bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors Affecting the Spread and Duration of Epidural Anesthesia with Ropivacaine
Authors: Higuchi Hideyuki , Adachi Yushi , Kazama Tomiei 
Published: July 2004

Background
Epidural anesthesia has an unpredictable extent and duration. Differences in the surface area of the lumbosacral dura, epidural fat volume, and epidural venous plexus velocity might explain the variability in the extent and duration of epidural anesthesia with ropivacaine.

Methods
Twenty-six healthy patients, aged 18-45 y, undergoing peripheral orthopedic surgery were enrolled. Dural surface area and posterior epidural fat volume were calculated from low thoracic, lumbar, and sacral axial magnetic resonance images obtained at 8-mm increments. Epidural venous plexus velocity at the L3-L4 disk level was derived from phase-contrast magnetic resonance images. The patients received 100 mg ropivacaine (1.0%) epidurally. The spread and duration of sensory anesthesia was assessed by pinprick, and that of motor block was assessed using a modified Bromage scale. Statistical correlation coefficients (rho) between magnetic resonance imaging and epidural anesthesia measurements were assessed by Spearman rank correlation. Stepwise multiple linear regression models were used to select important predictors of measures of epidural anesthesia.

Results
Dural surface area correlated with peak sensory block level (rho= -0.73, P = 0.0003) and onset time of caudal and cephalad block (rho = 0.62, P = 0.002; rho = -0.63, P = 0.002). Fat volume correlated with the regression to L5-S3 (rho = -0.44.44 to -0.54, P = 0.029 to 0.007). Epidural venous plexus velocity was significantly correlated with the regression to L3 (rho = -0.42, P = 0.038) and L4 (rho = -0.48, P = 0.017). Multiple regression analysis revealed that dural surface area was a significant predictive variable for the peak sensory block level (R = 0.61, P < 0.0001).

Conclusions
These findings indicate that dural surface area influences the spread of epidural anesthesia with ropivacaine and posterior fat volume influences the duration of epidural anesthesia in healthy patients within a narrow age range. Epidural venous plexus velocity might also influence the duration of epidural anesthesia with ropivacaine.
Early but No Long-term Benefit of Regional Compared with General Anesthesia for Ambulatory Hand Surgery
Authors: McCartney Colin J. L. , Brull Richard , Chan Vincent W. S. , Katz Joel , Abbas Sherif , Graham Brent , Nova Hugo , Rawson Regan , Anastakis Dimitri J. , von Schroeder Herbert 
Published: July 2004

Background
The purpose of this study was to determine whether either regional anesthesia (RA) or general anesthesia (GA) provided the best analgesia with the fewest adverse effects up to 2 weeks after ambulatory hand surgery.

Methods
Patients undergoing ambulatory hand surgery were randomly assigned to RA (axillary brachial plexus block; n = 50) or GA (n = 50). Before surgery, all patients rated their hand pain (visual analog scale) and pain-related disability (Pain-Disability Index). After surgery, eligibility for bypassing the postanesthesia care unit ("fast track") was determined, and pain, adverse effects, and home-readiness scores were measured. On postoperative days 1, 7, and 14, patients documented their pain, opioid consumption, adverse effects, Pain-Disability Index, and satisfaction.

Results
More RA patients were fast-track eligible (P < 0.001), whereas duration of stay in the postanesthesia care unit was shorter in the RA group (P < 0.001). Time to first analgesic request was longer in the RA group (P < 0.001), and opioid consumption was reduced before discharge (P < 0.001). In the RA group, the pain ratings measured at 30, 60, 90, and 120 min after surgery were lower (P < 0.001), and patients spent less time in the hospital after surgery (P < 0.001). More GA patients experienced nausea/vomiting during recovery in the hospital (P < 0.05). However, on postoperative days 1, 7, and 14, there were no differences in pain, opioid consumption, adverse effects, Pain-Disability Index, or satisfaction.

Conclusions
Despite significant reduction in pain before discharge from the hospital after ambulatory hand surgery, single-shot axillary brachial plexus block does not reduce pain at home on postoperative day 1 or up to 14 days after surgery when compared with GA. However, RA does provide other significant early benefits, including reduction in nausea and faster discharge from the hospital.
Detection of Neuropathic Pain in a Rat Model of Peripheral Nerve Injury
Authors: Hogan Quinn , Sapunar Damir , Modric-Jednacak Ksenija , McCallum J Bruce 
Published: July 2004

Background
Behavioral criteria that confirm neuropathic pain in animal injury models are undefined. Therefore, the authors sought clinically relevant measures that distinguish pain behavior of rats with peripheral nerve injury from those with sham injury.

Methods
The authors examined mechanical and thermal sensory sensitivity, comparing responses at baseline to responses after spinal nerve ligation (SNL group), sham nerve injury (sham group), or skin incision alone (control group).

Results
Substantial variance was evident in all sensory tests at baseline. After surgery, tests using brush, cold, or heat stimulation showed minimal distinctions between surgical groups. Postsurgical thresholds for flexion withdrawal from mechanical stimulation with von Frey fibers were decreased bilaterally in SNL and sham groups. In contrast, the probability of a complex hyperalgesia-type response with prolonged elevation, shaking, or licking of the paw was selectively increased on the ipsilateral side in the SNL group. Nonetheless, the effect of SNL on behavior was inconsistent, regardless of the sensory test. The behavioral measure that best distinguishes between SNL and sham groups and thereby best identifies animals with successful SNL-induced neuropathic pain is increased ipsilateral postsurgical probability of a hyperalgesia-type response to noxious mechanical stimulation. Using receiver operating characteristics analysis, mechanical hyperalgesia identifies a local SNL effect in approximately 60% of animals when specificity is required to be 90% or higher.

Conclusions
Simple withdrawal from von Frey tactile stimulation, although frequently used, is not a valid measure of peripheral nerve injury pain in rats, whereas a complex hyperalgesic-type response is a specific neuropathy-induced behavior.
Clonidine Prolongation of Lidocaine Analgesia after Sciatic Nerve Block in Rats Is Mediated via the Hyperpolarization-activated Cation Current, Not by α-Adrenoreceptors
Authors: Kroin Jeffrey S. , Buvanendran Asokumar , Beck Daniel R. , Topic Julie E. , Watts Daniel E. , Tuman Kenneth J. 
Published: July 2004

Background
Although clonidine is commonly combined with local anesthetics to extend duration of peripheral nerve block, the mechanism by which clonidine potentiates local anesthetic action in vivo is unclear.

Methods
Male Sprague-Dawley rats received percutaneous injections of 1% lidocaine with/without clonidine or epinephrine into the sciatic notch and duration of sensory blockade was quantified by inhibition of pinprick foot withdrawal. The antagonists prazosin or yohimbine were injected before lidocaine with clonidine or epinephrine to determine the role of alpha-adrenergic receptors. The role of the hyperpolarization-activated cation current (Ih) was evaluated by injecting the current blocker ZD 7288 as well as the current enhancers forskolin and 8-Br-cAMP before lidocaine alone or with 15 micrograms/ml clonidine.

Results
Mean duration of sensory block for lidocaine alone was 69 +/- 2 min. Sensory block duration increased monotonically with increasing doses of added clonidine or epinephrine. Preinjection of prazosin but not yohimbine prevented the increase in block duration seen with epinephrine. Neither alpha-adrenergic antagonist attenuated the extended duration of block with clonidine. ZD 7288 extended sensory blockade equivalent to the prolongation observed with clonidine. There was no additive effect when ZD 7288 and clonidine were combined, and a decreased duration of nerve block when either forskolin or 8-Br-cAMP preceded injection of lidocaine with clonidine.

Conclusions
The findings indicate that prolongation of duration of in vivo lidocaine nerve blockade by clonidine is not mediated by an alpha-adrenergic mechanism but likely involves the Ih current.
Experimentally biased model structure of the Hsc70/auxilin complex: Substrate transfer and interdomain structural change
Authors: Gruschus James M. , Greene Lois E. , Eisenberg Evan , Ferretti James A. 
Published: July 2004

AbstractA model structure of the Hsc70/auxilin complex has been constructed to gain insight into interprotein substrate transfer and ATP hydrolysis induced conformational changes in the multidomain Hsc70 structure. The Hsc70/auxilin system, which is a member of the Hsp70/Hsp40 chaperone system family, uncoats clathrin‐coated vesicles in an ATP hydrolysis‐driven process. Incorporating previous results from NMR and mutant binding studies, the auxilin J‐domain was docked into the Hsc70 ATPase domain lower cleft using rigid backbone/flexible side chain molecular dynamics, and the Hsc70 substrate binding domain was docked by a similar procedure. For comparison, J‐domain and substrate binding domain docking sites were obtained by the rigid‐body docking programs DOT and ZDOCK, filtered and ranked by the program ClusPro, and relaxed using the same rigid backbone/flexible side chain dynamics. The substrate binding domain sites were assessed in terms of conserved surface complementarity and feasibility in the context of substrate transfer, both for auxilin and another Hsp40 protein, Hsc20. This assessment favors placement of the substrate binding domain near D152 on the ATPase domain surface adjacent to the J‐domain invariant HPD segment, with the Hsc70 interdomain linker in the lower cleft. Examining Hsc70 interdomain energetics, we propose that long‐range electrostatic interactions, perhaps due to a difference in the pKa values of bound ATP and ADP, could play a major role in the structural change induced by ATP hydrolysis. Interdomain electrostatic interactions also appear to play a role in stimulation of ATPase activity due to J‐domain binding and substrate binding by Hsc70.
Kinetic traps in the folding/unfolding of procaspase‐1 CARD domain
Authors: Chen Yun‐Ru , Clark A. Clay 
Published: July 2004

AbstractWe have examined the folding and unfolding of the caspase recruitment domain of procaspase‐1 (CP1‐CARD), a member of the α‐helical Greek key protein family. The equilibrium folding/unfolding of CP1‐CARD is described by a two‐state mechanism, and the results show CP1‐CARD is marginally stable with a ΔG of 1.1 ± 0.2 kcal/mole and an m‐value of 0.65 ± 0.06 kcal/mole/M (10 mM Tris‐HCl at pH 8.0, 1 mM DTT, 25°C). Consistent with the equilibrium folding data, CP1‐CARD is a monomer in solution when examined by size exclusion chromatography. Single‐mixing stopped‐flow refolding and unfolding studies show that CP1‐CARD folds and unfolds rapidly, with no detectable slow phases, and the reactions appear to reach equilibrium within 10 msec. However, double jump kinetic experiments demonstrate the presence of an unfolded‐like intermediate during unfolding. The intermediate converts to the fully unfolded conformation with a half‐time of 10 sec. Interrupted refolding studies demonstrate the presence of one or more nativelike intermediates during refolding, which convert to the native conformation with a half‐time of about 60 sec. Overall, the data show that both unfolding and refolding processes are slow, and the pathways contain kinetically trapped species.
A classification of disulfide patterns and its relationship to protein structure and function
Authors: Gupta Abhas , Van Vlijmen Herman W.T. , Singh Juswinder 
Published: July 2004

AbstractWe report a detailed classification of disulfide patterns to further understand the role of disulfides in protein structure and function. The classification is applied to a unique searchable database of disulfide patterns derived from the SwissProt and Pfam databases. The disulfide database contains seven times the number of publicly available disulfide annotations. Each disulfide pattern in the database captures the topology and cysteine spacing of a protein domain. We have clustered the domains by their disulfide patterns and visualized the results using a novel representation termed the “classification wheel.” The classification is applied to 40,620 protein domains with 2–10 disulfides. The effectiveness of the classification is evaluated by determining the extent to which proteins of similar structure and function are grouped together through comparison with the SCOP and Pfam databases, respectively. In general, proteins with similar disulfide patterns have similar structure and function, even in cases of low sequence similarity, and we illustrate this with specific examples. Using a measure of disulfide topology complexity, we find that there is a predominance of less complex topologies. We also explored the importance of loss or addition of disulfides to protein structure and function by linking classification wheels through disulfide subpattern comparisons. This classification, when coupled with our disulfide database, will serve as a useful resource for searching and comparing disulfide patterns, and understanding their role in protein structure, folding, and stability. Proteins in the disulfide clusters that do not contain structural information are prime candidates for structural genomics initiatives, because they may correspond to novel structures.
Determination of enzyme mechanisms by molecular dynamics: Studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase
Authors: Reddy Swarnalatha Y. , Bruice Thomas C. 
Published: July 2004

AbstractMolecular dynamics (MD) simulations have been carried out to study the enzymatic mechanisms of quinoproteins, methanol dehydrogenase (MDH), and soluble glucose dehydrogenase (sGDH). The mechanisms of reduction of the orthoquinone cofactor (PQQ) of MDH and sGDH involve concerted base‐catalyzed proton abstraction from the hydroxyl moiety of methanol or from the 1‐hydroxyl of glucose, and hydride equivalent transfer from the substrate to the quinone carbonyl carbon C5 of PQQ. The products of methanol and glucose oxidation are formaldehyde and glucolactone, respectively. The immediate product of PQQ reduction, PQQH− [−HC5(O−) −C4( = O) −] and PQQH [−HC5(OH) −C4( = O) −] converts to the hydroquinone PQQH2 [−C5(OH) = C4(OH) −]. The main focus is on MD structures of MDH • PQQ • methanol, MDH • PQQH−, MDH • PQQH, sGDH • PQQ • glucose, sGDH • PQQH− (glucolactone, and sGDH • PQQH. The reaction PQQ → PQQH− occurs with Glu 171–CO2− and His 144–Im as the base species in MDH and sGDH, respectively. The general‐base‐catalyzed hydroxyl proton abstraction from substrate concerted with hydride transfer to the C5 of PQQ is assisted by hydrogen‐bonding to the C5 = O by Wat1 and Arg 324 in MDH and by Wat89 and Arg 228 in sGDH. Asp 297–COOH would act as a proton donor for the reaction PQQH− → PQQH, if formed by transfer of the proton from Glu 171–COOH to Asp 297–CO2− in MDH. For PQQH → PQQH2, migration of H5 to the C4 oxygen may be assisted by a weak base like water (either by crystal water Wat97 or bulk solvent, hydrogen‐bonded to Glu 171–CO2− in MDH and by Wat89 in sGDH).
Biophysical and kinetic analysis of wild‐type and site‐directed mutants of the isolated and native dehydroquinate synthase domain of the AROM protein
Authors: Park Alison , Lamb Heather K. , Nichols Charlie , Moore Jonathan D. , Brown Katherine A. , Cooper Alan , Charles Ian G. , Stammers David K. , Hawkins Alastair R. 
Published: July 2004

AbstractDehydroquinate synthase (DHQS) is the N‐terminal domain of the pentafunctional AROM protein that catalyses steps 2 to 7 in the shikimate pathway in microbial eukaryotes. DHQS converts 3‐deoxy‐D‐arabino‐heptulosonate‐7‐phosphate (DAHP) to dehydroquinate in a reaction that includes alcohol oxidation, phosphate β‐elimination, carbonyl reduction, ring opening, and intramolecular aldol condensation. Kinetic analysis of the isolated DHQS domains with the AROM protein showed that for the substrate DAHP the difference inKmis less than a factor of 3, that the turnover numbers differed by 24%, and that theKmfor NAD+differs by a factor of 3. Isothermal titration calorimetry revealed that a second (inhibitory) site for divalent metal binding has an approximately 4000‐fold increase inKDcompared to the catalytic binding site. Inhibitor studies have suggested the enzyme could act as a simple oxidoreductase with several of the reactions occurring spontaneously, whereas structural studies have implied that DHQS participates in all steps of the reaction. Analysis of site‐directed mutants experimentally test and support this latter hypothesis. Differential scanning calorimetry, circular dichroism spectroscopy, and molecular exclusion chromatography demonstrate that the mutant DHQS retain their secondary and quaternary structures and their ligand binding capacity. R130K has a 135‐fold reduction in specific activity with DAHP and a greater than 1100‐fold decrease in thekcat/Kmratio, whereas R130A is inactive.
The comparative study on the solution structures of the oxidized bovine microsomal cytochrome b5 and mutant V45H
Authors: Zhang Qi , Cao Chunyang , Wang Zhi‐Qiang , Wang Yun‐Hua , Wu Houming , Huang Zhong‐Xian 
Published: July 2004

AbstractA comparative study on the solution structures of bovine microsomal cytochrome b5 (Tb5) and the mutant V45H has been achieved by 1D and 2D 1H‐NMR spectroscopy to clarify the differences in the solution conformations between these two proteins. The results reveal that the global folding of the V45H mutant in solution is unchanged, but the subtle changes exist in the orientation of the axial ligand His39, and heme vinyl groups. The side chain of His45 in V45H mutant extends to the outer edge of the heme pocket leaving a cavity at the site originally occupied by the inner methyl group of Val45 residue. In addition, the imidazole ring of axial ligand His39 rotates counterclockwise by ∼3° around the His‐Fe‐His axis, and the 4‐heme vinyl group turns to the space vacated by the removed side chain due to the mutation. Furthermore, the helix III of the heme pocket undergoes outward displacement, while the linkage between helix II and III is shifted leftward. These observations are not only consistent with the pattern of the pseudocontact shifts of the heme protons, but also well account for the lower stability of V45H mutant against heat and urea.
Solution structure of the RWD domain of the mouse GCN2 protein
Authors: Nameki Nobukazu , Yoneyama Misao , Koshiba Seizo , Tochio Naoya , Inoue Makoto , Seki Eiko , Matsuda Takayoshi , Tomo Yasuko , Harada Takushi , Saito Kohei , Kobayashi Naohiro , Yabuki Takashi , Aoki Masaaki , Nunokawa Emi , Matsuda Natsuko , Sakagami Noriko , Terada Takaho , Shirouzu Mikako , Yoshida Mayumi , Hirota Hiroshi , Osanai Takashi , Tanaka Akiko , Arakawa Takahiro , Carninci Piero , Kawai Jun , Hayashizaki Yoshihide , Kinoshita Kengo , Güntert Peter , Kigawa Takanori , Yokoyama Shigeyuki 
Published: July 2004

AbstractGCN2 is the α‐subunit of the only translation initiation factor (eIF2α) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N‐terminus, which is termed the RWD domain after three major RWD‐containing proteins: RING finger‐containing proteins, WD‐repeat‐containing proteins, and yeast DEAD (DEXD)‐like helicases. In this study, we determined the solution structure of the mouse GCN2 RWD domain using NMR spectroscopy. The structure forms an α + β sandwich fold consisting of two layers: a four‐stranded antiparallel β‐sheet, and three side‐by‐side α‐helices, with an αββββαα topology. A characteristic YPXXXP motif, which always occurs in RWD domains, forms a stable loop including three consecutive β‐turns that overlap with each other by two residues (triple β‐turn). As putative binding sites with GCN1, a structure‐based alignment allowed the identification of several surface residues in α‐helix 3 that are characteristic of the GCN2 RWD domains. Despite the apparent absence of sequence similarity, the RWD structure significantly resembles that of ubiquitin‐conjugating enzymes (E2s), with most of the structural differences in the region connecting β‐strand 4 and α‐helix 3. The structural architecture, including the triple β‐turn, is fundamentally common among various RWD domains and E2s, but most of the surface residues on the structure vary. Thus, it appears that the RWD domain is a novel structural domain for protein‐binding that plays specific roles in individual RWD‐containing proteins.
Asymmetric amino acid compositions of transmembrane β‐strands
Authors: Chamberlain Aaron K. , Bowie James U. 
Published: July 2004

AbstractIn contrast to water‐soluble proteins, membrane proteins reside in a heterogeneous environment, and their surfaces must interact with both polar and apolar membrane regions. As a consequence, the composition of membrane proteins' residues varies substantially between the membrane core and the interfacial regions. The amino acid compositions of helical membrane proteins are also known to be different on the cytoplasmic and extracellular sides of the membrane. Here we report that in the 16 transmembrane β‐barrel structures, the amino acid compositions of lipid‐facing residues are different near the N and C termini of the individual strands. Polar amino acids are more prevalent near the C termini than near the N termini, and hydrophobic amino acids show the opposite trend. We suggest that this difference arises because it is easier for polar atoms to escape from the apolar regions of the bilayer at the C terminus of a β‐strand. This new characteristic of β‐barrel membrane proteins enhances our understanding of how a sequence encodes a membrane protein structure and should prove useful in identifying and predicting the structures of trans‐membrane β‐barrels.
Caspase activation, inhibition, and reactivation: A mechanistic view
Authors: Shi Yigong 
Published: July 2004

AbstractCaspases, a unique family of cysteine proteases, execute programmed cell death (apoptosis). Caspases exist as inactive zymogens in cells and undergo a cascade of catalytic activation at the onset of apoptosis. The activated caspases are subject to inhibition by the inhibitor‐of‐apoptosis (IAP) family of proteins. This inhibition can be effectively removed by diverse proteins that share an IAP‐binding tetrapeptide motif. Recent structural and biochemical studies have revealed the underlying molecular mechanisms for these processes in mammals and in Drosophila. This paper reviews these latest advances.