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At least 739 records · Page 41Linked to original sources
PubMed2003

Hydrodynamic micromanipulation of individual cells onto patterned attachment sites on biomicroelectromechanical system chips.

We report on a simple methodology to move selected single live cells to a desired location on a flat substrate, such as a patterned biomicroelectromechanical system chip. A macroscopic syringe-and-tube-based hydrodynamic manipulation system is used to achieve controlled cell navigation onto hydrophilic sites for cell attachment. Centimeter-per-second flow velocities generated by the system get downgraded to micrometers-per-second flow at the height of settled cells as a result of viscous flow in the medium. By pushing/pulling two syringes that produce two orthogonal flows, fine manipulation in any horizontal direction is feasible. After attachment of the desired cell(s) onto the selected hydrophilic site, all other unwanted cells are washed away from the surrounding hydrophobic surface with faster flow. This simple methodology is applicable for rapid cell pattern formation with high precision.

Animals↗
PubMed2006

Hydrodynamic dispersion in shallow microchannels: the effect of cross-sectional shape.

We highlight the fact that hydrodynamic dispersion in shallow microchannels is in most cases controlled by the width of the cross section rather than by the much thinner height of the channel. We identify the relevant time scales that separate the various regimes involved. Using the lubrication approximation, we provide simple formulas that permit a quantitative evaluation of dispersion for most shallow cross-sectional shapes in the "long-time" Taylor regime, which is effectively diffusive. Because of its relevance for microfluidic systems, we also provide results for the short-time "ballistic regime" (for specific initial conditions). The special cases of parabolic and quasi-rectangular shapes are considered due to their frequent use in microsystems.

Journal Article↗
PubMed2006

Visualization and modeling of the hydrodynamics of an impinging microjet.

The use of fluorescence confocal laser scanning microscopy (CLSM) for flow visualization is described, with a focus on elucidating the pattern of flow in the microjet electrode (MJE). The MJE employs a nozzle, formed from a fine glass capillary, with an inner diameter of approximately 100 microm, to direct solution at an electrode surface, using high velocity but at moderate volume flow rates. For CLSM visualization, the jetted solution contains a fluorescent probe, fluorescein at high pH, which flows into a solution buffered at low pH, where the fluorescence is extinguished, thereby highlighting the flow field of the impinging microjet. The morphology of the microjet and the hydrodynamic boundary layer are shown to be highly sensitive to the volume flow rate, with a collimated jet and thin boundary layer formed at the faster flow rates (approximately 1 cm(3) min(-1)). In contrast, at lower flow rates and for relatively large substrates, an unusual recirculation zone is observed experimentally for the first time. This effect can be eliminated by employing small substrates. The experimental observations have been quantified through numerical solution of the Navier-Stokes equations of continuity and momentum balance. The new insights provided by CLSM imaging demonstrate that flow in the MJE, and impinging jets in general, are more complex than predicted by classical models but are well-defined and quantifiable.

Journal Article↗
PubMed2006

Hydrodynamic tweezers: 1. Noncontact trapping of single cells using steady streaming microeddies.

A key need for dynamic single-cell measurements is the ability to gently position cells for repeated measurements without perturbing their behavior. We describe a new method that uses a gentle secondary flow to trap and suspend single cells, including motile cells, at predictable locations in 3-D. Trapped cells can be more dense or less dense than the surrounding medium. The cells are suspended without surface contact in one of four steady streaming eddies created by audible-frequency fluid oscillation (< or =1000 Hz) in a microchannel containing a single fixed cylinder (radius = 125 microm). Comparison of measured trap locations to computations of the eddy flow show that each trap is located near the eddy center, and the location is controlled via the oscillation frequency. We use the motile phytoplankton cell (Prorocentrum micans) to experimentally measure the trapping force, which is controlled via the oscillation amplitude. Trapping forces up to 30 pN are generated while exerting moderate shear stresses (shear stresses < or = 1.5 N/m2) on the trapped cell. The magnitude of this trapping force is comparable to that of optical tweezers or dielectrophoretic traps, without requiring an external field outside the physiological range for cells (the shear stresses are comparable to those found in arterial blood flow). The unique combination of predictable 3-D positioning, insensitivity to cell and medium properties, strong adjustable trapping forces, and a gentle fluid environment makes hydrodynamic tweezers a promising new option for noncontact trapping of single cells in suspension.

Animals↗
PubMed2007

Voltammetric monitoring of transient hydrodynamic flow profiles in microfluidic flow cells.

We consider the transition to steady-state flow in the inlet region of a hydrodynamic channel cell and show that a microelectrode positioned within this inlet region allows chronoamperometric results to be recorded, from which information about the extent of the development of the flow profile may be deduced as well as information about the precise dimensions of the microfluidic channel.

Journal Article↗
PubMed1986

Physicochemical and hydrodynamic characterization of P-57, a neurospecific calmodulin binding protein.

P-57 is a neurospecific calmodulin binding protein that was discovered by virtue of its unusual interactions with calmodulin-Sepharose [Andreasen, T. J., Luetje, C. W., Heideman, W., & Storm, D. R. (1983) Biochemistry 22, 4615-4618; Cimler, B. M., Andreasen, T. J., Andreasen, K. I., & Storm, D. R. (1985) J. Biol. Chem. 260, 10784-10788]. In contrast to other calmodulin binding proteins, P-57 has higher affinity for calmodulin-Sepharose in the absence of calcium compared to that in the presence of calcium. In this study, we report the chemical and physical properties of P-57 purified from detergent-solubilized bovine brain membranes. The amino acid composition of P-57 is distinctive in that it contains a single phenylalanine residue with no other aromatic amino acids and a relatively high percentage of proline and alanine. In the presence of 0.05% Lubrol PX, its predicted secondary structure from circular dichroism spectroscopy is 1% alpha-helix, 21% beta-sheet, and 78% random coil. The hydrodynamic characteristics of the protein-detergent complex and the molecular weight of the protein were determined by gel filtration and sucrose density gradient sedimentation in the presence and absence of calmodulin. The P-57-detergent complex has an apparent Stokes radius (Rs) of 4.58 nm and a sedimentation coefficient (S20,w) of 1.44 S while the Stokes radius and S20,w for the P-57-calmodulin-detergent complex are 5.33 nm and 2.32 S, respectively. Perrin analysis of a 5-[[[(iodoacetyl)amino]ethyl]amino]-1-naphthalenesulfonic acid (AEDANS) derivative of P-57 confirmed the Stokes radius determined by gel filtration.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acids↗
PubMed1987

Hydrodynamic properties of the chromaffin granule hydrogen ion pumping adenosinetriphosphatase.

We have determined the hydrodynamic properties of detergent-solubilized ATPase, which is coupled to H+ pumping in bovine adrenal chromaffin granules, by sedimentation equilibrium centrifugation and gel permeation chromatography. The protein solubilized with detergent containing phosphatidylserine sediments as a particle of 264,000 daltons and partial specific volume 0.829 cm3/g. Assuming a protein v of 0.73 and using the v measured for detergent and lipid mixed micelles of 0.93 cm3/g, we calculated that the protein component has a mass of 134,000 daltons and that the equivalent of approximately 1.5 micelles of detergent are bound per particle. The particle exhibits a Stokes radius of 43 A, which, together with the calculated particle volume, indicates an axial ratio close to 1. We conclude that the ATPase is an intrinsic membrane protein with a structure very different from that of mitochondrial F1F0 ATPase.

Adrenal Medulla↗
PubMed1987

Kinetic and hydrodynamic properties of transducin: comparison of physical and structural parameters for GTP-binding regulatory proteins.

Transducin is a member of the family of GTP-binding regulatory proteins that interact with cell surface receptors and that include Gs, Gi, and Go. Kinetic and physical properties of purified bovine transducin were characterized by the following results: (1) Initial rate analysis demonstrates a dissociative-type mechanism for the guanine nucleotide exchange process of transducin in the absence of rhodopsin. A second-order rate constant of kf = (1.7-2.7) X 10(-7) M-1 s-1 was determined for this reaction. (2) Equilibrium binding measurements indicated a Kd of 0.05-0.10 microM for guanosine 5'-O-(3-thiotriphosphate) (GTP gamma S) binding to transducin. (3) Neither the rate nor the extent of GTP gamma S binding was affected in the presence of up to 50 mM Mg2+, as compared to values obtained in the presence of excess ethylenediaminetetraacetic acid. (4) Sucrose density gradient ultracentrifugation gave S20,w values for transducin, its alpha subunit, and its beta gamma subunit complex of 4.23 +/- 0.25, 3.42 +/- 0.37, and 4.04 +/- 0.2, respectively. (5) Incubation of transducin in the presence of up to 20 mM Mg2+ did not alter its sedimentation behavior; however, the presence of guanine nucleotides did produce a shift in transducin's migration in the sucrose gradient. (6) Gel filtration over Sephacryl S-300 indicated that transducin elutes at a Stokes radius of 37.5 A and that transducin's alpha subunit displays a Stokes radius of 24 A. (7) A molecular mass of 68 kDa for transducin is derived from the determined hydrodynamic parameters. These results are compared with properties known for other G proteins, and functional differences between transducin and Gs, Gi, and Go are proposed in relation to the proteins' primary sequences.

Animals↗
PubMed1988

Structure of the Tet repressor and Tet repressor-operator complexes in solution from electrooptical measurements and hydrodynamic simulations.

The Tet repressor protein and tet operator DNA fragments and their complexes have been analyzed by electrooptical procedures. The protein shows a positive linear dichroism at 280 nm, a negative linear dichroism at 248 nm, and a strong permanent dipole moment of 3.5 X 10(-27) C m, which is independent of the salt concentration within experimental accuracy. Its rotation time constant of 40 ns indicates an elongated structure, which is consistent with a prolate ellipsoid of 100 A for the long axis and 40 A for the short axis. The time constant can also be fitted by a cylinder of length 78 A and diameter 37 A, which is consistent with nuclease protection data reported on repressor-operator complexes, if the cylinder axis is aligned parallel to the DNA axis. Addition of tetracycline induces changes of the limit dichroism but very little change of the rotation time constant. The rotation time constants observed for the operator DNA fragments show some deviations from the values expected from their contour length; however, these deviations remain relatively small. Formation of repressor-operator complexes leads to some increase of the DNA rotation time constants. Simulations by bead models demonstrate that these time constants can be explained without any major change of the hydrodynamic dimension of the components. The data for the complexes are fitted by bead models with smooth bending of the DNA corresponding to a radius of curvature of 500 A, but at the given accuracy, we cannot rule out that the DNA in the complex remains straight or is bent to a smaller radius of approximately 400 A. Thus, binding of the Tet repressor, which is a helix-turn-helix protein as judged from its sequence, to its operator seems to induce minor bending but does not induce strong bending of the DNA double helix.

DNA Transposable Elements↗
PubMed1988

Spectroscopic and hydrodynamic studies reveal structural differences in normal and transforming H-ras gene products.

We have recorded the circular dichroism spectra of the cellular and the viral H-ras gene products both in the absence and in the presence of guanine nucleotides and analyzed these spectra in terms of the secondary structure composition of these proteins. It is shown that the GTP complex of the ras proteins has a different secondary structure composition than the GDP complex and, furthermore, that there are differences in the secondary structure of the viral ras protein and the cellular ras protein. We have also recorded and analyzed the circular dichroism spectrum of the isolated guanine nucleotide binding domain of the Escherichia coli elongation factor Tu (EF-Tu), which has been considered as a model for the tertiary structure of the ras proteins [McCormick, F., Clark, B. F. C., LaCour, T. F. M., Kjeldgaard, M., Norskov-Lauritsen, L., & Nyborg, J. (1985) Science (Washington, D.C.) 230, 78-82]. Our data show that the guanine nucleotide binding domain of EF-Tu (30% alpha-helix and 16% beta-pleated sheet for the GDP complex) has quite a different secondary structure composition than the ras proteins (e.g., the cellular ras protein has 47% alpha-helix and 22% beta-pleated sheet for the GDP complex), indicating that the protein core comprising the guanine nucleotide binding site might be similar but that major structural differences must exist at the portion outside this core. Normal and transforming ras proteins also differ slightly in their hydrodynamic properties as shown by sedimentation velocity runs in the analytical ultracentrifuge.(ABSTRACT TRUNCATED AT 250 WORDS)

Cell Transformation, Neoplastic↗
PubMed1990

Slalom chromatography: size-dependent separation of DNA molecules by a hydrodynamic phenomenon.

Slalom chromatography, a size-dependent DNA fractionation method based on a new principle [Hirabayashi, J., & Kasai, K. (1989) Anal. Biochem. 178, 336-341], was systematically studied in detail. In this method, larger DNA fragments are eluted much later than smaller ones from columns packed with spherical microbeads. Elution of a series of DNA fragments was systematically examined by using columns packed with polymer-based packings of different diameter and different pore size for high-performance gel permeation chromatography. Packings of smaller diameter proved to be superior for resolving the smaller size range of DNA, while the reverse was the case for larger DNAs. Application of a faster flow rate led to larger retardation of every DNA fragment, while at the lowest flow rate applied (0.067 cm/min), all the fragments were eluted almost at the void volume. When the column temperature was lowered, retardation of DNA became larger. On the other hand, differences in the chemical nature and the pore size of packings, or in the hydrophobicity of the eluting solvent, had little effect on DNA retardation. Size-dependent fractionation of DNA was also achieved even on columns packed with nonporous packings having anionic groups (cation exchangers). In conclusion, these results confirmed the previous conclusion that slalom chromatography is not based on an adsorption or equilibrium phenomenon but should be attributed to a hydrodynamic phenomenon.

Animals↗
PubMed1982

Hydrodynamic properties of bovine cardiac troponin C.

The size and shape of bovine cardiac troponin C (TN-C) in solution have been examined by gel filtration, ultracentrifugation, and viscosity in the presence and absence of Ca2+. Cardiac TN-C (-Ca2+) has an intrinsic sedimentation coefficient, s020,w, of 1.87 S and a Stokes radius, RS, of 26.3 A as determined by gel chromatography on Sephacryl S-300. In 2 mM Ca2+, S020,w is increased to 2.04 S and RS is decreased to 24.3 A, indicating a conformational change to a more compact structure. Furthermore, the intrinsic viscosity of TN-C in the absence of Ca2+ (6.4 mL/g) is reduced to 5.4 mL/g when Ca2+ is added. Sedimentation equilibrium studies indicate that the effects of Ca2+ are not due to changes in the molecular weight of the protein. The hydrodynamic data suggest that TN-C is a moderately asymmetric protein with an axial ratio of 4--6.

Animals↗
PubMed1980

Hydrodynamic behavior of human and bacterial thymidylate synthetases and thymidylate synthetase--5-fluoro-2'-deoxyuridylate--5,10-methylenetetrahydrofolate complexes. Evidence for large conformational changes during catalysis.

The conformations of thymidylate synthetases from CCRF-CEM human leukemic cells and Lactobacillus casei were studied by hydrodynamic methods. Although the human enzyme has a molecular weight of 70 000--72 500, somewhat smaller than that of the L. casei enzyme, it has a larger Stokes radius and a lower sedimentation coefficient, indicating that the human enzyme is less spherical than the bacterial enzyme. Thymidylate synthetases from the human leukemic cells and the bacterial source both undergo substantial conformational changes upon the formation of a covalent ternary complex with the mechanism-based inhibitor 5-fluoro-2'-deoxyuridylate and 5,10-methylenetetrahydrofolate. The Stokes radius of both proteins decreases by 3.5% when the ternary complex is formed in spite of the 1.8% increase in molecular weight, and the sedimentation coefficient increases by 3.5% after appropriate corrections for the bound ligands. Ternary complex formation results in a more compact structure for both enzymes, with approximately the same reduction in the frictional ratio. Experiments with the bacterial enzyme indicate that approximately 70% of the total conformational change occurs upon binding of 1 mol of ligands/mol of enzyme. These results demonstrate that human and bacterial thymidylate synthetases undergo marked structural changes upon forming a ternary complex which is probably very similar to an activated complex formed with both substrates. These investigations also provide evidence for fundamental similarities in the mechanism of ternary complex formation with 5-fluoro-2'-deoxyuridylate and 5,10-methylenetetrahydrofolate, despite the marked differences in amino acid composition and the dissimilar conformations of these two enzymes obtained from widely divergent sources.

Binding Sites↗
PubMed1979

Shapes of proteins L1, L9, L25, and L30 from the 50S subunit of the Escherichia coli ribosome, determined by hydrodynamic studies.

Proteins L1, L9, L25, and L30, purified by a nondenaturing method from the 50S ribosomal subunit of Escherichia coli A19, have been characterized. The four proteins were studied under conditions which resemble those used for reconstitution experiments. These proteins have S020,W values of 2.0 S, 1.8 S, 1.8 S, and 1.0 S and D20,W values of 8.4 X 10(-7), 9.0 X 10(-7), 14.0 X 10(-7), and 15.0 X 10(-7) cm2/S. Apparent specific volumes at 20 degrees C are 0.738, 0.733, 0.700, and 0.735 mL/g for the four proteins. The respective molecular weights determined by sedimentation equilibrium are 25 000, 17 300, 12 000, and 6500. The intrinsic viscosity values for the four proteins are 4.0, 5.5, 3.6, and 3.2 mL/g. From these hydrodynamic parameters L1 and L9 appear to have globular or at most only slightly elongated shapes, whereas L25 and L30 appear to be definitely globular.

Electrophoresis, Polyacrylamide Gel↗
PubMed2001

Physical properties of human polynucleotide kinase: hydrodynamic and spectroscopic studies.

Human polynucleotide kinase (hPNK) is a putative DNA repair enzyme in the base excision repair pathway required for processing and rejoining strand-break termini. This study represents the first systematic examination of the physical properties of this enzyme. The protein was produced in Escherichia coli as a His-tagged protein, and the purified recombinant protein exhibited both the kinase and the phosphatase activities. The predicted relative molecular mass (M(r)) of the 521 amino acid polypeptide encoded by the sequenced cDNA for PNK and the additional 21 amino acids of the His tag is 59,538. The M(r) determined by low-speed sedimentation equilibrium under nondenaturing conditions was 59,600 +/- 1000, indicating that the protein exists as a monomer, in contrast to T4 phage PNK, which exists as a homotetramer. The size and shape of hPNK in solution were determined by analytical ultracentrifugation studies. The protein was found to have an intrinsic sedimentation coefficient, s(0)(20,w), of 3.54 S and a Stokes radius, R(s), of 37.5 A. These hydrodynamic data, together with the M(r) of 59 600, suggest that hPNK is a moderately asymmetric protein with an axial ratio of 5.51. Analysis of the secondary structure of hPNK on the basis of circular dichroism spectra, which revealed the presence of two negative dichroic bands located at 218 and 209 nm, with ellipticity values of -7200 +/- 300 and -7800 +/- 300 deg x cm(2) x d(mol(-1), respectively, indicated the presence of approximately 50% beta-structure and 25% alpha-helix. Binding of ATP to the protein induced an increase in beta-structure and perturbed tryptophan, tyrosine, and phenylalanine signals observed by aromatic CD and UV difference spectroscopy.

Adenosine Triphosphate↗
PubMed2003

The closely related estrogen-regulated trefoil proteins TFF1 and TFF3 have markedly different hydrodynamic properties, overall charge, and distribution of surface charge.

The human trefoil proteins TFF1 and TFF3 are expressed predominantly in the gastrointestinal tract. They are also expressed and regulated by estrogens in malignant breast epithelial cells. TFF1 and TFF3 are small cysteine-rich acidic secreted proteins of 60 and 59 amino acids with similar isoelectric points of 4.75 and 3.94, respectively. Each contains one trefoil domain that is characterized by several conserved features including six cysteine residues with conserved spacing. TFF1 and TFF3 form intermolecular disulfide bonds via an extra-trefoil domain cysteine residue and are present in vivo as monomers and homodimers and as complexes with other proteins. The TFF1 dimer is more active than the TFF1 monomer. In the present study the hydrodynamic and charge properties of TFF1 and TFF3 monomers and homodimers have been compared and shown to differ markedly. Notably, TFF1 is significantly more asymmetric than TFF3 (frictional coefficients 1.25 and 1.12, respectively, p < 0.001), and homodimerization of TFF1 results in a greater increase in asymmetry than for TFF3. The overall charges of TFF1 and TFF3 are very different at neutral pH. Titration curves predicted significant differences in charge across a wide pH range that agreed well with experimental data. The locations of charged amino acids in the primary sequences and in the tertiary structures of TFF1 and TFF3 were examined. This revealed interesting divergence in both the distribution and local topology of charged amino acid side chains. The significant differences between the shape, size, and surface charge of these two closely related molecules may account for their divergent biological activities.

Amino Acid Sequence↗
PubMed2006

Characterization of the hydrodynamic properties of the folding transition state of an SH3 domain by magnetization transfer NMR spectroscopy.

Protein folding kinetic data have been obtained for the marginally stable N-terminal Src homology 3 domain of the Drosophila protein drk (drkN SH3) in an investigation of the hydrodynamic properties of its folding transition state. Due to the presence of NMR resonances of both folded and unfolded states at equilibrium, kinetic data can be derived from NMR magnetization transfer techniques under equilibrium conditions. Kinetic analysis as a function of urea (less than approximately 1 M) and glycerol enables determination of alpha values, measures of the energetic sensitivity of the transition state to the perturbation relative to the end states of the protein folding reaction (the folded and unfolded states). Both end states have previously been studied experimentally by NMR spectroscopic and other biophysical methods in great detail and under nondenaturing conditions. Combining these results with the kinetic folding data obtained here, we can characterize the folding transition state without requiring empirical models for the unfolded state structure. We are thus able to give a reliable measure of the solvent-accessible surface area of the transition state of the drkN SH3 domain (4730 +/- 360 A(2)) based on urea titration data. Glycerol titration data give similar results and additionally demonstrate that folding of this SH3 domain is dependent on solvent viscosity, which is indicative of at least partial hydration of the transition state. Because SH3 domains appear to fold by a common folding mechanism, the data presented here provide valuable insight into the transition states of the drkN and other SH3 domains.

Animals↗
PubMed1999

Structural analysis of G-DNA in solution: A combination of polarized and depolarized dynamic light scattering with hydrodynamic model calculations.

Specific intra- and intermolecular quadruplex conformations of model G-DNA oligonucleotides have been identified from their translational and rotational diffusion coefficients in aqueous solution. The transport properties were determined by polarized and depolarized dynamic light scattering. A comparison with hydrodynamic model calculations provides detailed information about the size and shape of the molecules and allows one to distinguish between alternative intra- and intermolecular association. The potential of this combination of methods to elucidate biomolecular structures in solution, to characterize conformational changes, and follow intermolecular interaction processes due to a response to external stimuli has been discussed.

DNA↗