The molecular origin of birefringence in skeletal muscle. Contribution of myosin subfragment S-1.

The state of optical polarization of He-Ne laser light diffracted by single skinned frog skeletal muscle fibers has been determined after decoration of the thin filaments of rigor fibers with exogenous S-1. Light on the first diffraction order was analyzed using optical ellipsometry for changes occurring in total birefringence (delta nT) and total differential field ratio (rT) and the experimental results compared with theoretical predictions. Fibers were examined with SDS-gel electrophoresis and electron microscopy as independent assays of S-1 binding. The binding of S-1 to the thin filaments caused a significant increase in rT and a small but significant decrease in delta nT. Release of bound exogenous S-1 with magnesium pyrophosphate demonstrated that the effect of S-1 on the optical parameters was reversible and both electrophoresis and electron microscopy demonstrated the presence of S-1 specifically bound to the thin filaments. Model simulations based on the theory of Yeh, Y., and R. Baskin (1988. Biophys. J. 54:205-218) showed that the values of delta nT and rT were sensitive to the axial bonding angle of exogenous S-1 as well as to the volume fraction of added S-1. Analysis of the data in light of the model showed that an average axial S-1 binding angle of 68 degrees +/- 7 degrees best fit the data.     

Atomic solvation parameters applied to molecular dynamics of proteins in solution.

A solvation energy function for use in the molecular simulation of proteins is proposed. It is based on the accessible surface areas of atoms in the protein and on atomic solvation parameters derived from empirical vapor-to-water free energies of transfer of amino acid side-chain analogs. The energy function and its derivatives were added to the CHARMM molecular simulation program (Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., & Karplus, M., 1983, J. Comput. Chem. 4(2), 187-217). The effect of the added energy term was evaluated by 110 ps of molecular dynamics on the 26-residue protein melittin. The melittin monomer and tetramer were studied both with and without the added term. With the added energy term the monomer partially unfolded, while the secondary structure of the tetramer was preserved, in agreement with reported experiments (Brown, L.R., Lauterwein, J., & Wuethrich, K., 1980, Biochim. Biophys. Acta 622(2), 231-244; Lauterwein, J., Brown, L.R., & Wuethrich, K., 1980, Biochim. Biophys. Acta 622(2), 219-230).     

Chemotactic peptide binding by rabbit polymorphonuclear leukocytes. Presence of two compartments having similar affinities but different kinetics

N-Formylnorleucylleucylphenylalanine (f-Nle-LeuPhe) bound to rabbit peritoneal polymorphonuclear leukocytes at 4 degrees C exists in at least two compartments that can be differentiated by their off rates. The off rate of one compartment is similar to that of the receptor characterized previously, about 0.4 min-1 (Aswanikumar, S., Corcoran, B., Schiffmann, E., Day, A. R., Freer, R. J., Showell, H. J., Becker, E. L., and Pert, C. B. (1977) Biochem. Biophys. Res. Commun. 74, 810-817; Sullivan, S. J., and Zigmond, S. H. (1980) J. Cell Biol. 85, 703-711); the off rate of the second compartment is about 0.005 min-1. Lysis of the cells at 4 degrees C with 1% Triton does not affect the peptide release from either compartment. Accumulation of peptide at 4 degrees C into the fast off-rate compartment is rapid, reaching a plateau in about 5 min, while peptide in the slow off-rate compartment continues to increase for up to 4 h. The rate of accumulation in the slow off-rate compartment is approximately proportional to the amount of peptide bound to the fast off-rate compartment. Cells lysed at 4 degrees C before binding are still able to accumulate peptide into both compartments. Three possible models to explain the data are presented.     

Simultaneous measurement of electric birefringence and dichroism. A study on photosystem 1 particles.

We have developed a straightforward method to separate linear-dichroism and birefringence contributions to electric-field induced signals in a conventional birefringence setup. The method requires the measurement of electric birefringence for three different angular positions of the analyzer. It is demonstrated that the presence of linear dichroism can significantly influence the measured signals and lead to completely erroneous calculations of the birefringence signal and field-free decay times if its contribution is not taken into account. The new method is used to determine electric birefringence and linear dichroism of trimeric Photosystem 1 complexes from the cyanobacterium Synechocystis PCC 6803 in the detergents n-dodecyl-beta-D-maltoside and n-octyl-beta-D-glucoside. It is concluded that the orientation of the particles in the field is predominantly caused by a permanent electric dipole moment that is directed parallel to the symmetry axis of the particles. Comparison of the decay times obtained with dodecylmaltoside and octylglucoside supports a model in which the thickness of the disc-like complexes remains similar (7-8 nm) upon replacing dodecylmaltoside by octylglucoside, whereas the diameter increases from 14.4 +/- 0.2 to 16.6 +/- 0.2 nm because of an increased thickness of the detergent layer. This change in diameter is in good agreement with electron-microscopy results on Photosystem 2 complexes in dodecylmaltoside and octylglucoside (Dekker, J. P., E. J. Boekema, H. T. Witt, and M. Rögner. 1988. Biochim. Biophys. Acta 936:307-318). The value of approximately 16.6 nm for the diameter of Photosystem 1 trimers in dodecylmaltoside is in good agreement with recent results obtained from electron microscopy in combination with extensive image analysis (Kruip, J., E. J. Boekema, D. Bald, A. F. Boonstra, and M. Rögner. 1993. J. Biol. Chem. 268:23353-23360).     

Dynamics of the phosphate group in phospholipid bilayers. A 31P-1H transient Overhauser effect study.

Two recent studies have addressed the question of the dynamics of the phosphate in egg phosphatidylcholine multilayers by measurement and interpretation of 31P NMR spin-lattice relaxation. In the first (Milburn, M. P., and K. R. Jeffrey. 1987. Biophys. J. 52:791-799), the temperature dependences of the two contributions to the 31P relaxation rate, a dipolar interaction of the phosphorus with neighboring protons and a time-dependent anisotropic chemical shielding interaction were separately measured. A further study (Milburn, M. P., and K. R. Jeffrey. 1989. Biophys. J. 56:543-549) incorporated the anisotropic nature of phospholipid motions into the dynamic model of the headgroup motion by measuring the 31P spin-lattice relaxation time in oriented samples as a function of angle between the bilayer normal and the magnetic field. These angular dependent measurements were made at high field so that analysis could by made using the chemical shielding interaction because the 31P-1H dipolar interaction in phospholipid systems is complex and as such poorly understood. Nuclear Overhauser effect (NOE) studies have attempted to identify the important proton species contributing to the 31P-1H dipolar interaction (Yeagle, P. L., W. C. Hutton, C. Huang, and R. B. Martin. 1975. Biochemistry. 15:2121-2124) and despite some controversy in interpretation (Burns, R. A., R. E. Stark, D. A. Vidusek, and M. F. Roberts. 1983. Biochemistry. 22:5084-5090), it was generally agreed that the choline methyl and methylene protons are the major contributors to the 31P-1H NOE. To further understand the nature of the 31P-1H dipolar interaction, we carried out 31P-1H Transient Overhauser effect (TOE) measurements on egg phosphatidylcholine multilayers.(ABSTRACT TRUNCATED AT 250 WORDS)     

Calcium-dependent activation and deactivation of rod outer segment phosphodiesterase is calmodulin-independent

ATP-dependent activation and deactivation of retinal rod outer segment phosphodiesterase is affected by calcium [Kawamura, S. and Bownds, M. D., J. Gen. Physiol. 77:571-591(1981)]. Our data demonstrate that although calmodulin has been found in rod outer segments [Liu, Y. P. and Schwartz, H., Biochim. Biophys. Acta 526:186-193(1978); Kohnken, R. E. et al, J. Biol. Chem. 256:12517-12522(1981)], this protein is not involved in calcium-dependent phosphodiesterase activation at light levels at which calcium clearly affects this enzyme's activity. Furthermore, calmodulin does not mediate the calcium-dependent deactivation of phosphodiesterase.     

Comparison of the data, analysis, and results of X-ray absorption studies of cytochrome c oxidase

Differences in the methods of analysis of X-ray absorption data used by Powers et al. [Powers, L., Blumberg, W. E., Chance, B., Barlow, C., Leigh, J., Jr., Smith, J., Yonetani, T., Vik, S., & Peisach, J. (1979) Biochim. Biophys. Acta 547, 520-538; Powers, L., Chance, B., Ching, Y., & Angiolillo, P. (1981) Biophys. J. 34, 465-498] and Scott et al. [Scott, R., Schwartz, J., & Cramer S. (1986) Biochemistry 25, 5546-5555] are clarified. In addition, we compare the X-ray absorption data and results for resting cytochrome c oxidase reported by both groups using the same analysis method and conclude apart from any assumptions that the data are not identical.     

Response of rat liver glutaminase to pH. Mediation by phosphate and ammonium ions

The activity of rat liver glutaminase from sedimented fractions of freeze-thawed mitochondria is strongly affected by variation in pH over a physiologically relevant range at approximate physiological concentrations of activators. As pH increases from 7.1 to 7.7 at 0.7 mM ammonium and 10 mM phosphate, the S0.5 for glutamine decreases 3.5-fold, from 38 to 11 mM. This results in an 8-fold increase in reaction velocity at 10 mM glutamine. In addition, the M0.5 for phosphate activation decreases from 21 to 8.9 mM as pH increases from 7.1 to 7.7. This apparent effect of pH on the affinity of glutaminase for phosphate is similar to previous reports of the pH effect on activation by ammonium (Verhoeven, A. J., Van Iwaarden, J. F., Joseph, S. K., and Meijer, A. J. (1983) Eur. J. Biochem. 133, 241-244; McGivan, J. D., and Bradford, N. M. (1983) Biochim. Biophys. Acta 159, 296-302). Glutaminase does not respond to variation in pH between 7.1 and 7.7 when phosphate and ammonium are saturating. The effects of the two modifiers are additive. Each is still effective, as is pH, when the other is saturating. Therefore, it appears that the effects of pH on the apparent affinity of the enzyme for ammonium and phosphate account for the enzyme's response to pH. These results may help explain previous reports of minimal effects of pH on glutaminase at saturating concentrations of related substances (McGivan, J. D., Lacey, J. H., and Joseph, K. (1980) Biochim. J. 192, 537-542; Horowitz, M. L., and Knox, W. E. (1968) Enzymol. Biol. Clin. 9, 241-255; McGivan, J. D., and Bradford, N. M. (1983) Biochim. Biophys. Acta 759, 296-302). Glutaminase binds glutamine cooperatively with Hill coefficients ranging from 1.7 to 2.2, which suggests at least two and probably three or more interacting binding sites for glutamine. The strong response of liver glutaminase to pH and the fact that the reaction can supply metabolites for urea synthesis suggest a possible regulatory role of glutaminase in ureagenesis.     

Molecular cloning of rat intestinal mucin. Lack of conservation between mammalian species

We have prepared antisera to deglycosylated rat intestinal mucin and used it to obtain immunoreactive clones from a rat jejunum cDNA library. Four of these clones were sequenced, and all were found to be partial cDNAs that contained 18-base pair tandem repeats characteristic of a mucin. These cDNAs encoded a repetitive peptide with a consensus sequence of TTTPDV. Thus, they bear little resemblance to either of the two human intestinal mucin cDNAs isolated previously (Gum, J. R., Byrd, J. C., Hicks, J. W., Toribara, N. W., Lamport, D. T. A., and Kim, Y. S. (1989) J. Biol. Chem. 264, 6480-6487 and Gum, J. R., Hicks, J. W., Swallow, D. M., Lagace, R. E., Byrd, J. C., Lamport, D. T. A., Siddiki, B., and Kim, Y. S. (1990) Biochem. Biophys. Res. Commun. 171, 407-415). One of these rat mucin clones, designated RMUC 176, was chosen for further analysis. This clone recognized a band of approximately 9 kilobases when used to probe RNA blots. A strong hybridization band was present using rat small intestine and colon RNA but was not detectable when RNA isolated from heart, liver, or kidney was tested. The RMUC 176 clone and the two previously isolated human intestinal mucin cDNA clones were used to probe blots prepared from BamHI-digested DNA of various species. Here, the human probes detected fragments present only in human and chimpanzee DNA, whereas the RMUC 176 clone recognized fragments only in rat and mouse DNA. Thus, the repetitive portions of intestinal mucin genes are apparently not well conserved between phylogenetically distant species.     

Genetic engineering of Escherichia coli inorganic pyrophosphatase. Tyr55 and Tyr141 are important for the structural integrity.

Two tyrosines are supposed to be essential for the activity and to participate in the stabilization of Escherichia coli inorganic pyrophosphatase (PPiase) against heat denaturation [Samejima, T., Tamagawa, Y., Kondo, Y., Hachimori, A., Kaji, H., Takeda, A. and Shiroya, Y. (1988) J. Biochem. (Tokyo) 103, 766-772]. To locate these two tyrosines in the amino acid sequence, we substituted all the eight tyrosines of E. coli PPiase with phenylalanine and studied the properties of these YF mutant PPiases. Interestingly, substitution of the tyrosines (Tyr51, Tyr55 and Tyr141) conserved with the amino acid sequence of yeast PPiase [Lahti, R., Kolakowski, L. F., Heinonen, J., Vihinen, M., Pohjanoksa, K. and Cooperman, B. (1990) Biochim. Biophys. Acta 1038, 338-345] exerted the most drastic effects on the structure and activity of E. coli PPiase. PPiase variants YF51, YF55 and YF141 had 64%, 7% and 22% of the wild-type PPiase activity, respectively. Furthermore, PPiase variant YF141 had an increased sensitivity to heat denaturation, whereas mutant PPiase YF55 displayed a profound conformational change, as demonstrated by the binding of the fluorescent dye 9-(diethylamino)-5H-benzo(alpha) phenoxazine-5-one (Nile red) that monitors the hydrophobicity of protein surfaces. None of the tyrosines of E. coli PPiase seem to be essential for catalysis, but Tyr55 and Tyr141 are important for the structural integrity of E. coli PPiase.     

Percolation model of ionic channel dynamics.

The nonexponential closed-time distributions observed for ionic channels have been explained recently by quasi-one-dimensional models of structural diffusion (Millhauser, G. L., E. E. Salpeter, and R. E. Oswald. 1988. Proc. Natl. Acad. Sci. USA. 85: 1503-1507; Condat, C. A., and J. J?ckle. 1989. Biophys. J. 55: 915-925; Levitt, D. G. 1989. Biophys. J. 55: 489-498). We generalize this treatment by allowing for more complex trajectories using percolation theory. We assume that the gating transition depends on marginally connected conformational states leading to the observed spread in time scales.     

Gauging of the PhoE channel by a single freely diffusing proton

In the present study we combined a continuum approximation with a detailed mapping of the electrostatic potential inside an ionic channel to define the most probable trajectory for proton propagation through the channel (propagation along a structure-supported trajectory (PSST)). The conversion of the three-dimensional diffusion space into propagation along a one-dimensional pathway permits reconstruction of an ion motion by a short calculation (a few seconds on a state-of-the-art workstation) rather than a laborious, time-consuming random walk simulations. The experimental system selected for testing the accuracy of this concept was the reversible dissociation of a proton from a single pyranine molecule (8-hydroxypyrene-1,2,3-trisulfonate) bound by electrostatic forces inside the PhoE ionic channel of the Escherichia coli outer membrane. The crystal structure coordinates were used for calculation of the intra-cavity electrostatic potential, and the reconstruction of the observed fluorescence decay curve was carried out using the dielectric constant of the intra-cavity space as an adjustable parameter. The fitting of past experimental observations (Shimoni, E., Y. Tsfadia, E. Nachliel, and M. Gutman. 1993. Biophys. J. 64:472-479) was carried out by a modified version of the Agmon geminate recombination program (Krissinel, E. B., and N. Agmon. 1996. J. Comp. Chem. 17:1085-1098), where the gradient of the electrostatic potential and the entropic terms were calculated by the PSST program. The best-fitted reconstruction of the observed dynamics was attained when the water in the cavity was assigned epsilon 相似文献   

An investigation on the quinoprotein nature of some fungal and plant oxidoreductases.

The presence of pyrroloquinoline quinone (PQQ) as the organic cofactor of Dactylium dendroides galactose oxidase and lentil (Lens culinaris) seedling amine oxidase, purported PQQ-containing oxidoreductases (Van der Meer, R. A., Jongejan, J. A., and Duine, J. A. (1989) J. Biol. Chem. 264, 7792-7794; Citro, G., Verdina, A., Galati, R., Floris, G., Sabatini, S., and Finazzi-Argo', A. (1989) FEBS Lett. 247, 201-204), was reinvestigated using the nitro blue tetrazolium redoxcycling method (Paz, M. A., Gallop, P. M., Torrelio, B. M., and Flückiger, R. (1988) Biochem. Biophys. Res. Commun. 154, 1330-1337; Paz, M. A., Flückiger, R., Boak, A., Kagan, H. M., and Gallop, P. M. (1991) J. Biol. Chem. 266, 689-692) and the enzyme-linked immunosorbent assay with polyclonal antibodies against PQQ. The possible quinoprotein nature of the laccases from Polyporus versicolor and Rhus vernicifera was also investigated because of the similarities in spectroscopic and kinetic features of these enzymes and the laccase from Phlebia radiata, reported to be a PQQ protein (Karhunen, E., Niku-Paavola, M.-L., Viikari, L., Haltia, T., Van der Meer, R. A., and Duine, J. A. (1990) FEBS Lett. 267, 6-8). The presence of a quinonoid cofactor in lentil seedling amine oxidase is confirmed, whereas galactose oxidase and both laccases do not display any quinoprotein nature.     

Kinetics of the interaction of 2'(3')-O-(N-methylanthraniloyl)-ATP with myosin subfragment 1 and actomyosin subfragment 1: characterization of two acto-S1-ADP complexes.

We have used a fluorescent analogue of ATP, mantATP [2'(3')-O-(N-methylanthraniloyl)-adenosine 5'-triphosphate; Hiratsuka T. (1983) Biochim. Biophys. Acta 742, 496-508], and made a detailed kinetic study of the interaction of mantATP and mantADP with S1 and acto-S1. We have shown that these analogues behave like ATP and ADP, respectively. In addition, we have demonstrated that this analogue can distinguish between two acto-S1 complexes, the A-M.N (attached) and A.M.N (rigor-like) states [Geeves, M. A., Good, R. S., & Gutfreund, H. (1984) J. Muscle Res. Cell Motil. 5, 351-361]. Previously, these two states were observed with a pyrene label on Cys 374 of actin. This isomerization can now be monitored at two spatially distinct sites on the ternary complex, indicative of a major conformational change in the ternary complex. Also, we have measured the rate of ADP dissociation from both A-M.N and A.M.N directly and shown these to differ by a factor of 1000. Thus the results presented here support the model of Geeves et al. and are consistent with the A-M.N to A.M.N transition being coupled to the force-generating event of the crossbridge cycle.     

Determination of time-resolved fluorescence emission spectra and anisotropies of a fluorophore-protein complex using frequency-domain phase-modulation fluorometry

We report the first time-resolved fluorescence emission spectra and time-resolved fluorescence anisotropies obtained using frequency-domain fluorescence spectroscopy. We examined the fluorophore p-2-toluidinyl-6-naphthalenesulfonic acid (TNS) in viscous solvents and bound to the heme site of apomyoglobin using multifrequency phase fluorometers. Fluorescence phase shift and modulation data were obtained at modulation frequencies ranging from 1 to 200 MHz. For time-resolved emission spectra, the impulse response for the decay of intensity at each emission wavelength was obtained from the frequency response of the sample at the same emission wavelength. The decays have negative pre-exponential factors, consistent with a time-dependent spectral shift to longer wavelengths. These multiexponential decays were used to construct the time-resolved emission spectra, which were found to be in good agreement with earlier spectra obtained from time-domain measurements. Additionally, time-resolved anisotropies were obtained from the frequency-dependent phase angle differences between the parallel and perpendicularly polarized components of the emission. The rotational correlation times of TNS bound to apomyoglobin are consistent with those expected for this probe rigidly bound to the protein. TNS in propylene glycol also displayed a single exponential decay of anisotropy. These results, in conjunction with the previous successful resolution of multiexponential decays of fluorescence intensity (Lakowicz, J. R., Gratton, E., Laczko, G., Cherek, H., and Limkeman, M. (1984) Biophys. J., in press; Gratton, E., Lakowicz, J. R., Maliwal, B. P., Cherek, H., Laczko, G., and Limkeman, M. (1984) Biophys. J., in press) demonstrate that frequency-domain measurements provide information which is, at a minimum, equivalent to that obtainable from time-domain measurements.     

A hypothesis for the mechanism of sodium channel opening by batrachotoxin and related toxins

The mechanism of action of one class of sodium channel opening agents (batrachotoxinin, veratridine, aconitine and grayanotoxin) is proposed to involve complexation of a triad of agent oxygen atoms with the ε-ammonium ion of a channel lysing side chain, holding open the mouth or exit of the ion channel. This idea complements the oxygen triad model derived by structural considerations (Masutani, T., Seyama, I., Narahashi, T. and Iwasa, J. (1981) J. Pharm. Exp. Therap. 217,812) and extended by crystal structure comparisons (Codding, P.W. (1983) J. Am. Chem. Soc. 105, 3172). The mechanism is based on results for acetylcholine receptor ion channel gating, structure and function, using single group rotation (SGR) theory (cf. Kosower, E.M. (1983) Biochem. Biophys. Res. Commun. 111, 1022 and in press (1983);FEBS Lett. (1983) 155, 245; ibid. 157, 144; Biophys. J. (1983) 45, in press).     

Dissecting subsecond cadherin bound states reveals an efficient way for cells to achieve ultrafast probing of their environment

Cells continuously probe their environment with membrane receptors, achieving subsecond adaptation of their behaviour [Diez, G., Gerisch, G., Anderson, K., Müller-Taubenberger, A. and Bretschneider, T. (2006) Subsecond reorganization of the actin network in cell motility and chemotaxis. Proc. Natl. Acad. Sci. USA 102, 7601-7606, Shamri, R., Grabovsky, V., Gauguet, J.M., Feigelson, S., Manevich, E., Kolanus, W., Robinson, M.K., Staunton, D.E., von Andrian, U.H. and Alon, R. (2005) Lymphocyte arrest requires instantaneous induction of an extended LFA-1 conformation mediated by endothelium-bound chemokines. Nat. Immunol. 6, 497-606, Jiang, G., Huang, A.H., Cai, Y., Tanase, M. and Sheetz, M.P. (2006) Rigidity sensing at the leading edge through alpha(V)beta(3) integrins and RPTPalpha. Biophys. J. 90, 1804-2006]. Recently, several receptors, including cadherins, were found to bind ligands with a lifetime of order of one second. Here we show at the single molecule level that homotypic C-cadherin association involves transient intermediates lasting less than a few tens of milliseconds. Further, these intermediates transitionned towards more stable states with a kinetic rate displaying exponential decrease with piconewton forces. These features enable cells to detect ligands or measure surrounding mechanical behaviour within a fraction of a second, much more rapidly than was previously thought.     

Membrane structure and the tenuously maintained resistance to staining with N epsilon-dansyl-L-lysine shown by many cells

The ability to resist staining by N epsilon-dansyl-L-lysine is tenuously maintained in the majority of live nucleated cells taken from tissues concerned with immune function. Resistance is lost under a variety of nonphysiological conditions known to, or likely to, cause protein denaturation or aggregation. In contrast to that of dansyl-gamma-aminobutyrate, the fluorescence intensity of N epsilon-dansyl-L-lysine is only weakly enhanced by native proteins. This is further reduced on denaturation or aggregation of the proteins. It is unlikely, therefore, that cellular uptake of, and staining by, N epsilon-dansyl-L-lysine is a direct consequence of membrane protein denaturation/aggregation but may result from a decrease in protein-phospholipid interactions leading to formation of phospholipid domains. Previous work has indicated that such features are stained by N epsilon-dansyl-L-lysine (Humphries, G.M.K., Lovejoy, J.P., 1983, Biophys. J. 42:307-310; Humphries, G.M.K., Lovejoy, J.R., 1983, Biochem. Biophys. Res. Commun. 111:768-774). Although it appears likely that passage through a dansyl-lysine-staining state is a common, if not universal, prelude to cell death (as monitored by uptake of trypan blue), not all cells that lose resistance to dansyl-lysine staining are moribund. Resistance to staining is also lost by macrophages on binding to solid substrates and multivalent ligands. The possible physiological significance of this is discussed.