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Organization of actin filaments during polar body formation in eggs of Tubifex (Annelida, Oligochaeta).

Microfilaments in the Tubifex egg undergoing polar body formation can be decorated with heavy meromyosin (HMM). Since the HMM-arrowheads on filaments are dissociated by rinsing with ATP, they are identified as actin filaments. From metaphase through telophase of the second meiotic division, actin filaments are present in the cortex and in the meiotic apparatus. Consistent with the previous observations [26, 27], cortical filaments show stage-specific localization patterns. At metaphase the thick filamentous layer is localized at the animal pole, that means the region overlying the peripheral aster of the meiotic apparatus; filaments are organized in a meshwork. Upon the onset of anaphase chromosome movement, the filament meshwork mostly disappears and the remaining filaments are found to be solitary. Surrounding the animal pole region, but not extending over the animal pole, more and more filaments reappear during anaphase. As the polar body forms at the animal pole, filaments surrounding its base are organized into small bundles which are oriented randomly. By early telophase these filaments come to run circumferentially in the cortical layer (i.e. they form the contractile ring) engirding the cleavage furrow which develops at the base of the polar body. In the remaining cortex, filaments run along the surface and are oriented randomly. At all stages, adjacent filaments are often found to have opposite polarities; in favorable sections, HMM-decorated filaments appear to attach to the oolemma. The mechanism underlying the filament alignment of the contractile ring is discussed in relation to formation of the polar body.

Actins↗

Osteosarcoma cells in tissue culture. III. Actin filament distribution.

Microfilaments, especially actin, have been demonstrated in a variety of noncontractile cells. In earlier studies, the quantity as well as the distribution of these microfilaments has been used to differentiate normal murine fibroblasts from virally transformed cells. This study examines these differences in cells from spontaneously occurring, human osteosarcomas and normal human fibroblasts by transmission election microscopy and heavy meromyosin (HMM) decoration. Both the tumor cells and the normal fibroblasts were found to have subcortical bands of 7-nm microfilaments that labelled with HMM and were 150-300 nm in thickness. There was a central reticular pattern of microfilaments predominantly composed of 7-nm filaments in the fibroblasts but with a larger proportion of 10-nm filaments in the osteosarcoma cells. Arrowhead formation was present after mild Triton X-100 extraction and HMM decoration on only the 7-nm microfilaments, in both types of cells. Differences in the quantity of 10-nm filaments between cells in culture from spontaneously occurring human sarcomas and normal fibroblasts may account for differential surface responses, e.g., contact inhibition and saturation density. Unlike some evidence from viral transformation models, the data from this study do not support the hypothesis that tumorgenicity is linked mechanistically to decreases in polymerized cellular actin, at least not in cells from spontaneously occurring human sarcomas. The cellular behavior of human sarcomas, both in vitro and in vivo, may be a manifestation of differences both in structural proteins and cell surface proteins.

Actins↗

Electric potential at regions near the two specific thiols of heavy meromyosin determined by the fluorescence quenching technique. I. Effect of ATP.

Electric potentials at regions near the two specific thiol groups, SH1 and SH2, of the heavy meromyosin (HMM) molecule were studied by the fluorescence quenching technique. The effects of binding of ATP to HMM upon the electric potentials were also studied. N-(p(2-Benzimidazolyl)phenyl)maleimide (BIPM) was used as a thiol-directed fluorescent reagent. Prior to the labeling of SH2 with BIPM, the SH1 group was blocked with N-ethylmaleimide (NEM). Iodide ions (I-), thallium ions (Tl+), and acrylamide were used as quenchers of fluorescence. The sign of the electric potential was collectively determined from the dependence of the Stern-Volmer constants upon the ionic strength of solutions. 1. The region near SH1 was at a negative electric potential, whereas the electric potential at the region near SH2 was almost zero. 2. On the addition of ATP, the fluorescence intensity of BIPM bound to SH1 was unchanged, whereas that of BIPM bound to SH2 was greatly decreased to about 50% of the original level. The fluorescence intensity recovered as the added ATP was split into ADP and orthophosphate, and became saturated. The saturated level of the fluorescence intensity was, however, smaller than the original one, due to binding of the produced ADP to HMM. 3. On the addition of ATP, the negative electric potential at the region near SH1 was unchanged, whereas a negative electric potential with large gradient was newly introduced at the region near SH2. The value of the newly introduced electric potential was calculated on the basis of various assumptions. These results are discussed in connection with the functions of myosin.

Acrylamides↗

Microscopic observations on the interaction of heavy meromyosin-S-1 and actin in myofibrils.

The binding of the proteolytic myosin fragment, HMM-S-1, to the non-overlapping part of actin filaments in intact myofibrils can be demonstrated under the phase contrast microscope as a contrast reversal of striation. The same effect can be seen on ghost myofibrils (after myosin extraction) where the whole length of the I-filaments is bare. HMM-S-1-loaded ghost myofibrils contracted upon addition of ATP in agrement with the recent report of Oplatka et al. (1974a, b) but under the same conditions ghost myofibrils not treated with HMM-S-1) also contracted. If the ghosts were prepared under conditions more favourable to myosin extraction, contraction became nil or negligible even when we loaded then ghosts with S-1. Thus we attribute the effect described by Oplatka's group to a small numer of residual myosin filaments in the ghosts.

Actins↗

Investigation of the fluorescence of myosin and its fragments, heavy and light meromyosins, in concentrated solutions of neutral salts.

It is shown that when myosin and heavy (HMM) and light (LMM) meromyosins are treated with concentrated solutions of neutral salts there is change in a number of parameters of the fluorescence spectra of these proteins. For myosin and HMM this change takes place in the region of the same concentrations of LiCl, MgDl2, KSCN where there occurs dissociation of the light chains of the myosin molecule. Change in the fluorescence characteristics of myosin and HMM in the presence of these salts may be caused by two effects: change in the native conformation of the myosin molecule and dissociation of its light chains. The effect of salts on LMM fluorescence is in good agreement with general theory of the influence of concentrated salts on macromolecules.

Animals↗

Regulation of expressed truncated smooth muscle myosins. Role of the essential light chain and tail length.

Regulatory light chain (RLC) phosphorylation controls smooth muscle myosin's ability to act as a molecular motor. If thick filament-regulated myosins share a common structural basis for the "on-off" switch, then the interface between the RLC and essential light chain (ELC) should be as important in smooth muscle myosin as it is for calcium-dependent regulation in molluscan myosin (Xie, X., Harrison, D. H., Schlichting, I., Sweet, R. M., Kalabokis, V. N., Szent-Györgyi, A. G., and Cohen, C. (1994) Nature 368, 306-312). To test this hypothesis, a baculovirus expression system was used to obtain a truncated smooth muscle myosin that contained its native RLC and either smooth ELC, skeletal ELC, or no ELC. Movement of actin in a motility assay by heavy meromyosin (HMM) containing either skeletal or smooth ELC occurred at the same rate and in a phosphorylation-dependent manner. In contrast, substitution of skeletal RLC for smooth RLC produced an inactive molecule. HMM without an ELC moved actin at 25% the rate of control HMM, but the movement was phosphorylation-dependent even without an RLC/ELC interface. Poor regulation was observed, however, when the tail was truncated from 72 to 27 nm even though this species was primarily double-headed. These results suggest that the molecular changes induced at the active site by phosphorylation can occur independent of the ELC, but critically depend upon a stable coiled-coil tail that determines how the RLCs interact at the head/rod junction.

Actins↗

Formation of the stable myosin-ADP-aluminum fluoride and myosin-ADP-beryllium fluoride complexes and their analysis using 19F NMR.

The effects of aluminum fluoride and beryllium fluoride on smooth muscle myosin and its subfragments were studied. Mg(2+)-ATPase activity was inhibited in the presence of aluminum fluoride (beryllium fluoride). [3H]ADP bound to heavy meromyosin (HMM) in the presence of aluminum fluoride (beryllium fluoride) and was not dissociated after 3 days of dialysis demonstrating that [3H]ADP was trapped in HMM. These results suggest the formation of a stable HMM-ADP-fluoroaluminate (fluoroberyllate) complex. The intrinsic tryptophane fluorescence intensity was increased in the presence of ADP and aluminum fluoride (beryllium fluoride). Acto-S1 was dissociated upon the formation of S1-ADP-fluoroberyllate and actin destabilized S1-ADP-fluoroberyllate complex, while S1-ADP-fluoroaluminate failed to bind to actin. Furthermore, when S1 formed the complex with actin, nucleotide trapping did not occur in the presence of fluoraluminate. These results indicated that the myosin-ADP-fluoroberyllate complex resembles a weak binding state while myosin-ADP-fluoroaluminate complex is a distinct conformation although the binding to actin was also weak. The structure of the ternary complex was investigated using 19F NMR. The 19F NMR spectrum of the S1-ADP-fluoroaluminate complex showed a peak at -66.7 ppm which is due to the binding of fluoraluminate to S1. The peak was not observed when 5'-adenylylimidodiphosphate was substituted for ADP suggesting that aluminum fluoride plays a role as a phosphate analogue. The stoichiometry of the bound fluoride was determined to be 3.8 mol/mol S1 suggesting that the bound species is AlF-4.

Adenosine Diphosphate↗

Stereoselective metabolism of rac-mexiletine by the fungus Cunninghamella echinulata yields the major human metabolites hydroxymethylmexiletine and p-hydroxymexiletine.

rac-Mexiletine is an orally effective class 1b antiarrhythmic agent used to treat ventricular arrhythmias. In vivo experiments have demonstrated. It is predominantly metabolized by the liver with < 10% excreted as unchanged drug. The major mammalian metabolites have been identified as p-hydroxymexiletine (PHM) and hydroxymethylmexiletine (HMM). The purpose of our study was to determine whether the fungus Cunninghamella echinulata, which possesses a cytochrome P450 system analogous to that found in humans, could be used as a suitable in vitro model for studying the oxidative metabolism of rac-mexiletine. To accomplish this, a high performance liquid chromatographic assay was used that was capable of simultaneously quantifying the enantiomers of mexiletine, HMM, and PHM. Utilizing this procedure, it was demonstrated that C. echinulata stereoselectively converted rac-mexiletine into HMM (4% of added drug) and PHM (32% of added drug) after an incubation period of 50 hr. In addition, metabolite biosynthesis could be optimized by altering fermentation media components. Seven media values and seven pH values were evaluated. It was determined that a medium at pH 7.0 containing yeast extract and sucrose yielded optimal amounts of metabolites.

Anti-Arrhythmia Agents↗

Polymerization polarity of actin.

The actin polymer, like the thin filaments of muscle, is known to be polarized as demonstrated by the well known "HMM decoration" technique to give a "herringbone" pattern pointing in one direction. The question "Does polymer formation proceed unidirectionally, or bidirectionally?" was raised and tested experimentally. Short fragments of actin polymers were prepared, fully decorated with HMM and these decorated fragments were used as initiation centers for further actin polymerization without HMM. The resultant polymers showing both decorated and undecorated portions were examined and found to consist of a large majority of "spears" i.e., the added undecorated polymer extended in the direction opposite to that direction pointed by the "herringbone" pattern. However, a few cases of polymers indicating the opposite direction of polymerization were also found. Analysis leads to the conclusion that actin polymerization is unidirectional, although further experimentation is necessary to establish this completely.

Actins↗

Predicting peptides that bind to MHC molecules using supervised learning of hidden Markov models.

The binding of a major histocompatibility complex (MHC) molecule to a peptide originating in an antigen is essential to recognizing antigens in immune systems, and it has proved to be important to use computers to predict the peptides that will bind to an MHC molecule. The purpose of this paper is twofold: First, we propose to apply supervised learning of hidden Markov models (HMMs) to this problem, which can surpass existing methods for the problem of predicting MHC-binding peptides. Second, we generate peptides that have high probabilities to bind to a certain MHC molecule, based on our proposed method using peptides binding to MHC molecules as a set of training data. From our experiments, in a type of cross-validation test, the discrimination accuracy of our supervised learning method is usually approximately 2-15% better than those of other methods, including backpropagation neural networks, which have been regarded as the most effective approach to this problem. Furthermore, using an HMM trained for HLA-A2, we present new peptide sequences that are provided with high binding probabilities by the HMM and that are thus expected to bind to HLA-A2 proteins. Peptide sequences not shown in this paper but with rather high binding probabilities can be obtained from the author.

Algorithms↗

Actin-like filaments in the Sertoli cell junctional specializations in the swine and mouse testis.

Microfilaments at the junctional specializations between adjacent Sertoli cells and between the Sertoli cell and the late spermatid of the mouse and swine testes bind HMM and form arrowhead complexes with a periodicity of about 35 nm. The arrowhead formation is inhibited when the tissues are treated with HMM in the presence of ATP. These observations show that the microfilaments are actin-like in nature. The functional significance of these filaments in the Sertoli cell is discussed.

Actins↗

The identification and localization of actin and actin-like filaments in lactating guinea pig mammary gland alveolar cells.

Cytochalasin B, a microfilament-altering drug, inhibits lactose synthesis in lactating guinea pig mammary gland [Biochim. Biophys. Acta 392:20, 1975] but not primary by inhibiting glucose transport [Eur. J. Cell Biol. 20:150, 1979]. In order to study the possible role of microfilaments in lactose synthesis and secretion, we isolated both the alveolar (milk-secreting) and myoepithelial (contractile) cells from lactating mammary gland. Light microscopy shows that the alveolar cell fraction (viability approximately 71%) is homogenous and that the cells retain strong polarity of secretory structures in the apical region. Two proteins were extracted from the alveolar cell fraction. One (mol wt 42,000) comigrates with skeletal muscle actin on SDS-PAGE gels. The other, a high-molecular-weight (180,000) protein (HMWP) may be analogous to actin-binding protein or clathrin. An extract from the myoepithelial cell fraction also contains a protein that comigrates with actin but no HMWP. Whole tissue extract contains the 42K protein, and a 185K HMWP. Examination of the alveolar cell extract by electron microscopic (EM) negative staining revealed meshworks of multistranded, interconnecting filaments, with attached globular structures (100-200 A) (possibly the HMWP) and single filaments (40-60 A diameter) branching off. To localize these filamentous structures in situ, whole tissue was glycerinated and incubated with rabbit skeletal muscle heavy meromyosin (HMM). Masses of filaments in myoepithelial cells served as convenient standards for HMM decoration. Decorated filaments have cross-arms or projections, unlike the narrow, smooth filaments of control tissue. Decorated filaments in alveolar cells are located beneath the plasma membrane, in close association with secretory vacuoles, and near the Golgi apparatus; filaments near the latter two are often oriented perpendicular to the plasma membrane. Microvesicles are embedded in meshworks under the plasmalemma and near the Golgi apparatus. Intermediate-sized (85-115 A diameter), non-decorated filaments diverge from the meshworks of decorated filaments. Micro-vesicles are associated with intermediate-sized filaments as well. The association of actin-like filaments with secretory vacuoles and microvesicles and their location in areas of the cell concerned with biosynthetic activities suggest a possible function in the intracellular transport of secretory products.

Actins↗

Electron paramagnetic resonance and nanosecond fluorescence depolarization studies on creatine-phosphokinase interaction with myosin and its fragments.

Recent reports in the literature have indicated a physical association of creatine-phosphokinase (CPK) with the tail portion of the myosin molecule. The present paper describes further studies on the interaction of CPK with myosin and myosin fragments, using the techniques of electron paramagnetic resonance (EPR) and nanosecond fluorescence depolarization. From EPR work, spin-labeled CPK appears to interact with myosin, tail-less myosin (heavy meromyosin [HMM]), and myosin heads (subfragment-1 [S1]), the extent of interaction being proportional to the S1 content of myosin or its fragments. Spin-labeled CPK did not evidence interaction with the headless myosin "rods," with myosin tails (light meromyosin [LMM]), with S2 necks (which connect S1 to the rest of the myosin molecule), or with actin. When a fluorescent dye is directed to the essential epsilon-amino group of CPK, nanosecond fluorescence depolarization studies indicate a substantial interaction with myosin, HMM, and S1, but very little with F-actin. When the "fast-reacting" thiol of the S1 moiety or the "essential thiol" of CPK was labeled with either a fluorescent dye or a spin label, no interaction between CPK and myosin (or S1) was detected.

Actins↗

Does myosin-substrate interaction in vitro result in a delocalized conformation change?

The effect of substrate on the far UV (185-250 nm) and near UV (250-325 nm) circular dichroism (CD) of myosin and heavy meromyosin (HMM) was studied. The following results were obtained with the addition of ATP (during various conditions of hydrolysis), ADP, and pyrophosphate: (1) no changes were observed in the far UV CD, (2) ATP and ADP perturbed the near UV CD only at spectral regions below 280 nm coinciding with the regions of their optical activity, (3) the optically inactive pyrophosphate caused no change in the near UV CD, and (4) myosin and HMM gave exactly the same results. These results suggest that myosin-substrate interaction in vitro does not result in a delocalized conformational change.

Adenosine Diphosphate↗

Vascularization of cutaneous melanoma involves vessel co-option and has clinical significance.

This study was undertaken to determine the role and the fate of the peritumoural vascular plexus during the vascularization of human malignant melanoma (hMM) and in an appropriate murine melanoma model system. The prognostic significance of the vascularity of different tumour areas was also evaluated. Despite morphometry revealing several-fold higher microvessel densities (MVDs) in the peritumoural tissue than at the centre of the tumour, the development of visceral metastases of hMM was exclusively correlated with the MVD of the tumour centre. Furthermore, the 5-year survival of the patient group with low tumour centre MVD (<30/mm(2), n=29) was 100%, compared to 1/16 patients alive with high tumour centre MVD (>30/mm(2), n=16). Morphometric analysis and three-dimensional reconstruction of vessel networks of both human and murine melanomas showed clearly that the peritumoural vascular plexus present at the melanoma base is continuously being incorporated into the growing tumour mass. Once vessels become incorporated, sprouting ceases and the proliferating endothelial cells (EC) take part only in vessel dilatation. Moreover, the immunohistochemical and ultrastructural characterization of microvessels demonstrated that the pericyte coverage of endothelial tubes was complete in all of the investigated areas, in both human and murine melanomas.

Analysis of Variance↗

Protein classification based on text document classification techniques.

The need for accurate, automated protein classification methods continues to increase as advances in biotechnology uncover new proteins. G-protein coupled receptors (GPCRs) are a particularly difficult superfamily of proteins to classify due to extreme diversity among its members. Previous comparisons of BLAST, k-nearest neighbor (k-NN), hidden markov model (HMM) and support vector machine (SVM) using alignment-based features have suggested that classifiers at the complexity of SVM are needed to attain high accuracy. Here, analogous to document classification, we applied Decision Tree and Naive Bayes classifiers with chi-square feature selection on counts of n-grams (i.e. short peptide sequences of length n) to this classification task. Using the GPCR dataset and evaluation protocol from the previous study, the Naive Bayes classifier attained an accuracy of 93.0 and 92.4% in level I and level II subfamily classification respectively, while SVM has a reported accuracy of 88.4 and 86.3%. This is a 39.7 and 44.5% reduction in residual error for level I and level II subfamily classification, respectively. The Decision Tree, while inferior to SVM, outperforms HMM in both level I and level II subfamily classification. For those GPCR families whose profiles are stored in the Protein FAMilies database of alignments and HMMs (PFAM), our method performs comparably to a search against those profiles. Finally, our method can be generalized to other protein families by applying it to the superfamily of nuclear receptors with 94.5, 97.8 and 93.6% accuracy in family, level I and level II subfamily classification respectively.

Algorithms↗

Cellular localization of high-molecular-mass heat shock proteins in murine cells.

We have previously prepared an antiserum raised against hsp105 of murine FM3A cells. The anti-hsp105 serum reacted to two isoforms of high-molecular-mass heat shock protein (HMM-HSP) having a molecular mass of 105,000 Da (hsp105A and hsp105B) in FM3A cells. While hsp105A and hsp105B were both synthesized and accumulated under non-stressed conditions, upon exposure to heat shock much more hsp105B was induced than hsp105A. When the cellular distribution of these hsp105s in murine 3T3 Swiss albino and C3H 10T1/2 cells was examined by immunofluorescence methods using the anti-hsp105 serum, the HMM-HSPs were localized in the cytoplasm and nuclei and were never found in the nucleoli of both 3T3 and C3H cells under non-stressed and stressed conditions.

3T3 Cells↗

Sequence, structural, functional, and phylogenetic analyses of three glycosidase families.

Glycosidases, which cleave the glycosidic bond between a carbohydrate and another moiety, have been classified into over 63 families. Here, a variety of computational techniques have been employed to examine three families important in normal and abnormal pathology with the aim of developing a framework for future homology modeling, experimental and other studies. Family 1 includes bacterial and archaeal enzymes as well as lactase phlorizin-hydrolase and klotho, glycosidases implicated in disaccharide intolerance II and aging respectively. A statistical model, a hidden Markov model (HMM), for the family 1 glycosidase domain was trained and used as the basis for comparative examination of the conserved and variable sequence and structural features as well as the phylogenetic relationships between family members. Although the structures of four family 1 glycosidases have been determined, this is the first comparative examination of all these enzymes. Aspects that are unique to specific members or subfamilies (substrate binding loops) as well those common to all members (a beta/alpha)8 barrel fold) have been defined. Active site residues in some domains in klotho and lactase-phlorizin hydrolases differ from other members and in one instance may bind but not cleave substrate. The four invariant and most highly conserved residues are not residues implicated in catalysis and/or substrate binding. Of these, a histidine may be involved in transition state stabilization. Glucosylceramidase (family 30) and galactosylceramidase (family 59) are mutated in the lysosomal storage disorders Gaucher disease and Krabbe disease, respectively. HMM-based analysis, structure prediction studies and examination of disease mutations reveal a glycosidase domain common to these two families that also occurs in some bacterial glycosidases. Similarities in the reactions catalyzed by families 30 and 59 are reflected in the presence of a structurally and functionally related (beta/alpha)8 barrel fold related to that in family 1.

Amino Acid Sequence↗