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Quantitation of specific fragments in DNA restriction digests: application to the cohesive fragments in lambda DNA digests.

A procedure for the quantitation of reactions between specific members of a set of DNA restriction fragments is presented. Quantitation of the cohesive fragments in NruI nuclease digests of lambda DNA is used as an example. Restriction fragments are resolved on agarose gels and their amounts are estimated from densitometer scans of photographic negatives of ethidium bromide-stained gels. A linear relationship is found between the peak height of given fragment on the scan and the logarithm of the molecular weight of the fragment, arising in part from the stoichiometry of the digest; this relationship allows simple interpolation between the peak heights of the nonreacting fragments in each gel lane to determine the theoretical maximal amount of each reactive fragment in that gel lane. Similar procedures should be applicable to enzymatic ligation or to site-specific cleavage of specific restriction fragments or to autoradiographic detection of the fragments. Since each lane of the gel is analyzed independently, the method is largely self-correcting for variations in amounts applied to the gel.

Bacteriophage lambda

Precise localization of the alpha-globin gene cluster within one of the 20- to 300-kilobase DNA fragments released by cleavage of chicken chromosomal DNA at topoisomerase II sites in vivo: evidence that the fragments are DNA loops or domains.

We have mapped the position of the alpha-globin gene cluster in the 20- to 300-kilobase fragments of chromosomal DNA isolated from growing chicken HD3 erythroblastoid cells exposed to 4'-demethylepipodophyllotoxinthenylidene beta-D-glucoside. This epipodophyllotoxin traps functioning topoisomerase II molecules, the denaturation of which cleaves DNA and reveals their reaction sites. The DNA fragments, prepared by centrifugation in sucrose gradients, bind selectively to glass-fiber filters and are protected from lambda 5'-exonuclease, properties compatible with the presence of a topoisomerase II subunit bound to their 5' ends. Restriction enzyme cleavage of the fragments and hybridization with cloned alpha-globin-region probes reveal additional distinctive bands not seen in control DNA, allowing the localization of fragment ends near this gene cluster. The terminal regions of fragments from sucrose gradients or from field-inversion electrophoresis gels were also used to probe cloned regions of the gene cluster. Both approaches show that this cluster of three genes, which is not expressed in these cells, is located at a specific position in a approximately 20-kilobase DNA fragment. The upstream end of this fragment lies in a region that contains a site of DNA attachment to the nuclear matrix mapped by both in vivo and in vitro methods, and its downstream end is flanked by approximately 80% A + T sequences characteristic of matrix-attachment regions. These observations suggest that the DNA fragments are formed because topoisomerase II molecules can specifically and readily integrate into DNA at matrix-attachment regions and that the fragments represent entire DNA loops or domains.

Animals

Mechanical impactor employing Nitinol probes to fragment human calculi: fragmentation efficiency with flexible endoscope deflection.

The Browne Pneumatic Impactor (BPI; Browne Medical Systems, Minneapolis, MN) is a new mechanical lithotripter that relies on a pneumatically driven metal probe. It can be employed through both rigid and actively deflectable flexible endoscopes. Prior in vivo studies have shown excellent fragmentation of hard human calculi while employing the BPI with active endoscope deflection of as much as 45 degrees. In this study, we set out to define the efficiency of stone fragmentation with active endoscope deflection and to quantify the extent of retrograde stone migration that is often noted when mechanical lithotripters are employed. Pressure transducer testing of the BPI revealed an inverse relation between increased deflection of the endoscope and transduced voltage. Calculus fragmentation tests showed that as the endoscope was actively deflected to 90 degrees, the BPI still was able to fragment human calcium oxalate monohydrate calculi into extractable fragments with as few as six pulses. The maximum active endoscope deflection was 95 degrees with the 0.020-inch Nitinol probe passed through the working channel. At this deflection, the BPI was able to fragment an 8 mm pure calcium oxalate monohydrate calculus into two fragments after 14 pulses. Retrograde migration was evaluated by employing the BPI in a simulated ureter in a waterbath. The travel distance of a 5-mm 5-g calculus with one pulse averaged 12.2 mm (range 1-44 mm). Smaller, less dense calculi travelled farther. A rebound effect was occasionally noted, and this was associated with an off-center delivery. In conclusion, the BPI is an efficient mechanical lithotrite able to fragment hard human calculi when employed with active endoscope deflection of as much as 95 degrees. Delivered energy decreased with active endoscope deflection, but this change did not prevent fragmentation. Retrograde migration was an important variable more notable with smaller calculi.

Alloys

Enantioselectivity of bovine serum albumin-bonded columns produced with isolated protein fragments. II. Characterization of protein fragments and chiral binding sites.

Enantioselectivity of bovine serum albumin (BSA)-bonded columns produced with isolated protein fragments has been investigated. The BSA fragment, BSA-FG75, was isolated by size exclusion chromatography following peptic digest of BSA. The isolated BSA-FG75 was further fractionated to two fractions, BSA-F1 and BSA-F2, by anion-exchange chromatography. BSA-F1 and BSA-F2 had molecular mass of about 35000 daltons, estimated by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry, BSA-F1 has amino acid residues 1-307 estimated by electrospray ionization (ESI) mass spectrometry, while BSA-F2 is an N-terminal half BSA fragment. The BSA, BSA-FG75, BSA-F1 and BSA-F2 proteins were bound to aminopropyl-silica gels activated by N,N'-disuccinimidyl carbonate. The bound amounts of the BSA fragments were 2.2-2.7 times more than that of the intact BSA. Chiral recognition of 2-arylpropionic acid derivatives, benzodiazepines, warfarin and benzoin was obtained with the BSA fragment-bonded columns. The non-enantioselective interactions of benzoin and benzodiazepines except for clorazepate with BSA fragments were increased with protein surface coverages, while those of 2-arylpropionic acid, clorazepate and warfarin were decreased. The BSA fragment columns gave higher enantioselectivity for lorazepam and benzoin, and lower enantioselectivity for other compounds tested, compared with the BSA column. These results might be due to changes in the globular structure of the BSA fragment and/or changes in the local environment around the binding sites.

Benzodiazepines

Reconstitution of Escherichia coli RNase HI from the N-fragment with high helicity and the C-fragment with a disordered structure.

The Escherichia coli RNase HI variant with the Lys86-->Ala mutation is purified in two forms, as nicked and intact proteins. The nicked K86A protein, in which the N-fragment (Met1-Lys87) and the C-fragment (Arg88-Val155) remain associated, is enzymatically active. These N- and C-fragments were isolated and examined for reassociation. These peptides did not associate to form the nicked K86A protein at pH 3.0 in the absence of salt, but were associated, with a yield of 30-80%, when the pH was raised to 5.5 or when salt was added. Measurements of the CD spectra show that the alpha-helices are partially formed in the N-fragment at pH 3.0 in the absence of salt and are almost fully formed either at pH 5.5 or at pH 3.0 in the presence of 0.15 M NaCl. In contrast, the C-fragment remains almost fully disordered under these conditions. The N-fragment with this high (native-like) helicity shows the characteristics of a molten globule with respect to the content of the secondary and tertiary structures, the ability to bind a fluorescent probe (1-anilinonaphthalene-8-sulfonic acid), and the behavior on the thermal transition. These results suggest that the N-fragment contains an initial folding site, probably the alpha I-helix, and the completion of the folding in this site provides a surface that facilitates the folding of the C-fragment. This folding process may represent that of the intact RNase HI molecule.

Binding Sites

Characterization of chromosome fragmentation in two protozoans and identification of a candidate fragmentation sequence in Euplotes crassus.

Following the sexual cycle, hypotrichous ciliated protozoans fragment a set of their micronuclear chromosomes to generate the thousands of short, linear DNA molecules present in the transcriptionally active macronucleus. We have used a hybrid selection procedure to examine macronuclear DNA molecules for subtelomeric length heterogeneity to determine whether chromosome fragmentation occurs at unique or multiple sites. The results suggest that multiple, but closely spaced, chromosome fragmentation sites are used by Oxytricha nova. In contrast, Euplotes crassus uses unique chromosome fragmentation sites in a reproducible manner to generate the ends of macronuclear DNA molecules. Additional studies compared DNA sequences in the vicinity of chromosome fragmentation sites in an attempt to define cis-acting sequences that direct the fragmentation process. A conserved sequence was found near chromosome fragmentation sites in E. crassus. The location of the conserved sequence suggests that chromosome fragmentation involves staggered cuts of the micronuclear DNA molecules.

Animals

Immunological characterization of papain-induced fragments of Clostridium botulinum type A neurotoxin and interaction of the fragments with brain synaptosomes.

After treatment of Clostridium botulinum type A neurotoxin with papain, three fragments (Mrs, 101,000, 45,000, and 43,000) were purified by hydrophobic and ion-exchange chromatography with a high-performance liquid chromatographic system. Immunoblotting analyses with monoclonal antibodies showed that the 101,000-dalton fragment consisted of the light chain and a part of the heavy chain (H-1 fragment) linked together by a disulfide bond, and the other two fragments were correlated to the remaining portion of the heavy chain (H-2 fragment). The 45,000- and 43,000-dalton fragments effectively competed for binding of the 125I-labeled neurotoxin to synaptosomes, while no inhibition was observed with the 101,000-dalton fragment. The results indicate that the H-2 fragment interacts with the binding site on the neural membrane. The binding of the neurotoxin was impaired by treatment of synaptosomes with neuraminidase. Incorporation of gangliosides into neuraminidase-treated synaptosomes resulted in the restoration of binding. The results suggest that gangliosides are one of the components of the toxin-binding site.

Animals

Bleeding times in rats treated with heparin, heparin fragments of high and low anticoagulant activity and chemically modified heparin fragments of low anticoagulant activity.

A template bleeding time study in the rat was undertaken to see if it is possible to correlate bleeding times with the molecular weight, anticoagulant activity or chemical composition of heparin or heparin-derived compounds. Heparin from porcine intestinal mucosa (PM-heparin) and from bovine lung (BL-heparin) as well as heparin fragments from these sources were compared. Heparin fragments of low anticoagulant activity were prepared by affinity chromatography on immobilized antithrombin as well as by chemical modification. A heparin fragment of high affinity for antithrombin (HA-fragment) caused a marked and dose-dependent increase in bleeding time while the corresponding heparin fragment with low affinity for antithrombin (LA-fragment) had a marginal and non-dose dependent effect on the bleeding time. Similar results were also obtained with PM-heparin with high and low affinity for antithrombin. A high anti-FXa activity was not always correlated with a marked bleeding tendency. Provided that a fragment was devoid of activated partial thromboplastin time (APTT) activity, it was not possible to provoke a bleeding time of 20 min or longer, although the compound was administered at a dose of 1,088 U/kg (anti-FXa activity). On the other hand, a N-acetylated chemically oversulphated heparin fragment, with a very low anti-FXa activity (1 U/mg) and with an APTT activity of 34 U/mg, caused a bleeding time of 20 min or longer in 70% of the animals after injection of the same number of APTT units, 1,088 U/kg. These data indicate that the APTT activity is a better and more sensitive indicator of the bleeding than is the anti-FXa activity.

Acetylation

Enzymatic fragmentation of tetanus toxin. Identification and characterization of an atoxic, immunogenic fragment.

Purified filtrate tetanus toxin was subjected to limited digestion with papain and the resulting fragments were separated by gel exclusion chromatography and characterized. One atoxic fragment was shown to react with antiserum against tetanus toxoid and was capable of inducing antibodies in rabbits that neutralized native tetanus toxin, The fragment had an estimated molecular weight of 56,000 by SDS polyacrylamide gel electrophoresis and 62,000 by sedimentation equilibrium. In the presence of a reducing agent, the fragment yielded two components with approximatec molecular weights of 23,000 and 32,000. Thus, it appears that the atoxic, immunogenic fragment is composed of two peptides joined by at least one disulfide bond. The fragment was examined by circular dichroism and data analysis indicated the presence of considerable beta-structure, but little, if any, alpha-helicity. This is significantly different from the estimates for filtrate toxin. 29% alpha-helicity and 23% beta-structure. Above 250 nm, the circular dichroic spectrum of the fragment was also distinct from that of intact toxin.

Amino Acids

Protein fragments as models for events in protein folding pathways: protein engineering analysis of the association of two complementary fragments of the barley chymotrypsin inhibitor 2 (CI-2).

Two fragments of chymotrypsin inhibitor-2, CI-2(20-59) and CI-2(60-83), derived from cyanogen bromide cleavage at Met-59, associate to give a native-like structure. We analyze the kinetics and equilibria of association of mutant fragments derived from cleaving mutant proteins at the same methionine residue. The changes in free energy of association have been measured both from isothermal studies of the binding of fragments and from thermal denaturation of the complexes. In general, there is a good correlation between the changes on mutation of the free energy of association of fragments and the changes in free energy of folding of the uncleaved parent protein. The notable exceptions are for residues in regions of the fragments that form nonnative hydrophobic clusters in the isolated fragments; mutation of the hydrophobic residues involved in these clusters decreases the equilibrium constant for formation of the noncovalent complex less than it does the equilibrium constant for folding of intact protein. The dissociated fragments must be destabilized by mutation of those hydrophobic residues, but to a lesser extent than is the complex itself. These clusters are thus less important energetically in the denatured state of the intact protein. The second-order rate constants for the major phase of association change with mutation, similar results being obtained from fluorescence measurements of the regain of tertiary structure and from circular dichroism measurements of the regain of secondary structure. The rate constants for association correlate well, in general, with the rate constants of refolding of the respective uncleaved proteins.(ABSTRACT TRUNCATED AT 250 WORDS)

Circular Dichroism

Development of a cleavage-site-specific monoclonal antibody for detecting metalloproteinase-derived aggrecan fragments: detection of fragments in human synovial fluids.

We have developed a monoclonal antibody AF-28 that specifically recognizes a neo-epitope on polypeptides with N-terminal FFGVG ... sequences. This sequence is found at the N-terminus of aggrecan fragments that have been digested with matrix metalloproteinases (MMPs). By immunoblotting, monoclonal antibody AF-28 specifically detected G2 fragments derived from an aggrecan G1-G2 substrate digested with stromelysin, collagenase, gelatinase and matrilysin, but failed to detect G2 fragments obtained from elastase, trypsin or cathepsin B digests. Undigested G1-G2 was not detected. In addition, AF-28 antibody detected fragments derived from whole aggrecan and this detection did not require prior treatment with chondroitinase or keratanase. Competition experiments confirmed that peptides containing internal ... FFGVG ... sequences were not detected by the antibody, while native MMP-digested aggrecan fragments and a synthetic 32-mer peptide with FFGVG ... N-termini were equally competitive on a molar basis. An FFGVG 5-mer, and an FGVGGEEDI9-mer which lacked the N-terminal phenylalanine residue, were 50 times and 230 times respectively less competitive than the FFGVG ... 32-mer. Two fragments from the interglobular domain, F342-F373 and F342-D441, that are predicted products of G1-G2 digestion by neutrophil collagenase but have not previously been detected, could be detected with AF-28. The epitope recognized by AF-28 was also detected in human synovial fluids by Western blot analysis. A broad band of 100-200 kDa was detected in some patients and a dominant band of 40-60 kDa was found in two patients. The size of this small fragment corresponds with that seen for the porcine F342-E373 product and may represent the natural physiological product of aggrecan cleaved in vivo at both the MMP site (... DIPEN341 decreases F342FGVG ...) and the aggrecanase site (... ITEGE373 decreases A374RGSVI ...).

Aggrecans

Endotoxin-neutralizing properties of the 25 kD N-terminal fragment and a newly isolated 30 kD C-terminal fragment of the 55-60 kD bactericidal/permeability-increasing protein of human neutrophils.

The bactericidal/permeability-increasing protein (BPI) of polymorphonuclear leukocytes (PMN) is a potent cytotoxin, specific for Gram-negative bacteria, that also inhibits endotoxin activity by neutralizing isolated bacterial lipopolysaccharides (LPS). We have previously shown that an isolated 25 kD N-terminal fragment of human BPI carries all the antibacterial activities of the parent 55-60 kD molecule. In this study we have compared the LPS-neutralizing activities of human holo-BPI, the N-terminal fragment and a 30 kD C-terminal fragment that we have now isolated. We show that the N-terminal fragment also has LPS-neutralizing activity as detected by inhibition (up to 95%) of (a) activation by LPS of procoagulant proteases in Limulus amebocyte lysates, (b) LPS "priming" of PMN, and (c) LPS-mediated production of tumor necrosis factor in whole human blood. Holo-BPI and the 25 kD fragment have similar neutralizing potency (in nanomolar range) in all assays toward "smooth" LPS from Escherichia coli O111:B4 and O55:B5 (possessing long chain polysaccharide or O-antigen), and "deep rough" LPS from Salmonella minnesota Re595 mutant (possessing no O-antigen). The C-terminal fragment of BPI is devoid of antibacterial activity when tested against BPI-sensitive E. coli J5, but does have endotoxin-neutralizing activity. This activity is weak relative to holo-BPI and the 25 kD N-terminal fragment in the Limulus and PMN-priming assay, but is comparable for inhibition of TNF production in whole blood. We conclude that the principal determinants for LPS recognition and neutralization, like those for antibacterial action, reside in the N-terminal half of the BPI molecule, but that sites within the C-terminal half can also contribute to BPI-LPS interaction once LPS is detached from the bacterial envelope.

Antimicrobial Cationic Peptides

Cloning of a DNA fragment displaying restriction fragment length polymorphisms between the genomes of spontaneously hypertensive and Wistar-Kyoto rats.

A 3 kilobase (kb) EcoRI fragment cloned from the genome of the spontaneously hypertensive rat (SHR) displayed restriction fragment length polymorphism (RFLP) compared with the genome of the Wistar-Kyoto rat (WKY) when total genomic Southern blot analysis was performed for two restriction enzymes, PstI and PvuII. Sequencing of the DNA fragment cloned from genomic SHR and WKY libraries revealed that this 3 kb EcoRI fragment harbours three point mutations. Two of them (C to T and A to T) are situated in the middle of the restriction sites for PstI and PvuII, thus disrupting the recognition sites for these enzymes in the SHR genome. Southern blot analysis using total complementary (c) DNA obtained from cDNA libraries of aortic smooth muscle cells from SHR and a whole WKY kidney, with this 3 kb EcoRI fragment as a probe, showed polymorphic bands suggesting that these point mutations are reflected in the sequences of messenger (m) RNA transcribed from the gene encoded in this 3 kb fragment. Detection of two bands by a Northern blot analysis for RNA from various SHR tissues indicates that this 3 kb fragment is actively transcribed in vivo.

Animals

The amino acid sequence of fragment A, an enzymically active fragment of diphtheria toxin. III. The chymotryptic peptides, the peptides derived by cleavage at tryptophan residues, and the complete sequence of the protein.

Fragment A (21,145 daltons in its longest known form) may be derived from diphtheria toxin (60,000 daltons) by mild tryptic digestion and reduction. Purified Fragment A consists of a mixture of 3 molecules of 190, 192, and 193 residues; the first 190 residues are in common and correspond to the NH2-terminal region the toxin. All three species of Fragment A are active in catalyzing ADP ribosylation of elongation factor 2, an essential component of protein synthesis. This reaction inactivates the factor and is responsible for the toxin's action in inhibiting protein synthesis in animal cells. It is believed that Fragment A or similar enzymically active fragments released into the cytosol of toxin-treated cells mediate this inhibition. The complete amino acid sequence of Fragment A has been determined from 32 chymotryptic peptides, three peptides derived by chemical cleavage of Fragment A at its 2 tryptophan residues, five cyanogen bromide peptides, and six tryptic peptides from the maleylated protein.

Adenosine Diphosphate Sugars

Chemical modification of bovine prothrombin fragment 1 in the presence of Tb3+ ions. Sequence studies on 3-gamma-MGlu-fragment.

Chemical modification of the gamma-carboxyglutamyl (Gla) residues of bovine prothrombin fragment 1 using the formaldehyde-morpholine method in the presence of 100 Kappm Tb3+ ions at pH 5.0 provided a modified protein containing 3 gamma-methyleneglutamyl residues (gamma-MGlu) and 7 Gla residues (bovine 3-gamma-MGlu-fragment 1). The modified protein bound the same number of Ca2+ ions as the native protein (six to seven), exhibited 28Mg2+-binding properties identical to native fragment 1 (five Mg2+ ions bound), exhibited the metal ion-promoted quenching of the intrinsic fluorescence in a manner similar to the native protein, but did not bind to phosphatidylserine (PS)/phosphatidylcholine (PC) vesicles in the presence of Ca2+ ions. Modification of the bovine protein using [14C]formaldehyde-morpholine provided a 14C-labeled 3-gamma-MGlu-fragment 1 suitable for sequence analysis. Edman sequencing of the peptides released by a tryptic digest of the reduced and carboxymethylated bovine [14C]3-gamma-MGlu-fragment 1 indicated that Gla residues at positions 7, 8, and 33 had been converted to [14C]gamma-methyleneglutamyl residues. In addition Lys97 was found to contain a 14C label. Similar analysis of the human [14C]3-gamma-MGlu-fragment 1 indicated that Gla residues at positions 7 and 32 were major modification sites and that Gla residues at positions 6 and 14 were partially modified. Lysine 96 was also modified in the human protein. The incorporation of a 14C label at Lys97 in bovine 3-gamma-MGlu-fragment 1 protein is not responsible for the loss of Ca2+-promoted binding to PS/PC vesicles. We suggest that Gla residues 7, 8, and 33 are elements of the first Ca2+-binding site; occupancy of this site establishes the Ca2+-specific conformation which is essential for the Ca2+-promoted interaction of the bovine protein with PS/PC vesicles. These studies also suggest that the loss of Gla residues at positions 7 and 32 prevents the formation of the initial Ca2+-binding site in the human protein.

Amino Acid Sequence

[Studies in the fibrinogen molecule D fragment inactivation protecting fragment].

The interaction was studied between two fragments of bovine fibrinogen isolated from its tryptic hydrolysate: the D fragment, an inhibitor of fibrin-monomer polymerization, and the protector, a fragment inactivating the D fragment. This reaction is relatively rapid: it is completed for several minutes at room temperature and at 37 degrees and is slowed down at 5 degrees. However, the reached level of the D fragment inactivation does not depend upon temperature (within a range from 5 degrees to 37 degrees). Dilution of the incubation mixture under applied conditions caused no dissociation of the D fragment-protector complex. Inactivation of the D fragment by the protector depends on the solution ionic strength; ionic strength 0.13-0.16 is optimal.

Animals

Mercaptan-induced fragmentation of a subunit-like proteolytic fragment of immunoglobulin M.

Limited papain hydrolysis of immunoglobulin M (IgM) produces a subunit-like proteolytic fragment designated IgM(p) (Inman & Hazen, 1968). In the presence of mercaptans, IgM(p) partially dissociated into Fc(mu)-like and Fab(mu) fragments. Treatment of residual IgM (that remaining after a papain digestion) with 2mm-mercaptoethylamine resulted in fragmentation of the same type that occurs in a routine limited digestion of IgM with papain, although exogenous enzyme was not added to the mixture. When IgM was hydrolysed with (14)C-labelled papain, a small quantity of the enzyme was found to be associated with the residual IgM and IgM(p) fractions. IgM and IgM 7S subunit (IgM(s)) that had been exposed to papain in the absence of activating mercaptan and separated from the enzyme by gel filtration also fragmented when subsequently treated with 2mm-mercaptoethylamine. The fragments resembled those produced during a typical limited papain digestion of IgM. It was concluded that mercaptoethylamine induced fragmentation of IgM(p) by activating adsorbed papain.

Carbon Isotopes

Limited enzymatic cleavage of pig immunoglobulin G and of specific antibodies. III. Large-scale isolation of tryptic fragments of antibodies and of non-specific immunoglobulin and characteristics of the Fc fragment.

Precipitating and non-precipitating anti-Dnp antibodies and S-sulpho non-specific IgG in gram quantities were subjected to limited cleavage by trypsin. Upon gel chromatography on Sephadex G-100 the fraction of Fab and Fc fragments was separated from incompletely split molecules and from tFc' fragments. The Fab and Fc fragments were separated from each other either by ion-exchange chromatography on QAE-Sephadex or by preparative electrophoresis in starch block. Both Fab and Fc fragments appeared to be heterogeneous as to electric charge. The Fc fragments were characterized by amino acid composition and N-terminal amino acids. The Fc fragment of non-specific IgG was cleaved by cyanogen bromide, and a C-terminal peptide containing 18 residues was isolated. Partial amino acid sequence of this peptide pointed to a high degree of homology with immunoglobulins of other animal species.

Amino Acids