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Query: UNIPROT:P06889 (Mol)
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The conformations of known tryptic limited proteolytic sites have been analysed and compared to the structures of the binding regions of serine proteinase inhibitors, as they are found when complexed to a serine proteinase. Conformational parameters studied include main-chain torsion angles, root-mean-square fits, accessibility, mobility and protrusion indices. As observed before, the inhibitors share a common main-chain conformation at the binding loop from P3-P'3 (Schechter & Berger notation), which is maintained throughout all the serine proteinase inhibitor families for which X-ray data is available, despite lack of similarity in the rest of the protein. This canonical structure is not found amongst the limited proteolytic sites (or nicksites), which differ markedly from the inhibitor binding loop conformation, and also amongst themselves. The experimentally determined nicksites are in general both accessible and protruding; as are the inhibitor binding loops, as well as being typically flexible regions of structure, as denoted by elevated temperature factors from crystallographic determinations. For cleavage by serine proteinases these loops must radically alter their local conformations and a large motion of the loop relative to the structure, in some cases, would be required to orientate these sites for cleavage.
J Mol Biol 1991 Jul 20
PMID:Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors. 185 71

A diverse array of cellular and evolutionary forces--including unequal crossing-over, magnification, compensation, and natural selection--is at play modulating the number of copies of ribosomal RNA (rRNA) genes on the X and Y chromosomes of Drosophila. Accurate estimates of naturally occurring distributions of copy numbers on both the X and Y chromosomes are needed in order to explore the evolutionary end result of these forces. Estimates of relative copy numbers of the ribosomal DNA repeat, as well as of the type I and type II inserts, were obtained for a series of 96 X chromosomes and 144 Y chromosomes by using densitometric measurements of slot blots of genomic DNA from adult D. melanogaster bearing appropriate deficiencies that reveal chromosome-specific copy numbers. Estimates of copy number were put on an absolute scale with slot blots having serial dilutions both of the repeat and of genomic DNA from nonpolytene larval brain and imaginal discs. The distributions of rRNA copy number are decidedly skewed, with a long tail toward higher copy numbers. These distributions were fitted by a population genetic model that posits three different types of exchange events--sister-chromatid exchange, intrachromatid exchange, and interchromosomal crossing-over. In addition, the model incorporates natural selection, because experimental evidence shows that there is a minimum number of functional elements necessary for survival. Adequate fits of the model were found, indicating that either natural selection also eliminates chromosomes with high copy number or that the rate of intrachromatid exchange exceeds the rate of interchromosomal exchange.
Mol Biol Evol 1991 Jul
PMID:Evolution of ribosomal RNA gene copy number on the sex chromosomes of Drosophila melanogaster. 192 6

The pentameric 71-domain structure of human and mouse immunoglobulin M (IgM) was investigated by synchrotron X-ray solution scattering and molecular graphics modelling. The radii of gyration RG of human IgM Quaife and its Fc5, IgM-S, Fab'2 and Fab fragments were determined as 12.2 nm, 6.1 nm, 6.1 nm, 4.9 nm and 2.9 nm in that order. The RG values were similar for mouse IgM P8 and its Fab'2 and Fab fragments, despite the presence of an additional carbohydrate site. The IgM scattering curves, to a nominal resolution of 5 nm, were compared with molecular graphics models based on published crystallographic alpha-carbon co-ordinates for the Fab and Fc structures of IgG. Good curve fits for Fab were obtained based on the crystal structure of Fab from IgG. A good curve fit was obtained for Fab'2, if the two Fab arms were positioned close together at their contact with the C mu 2 domains. The addition of the Fc fragment close to the C mu 2 domains of this Fab'2 model, to give a planar structure, accounted for the scattering curve of IgM-S. The Fc5 fragment was best modelled by a ring of five Fc monomers, constrained by packing considerations and disulphide bridge formation. A position for the J chain between two C mu 4 domains rather than at the centre of Fc5 was preferred. The intact IgM structure was best modelled using a planar arrangement of these Fab'2 and Fc5 models, with the side-to-side displacement of the Fab'2 arms in the plane of the IgM structure. All these models were consistent with hydrodynamic simulations of sedimentation data. The solution structure of IgM can therefore be reproduced quantitatively in terms of crystallographic structures for the fragments of IgG. Putative Clq binding sites have been identified on the C mu 3 domain. These would become accessible for interaction with Clq when the Fab'2 arms move out of the plane of the Fc5 disc in IgM, that is, a steric mechanism exposing pre-existing Clq sites. Comparison with a solution structure for Clq by neutron scattering shows that two or more of the six globular Clq heads in the hexameric head-and-stalk structure are readily able to make contacts with the putative Clq sites in the C mu 3 domains of free IgM if if the Clq arm-axis angle in solution is reduced from 40 degrees-45 degrees to 28 degrees. This could be the trigger for Cl activation.
J Mol Biol 1991 Oct 20
PMID:Solution structure of human and mouse immunoglobulin M by synchrotron X-ray scattering and molecular graphics modelling. A possible mechanism for complement activation. 194 55

Continuation of early evolutionary bonding between tRNAs would provide a solution to residence time problems between peptidyl-tRNA and mRNA. It could also improve the speed of peptide bond formation by holding the amino acid close to the growing peptide. The tRNA clover leaf structure would allow each tRNA to form a T psi C(GA)-loop bond to one side and a D-loop bond to the other, hence fixing itself within a group of tRNAs, all attached to the mRNA. This can be developed into a system for peptide elongation in which bonds are made and broken in an ordered sequence, with each step triggering the next. This leads to a model system that fits with some recent proposals for a three-site ribosome.
J Mol Evol 1991 Nov
PMID:The use of bonding between tRNAs to implement early peptide synthesis. 196 Jul 43

To isolate peroxisomes from Saccharomyces cerevisiae of a quality sufficient for in vitro import studies, we optimized the conditions for cell growth and for cell fractionation. Stability of the isolated peroxisomes was monitored by catalase latency and sedimentability of marker enzymes. It was improved by (i) using cells that were shifted to oleic acid medium after growth to stationary phase in glucose precultures, (ii) shifting the pH from 7.2 to 6.0 during cell fractionation, and (iii) carrying out equilibrium density centrifugation with Nycodenz containing 0.25 M sucrose throughout the gradient. A concentrated peroxisomal fraction was used for in vitro import of catalase A. After 2 h of incubation, 62% of the catalase was associated with, and 16% was imported into, the organelle in a protease-resistant fashion. We introduced immunofluorescence microscopy for S. cerevisiae peroxisomes, using antibodies against thiolase, which allowed us to identify even the extremely small organelles in glucose-grown cells. Peroxisomes from media containing oleic acid were larger in size, were greater in number, and had a more intense fluorescence signal. The peroxisomes were located, sometimes in clusters, in the cell periphery, often immediately adjacent to the plasma membrane. Systematic immunofluorescence observations of glucose-grown S. cerevisiae demonstrated that all such cells contained at least one and usually several very small peroxisomes despite the glucose repression. This finding fits a central prediction of our model of peroxisome biogenesis: peroxisomes form by division of preexisting peroxisomes; therefore, every cell must have at least one peroxisome if additional organelles are to be induced in that cell.
Mol Cell Biol 1991 Jan
PMID:Peroxisomes in Saccharomyces cerevisiae: immunofluorescence analysis and import of catalase A into isolated peroxisomes. 198 44

The structure of the small squash trypsin inhibitor CMTI-I is refined by directly minimizing the difference between the observed two-dimensional nuclear Overhauser enhancement (NOE) intensities and those calculated by the full relaxation matrix approach. To achieve this, a term proportional to this difference was added to the potential energy function of the molecular dynamics program X-PLOR. Derivatives with respect to atomic co-ordinates are calculated analytically. Spin diffusion effects are thus accounted for fully during the refinement. Initial structures for the refinement were those determined recently by solution nuclear magnetic resonance using the isolated two-spin approximation to derive distance range estimates. The fits to the nuclear magnetic resonance data improve significantly with only small shifts in the refined structures during a few cycles of conjugate gradient minimization. However, larger changes (approximately 1 A) in the conformation occur during simulated annealing, which is accompanied by a further reduction of the difference between experimental and calculated two-dimensional NOE intensities. The refined structures are closer to the X-ray structure of the inhibitor complexed with trypsin than the initial structures. The root-mean-square difference for backbone atoms between the initial structures and the X-ray structure is 0.96 A, and that between the refined structures and the X-ray structure 0.61 A.
J Mol Biol 1991 Jun 05
PMID:Relaxation matrix refinement of the solution structure of squash trypsin inhibitor. 205 85

The convulsant and/or anticonvulsant activity of unsubstituted and mono-alkyl-substituted cyclopentanones and cyclohexanones were examined by testing the ability of these compounds to produce seizures or to inhibit seizures induced by pentylenetetrazol and maximal electroshock in CF-1 mice. In addition, these compounds were tested for their ability to bind to the picrotoxin receptor. The unsubstituted compounds, cyclopentanone and cyclohexanone, prevented both pentylnetetrazol- and maximal electroshock-induced seizures. Cyclopentanones and cyclohexanones with small (less than 3 carbon atoms) alkyl substituents in the 2-position were also anticonvulsant; all of these compounds, except 2-ethylcyclohexanone, blocked both pentylenetrazol- and maximal electroshock-induced seizures. 2-Ethylcyclohexanone was very effective against pentylenetetrazol seizures but did not prevent maximal electroshock seizures. Cyclohexanones with larger alkyl substituents in the 2-position, 2-propylcyclohexanone and 2-t-butylcyclohexanone, caused clonic seizures following injection into mice. Of the cyclopentanones and cyclohexanones with alkyl substitutions in the 3-position that were studied, one was an anticonvulsant (3-methylcyclopentanone), one was a mixed convulsant/anticonvulsant (3-ethylcyclohexanone), and the other two (3-ethylcyclopentanone and 3-t-butylcyclohexanone) were convulsants. Finally, two cyclohexanones with alkyl substituents in the 4-position were studied. Both 4-ethylcyclohexanone and 4-t-butylcyclohexanone produced convulsions when injected into mice. All the neuroactive cyclopentanones and cyclohexanones competitively displaced [35S]t-butylbicyclophosphorothionate, a ligand specific for the picrotoxin receptor, from rat brain membranes. The convulsant compounds were generally more potent than the anticonvulsants. The cyclohexanones were more potent than their corresponding cyclopentanones and the binding potency of both increased as the size of the alkyl substituent increased. These results suggest that cyclopentanone, cyclohexanone, and their alkyl-substituted derivatives act at the picrotoxin receptor to increase or decrease neuronal activity. Thus, they appear to have sites and mechanisms of action similar to those of the neuroactive gamma-butyrolactones and gamma-thiobutyrolactones.
Mol Pharmacol 1990 Jan
PMID:Convulsant and anticonvulsant cyclopentanones and cyclohexanones. 215 13

N-Methyl-D-aspartate (NMDA) receptors mediate important physiological and pathological processes, including long term potentiation and neuronal excitotoxicity. Elucidation of mechanisms underlying NMDA receptor functioning will promote understanding of the molecular bases of NMDA receptor-mediated processes. The localization of the phencyclidine (PCP) receptor within the ionophore of the NMDA receptor-gated ion channel permits the binding of PCP receptor ligands to serve as a functional marker of channel activation. We have previously demonstrated that the highly selective PCP receptor ligand [3H]MK-801 displays multiexponential kinetics of association, indicating that the NMDA receptor functions according to a multistate model. Using the fast component of [3H]MK-801 binding to PCP receptors as a marker for activated NMDA channels, we demonstrate here a Hill coefficient of 2 for activation of NMDA channels by L-glutamate. A multistate model of NMDA receptor functioning analogous to the model known to account for the functioning of nicotinic cholinergic and gamma-aminobutyric acidA receptors fits well to our experimental data, supporting the concept that the NMDA receptor is properly classified in the Class 1 superfamily of ligand-gated channels.
Mol Pharmacol 1990 May
PMID:Rat brain N-methyl-D-aspartate receptors require multiple molecules of agonist for activation. 216 56

An equation for calculating the distances between the atoms involved in forming an idealized hydrogen bond in a parallel or antiparallel beta-barrel has been derived by adjusting the corresponding data given by Pauling and Corey for a beta-sheet. Based on these distances, a geometrical optimization method was developed, by which one can generate various idealized beta-barrels: parallel or antiparallel, tilted or non-tilted, right-tilted or left-tilted. For each type of idealized beta-barrel thus obtained, the corresponding conformation and characteristic geometric parameters as well as their relationship are analyzed and discussed. Since the strand in a tilted beta-barrel traces a curve rather than a straight line on a cylinder-like surface, a regular chain in which the dihedral angles of each residue are the same cannot form a tilted beta-barrel but only a non-tilted beta-barrel. As observed, the strands of a right-tilted beta-barrel possess a very strong right-handed twist. The radii of the idealized tilted parallel and antiparallel beta-barrels are greater than those of the corresponding non-tilted ones by approximately 1 A and approximately 1.5 A, respectively. Consequently, there is relatively more room for a tilted beta-barrel to accommodate the internal side-chains, suggesting that a conformational change from a non-tilted beta-barrel to a tilted one would ease the repulsion among the crowded internal side-chains so as to make the structure more stable. The values of root-mean-square fits indicate that the idealized right-tilted beta-barrels coincide quite well with the observed beta-barrels in both parallel and antiparallel cases.
J Mol Biol 1990 May 20
PMID:Conformational and geometrical properties of idealized beta-barrels in proteins. 234 9

Pharmacokinetics, subcellular distribution (SCD), and covalent binding of a single dose of 1 microCi of [S-methyl-3H]bleomycin ([3H]-BLM]) in combination with one unit of unlabeled bleomycin were studied in hamsters following intratracheal (IT) injection. The radioactivity decreased from the lung biexponentially with time. The apparent half-time of absorption for the alpha-phase was 1.1 and 17.9 hr for the beta-phase. The plasma disappearance curve of [3H]BLM fits to a two-compartmental model with the apparent half-life removal for the alpha-phase being 1.6 hr and for the beta-phase 116.9 hr. The radioactivity was detected in all studied tissues. The radioactivity from spleen, testicle, liver, fat, RBC, brain, adrenal, and kidney manifested only the alpha-phase of the disappearance curve, while the beta-phase was complicated by redistribution processes. Of the eight tissues, the spleen had the shortest (2.0 hr) and kidney the longest (12.1 hr), and the remaining tissues had half-lives which ranged from 4 to 10 hr. The SCD study revealed that 85 to 95% of the total radioactivity in the lung and liver homogenate was associated with the soluble fraction (SF) at 30 min after treatment, thereafter, the radioactivity from both tissues gradually decreased to 60% of the total at 24 hr. The SF of the lung homogenate had the highest specific radioactivity (SRA) of any of the fractions during the period between 0.5 and 6 hr. The SRA, however, decreased biexponentially and attained a value similar to that of the mitochondrial and microsomal fractions at 12 and 24 hr after treatment. In the case of liver, the SF had the highest, the nuclear the lowest, and mitochondrial and microsomal fractions the same level of SRA at 30 min. Thereafter, the SRA of all fractions were increased with time. A significant amount of radioactivity from [3H]BLM was covalently bound to lung, liver, and plasma proteins. The SF of the lung contained an increasing amount of radioactivity covalently bound after 1.5 hr of [3H]BLM injection and nearly all radioactivity measured in the plasma was covalently bound. It was concluded from the findings of this study that the presence of a major portion of [3H]BLM in the SF of the lung and its covalent linkage with the proteins of this fraction might initiate the complex sequence of events at the metabolic level necessary for the pneumotoxicity.
Exp Mol Pathol 1986 Oct
PMID:Pharmacokinetics, subcellular distribution, and covalent binding of [3H]bleomycin in hamsters after intratracheal administration. 242 61


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