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At least 1,207 records · Page 67Linked to original sources
PubMed2003

Arm sequences contribute to the architecture and catalytic function of a lambda integrase-Holliday junction complex.

lambda integrase (Int) mediates recombination between attachment sites on lambda phage and E. coli DNAs. With the assistance of accessory proteins that induce DNA loops, Int bridges pairs of distinct arm- and core-type DNA binding sites to form synapsed recombination complexes, which then recombine via a Holliday junction (HJ) intermediate. We show that, in addition to promoting the proper positioning of Int protomers, the arm sequences facilitate the catalytic activities of the Int tetramer, independent of accessory proteins or physical continuity between the arm and core sites. We have determined the architecture of ternary complexes containing a HJ, Int, and P'1,2 arm-type DNA. These structures accommodate simultaneous binding of Int to direct-repeat arm sites and indirect-repeat core sites and afford a new view of the higher-order recombinogenic complexes.

Bacteriophage lambda↗
PubMed1996

Recognition of the T-arm of tRNA by tRNA (m5U54)-methyltransferase is not sequence specific.

tRNA (m5U54)-methyltransferase (RUMT) catalyzes the methylation of U54 of tRNAs. In contrast to enzymes which recognize a particular tRNA, RUMT recognizes features common to all tRNAs. We have shown that these features reside in the T-arm of tRNA and constructed a minimal consensus sequence for RUMT recognition and catalysis (Gu et al., 1991b). Here, we have mutated each conserved T-loop residue and conserved T-stem base pair to bases or base pairs which are not observed in Escherichia coli tRNA. The substrate specificity of RUMT for 30 in vitro synthesized T-arm mutants of tRNAPhe and 37 mutants of the 17-mer analog of the T-arm derived from tRNA1Val was investigated. A 2-5 base pair stem was essential for recognition of the T-arm by RUMT, but the base composition of the stem was unimportant. The 7-base size of the T-loop maintained by the stem was essential for RUMT recognition. For tRNA, most base substitutions in the 7-base loop did not eliminate RUMT activity, except for any mutation of the methyl acceptor U54 and the C56G mutation. The effect of base and base pair mutations on Kcat or the rate of methylation by RUMT was more striking than the effect on the Kd for binding to RUMT. In comparison with mutations in the T-loop of intact tRNA, base mutation in the T-loop of the 17-mer T-arm had a more deleterious effect on binding and methylation. Surprisingly, recognition of tRNA by RUMT appears to reside in the three-dimensional structure of the seven-member T-loop rather than in its primary structure.

Base Sequence↗
PubMedDate not supplied

Parameters affecting the efficiency of affinity-based reversed micellar extraction and separation (ARMES) in glycoprotein purification.

Affinity-based reversed micellar extraction and separation (ARMES) is an effective method for purifying both low and high molecular weight glycoproteins via liquid-liquid extraction. A range of extraction conditions were examined to gain insight into the mechanism of ARMES. Concanavalin A (Con A) was used as the model affinity ligand to bind soybean peroxidase (SBP) and beta-galactosidase as model glycoproteins. Factorial design was used to investigate the effect of various system variables on the extraction of SBP via ARMES. A quadratic model described the systems well, resulting in a standard deviation of 7% between calculated and experimental extraction efficiencies. Sensitivity analysis suggested that the key criteria in ARMES were the NaCl concentration and pH of the aqueous feed phase. Extraction of both glycoproteins decreased above pH 7 but fell to zero only at pH values significantly above the pI of the model glycoproteins and the Con A affinity ligand. It is proposed that the complex of the affinity lectin with the glycoprotein results in a sufficiently hydrophobic species that can be extracted into a reversed micellar organic phase even at pH's far above the pI's of the individual proteins that comprise the complex. This finding has practical considerations for the use of ARMES in the resolution and purification of protein glycoforms.

Glycoproteins↗
PubMed1999

Side Arm Effects on Cyclen-Alkali Metal Cation Complexation: Highly Selective and Three-Dimensional Encapsulation of Na(+) Ion.

A variety of armed cyclens were prepared in which ester, amide, nitrile, and pyridine moieties were attached as cation-ligating side arms to a 12-membered ring. Ester-, amide-, and pyridine-armed cyclens nicely accommodated a Na(+) ion in a three-dimensional fashion and clearly discriminated the cation from Li(+) and K(+) ions. They extracted Na(+) ion more efficiently and selectively than common Na(+) ion-selective ligands. X-ray diffraction, FAB-MS, (23)Na NMR binding studies, and computer modeling experiments demonstrated that the cyclens having ester-, amide-, and pyridine-functionalized side arms formed highly selective encapsulated Na(+) complexes via a cooperative action of parent cyclen and side arms.

Journal Article↗
PubMed2004

Multiarm molecular brushes: effect of the number of arms on the molecular weight polydispersity and surface ordering.

Individual molecules of multiarm starlike molecular brushes were visualized by atomic force microscopy. In the studied series of brushes, the number of arms varied from one for a linear chain to four, while the length of the side chains was kept approximately constant. Molecular visualization provided a unique opportunity for independent size characterization of the brush arms separately from that of the entire molecule. In agreement with the Schulz-Flory theory for chain coupling, the polydispersity of the total length was significantly lower than that of the arm length. The variation in polydispersity had an effect on molecular ordering. Lateral compression of the starlike brushes caused a transition from an extended dendritic-like conformation to a compact disklike conformation. In contrast to one-, two-, and three-arm brushes, the four-arm molecules with a lower polydispersity index of 1.04 demonstrated local hexagonal order.

Journal Article↗
PubMed1984

Modifying an underlying component of perceived arm length: adaptation of tactile location induced by spatial discordance.

In four experiments we examined the adaptation and aftereffect that resulted from a treatment yielding tactile/kinesthetic length discordance between the arms. Perceived discordance diminished with trials and tended to zero. Subsequent visual/tactile cross-modal judgments of distance showed the aftereffect to be a change in the perceived location of an unseen probed spot on each hand with respect to the location of a truly coincident visual marker. This occurred toward the body for the probed spot on one arm and away from the body on the other. There were three other main findings: (a) Arm movement was not a necessary condition for adaptation or aftereffect; (b) with intrinsic length information about the right arm present, but touch information from the right index finger absent during treatment, adaptation and aftereffect were abolished; (c) aftereffects of tactile location that were manifest at the hand and wrist tended to zero when a point close to the elbow was tested with a cross-modal procedure. The experiments provide evidence that the mapping of the tactile sheet onto an internal length domain had been modified by the treatment. The sensory consequences of the treatment led many subjects to report spontaneously that their arms felt to be of different lengths.

Adaptation, Physiological↗
PubMed1996

Partial hippocampal kindling affects retention but not acquisition and place but not cue tasks on the radial arm maze.

The performance of rats that were partially kindled in the hippocampus was assessed on an 8-arm radial arm maze with 4 baited arms. In rats first trained and then kindled, deficits were found on a place task in which rats reached the goal arms of the maze using salient extramaze spatial cues, but not on an intramaze cue task in which rats reached the goal arms using salient intramaze cues. Acquisition of a new place task on the maze was not different between kindled and control rats. In conclusion, partial hippocampal kindling disrupted the retention but not the acquisition of a spatial or place task; retention of a nonspatial cue task was not disrupted.

Animals↗
PubMed2005

Genomic and gene expression profiling of minute alterations of chromosome arm 1p in small-cell lung carcinoma cells.

Genetic alterations occurring on human chromosome arm 1p are common in many types of cancer including lung, breast, neuroblastoma, pheochromocytoma, and colorectal. The identification of tumour suppressors and oncogenes on this arm has been limited by the low resolution of current technologies for fine mapping. In order to identify genetic alterations on 1p in small-cell lung carcinoma, we developed a new resource for fine mapping segmental DNA copy number alterations. We have constructed an array of 642 ordered and fingerprint-verified bacterial artificial chromosome clones spanning the 120 megabase (Mb) 1p arm from 1p11.2 to p36.33. The 1p arm of 15 small-cell lung cancer cell lines was analysed at sub-Mb resolution using this arm-specific array. Among the genetic alterations identified, two regions of recurrent amplification emerged. They were detected in at least 45% of the samples: a 580 kb region at 1p34.2-p34.3 and a 270 kb region at 1p11.2. We further defined the potential importance of these genomic amplifications by analysing the RNA expression of the genes in these regions with Affymetrix oligonucleotide arrays and semiquantitative reverse transcriptase-polymerase chain reaction. Our data revealed overexpression of the genes HEYL, HPCAL4, BMP8, IPT, and RLF, coinciding with genomic amplification.

Animals↗
PubMed2001

Deletions of chromosome 13 in multiple myeloma identified by interphase FISH usually denote large deletions of the q arm or monosomy.

Deletions of the long arm of chromosome 13 (13q-) are observed in patients with multiple myeloma (MM), are rarely observed in the monoclonal gammopathy of undetermined significance (MGUS) and have been associated with a worsened prognosis in MM. However, no minimally deleted region in the 13q arm has been defined at 13q, and consequently no tumor suppressor genes have yet been identified that are important for disease pathogenesis. We attempted to characterize these chromosome 13q deletions at the molecular cytogenetic level. We studied 351 newly diagnosed patients, entered into the E9486/E9487 clinical study of the Eastern Cooperative Oncology Group. Fluorescent in situ hybridization (FISH) combined with immune fluorescent detection (cIg-FISH) of clonal plasma cells (PC) and cytomorphology were used to analyze interphase, bone marrow (BM) cell, cytospin slides. We simultaneously used DNA probes for the following locus specific probes (LSI); LSI 13 (Rb) and D13S319, which hybridize to 13q14. We subsequently studied distal deletions using the D13S25 probe (13q14.3) and a subtelomeric probe (13qSTP) for the 13q-arm (D13S327) in 40 cases with documented LSI 13 (Rb)/D13S319 deletion and 40 without deletion of these loci. Of 325 evaluable patients, we found 13q deletions in 176 (54%) using LSI 13 (Rb) and D13S319 probes. Of 40 patients with LSI 13 (Rb)/D13S319 deletions, 34 (85%) had coexistent deletion of both D13S25/13qSTP. These results indicate that chromosome 13 deletions in MM involve loss of most if not all of the 13q arm perhaps even indicating monosomy. In six cases the 13qSTP signal was conserved, but D13S25 was lost indicating large interstitial deletions involving 13q14. In 39 of the 40 cases without LSI 13 (Rb)/D13S319 deletions, the normal pattern of two pairs of signals was observed for D13S25/13qSTP. Deletions involving 13q14 are very common in MM as detected by cIg-FISH. These deletions appear to predominantly involve loss of large segments of the 13q arm or monosomy 13, and only occasionally represent an interstitial deletion.

Adult↗
PubMed1998

Mutational analysis of the NH2-terminal arms of the trp repressor indicates a multifunctional domain.

The NH2-terminal arms of the Escherichia coli trp repressor have been implicated in three functions: formation of repressor-operator complexes via association with non-operator DNA; stabilization of repressor oligomers bound to DNA; and oligomerization of the aporepressor in the absence of DNA. To begin to examine the structural aspects of the arms that are responsible for these varied activities, we generated an extensive set of deletion and substitution mutants and measured the activities of these mutants in vivo using reporter gene fusions. Deletion of any part of the arms resulted in a significant decrease in repressor activity at both the trp and the trpR operons. Positions 4, 5 and 6 were the most sensitive to missense changes. Most substitutions at these positions resulted in repressors with less than 5% of the activity of the wild-type trp repressor. A large percentage of the missense mutants were more active than the wild-type repressor in medium containing tryptophan and less active in medium without tryptophan. This phenotype can be explained in terms of altered oligomerization of both the repressor and the aporepressor. Also, nine super-repressor mutants, resulting from substitutions clustered at both ends of the arms, were found. Our results support the hypothesis that the NH2-terminal arm of the trp repressor is a multifunctional domain and reveal structural components likely to be involved in the various functions.

Bacterial Proteins↗
PubMed2002

Role of syndecan in the elongation of postoral arms in sea urchin larvae.

Ac-SYN is the core protein of a cell surface proteoglycan of the sea urchin Anthocidaris crassispina. To examine the functions of Ac-SYN, embryos were cultured in the presence of affinity-purified antibody against Ac-SYN. At the late pluteus stage, severe inhibition of elongation of the postoral arms was seen in treated embryos compared with control embryos. Blastocoeleic microinjection of the antibody did not affect morphogenesis. The relationship between the number of cells in the postoral arms and the length of the postoral rods was investigated in normal embryos. This showed that postoral arm elongation has two phases: the first phase accompanies the increase in cell numbers while the second does not. The syndecan antibody inhibited the increase in cell numbers in the postoral arms. Furthermore, in the treated embryos, cell numbers continued to increase normally until 31 h post fertilization (hpf), while cell division stopped after 31 hpf. These results suggest that Ac-SYN participates in postoral arm formation via cell division in sea urchin embryos.

Animals↗
PubMed2002

Forearm reactive hyperemic blood flow and arm-cranking exercise capacity in healthy and heart failure subjects.

BACKGROUND: The relationship between lower limbs maximal vasodilatory capacity and exercise capacity in congestive heart failure (CHF) and healthy subjects has been well-documented. However, the relationship between upper limbs maximal vasodilatory capacity and exercise is less well-established. METHODS AND RESULTS: Twelve patients with CHF, 16 age-matched normal subjects, and 11 very fit individuals underwent an arm-cranking exercise test using maximal oxygen uptake (arm VO(2max)) and measurements of peak forearm reactive hyperemic blood flow. Despite similar forearm strength, arm VO(2max) was significantly reduced in patients with CHF when compared to normal and very fit individuals (13.9 +/- 2.9, 23.5 +/- 4.8, and 36.4 +/- 8.5 mL/kg/min, respectively, P <.05). Similarly, peak reactive hyperemia was lower in CHF patients as compared to normal and very fit individuals (18.6 +/- 5.9, 24.3 +/- 5.8, and 41.1 +/- 8.1 mL/100 mL/min, respectively, P <.05). There was a strong relationship between peak reactive hyperemic blood flow and arm VO(2max) (r =.75; P <.001) in all subjects. CONCLUSIONS: These results suggest a significant relationship between forearm vasodilatory capacity and arm-cranking VO(2max) in CHF patients, sedentary, and very fit individuals.

Adult↗
PubMed1989

Massive pulmonary embolism: triple-armed therapy.

Many patients who suffer a massive pulmonary embolus die despite emergent therapy. In these desperately ill patients an aggressive, combined method of management was initiated to improve their chances and quality of survival. During a 5-year period 10 patients were treated with (1) low-dose topical, intrapulmonary thrombolytic therapy to dissolve thrombus, (streptokinase or urokinase); (2) anticoagulation to prevent thrombus propagation (heparin); and (3) the simultaneous insertion of a Greenfield filter to prevent the early, recurrent, and therefore potentially fatal pulmonary embolus--"triple-armed therapy." Thrombolytic therapy was administered through a Swan-Ganz catheter wedged against the pulmonary embolus. During the same interval 10 other patients also sustained massive pulmonary emboli but were treated only with systemic heparin. Serial pulmonary arteriography was performed daily. The patients treated by triple-armed therapy responded favorably with a rapid (less than 6 hours), significant improvement in PaO2, pulmonary artery pressure, cardiac output, pulmonary vascular resistance, and blood pressure, compared with patients treated with continuous heparin alone. Nine patients in the triple-armed therapy group survived whereas only six in the heparin group survived. Two additional patients were treated by triple-armed therapy and had thrombolysis with triple-armed therapy with tissue plasminogen activator; these patients demonstrated the most rapid improvement in cardiorespiratory dynamics and arteriographic clearance of emboli. This management protocol shows promise for patients who sustain a massive pulmonary embolus, because it reduces the morbidity associated with pulmonary embolectomy while avoiding the hazards associated with systemic thrombolytic therapy.

Aged↗
PubMed1994

Design of a "minimAl" homeodomain: the N-terminal arm modulates DNA binding affinity and stabilizes homeodomain structure.

This report investigates the sequence specificity requirements for homeodomain structure and DNA binding activity by the design and synthesis of a "minimAl" homeodomain (for minimalist design and alanine scanning mutagenesis) which contains the consensus residues and in which all nonconsensus residues have been replaced with alanine. The murine homeodomain Msx served as the prototype for the minimAl homeodomain, Ala-Msx. We show that Ala-Msx binds to DNA specifically, albeit with lower affinity than Msx. A derivative of the minimAl homeodomain, Ala-Msx(NT), which contains a native rather than an alanine-substituted N-terminal arm, has similar DNA binding affinity as Msx. We show that the native N-terminal arm stabilizes the tertiary structure of the minimAl homeodomain. Although Ala-Msx resembles a molten-globule protein, the structure of Ala-Msx(NT) is similar to Msx. The requirement for an intact N-terminal arm is not unique to the minimAl homeodomain, since the N-terminal arm also promotes high-affinity binding activity and appropriate tertiary structure of Msx. Therefore, the homeodomain "scaffold" consists of consensus residues, which are sufficient for DNA recognition, and nonconsensus residues in the N-terminal arm, which are required for optimal DNA binding affinity and appropriate tertiary structure. MinimAl design provides a powerful strategy to probe homeodomain structure and function. This approach should be of general utility to study the sequence specificity requirements for structure and function of other DNA-binding domains.

Alanine↗
PubMed2006

The N-terminal arm of small heat shock proteins is important for both chaperone activity and substrate specificity.

Small heat shock proteins (sHSPs) are a ubiquitous class of molecular chaperones that interacts with substrates to prevent their irreversible insolubilization during denaturation. How sHSPs interact with substrates remains poorly defined. To investigate the role of the conserved C-terminal alpha-crystallin domain versus the variable N-terminal arm in substrate interactions, we compared two closely related dodecameric plant sHSPs, Hsp18.1 and Hsp16.9, and four chimeras of these two sHSPs, in which all or part of the N-terminal arm was switched. The efficiency of substrate protection and formation of sHSP-substrate complexes by these sHSPs with three different model substrates, firefly luciferase, citrate synthase, and malate dehydrogenase (MDH) provide new insights into sHSP/substrate interactions. Results indicate that different substrates have varying affinities for different domains of the sHSP. For luciferase and citrate synthase, the efficiency of substrate protection was determined by the identity of the N-terminal arm in the chimeric proteins. In contrast, for MDH, efficient protection clearly required interactions with the alpha-crystallin domain in addition to the N-terminal arm. Furthermore, we show that sHSP-substrate complexes with varying stability and composition can protect substrate equally, and substrate protection is not correlated with sHSP oligomeric stability for all substrates. Protection of MDH by the dimeric chimera composed of the Hsp16.9 N-terminal arm and Hsp18.1 alpha-crystallin domain supports the model that a dimeric form of the sHSP can bind and protect substrate. In total, results demonstrate that sHSP-substrate interactions are complex, likely involve multiple sites on the sHSP, and vary depending on substrate.

Amino Acid Sequence↗
PubMed1993

Are the Orientations of the Head and Arm Related During Pointing Movements?

The head, eye, and shoulder are each free to rotate around three mutually orthogonal axes. These three degrees of freedom allow a given gaze or pointing direction of the eye, head, or arm to be obtained in many different possible orientations. Unlike translations in three dimensions, three-dimensional (3-D) rotations are noncommutative. Therefore, the orientation of a rigid body following sequential rotations about two different axes depends on the order of the rotations. In this article, we demonstrate that only two degrees of freedom are used during orienting movements of the head and pointing movements of the arm. This provides a unique orientation of head and arm for each gaze or pointing direction despite the noncommutativity of three-dimensional rotations. This observation is in itself not new. We found, however, that (a) the two-dimensional lquot;rotation surface,rquot; which describes the orientation of the head for all gaze directions, is curved, unlike the analogous flat plane for the eye. (b) The rotation surface for the head is curved differently than that for the arm. This result argues against the hypothesis that the orientations of head and arm are directly coupled during pointing. It also implies that the orientation of the eye in space during gaze shifts of the eye and head is not uniquely determined for a given direction of gaze. This finding argues against a perceptual basis for the reduction of rotational degrees of freedom.

Journal Article↗
PubMed2006

Substrate oxidation during incremental arm and leg exercise in men and women matched for ventilatory threshold.

The aim of this study was to determine the variations in substrate utilization between men and women matched for ventilatory threshold (Tvent) during incremental arm cranking and leg cycling exercise at 70, 85, 100 and 115% of the mode-specific Tvent. Recreationally active men (n=12) and women (n=10) with similar values for percentage of peak oxygen consumption at Tvent participated in the study. Ventilatory equivalence, excess CO2 and modified V-slope methods were used concurrently to determine Tvent. The participants performed 5 min of exercise at each of 70, 85, 100 and 115% Tvent during both arm cranking and leg cycling exercise. The females were tested during the early follicular phase for all trials. A two-way mixed-design analysis of variance was performed to test for differences between the sexes. When carbohydrate and fat oxidation were expressed relative to total fat-free mass, carbohydrate oxidation during arm cranking and leg cycling was significantly higher in men than women at each percentage of Tvent. In contrast, women showed significantly higher fat oxidation across intensities during both arm cranking and leg cycling. Our results suggest that when substrate utilization is expressed relative to total fat-free mass, women appear to maintain a higher rate of fat and lower rate of carbohydrate oxidation than men during both incremental arm cranking and leg cycling exercise relative to Tvent.

Adult↗
PubMed1991

The proximal portion of Chlamydomonas flagella contains a distinct set of inner dynein arms.

A specific type of inner dynein arm is located primarily or exclusively in the proximal portion of Chlamydomonas flagella. This dynein is absent from flagella less than 6 microns long, is assembled during the second half of flagellar regeneration time and is resistant to extraction under conditions causing complete solubilization of two inner arm heavy chains and partial solubilization of three other heavy chains. This and other evidence described in this report suggest that the inner arm row is composed of five distinct types of dynein arms. Therefore, the units of three inner arms that repeat every 96 nm along the axoneme are composed of different dyneins in the proximal and distal portions of flagella.

Cell Movement↗