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PubMed1977

Affinity chromatography of myosin, heavy meromyosin, and heavy meromyosin subfragment one on F-actin columns stabilized by phalloidin.

A method of affinity chromatography based on the trapping of actin filaments within agarose gel beads is described. This method can be used for the purification of myosin and its active proteolytic subfragments, as well as for studies on the interaction between actin and these proteins. Actin columns stabilized by phalloidin bind myosin, heavy meromyosin (HMM), and heavy meromyosin subfragment 1 (HMM-S1) specifically and reversibly. The effect of pyrophosphate and KCl on the dissociation of actomyosin, acto-HMM, or acto-HMM-S1 complex is reported. We also describe the single-step purification of myosin from a crude rabbit psoas muscle extract.

Actins↗

PubMedDate not supplied

Coexistence of two biochemically distinct phospholipase A2 activities in human platelet, monocyte, and neutrophil.

The cell-associated phospholipase A2 (PLA2) activities of the human platelet, neutrophil, and monocyte were simultaneously characterized, utilizing the biochemical differences observed between the 14 kDa (kilodalton), type II PLA2 isolated from inflammatory human synovial joint fluid (HSF) and the arachidonic acid (AA) specific, 85-kDa high molecular mass (HMM) PLA2 isolated from the cytosol of a U937 monocytic cell line. The HSF PLA2 can be distinguished from the HMM PLA2 by its resistance to acid treatment, sensitivity to a sulfhydryl reducing agent, lack of preference for the fatty acid on the sn-2 position of phospholipid substrate, and inhibition by the C-7 phosphonate-phospholipid transition-state PLA2 inhibitor. Evaluation of all three cell types revealed that HMM-like PLA2 activity was found predominantly in the cytosolic fractions, although detection in neutrophil cytosol required more concentrated preparations and the use of high specific activity [3H]AA-labeled Escherichia coli. HSP-PLA2-like activity was measured in microsomal and cytosolic fractions of all three cell types, but was found in neutrophil cytosol only after treatment with acid. Further HMM-PLA2-specific interfering agents in neutrophil cytosol were observed and exemplifies one problem in assigning the existence of this enzyme in crude broken cell preparations using activity measurements alone. The role that these two enzymes play in eicosanoid production of the respective cell types remains to be studied.

Arachidonic Acid↗

PubMed1980

Fluorescent staining of microfilaments with heavy meromyosin labeled with N-(7-dimethylamino-4-methylcoumarinyl) maleimide.

For fluorescent staining of microfilaments in cells, heavy meromyosin (HMM) or subfragment-1 (S-1) was labeled with a novel thiol-directed fluorescent dye, N-(7-dimethylamino-4-methylcoumarinyl) maleimide (DACM), instead of the usual dyes, such as fluorescein-isothiocyanate (FITC). DACM-labeled HMM or S-1 gave characteristic fluorescence patterns to a variety of cell types similar to those reported with the use of FITC-labeled HMM or S-1 or with immunofluorescence techniques using anti-actin antibody. The fluorescence of DACM was fairly photoresistant as compared with FITC, so that HMM or S-1 required only 1 mol of the dye per myosin head. Consequently, F-actin need not be used to preserve the actin binding activity of the myosin fragments when labeling with the dye.

Animals↗

PubMed2002

Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model approach.

BACKGROUND: Most profile and motif databases strive to classify protein sequences into a broad spectrum of protein families. The next step of such database studies should include the development of classification systems capable of distinguishing between subfamilies within a structurally and functionally diverse superfamily. This would be helpful in elucidating sequence-structure-function relationships of proteins. RESULTS: Here, we present a method to diagnose sequences into subfamilies by employing hidden Markov models (HMMs) to find windows of residues that are distinct among subfamilies (called signatures). The method starts with a multiple sequence alignment (MSA) of the subfamily. Then, we build a HMM database representing all sliding windows of the MSA of a fixed size. Finally, we construct a HMM histogram of the matches of each sliding window in the entire superfamily. To illustrate the efficacy of the method, we have applied the analysis to find subfamily signatures in two well-studied superfamilies: the cadherin and the EF-hand protein superfamilies. As a corollary, the HMM histograms of the analyzed subfamilies revealed information about their Ca2+ binding sites and loops. CONCLUSIONS: The method is used to create HMM databases to diagnose subfamilies of protein superfamilies that complement broad profile and motif databases such as BLOCKS, PROSITE, Pfam, SMART, PRINTS and InterPro.

Binding Sites↗

PubMed2006

Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.

BACKGROUND: Horizontal gene transfer (HGT) is considered a strong evolutionary force shaping the content of microbial genomes in a substantial manner. It is the difference in speed enabling the rapid adaptation to changing environmental demands that distinguishes HGT from gene genesis, duplications or mutations. For a precise characterization, algorithms are needed that identify transfer events with high reliability. Frequently, the transferred pieces of DNA have a considerable length, comprise several genes and are called genomic islands (GIs) or more specifically pathogenicity or symbiotic islands. RESULTS: We have implemented the program SIGI-HMM that predicts GIs and the putative donor of each individual alien gene. It is based on the analysis of codon usage (CU) of each individual gene of a genome under study. CU of each gene is compared against a carefully selected set of CU tables representing microbial donors or highly expressed genes. Multiple tests are used to identify putatively alien genes, to predict putative donors and to mask putatively highly expressed genes. Thus, we determine the states and emission probabilities of an inhomogeneous hidden Markov model working on gene level. For the transition probabilities, we draw upon classical test theory with the intention of integrating a sensitivity controller in a consistent manner. SIGI-HMM was written in JAVA and is publicly available. It accepts as input any file created according to the EMBL-format.It generates output in the common GFF format readable for genome browsers. Benchmark tests showed that the output of SIGI-HMM is in agreement with known findings. Its predictions were both consistent with annotated GIs and with predictions generated by different methods. CONCLUSION: SIGI-HMM is a sensitive tool for the identification of GIs in microbial genomes. It allows to interactively analyze genomes in detail and to generate or to test hypotheses about the origin of acquired genes.

Algorithms↗

PubMed2006

Hidden Markov model variants and their application.

Markov statistical methods may make it possible to develop an unsupervised learning process that can automatically identify genomic structure in prokaryotes in a comprehensive way. This approach is based on mutual information, probabilistic measures, hidden Markov models, and other purely statistical inputs. This approach also provides a uniquely common ground for comparative prokaryotic genomics. The approach is an on-going effort by its nature, as a multi-pass learning process, where each round is more informed than the last, and thereby allows a shift to the more powerful methods available for supervised learning at each iteration. It is envisaged that this "bootstrap" learning process will also be useful as a knowledge discovery tool. For such an ab initio prokaryotic gene-finder to work, however, it needs a mechanism to identify critical motif structure, such as those around the start of coding or start of transcription (and then, hopefully more).For eukaryotes, even with better start-of-coding identification, parsing of eukaryotic coding regions by the HMM is still limited by the HMM's single gene assumption, as evidenced by the poor performance in alternatively spliced regions. To address these complications an approach is described to expand the states in a eukaryotic gene-predictor HMM, to operate with two layers of DNA parsing. This extension from the single layer gene prediction parse is indicated after preliminary analysis of the C. elegans alt-splice statistics. State profiles have made use of a novel hash-interpolating MM (hIMM) method. A new implementation for an HMM-with-Duration is also described, with far-reaching application to gene-structure identification and analysis of channel current blockade data.

Alternative Splicing↗

PubMed2005

Orientation of the myosin light chain region by single molecule total internal reflection fluorescence polarization microscopy.

To study the orientation and dynamics of myosin, we measured fluorescence polarization of single molecules and ensembles of myosin decorating actin filaments. Engineered chicken gizzard regulatory light chain (RLC), labeled with bisiodoacetamidorhodamine at cysteine residues 100 and 108 or 104 and 115, was exchanged for endogenous RLC in rabbit skeletal muscle HMM or S1. AEDANS-labeled actin, fully decorated with labeled myosin fragment or a ratio of approximately 1:1000 labeled:unlabeled myosin fragment, was adhered to a quartz slide. Eight polarized fluorescence intensities were combined with the actin orientation from the AEDANS fluorescence to determine the axial angle (relative to actin), the azimuthal angle (around actin), and RLC mobility on the <<10 ms timescale. Order parameters of the orientation distributions from heavily labeled filaments agree well with comparable measurements in muscle fibers, verifying the technique. Experiments with HMM provide sufficient angular resolution to detect two orientations corresponding to the two heads in rigor. Experiments with S1 show a single orientation intermediate to the two seen for HMM. The angles measured for HMM are consistent with heads bound on adjacent actin monomers of a filament, under strain, similar to predictions based on ensemble measurements made on muscle fibers with electron microscopy and spectroscopic experiments.

Actins↗

PubMed2001

Objective laparoscopic skills assessments of surgical residents using Hidden Markov Models based on haptic information and tool/tissue interactions.

UNLABELLED: Laparoscopic surgical skills evaluation of surgery residents is usually a subjective process, carried out in the operating room by senior surgeons. By its nature, this process is performed using fuzzy criteria. The objective of the current study was to develop and assess an objective laparoscopic surgical skill scale using Hidden Markov Models (HMM) based on haptic information, tool/tissue interactions and visual task decomposition. METHODS: Eight subjects (six surgical trainees: first year surgical residents 2 x R1, third year surgical residents 2 x R3 fifth year surgical residents 2 x R5; and two expert laparoscopic surgeons: 2 x ES) performed laparoscopic cholecystectomy following a specific 7 steps protocol on a pig. An instrumented laparoscopic grasper equipped with a three-axis force/torque sensor located at the proximal end with an additional force sensor located on the handle, was used to measure the forces and torques. The hand/tool interface force/torque data was synchronized with a video of the tool operative maneuvers. A synthesis of frame-by-frame video analysis was used to define 14 different types of tool/tissue interactions, each one associated with unique force/torque (F/T) signatures. HMMs were developed for each subject representing the surgical skills by defining the various tool/tissue interactions as states and the associated F/T signatures as observations. The statistical distance between the HMMs representing residents at different levels of their training and the HMMs of expert surgeons were calculated in order to generate a learning curve of selected steps during laparoscopic cholecystectomy. RESULTS: Comparison of HMM's between groups showed significant differences between all skill levels, supporting the objective definition of a learning curve. The major differences between skill levels were: (i) magnitudes of F/T applied (ii) types of tool/tissue interactions used and the transition between them and (iii) time intervals spent in each tool/tissue interaction and the overall completion time. The objective HMM analysis showed that the greatest difference in performance was between R1 and R3 groups and then decreased as the level of expertise increased, suggesting that significant laparoscopic surgical capability develops between the first and the third years of their residency training. The power of the methodology using HMM for objective surgical skill assessment arises from the fact that it compiles enormous amount of data regarding different aspects of surgical skill into a very compact model that can be translated into a single number representing the distance from expert performance. Moreover, the methodology is not limited to in-vivo condition as demonstrated in the current study. It can be extended to other modalities such as measuring performance in surgical simulators and robotic systems.

Animals↗

PubMed1979

Disposition and metabolism of pentamethylmelamine and hexamethylmelamine in rabbits and humans.

The disposition and metabolism of pentamethylmelamine (PMM) and hexamethylmelamine (HMM) were studied in the rabbit, and the disposition of PMM was studied in humans. Parent compound and metabolites were identified by thin-layer chromatography, gas chromatography, and gas chromatography/mass spectrometry analyses. Plasma elimination in both species following i.v. administration of each drug was best described by a two-compartment open model. Both compounds were extensively demethylated with less than 1% of the total dose administered recovered in the urine over 24 hr. The areas under the plasma time-concentration curves of PMM and HMM following p.o. administration to rabbits were 5 and 25% of the areas following i.v. administration. Gastrointestinal absorption was rapid and efficient with 75 to 89% of drug equivalents recoverable in the urine after p.o. administration of [ring-14C]PMM or [ring-14C]HMM to rabbits. Reduced bioavailability of PMM and HMM p.o. appears to be a consequence of rapid metabolism presumably in the liver.

Altretamine↗

PubMed2002

[Hidden Markov model used in protein sequence analysis].

Hidden Markov model (HMM) used in the research of protein is a new field of bioinformatics. Nowadays large amount of data about protein sequences and structures have been obtained. Traditional methods of protein analysis are no longer used. Biologists have updated their research methods with computer technology and statistics, which can deal with large amount of data. HMM can be used to distinguish protein sequence with the same characteristics. A family of protein from SCOP database was selected, through which a HMM model representing the family was obtained, and then the model was utilized to analyze protein sequences. Results indicate that HMM can express particular family of protein, and recognize the given protein sequences of the family from many sequences.

Algorithms↗

PubMed2001

Development of molecular monitoring methods for the evaluation of the activity of sulfate- and metal reducing bacteria (SMRBS) as an indication of the in situ immobilisation of heavy metals and metalloids.

Sulfate- and metal reducing bacteria (SMRBs) are known for their capacity to reduce and precipitate heavy metals and metalloids (HMM) as metalsulfides (Luptáková A et al, 1998), which have the characteristic of forming stable precipitates due to their very low solubility product. Therefore, we examined the potential of using the activity of SMRBs to create a bioreactive zone or barrier for the in situ precepitation of heavy metals as a remediation strategy for heavy metal contaminated groundwater. In order to obtain insight in the ongoing biological processes for using this information to direct or optimize the in situ HMM- precipitation process, a monitoring strategy for sulfate- reduction activity of SMRBs must be designed using molecular methods. Here, we report the results of batch and column experiments which demonstrate the feasibility to stimulate the endogenous SRB- population, resulting in the in situ precipitation of HMM as sulfide complexes. Moreover, the sustainability of the in situ HMM precipitation wa s shown. For the development of molecular monitoring methods, the community structures of different bacterial consortia, obtained from bioreactors, was analysed by shotgun cloning of total community DNA followed by sequencing of the 16S rRNA- gene. The SRB- specific 16S rRNA- primerset SRB385R- 907F was used but this specificity to specifically amplify the 16S rRNA- gene of SRBs was low. Also, the dsr (dissimilatory sulfite reductase)- gene specific DSR1F- DSR4R primerset showed sometimes after amplification of the dsr- genes as part of the community structure analysis satellite bands on agarose gel. Present work is concentrating on the isolation and identification of SRB- strains in the different bacterial cultures. Shotgun cloning of the 16S rRNA- and dsr- gene of the strains and total community DNA will give the information that is necessary for the optimization of existing SRB- specific primers and design of new primers. These primers will be used for the development of monitoring techniques.

Alkaloids↗

PubMed1979

Interaction of actin with myosin A and heavy meromyosin.

Ca2+ "free" actomyosin suspensions as well as actin heavy meromyosin (HMM) solutions in the presence of Ca2+ showed no contractile response (superprecipitation) and had low steady-state Mg2+-ATPase activity. Under the same experimental conditions both the enzymatic activity increased and contractile response was restored if the solubility of the proteins was depressed by the addition of polyethylene glycol 4000 (PEG-4000). The stability of the enzymatically active actomyosin or actin HMM complexes was 10 times lower in cleared solutions than in the insoluble actomyosin or actin HMM suspensions. It was concluded that soluble actomyosin or actin HMM solutions are inadequate test tube models for studying muscular contraction.

Adenosine Triphosphatases↗

PubMed1991

The mechanism of ATP hydrolysis by smooth muscle myosin and subfragments using steady state titration and 18O exchange.

The mechanisms of increases in the ATPase rates of smooth muscle acto-myosin, acto-heavy meromyosin (HMM) and acto-subfragment 1 (S1) were investigated using steady state titration and 18O exchange. Phosphorylation increased the phosphate release rates both from acto-myosin and acto-HMM. Steady state titration at high enzyme concentrations and 18O exchange at substoichiometric ATP concentrations showed that gizzard myosin was kinetically homogeneous, whereas HMM and S1 prepared by various published methods were heterogeneous. At high ATP concentrations, a small population of HMM and S1 hydrolyzed ATP with a low amount of oxygen exchange.

Adenosine Triphosphate↗

PubMed1989

Coupling of the enzymic activities of myosin ATPase and creatine kinase and its role in muscular contraction.

During muscular contraction the regeneration of ATP, catalysed by creatine kinase (CK), keeps pace with the hydrolysis of ATP by myosin ATPase posing the question of its regulatory mechanism. In the background of F-actin activation of heavy meromyosin (HMM) ATPase activity we have investigated in vitro the role of F-actin in regulating CK's activity in the absence and presence of HMM. For the coupled enzyme system we have also looked into the roles played by the individual reactants. F-actin has been found to appreciably increase CK's activity in the absence of HMM. While HMM alone inhibited CK's activity, there was a several fold increase when F-actin was also present. By a process of elimination we conclude that none of the reactants apart from H+ could be involved in regulating CK's activity in the coupled enzyme system. As no change in the pH of reaction mixture was observed during the reaction, we further conclude that the two enzymic reactions are coupled by proton transfer along F-actin. Implications of the findings for PCr-Cr shuttle and movements of ATP and ADP in sarcomere are discussed.

Actins↗

PubMed1988

Effect of caldesmon on the ATPase activity and the binding of smooth and skeletal myosin subfragments to actin.

We have previously shown that inhibition of the ATPase activity of skeletal muscle myosin subfragment 1 (S1) by caldesmon is correlated with the inhibition of S1 binding in the presence of ATP or pyrophosphate (Chalovich, J., Cornelius, P., and Benson, C. (1987) J. Biol Chem. 262, 5711-5716). In contrast, Lash et al. (Lash, J., Sellers, J., and Hathaway, D. (1986) J. Biol. Chem. 261, 16155-16160) have shown that the inhibition of ATPase activity of smooth muscle heavy meromyosin (HMM) by caldesmon is correlated with an increase in the binding of HMM to actin in the presence of ATP. We now show, in agreement, that caldesmon does increase the binding of smooth muscle HMM to actin-tropomyosin while decreasing the ATPase activity. The effect of caldesmon on the binding of smooth HMM is reversed by Ca2+-calmodulin. Caldesmon strengthens the binding of smooth S1.ATP and skeletal HMM.ATP to actin-tropomyosin but to a lesser extent than smooth HMM.ATP. Furthermore, this increase in binding of smooth S1.ATP and skeletal HMM.ATP does not parallel the inhibition of ATPase activity. In contrast, in the absence of ATP, all smooth and skeletal myosin subfragments compete with caldesmon for binding to actin. Thus, the effect that caldesmon has on the binding of myosin subfragments to actin-tropomyosin depends on the source of myosin, the type of subfragment, and the nucleotide present. The inhibition of actin-activated ATP hydrolysis by caldesmon, however, is not greatly different for different smooth and skeletal myosin subfragments. Evidence is presented that caldesmon inhibits actin-activated ATP hydrolysis by attenuating the productive interaction between myosin and actin that normally accelerates ATP hydrolysis. The increased binding seen by some myosin subfragments, in the presence of ATP, may be due to binding of these subfragments to a nonproductive site on actin-caldesmon. The subfragments which show an increase in binding in the presence of ATP and caldesmon appear to bind directly to caldesmon as demonstrated by affinity chromatography.

Actins↗

PubMed1988

Two pathways for oxygen exchange by heavy meromyosin and their dependence on actin.

In the hydrolysis of MgATP by acto heavy meromyosin (HMM) there are two enzymatic pathways that differ in the properties of their intermediate oxygen exchange; one of these is designated the low exchange pathway (P1); the other is designated the high exchange pathway (P2). A plot of the P1 flux versus the actin concentration gives a sigmoid curve, whereas the corresponding curve for the P2 flux rises in an approximately hyperbolic manner. At low concentrations of actin, where the sigmoid curve of the P1 flux is in a lag phase, the major flux is along P2; but at higher concentrations of actin, as the P1 curve rises sharply, the flux along P1 comes to predominate. Even at the highest levels of actin, at saturating levels for both pathways, the kinetics of exchange along P1 and P2 are significantly different. In addition to these differences in the actin dependence, the flux of P1 relative to P2 is markedly inhibited by KCl. Therefore, which of the two pathways dominates during the hydrolysis of MgATP by HMM is strongly dependent on experimental conditions. The findings suggest that P1 involves the interaction of HMM with two actin units whereas P2 involves the interaction of HMM with one actin unit. The results are discussed in relation to a kinetic scheme based on this proposal.

Actins↗

PubMed1986

Effect of phenobarbital pretreatment on the metabolism and antitumor activity of hexamethylmelamine.

The effect of phenobarbital (PB) pretreatment on the N-demethylation and antitumor activity of hexamethylmelamine (HMM) was investigated in mice. In mice pretreated with PB, the levels of HMM in plasma, liver, and M5076 tumor were much lower than in mice treated with HMM alone. Plasma area under the curve (AUC) values were 15 +/- 4 versus 37 +/- 28 micrograms/ml X min, liver AUC values were 43 +/- 13 versus 246 +/- 5 micrograms/g X min, and tumor AUC values were 37 +/- 14 versus 109 +/- 24 micrograms/g X min. All of the N-demethylated metabolites except N2N4 dimethylmelamine in plasma, liver, and tumor also reached much lower levels in mice pretreated with PB. The antitumor activity of HMM was significantly antagonized by PB treatment in both M5076 reticular cell sarcoma and PC6 plasmocytoma of the mouse.

Altretamine↗

PubMed1986

Role of hexamethylmelamine in the treatment of ovarian cancer: where is the needle in the haystack?

Hexamethylmelamine (HMM) was selected for development as an antineoplastic agent because it demonstrated activity in a variety of preclinical tumor models. Its mechanism of action is unknown. It has been used in clinical trials since 1964. The clinical toxic effects have consisted of signs and symptoms involving the following systems: gastrointestinal (nausea, vomiting, anorexia), hematologic (leukopenia, mild anemia), and neurologic (critical depression, hallucinations, peripheral motor and sensory deficits). Antitumor activity against advanced ovarian cancer was demonstrated in phase I trials and the drug was quickly incorporated into trials which utilized drug combinations. The majority of these have consisted of phase II trials without an identified control population. As might be predicted, all of the HMM-containing combinations are active. However, the contribution of HMM to the antitumor activity of the combination remains conjectural. Thus, in spite of greater than 15 years of clinical trials with a drug that has single-agent activity, the questions regarding the role of HMM in the treatment of ovarian cancer remain unanswered.

Altretamine↗