a critical point by either lowering the temperature or increasing the hydrostatic pressure, critical concentration fluctuations are observed. If one component of a binary mixture is charged, electrostatic interactions can be used to induce phase separation at constant temperature. This is demonstrated for Ca2(+)-driven demixing in alloys of lecithin and negatively charged phosphatidylglycerol. The influence of the various concepts for the induction of lateral structure formation in lipid membranes on integral functional units like ionophores is demonstrated by analysing the single channel current fluctuations of gramicidin in bimolecular lipid membranes. Ca2+, as well as polyelectrolyte-induced phase separations are shown and discussed as examples for the important (lateral) order-function relationship in biomembranes.

Electrochemistry↗

PubMed1992

Structure and RNA content of the prosomes.

Duck erythroblasts prosomes were analysed by small angle neutron scattering (SANS), dynamic light scattering and (cryo-)electron microscopy. A molecular weight of approximately 720,000 +/- 50,000, a radius of gyration of 64 +/- 2 A and a hydrodynamic radius of approximately 86 A were obtained. Electron micrographs show a hollow cylinder-like particle with a diameter of 120 A, a height of 170 A and a diameter of 40 A for the cavity, built of four discs, the two outer ones being more pronounced than those in the center. Results from SANS indicate less then 5% of RNA in the purified prosomes, but nuclease protection assays confirm its presence.

Animals↗

PubMed1983

Self-assembly of brome mosaic virus protein into capsids. Initial and final states of aggregation.

The pH and ionic strength dependence of the states of aggregation of brome mosaic virus protein has been investigated by small angle neutron scattering, quasielastic light-scattering, analytical centrifugation and electron microscopy. At pH above neutrality, protein oligomers are found in dynamical equilibrium, comprising monomers, dimers and aggregates of higher molecular weight. By lowering the pH, capsids assemble spontaneously with dimensions in solution which depend on ionic strength. If formed by dialysis, they contain 180 monomers, but are 30 A larger in diameter than the native virus. If formed by pH-jump, they contain less monomers: the deficiency decreases with decreasing the final pH and the initial protein concentration. Upon dehydration for electron microscopy, capsids contract by 10%.

Capsid↗

PubMed1989

Lateral order in mixed lipid bilayers and its influence on ion translocation by gramicidin: a model for the structure-function relationship in membranes.

The temperature-composition phase diagram of dimyristoylphosphatidylcholine and dipentadecylphosphatidylglycerol (DiC15PG) was determined by mass densitometry. For a mixture containing 30 mol% DiC15PG, the homogeneous distribution of the 2 components is demonstrated in the fluid state at T = 35 degrees C by small-angle neutron scattering in combination with the inverse contrast variation method. By the same technique, the coexistence of fluid and condensed phases at T = 23.3 degrees C could be shown in agreement with the densitometric data. Furthermore, it is demonstrated that Ca++ induces, even at T = 35 degrees C, separation into 2 fluid phases. A corresponding phase separation is found in bimolecular lipid membranes ("black films") by analysis of the single-channel conductance fluctuations of gramicidin A incorporated into an equimolarly mixed membrane of neutral lecithin and charged phosphatidic acid. The results are discussed as primary examples on the model-membrane level for the important structure-function relationship of biomembranes.

Calcium↗

PubMed1992

Structural dynamics of translating ribosomes.

We describe three groups of small angle neutron scattering (SANS) experiments with translating ribosomes: 1) regular protonated (normal abundance hydrogen) particles; 2) two isotopic hybrid particles which are reconstituted from one protonated and the other deuterated subunit; 3) four isotypic hybrid particles differing from each other by the extent of protein and RNA deuteration. Using the SANS contrast variation method the radii of gyration of protein and RNA components in both ribosomal subunits as well as the intersubunit distance in the pre- and post-translocation states were determined. The results obtained suggest the following model of the ribosome as a dynamic machine. The ribosome oscillates between two major conformers differing in geometrical dimensions. The 'active' (pulsating) part of the ribosome is the 30S subunit. We believe that the movement of its 'head' relative to the passive 50S subunit is the main mechanical act of translocation. The radius of gyration of the 30S subunit and the intersubunit distance change upon the movement. This is corroborated by neutron scattering data.

Bacterial Proteins↗

PubMed1994

Conformational changes in yeast phosphoglycerate kinase upon substrate binding.

Small-angle neutron scattering (SANS) was used to measure the radius of gyration (Rg) of solutions of phosphoglycerate kinase (PGK) in a variety of substrate environments in D2O. The Rg of 24.0 A was measured for native PGK. A decrease in Rg was observed for the following: 23.7 A for PGK+sulphate; 23.5 A for PGK+ beta, gamma-bidentate Cr(H2O)4ATP (CrATP); 23.3 A for PGK + 3-phospho-D-glycerate (PGA)+CrATP; 22.9 A for PGK+CrATP+sulphate; 22.6 A for PGK+PGA+CrATP+sulphate. The statistical error was about +/- 0.3 A, which is less than systematic effects in this system. These results are consistent with catalysis by a hinge-bending motion of the enzyme. Since CrATP is not hydrolyzed, these results represent the conformational states of the bound substrates in the catalytically relevant ternary complex in the absence of product formation. The second virial coefficient is also measured for this system and this is consistent with that calculated from the protein volume only.

Catalysis↗

PubMed1994

How random is a highly denatured protein?

There has been renewed interest in determining the physicochemical properties of denatured states of proteins. In many denatured states there is evidence for the existence of nonrandom configurational distributions. Here we examine the small-angle neutron scattering profile of yeast phosphoglycerate kinase in the native state and in highly denaturing conditions. We show that the denatured protein scattering profile can be interpreted using a model developed for synthetic polymers in which the chain behaves as a random coil in a good solvent, i.e. with excluded volume interactions. The implications of this result for our appreciation of the protein folding process are discussed.

Journal Article↗

PubMedDate not supplied

Activation of recA protein: the salt-induced structural transition.

Purified recA protein is induced by high salt concentrations to hydrolyse ATP even in the absence of DNA. By small angle neutron scattering we show that this salt activation results from a structural transition of the protein filament in the presence of ATP gamma S from the inactive, compact form (a helical polymer of pitch 70 A and cross-sectional radius of gyration Rc 40 A) to the open form (a helical filament of pitch 95 A and Rc 35 A, which are the same structural parameters as in the ATPase active complex with DNA and ATP), without detectable change in the degree of association. We conclude that activation of recA is due to the same structural change whether induced by the binding of DNA or by salt. Indeed, the other enzymatic activity of recA, the proteolytic cleavage of the lexA repressor, is found to be inducible by the same salt concentrations as those of the structural transition.

Acetates↗

PubMed2004

Partial specific volume and solvent interactions of amphipol A8-35.

Amphipols are small amphiphilic polymers that can stabilize and keep soluble membrane proteins in aqueous solutions in the absence of detergent. A prerequisite to solution studies of membrane protein/amphipol complexes is the determination of the partial specific volume v2 and effective charge z of the polymer. The ratio (R) of the buoyant molar masses of particles in D2O and H2O solutions, obtained from sedimentation velocity (sH/sD method) and sedimentation equilibrium experiments, and their contrast match point (CMP), determined in small-angle neutron scattering experiments, depend on v2 and z. When z is known, v2 can be estimated from R with a good accuracy as long as v2 is close to 1. The effects of labile H/D exchange and of polyelectrolyte counter-ion dissociation in general cannot be neglected. The accuracy, advantages, and limits of the sH/sD method have been studied in details using model macromolecules (DNA, protein, and polysaccharide). The sH/sD method appears particularly advantageous for the study of heterogeneous samples. Measurements of density, sD/sH buoyant molar masses in H2O, D2O, and D2(18)O, and CMP of hydrogenated and partially deuterated A8-35, a polyacrylate-based amphipol containing 35 underivatized carboxylates per 100 monomers, led to a consistent description of its buoyancy and charge properties.

Carbon↗