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At least 19 recordsLinked to original sources
PubMed1991

Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops.

Thermodynamic parameters for internal loops of unpaired adenosines in oligoribonucleotides have been measured by optical melting studies. Comparisons are made between helices containing symmetric and asymmetric loops. Asymmetric loops destabilize a helix more than symmetric loops. The differences in free energy between symmetric and asymmetric loops are roughly half the magnitude suggested from a study of parameters required to give accurate predictions of RNA secondary structure [Papanicolaou, C., Gouy, M., & Ninio, J. (1984) Nucleic Acids Res. 12, 31-44]. Circular dichroism spectra indicate no major structural difference between helices containing symmetric and asymmetric loops. The measured sequence dependence of internal loop stability is not consistent with approximations used in current algorithms for predicting RNA secondary structure.

Base Sequence↗
PubMedDate not supplied

Strength characteristics and failure modes of locking-loop and three-loop pulley suture patterns in equine tendons.

Size 3-0 polydioxanone was used as a single strand, single braid (3 strands), or double braid (6 strands) to create six suture material-pattern combinations for equine tenorrhaphy: single-strand locking loop, single-braid locking loop, double-braid locking loop, single-strand three-loop pulley, single-braid three-loop pulley, and double-braid three-loop pulley. Maximum load to failure for the single-strand locking loop (46.1 +/- 2.9 newtons [N]) was less than for all other sutures (range, 103-155 N). The load required to form a 2 mm gap between tendon ends was greater for the single-braid three-loop pulley (66.7 +/- 6.9 N) and double-braid three-loop pulley (85.4 +/- 17.7 N) than any other sutures. The load required to produce a 10 mm gap was least for the single-strand locking loop (34.3 +/- 3.9 N) and greatest for the double-braid three-loop pulley (131.5 +/- 27.5 N). Gap between tendon ends at maximum load was greater for the single-braid (18.1 +/- 0.9 mm) and double-braid (19.2 +/- 2.2 mm) locking loops than for any other sutures. Suture material broke in 53% of the locking-loop tests but in only 17% of the three-loop pulley tests. Tendon matrix disruption accounted for 43% of the locking-loop failures and 77% of the three-loop pulley failures. The three-loop pulley pattern provided more support, less tendon distraction, and less tendon matrix constriction and distortion than the locking-loop pattern.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1990

Furosemide acts on short loop of descending thin limb, but not on long loop.

In order to elucidate the tubular sites of action of loop diuretics such as furosemide, bumetanide and ethacrynic-cysteine complex within isolated rat descending thin limbs, cellular ATP was measured by luciferin-luciferase technique. When short descending thin limbs of Henle's loop (SDL) were incubated in the absence of exogenous substrate at 37 degrees C, cellular ATP content was decreased in a time-dependent manner (up to 49% after 60 min). This ATP decrease, however, was retarded significantly in the presence of loop diuretics at 60 min. The mean percentage of change in ATP compared with the control for each loop diuretic in SDL was as follows: 10(-5) M furosemide, 178%; 10(-5) M bumetanide, 189%; and 10(-7) M ethacrynic-cysteine complex, 154%; respectively. To the contrary, cellular ATP in long descending thin limb of Henle's loop (LDL) was not changed by loop diuretics compared with the control. A similar protection against ATP depletion was observed in the medullary thick ascending limb of Henle's loop, in which the mean percentage was as follows: 10(-5) M furosemide, 163%; 10(-5) M bumetanide, 187%; and 10(-7) M ethacrynic-cysteine complex, 134%. Similarly to LDL, the cellular ATP did not change in outer medullary collecting tubule. From these results, we conclude that loop diuretics act on the isolated rat SDL, but not on LDL.

Adenosine Triphosphate↗
PubMed2026

R-loops and D-loops: a delicate balance in genomic stability and instability.

R-loops and D-loops are three-stranded nucleic acid structures that have emerged as central regulators of genome stability, gene expression, and DNA metabolism. R-loops form co-transcriptionally or post-transcriptionally when nascent RNA re-anneals with the template DNA strand, generating an RNA: DNA hybrid that displaces the non-template strand into a single-stranded state. These structures are enriched at CpG island promoters, transcription termination sites, and immunoglobulin class-switch regions, where they coordinate transcription regulation, chromatin remodeling, and DNA damage signaling. D-loops are formed when a single-stranded DNA segment pairs with one strand of a duplex and displaces the other, arising through context-dependent mechanisms that include RAD51- or DMC1-mediated strand invasion in homologous recombination, shelterin-assisted invasion at telomeres, and replication-coupled strand displacement at the mitochondrial DNA origin. They serve as indispensable intermediates in double-strand break repair, telomere maintenance, and mitochondrial DNA replication. Recent cryo-electron microscopy studies have resolved the stepwise RAD51-mediated strand exchange mechanism at near-atomic resolution, substantially advancing structural understanding of D-loop biogenesis. Despite their differences in molecular composition, both structures remodel Watson-Crick base pairing and, when dysregulated, are associated with replication fork stalling, transcription-replication conflicts, and aberrant recombination. This review systematically compares the structural features, formation mechanisms, regulatory networks, and biological functions of R-loops and D-loops, with emphasis on their convergent roles in safeguarding genome integrity. We further discuss rapidly evolving detection technologies and emerging therapeutic strategies targeting these structures in cancer and neurodegeneration, identifying key unresolved questions for future investigation.

Genomic Instability↗
PubMed1987

Structural features of the terminal loop region of frog retinal rod outer segment disk membranes: II. Organization of the terminal loop complex.

In addition to a lipid bilayer component (Corless, Fetter, and Costello: J. Comp. Neurol. 257:1-8, '87), the terminal loop region of frog rod outer segment (ROS) disks displays a clustering of discrete elements referred to as the terminal loop complex. It consists of (1) semicircular or crescentic densities within the terminal loop, (2) linear interdisk densities spanning the cytoplasm near terminal loops, and (3) distinctive freeze-fracture particles associated with the terminal loop, located between 1 and 2. The linear interdisk densities are organized on a two-dimensional lattice that appears to ensheath completely the lamellar domains of all ROS disks. Indirect evidence is presented for a net axial alignment of intraloop densities. We interpret the large freeze-fracture particles of the terminal loop region to reflect transmembrane components that connect the interdisk and intraloop densities. Thus, we propose that the entire terminal loop (TL) complex is organized on a two-dimensional net. We further infer that each TL complex is organized as a dimeric unit and that such dimers interact axially and laterally to generate the observed lattice structure. It is suggested that one component of the terminal loop complex is the high molecular weight protein localized along the disk perimeter by Papermaster, Schneider, Zorn, and Kraehenbuhl (J. Cell. Biol. 78:415-425, '78).

Animals↗
PubMed1988

Recurring loop motif in proteins that occurs in right-handed and left-handed forms. Its relationship with alpha-helices and beta-bulge loops.

A common feature of alpha-helices in proteins is a loop at the C-terminal end, with a characteristic hydrogen bond pattern. It is noted that several loops with the same structural features occur independently of alpha-helices; two are even situated at the loop ends of beta-hairpins. The name paperclip is suggested for loops possessing the appropriate hydrogen bonds. A number of features of paperclips are described: they exist in two classes, depending on the number of residues at the loop end; one class is very much commoner than the other. Two paperclips are found that belong to the common class, except that the main-chain conformation of each is the mirror image of that normally found. The majority of paperclips are shown to have tightly clustered sets of main-chain dihedral angles. These are somewhat similar to, but distinct from, a subgroup of another common family of loops that have been called beta-bulge loops; in the latter, the dihedral angles are also tightly clustered. The high degree of clustering in both cases is likely to be a result of steric constraints associated with hydrogen bond patterns at the ends of loops.

Amino Acid Sequence↗
PubMed1986

Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations.

We describe a method for predicting the conformations of loops in proteins and its application to four of the complementarity determining regions [CDRs] in the crystallographically determined structure of MCPC603. The method is based on the generation of a large number of randomly generated conformations for the backbone of the loop being studied, followed by either minimization or molecular dynamics followed by minimization starting from these random structures. The details of the algorithm for the generation of the loops are presented in the first paper in this series (Shenkin et al. [submitted]). The results of minimization and molecular dynamics applied to these loops is presented here. For the two shortest CDRs studied (H1 and L2, which are five and seven amino acids long), minimizations and dynamics simulations which ignore interactions of the loop amino acids beyond the carbon beta replicate the conformation of the crystal structure closely. This suggests that these loops fold independently of sequence variation. For the third CDR (L3, which is nine amino acids), those portions of the CDR near its base which are hydrogen bonded to framework are well replicated by our procedures, but the top of the loop shows significant conformational variability. This variability persists when side chain interactions for the MCPC603 sequence are included. For a fourth CDR (H3, which is 11 amino acids long), new low-energy backbone conformations are found; however, only those which are close to the crystal are compatible with the sequence when side chain interactions are taken into account. Results from minimization and dynamics on single CDRs with all other CDRs removed are presented. These allow us to explore the extent to which individual CDR conformations are determined by interactions with framework only.

Binding Sites, Antibody↗
PubMed1985

The pelvic ileal reservoir. An experimental comparison of the 3-loop and 2-loop systems.

In an experimental study the function of the 3-loop (Parks) pelvic ileal reservoir was compared with that of the 2-loop (Utsunomiya) reservoir. Both types achieved satisfactory degrees of continence and evacuation when tested in the defunctioned state. Following restoration of intestinal continuity, the stools of dogs with 3-loop pouches were usually liquid (69 percent) compared to the more formed stools (72 percent) in the 2-loop group, P less than 0.001. At postmortem the reservoirs of the 3-loop group were found to have undergone much greater dilatation (P less than 0.05). These findings suggest that construction of the 3-loop (Parks) pelvic reservoir may lead to retention with overflow if catheterization is not used. It is not clear whether the superior function of the 2-loop pouch is attributable to better motor function or the absence of an efferent limb which allows it to be placed deep in the pelvis.

Animals↗
PubMed1991

AraC-DNA looping: orientation and distance-dependent loop breaking by the cyclic AMP receptor protein.

The arabinose operon promoter, pBAD, is negatively regulated in the absence of arabinose by AraC protein, which forms a DNA loop by binding to two sites separated by 210 base-pairs, araO2 and araI1. pBAD is also positively regulated by AraC-arabinose and the cyclic AMP receptor protein, CRP. We provide evidence that CRP breaks the araO2-araI1 repression loop in vitro. The ability of CRP to break the loop in vitro and to activate pBAD in vivo is dependent upon the orientation and distance of the CRP binding site relative to araI1. An insertion of one DNA helical turn, 11 base-pairs, between CRP and araI only partially inhibits CRP loop breaking and activation of pBAD, while an insertion of less than one DNA helical turn, 4 base-pairs, not only abolishes CRP activation and loop breaking, but actually causes CRP to stabilize the loop and increases the araO2-mediated repression of pBAD. Both integral and non-integral insertions of greater than one helical turn completely abolish CRP activation and loop breaking in vitro.

AraC Transcription Factor↗
PubMed1992

Loop memory of posterior chamber intraocular lenses of various sizes, designs, and loop materials.

Looped intraocular lenses (IOLs) fixate by exerting centripetal pressure on the ocular tissues. The ability of the flexible loops to maintain pressure depends on their rigidity (i.e., resistance to flexion) and their "memory" (i.e., ability to restore original configuration after a long period of compression). We studied the memory of 30 different posterior chamber IOLs, with loops made of polypropylene (PP) and poly(methyl methacrylate) (PMMA), of various diameters, styles, and designs. The lenses were inserted into plastic wells, 9.5 mm in diameter, and immersed in water (37 degrees C) for one month. They were then placed on an open plate and allowed to re-expand for one month. Loop memory was calculated as the difference in diameter between the initial (pretest) measurement and measurements taken during the compression and release periods. The results showed that short (12.0 to 12.5 mm) IOLs had relatively better memory than longer (13.5 to 14.0 mm) IOLs. Those with PP loops expanded more and for longer periods than those comparable size and design with PMMA loops. One-piece, all-PMMA lenses exhibited the best loop memory. These lenses have the high rigidity of the PMMA material and the good memory of the design. Thus, the total IOL diameter can be reduced to 12.0 mm while providing long-term constant pressure on the capsular bag to maintain stable fixation.

Equipment Design↗
PubMed1992

Comparative NMR study of A(n)-bulge loops in DNA duplexes: intrahelical stacking of A, A-A, and A-A-A bulge loops.

We have prepared a series of deoxyoligonucleotide duplexes of the sequence d(G-C-A-T-C-G-X-G-C-T-A-C-G).d(C-G-T-A-G-C-C-G-A-T-G-C), in which X represents either one (A), two (A-A), or three (A-A-A) unpaired adenine basis. Using two-dimensional proton and phosphorus NMR spectroscopy, we have characterized conformational features of these bulge-loop duplexes in solution. We find that Watson-Crick hydrogen bonding is intact for all 12 base pairs, including the GC bases that flank the bulge loop. Observation of NOE connectivities in both H2O and D2O allows us to unambiguously localize all of the bulged adenine residues to intrahelical positions within the duplex. This is in contrast to an earlier model for multiple-base bulge loops in DNA [Bhattacharyya, A., & Lilley, D. M. J. (1989) Nucleic Acids Res. 17, 6821-6840], in which all but the most 5' bulged base are looped out into solution. We find that insertion of two or three bases into the duplex results in the disruption of specific sequential NOEs for the base step across from the bulge loop site on the opposite strand. This disruption is characterized by a partial shearing apart of these bases, such that certain sequential NOEs for this base step are preserved. We observe a downfield-shifted phosphorus resonance, which we assign in the A-A-A bulge duplex to the 3' side of the last bulged adenine residue. Proton and phosphorus chemical shift trends within the An-bulge duplex series indicate that there is an additive effect on the structural perturbations caused by additional unpaired bases within the bulge loop. This finding parallels previous observations [Bhattacharyya, A., & Lilley, D. M. J. (1989) Nucleic Acids Res. 17, 6821-6840; Hsieh, C.-H., & Griffith, J. D. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 4833-4837] on the magnitude of the induced bending of DNA duplexes by multiple-base bulge loops.

Adenine↗
PubMed1985

Coupling of a loop diuretic-sensitive Na+ influx with the net loop diuretic-sensitive K+ efflux in mouse NIH 3T3 cells.

Mouse 3T3 fibroblasts have a loop diuretic sensitive Na+ transport system, responsible for more than 50% of the total Na+ influx. This transport system is dependent on the simultaneous presence of all three ions; Na+, K+, (Rb+) and Cl- in the extracellular medium. The same requirement for these three ions was also found for the loop diuretic-sensitive K+ efflux. In addition, the sensitivities of Na+ influx and Rb+ efflux for the two loop diuretics, furosemide and bumetanide were found to be similar. The similar ionic requirement and sensitivity towards loop diuretics of the two fluxes, support the hypothesis, that this loop diuretic-sensitive Na+ influx in mouse 3T3 cells, is accompanied by the net loop diuretic-sensitive K+ efflux.

Animals↗
PubMed1989

Open-loop and closed-loop optokinetic nystagmus in squirrel monkeys (Saimiri sciureus) and in man.

Horizontal optokinetic nystagmus (OKN) was measured in 3 normal Squirrel monkeys by means of the electromagnetic search coil technique. Binocular and monocular stimulation of each eye to the left and right by moving vertical stripe patterns of 2.37 or 15 degree period were applied at angular velocities of 0.5 to 400 deg/s. After measurement of horizontal OKN under normal conditions, open-loop OKN gain was determined by monocular stimulation of an eyeball immobilized by means of retrobulbar injections of 11 units botulinum toxin (BoTx type A) and compared with the pre-injection data or with monocular stimulation of the other eye, which remained mobile. In normal Squirrel monkeys gain of optokinetic nystagmus reached values between 0.8 and 0.97 at angular velocities below 1.5 deg/s. Gain under these conditions was related to stimulus angular velocities Vs, i.e. Ge = Ve/Vs. A slightly higher gain was found for binocular than for monocular stimulation. No significant differences were found in OKN when monocular stimulation in the naso-temporal and in the temporo-nasal direction was applied. The upper cut-off angular velocity (-3 dB-point) reached values of 180-230 deg/s, significantly above those observed in man under similar stimulus conditions. Monocular optokinetic stimulation of an immobilized eye led to vigorous optokinetic nystagmus and OKAN of the other eye, whereby maximum gain (Gi = Ve/Vr) was found to be between 20 and 30 at lower retinal stimulus velocities (2-5 deg/s). Gain was related to retinal stimulus velocity Vr. Increase in Vr above 10 deg/s led to a decrease in gain with a slope of about 20 dB per decade. Measurement of gain of closed-loop OKN related to retinal stimulus velocity Vr (which was determined by the difference between Vs and Ve) led to a similar dependence of OKN as in closed-loop stimulus conditions. Differences in sensitivity between the temporal and the nasal visual hemifield stimulation evoking horizontal open-loop OKN are described. Directional selectivity appeared in these experiments. Open-loop OKN data from a human subject are reported. With highly attentive horizontal optokinetic gaze nystagmus, Ve depended on the duration of the pursuit phases of OKN. Ve accelerated with the duration of the individual slow phase of OKN and was reset by each backward saccade (of the covered mobile eye). OKN gain was considerably smaller when the subject intentionally pursued as many stripes as possible of the 1.15 degree period stripe pattern (gain related to Vr about 1.5-3).(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1992

Mutational and proteolytic studies on a flexible loop in glutathione synthetase from Escherichia coli B: the loop and arginine 233 are critical for the catalytic reaction.

The function of the flexible loop which is disordered in crystal structure analysis of glutathione synthetase from Escherichia coli B has been investigated by limited proteolysis and kinetic measurements for the wild-type and mutant enzymes. Proteolysis of the intact enzyme using arginyl endopeptidase or trypsin brought about a time-dependent decrease in the enzymatic activity and the production of protein fragments. SDS-polyacrylamide gel electrophoresis and peptide sequence analysis showed that only a peptide bond between arginine 233 and glycine 234 in the loop was cleaved. Further, native polyacrylamide gel electrophoresis revealed that the cleaved enzyme retained almost the same quaternary structure as that of the wild-type enzyme. Upon protease treatment, the presence of substrates, ATP and/or gamma-L-glutamyl-L-cysteine (gamma-Glu-Cys), protected the loop from cleavage, but the presence of glycine was not capable of protecting it. In addition, replacement of arginine 233 in the loop with lysine by site-directed mutagenesis increased the Michaelis constants for gamma-Glu-Cys and glycine by factors of 28 and 213, respectively. The protection against cleavage on a similar protease incubation of this mutant enzyme was also observed in the presence of ATP and/or gamma-Glu-Cys, but the effect in the presence of both substrates was half as large as that for the wild-type enzyme. These results suggest that the loop covers the active site while ATP and gamma-Glu-Cys bind there and that it protects the unstable gamma-Glu-Cys phosphate intermediate from decomposition by bulk water.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1975

Experimental production of elevated serum folate in dogs with intestinal blind loops. II. Nature of bacterially produced folate coenzymes in blind loop fluid.

Jejunal and ileal blind loops were constructed in separate groups of dogs and the folate coenzymes present in these loops were investigated. Although only those dogs with high blind loops had appreciably elevated folate levels active for Lactobacillus casei but not Streptococcus faecalis, every blind loop appeared to contain four folate compounds--5-formyltetrahydrofolic acid, 5-methyltetrahydrofolic acid, tetrahydrofolic acid and a compound tentatively identified as 5-formyltetrahydrofolic triglutamate. Why increased levels of 5-methyltetrahydrofolate alone are present in the serum of dogs with a high blind loop is discussed.

Animals↗
PubMed1992

Common features of the conformations of antigen-binding loops in immunoglobulins and application to modeling loop conformations.

Using database screening techniques we have examined the relationship between antigen-binding loops in immunoglobulins, and regions of similar conformation in other protein families. The conformations of most antigen-binding loops are not unique to immunoglobulins. But in many cases, the geometrical relationship between the loop and the peptides flanking it differs between the immunoglobulins and other structures with the same loop. We assess model building by data base screening, compared with that based on canonical structures.

Amino Acid Sequence↗
PubMed1987

The role of visual reafferents during a pointing movement: comparative study between open-loop and closed-loop performances in monkeys before and after unilateral electrolytic lesion of the substantia nigra.

In order to elucidate the compensatory role of visual feedback during movement, two experiments were designed to compare the motor performances of Papio papio baboons depending on whether the animals were able to visually control the limb trajectory (visual closed-loop condition) or not (visual open-loop condition). The visuomotor task used consisted of making trained pointing movements towards a stationary target. In experiment A, the baboons were successively presented with these two experimental conditions. The abolition of visual control was found to cause no change in either reaction time (RT) or movement time (MT), but brought about extensive pointing errors. It was also associated with a conspicuous increase in the mean velocity and the mean length of the trajectories. In experiment B, two groups of baboons were used. The monkeys in the first group were required to perform under closed loop conditions. The second group performed the pointing movement under open loop conditions. Once criterion was reached by each animal, a unilateral electrolytic lesion of the substantia nigra (SN) was performed. A comparison between the post operative performances of the animals in the two groups showed that suppression of visual cues resulted in a lengthening of the RT and a slowing of the movement speed. Moreover when visual feedback was lacking, the amplitude of the movement decreased and the finger fell short of the target. During the last post operative period, suppression of visual feedback brought about a more rapid return of RTs to their preoperative level and a more durable slowing of movement speed than with normal vision. The discussion deals with the role of visual feed-back in the control of movement preparation and execution, and with the change in mode of motor control caused by lesion of the SN. Partial exclusion of the SN might bring about a shift from the feedforward to a feedback mode relying more heavily on visual cues.

Animals↗