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W C Johnson

Publications and source records attributed to W C Johnson.

At least 109 records · Page 6Linked to original sources
PubMed1987

Prediction of the tertiary structure of the alpha-subunit of tryptophan synthase.

The tertiary structure of the alpha-subunit of tryptophan synthase was proposed using a combination of experimental data and computational methods. The vacuum-ultraviolet circular dichroism spectrum was used to assign the protein to the alpha/beta-class of supersecondary structures. The two-domain structure of the alpha-subunit (Miles et al.: Biochemistry 21:2586, 1982; Beasty and Matthews: Biochemistry 24:3547, 1985) eliminated consideration of a barrel structure and focused attention on a beta-sheet structure. An algorithm (Cohen et al.: Biochemistry 22:4894, 1983) was used to generate a secondary structure prediction that was consistent with the sequence data of the alpha-subunit from five species. Three potential secondary structures were then packed into tertiary structures using other algorithms. The assumption of nearest neighbors from second-site revertant data eliminated 97% of the possible tertiary structures; consideration of conserved hydrophobic packing regions on the beta-sheet eliminated all but one structure. The native structure is predicted to have a parallel beta-sheet flanked on both sides by alpha-helices, and is consistent with the available data on chemical cross-linking, chemical modification, and limited proteolysis. In addition, an active site region containing appropriate residues could be identified as well as an interface for beta 2-subunit association. The ability of experimental data to facilitate the prediction of protein structure is discussed.

Amino Acid Sequence↗
PubMed1987

Early diagnosis of pancreatic infection by computed tomography-guided aspiration.

We performed 92 computed tomography-guided percutaneous needle aspirations of pancreatic inflammatory masses in 60 patients suspected of harboring pancreatic infection. Thirty-six patients (60%) were found by Gram stain and culture to have a total of 41 separate episodes of pancreatic infection. Among 42 aspirates judged to be infected by computed tomography-guided aspiration, all but one were confirmed by surgery or indwelling catheter drainage. Among 50 aspirates judged to be sterile, no subsequent evidence of infection was found. All patients tolerated the procedure well and no complications were noted. As a result of this technique, we observed that pancreatic infection occurs earlier than has been previously appreciated (within 14 days of the onset of pancreatitis in 20 of the 36 patients) and that infection may recur during prolonged bouts of pancreatitis. We conclude that guided aspiration is a safe, accurate method for identifying infection of the pancreas at an early stage.

Acute Disease↗
PubMed1987

Treatment of claudication with pentoxifylline: are benefits related to improvement in viscosity?

Forty-five patients with short-distance claudication were treated with pentoxifylline. The initial claudication distance increased significantly (32.5 m, p = 0.02) and the absolute claudication distance (ACD) increased significantly (49.5 m, p = 0.001) while the patients were receiving pentoxifylline. Patients with initial elevated viscosity levels were more likely to have decreased viscosity with pentoxifylline than were patients with normal viscosity levels (p = 0.01). No significant improvement in ACD or viscosity was noted in 51% of patients. Both ACD and viscosity improved in 15% of patients, viscosity improved without improvement in ACD in 9%, and ACD improved without improvement in viscosity in 25%.

Blood Viscosity↗
PubMed1987

Burkitt's lymphoma with ileocecal and subdiaphragmatic masses.

Approximately 25 new cases of American Burkitt's lymphoma (ABL) are diagnosed and reported yearly. Black patients presenting with ABL occur in less than 5 percent of the reported cases. A 47-year-old black man with ABL and ileocecal masses typical of the disease is presented. Symptoms, physical findings, and radiologic features of the disease are assessed. The combined modality of aggressive surgical extirpation and chemotherapy may improve remission and survival time by reduction of tumor burden.

Burkitt Lymphoma↗
PubMed1986

Conformational analysis of thymidylate synthase from amino acid sequence and circular dichroism.

Circular dichroism studies were carried out in the vacuum ultraviolet region for thymidylate synthase from Lactobacillus casei and its ligand complexes. The CD spectrum was analyzed for secondary structure by our method and the variable selection method, and both gave similar results. Our method predicts 33% alpha-helix, 25% (23% antiparallel and 2% parallel) beta-sheet, 20% turns, and 16% other structure. The secondary structure of this protein was also predicted from the amino acid sequence by four different methods. Though there is a variation in the prediction among these methods, the prediction of 32% alpha-helix and 23% beta-sheet by combining the four methods is in excellent agreement with our CD results. Further, the location of the predicted regions of alpha-helices and beta-strands along the sequence and the CD characteristics strongly suggest that this protein belongs to an alpha + beta structural class. Binding of the inhibitor FdUMP or the cofactor 5,10-methylenetetrahydrofolate did not change the CD spectrum. However, when both ligands were present, there was a significant change in the CD spectrum and the maximum changes occurred when the concentration of FdUMP was 1 mol/mol of enzyme. The addition of FdUMP and cofactor causes, respectively, a 5% and 6% decrease in beta-sheet and beta-turns and about an 8% increase in "other" structure.

Amino Acid Sequence↗
PubMed1986

Analysis of protein circular dichroism spectra for secondary structure using a simple matrix multiplication.

Inverse circular dichroism (CD) spectra are presented for each of the five major secondary structures of proteins: alpha-helix, antiparallel and parallel beta-sheet, beta-turn, and other (random) structures. The fraction of the each secondary structure in a protein is predicted by forming the dot product of the corresponding inverse CD spectrum, expressed as a vector, with the CD spectrum of the protein digitized in the same way. We show how this method is based on the construction of the generalized inverse from the singular value decomposition of a set of CD spectra corresponding to proteins whose secondary structures are known from X-ray crystallography. These inverse spectra compute secondary structure directly from protein CD spectra without resorting to least-squares fitting and standard matrix inversion techniques. In addition, spectra corresponding to the individual secondary structures, analogous to the CD spectra of synthetic polypeptides, are generated from the five most significant CD eigenvectors.

Chemical Phenomena↗
PubMed1986

Staged infrainguinal revascularization: initial prosthetic above-knee bypass followed by a distal vein bypass for recurrent ischemia. A valid concept for extending limb salvage?

Optimal infrainguinal revascularization should provide limb salvage for the longest duration of time. It is not known whether limb salvage is longer with an initial below-knee popliteal or tibial in situ saphenous vein graft or with staged bypasses; that is, an initial above-knee popliteal prosthetic bypass if feasible, followed by a more distal vein graft should the above-knee prosthetic graft fail. A retrospective review of 197 lower extremity vascular reconstructions performed since 1976 utilizing polytetrafluoroethylene (PTFE), umbilical vein, or in situ saphenous vein was completed. The data were analyzed for differences in limb salvage and prevention of limb threatening ischemia among three subgroups: above-knee prosthetic bypass, below-knee or tibial in situ saphenous vein bypass, and staged reconstructions (above-knee prosthetic bypass with subsequent in situ bypass). The groups were similar with respect to severity of limb threatening ischemia as indicated by mean preoperative ankle-brachial indices. Cumulative secondary limb salvage at 36 months was 73 percent for prosthetic grafts in the above-knee position, 78 percent for in situ saphenous vein grafts in the below-knee or tibial position, and 87 percent for staged reconstruction with an initial prosthetic graft to the above-knee position followed by a distal in situ vein bypass when the prosthetic graft fails.

Arteriosclerosis↗
PubMed1986

Treatment of pitted scars: punch transplant technique.

This paper describes an operation for treatment of pitted scars of the face. After local anesthesia, the pitted scar is removed by a cutaneous punch. Donor grafts are obtained from the postauricular skin and held in place using a Steri-Strip or other method. The graft is placed so that it will be level or slightly elevated. The dressing is removed at 2 days and the graft site is cleaned with hydrogen peroxide. After 3 to 4 weeks, the area is levelled by a dermabrasion or other technique. Expected results and complications are discussed.

Cicatrix↗
PubMed1986

The role of computed tomography in symptomatic aortic aneurysms.

Forty-seven patients with an abdominal aortic aneurysm (AAA) and recent onset of abdominal or back pain were evaluated by emergency computed tomography (CT) to identify those patients with a confined rupture, and unstable aneurysm, nonaneurysmal cause of pain and a stable AAA. CT suggested that 25 per cent of these had a confined rupture and should undergo emergency surgical treatment. Rupture was confirmed at operation in one-half of these instances. Thirteen per cent avoided operation since other significant pathologic factors were identified. The remaining 47 per cent benefited from optimal preoperative evaluation and semielective surgical treatment. No patient ruptured an AAA during the delay for complete preoperative evaluation and preparation. Additionally, a preoperative CT is useful to identify patients with an unsuspected iliac, suprarenal, thoracic or inflammatory aneurysm. Thus, we believe that CT has a particularly important role in the evaluation of the symptomatic AAA, adding it to the list of indications for CT evaluation of difficult aortic disorders.

Aorta, Abdominal↗
PubMed1985

Base tilt of DNA in various conformations from flow linear dichroism.

We have measured the isotropic absorption (Aiso) and linear dichroism (LD) of Escherichia coli DNA in 0.01 M Na+ (10.4 base pairs per turn of B form), 5.5 M NH4F (10.2 base pairs per turn of B form), and 80% trifluoroethanol (A form) into the vacuum UV spectral region. The reduced dichroism spectrum (LD divided by Aiso) of DNA in the A conformation differed from those of the B conformations, demonstrating that LD is a sensitive method for distinguishing DNA conformation. The reduced dichroism spectra of the B conformations were similar, indicating little change in the orientation of the bases for DNA in high salt. The wavelength dependence of the reduced dichroism indicates that the angle between the base planes and the helix axis is less than 76 degrees for all three conformations of DNA.

Base Composition↗
PubMed1985

Evidence for Z-form RNA by vacuum UV circular dichroism.

Circular dichroism (CD) spectra in the vacuum UV region for different conformations of poly d(G-C) X poly d(G-C) and poly r(G-C) X poly r(G-C) are very characteristic. The CD of the RNA in the A-form (6 M NaClO4 and 22 degrees C) is very similar to that of the DNA in 80% alcohol where it is believed to be in the A-form. With the exception of the longest wavelength transition, the CD of the RNA in 6 M NaClO4 at 46 degrees C is similar to the CD of the DNA under conditions where it is believed to be in the Z-form (2 M NaClO4). This substantiates that poly r(G-C) X poly r(G-C) assumes a left-handed Z-conformation in 6 M NaClO4 above 35 degrees C. CD spectra for the left-handed Z-forms of both the RNA and DNA are characterized by an intense negative peak at 190-195 nm, a crossover at about 184 nm, and an intense positive peak below 180 nm. The right-handed A- and B-forms of RNA and DNA all have an intense positive peak in their CD spectra near 186 nm. The large difference in CD in the range 185-195 nm for right- and left-handed conformations of nucleic acids can be used to identify the sense of helix winding.

Circular Dichroism↗
PubMed1985

Circular dichroism studies of acetylcholinesterase conformation. Comparison of the 11 S and 5.6 S species and the differences induced by inhibitory ligands.

Circular dichroism studies were carried out in the vacuum ultraviolet region for 11 S and 5.6 S species of acetylcholinesterase from Torpedo. As the 5.6 S acetylcholinesterase forms larger oligomers in the absence of detergent, the CD spectrum was measured both with and without detergent. Secondary structure analysis of the CD spectrum for 11 S acetylcholinesterase shows 33% alpha-helix, 23% beta-sheet (14% antiparallel and 9% parallel), 17% turns and 26% other structure. Binding of edrophonium to the active site of 11 S acetylcholinesterase increases alpha-helix, while binding of propidium to the peripheral site increases beta-sheet. The beta-sheet content is slightly higher for 5.6 S than 11 S acetylcholinesterase in water. When the detergent is added to 5.6 S acetylcholinesterase, the 190 nm and 220 nm bands become less intense, although the analyses of the two spectra are similar. No significant change is observed for the 5.6 S form in either solvent on binding ligands. The prediction of both parallel and antiparallel beta-sheet suggests that at least one domain in these multidomain proteins belongs to the alpha/beta tertiary structural type.

Acetylcholinesterase↗
PubMed1985

Expanded criteria for percutaneous abscess drainage.

The original criteria for percutaneous abscess drainage were limited to simple abscesses (well-defined, unilocular) with safe drainage routes. We expanded these entry criteria to include complex abscesses (loculated, ill-defined, or extensively dissecting abscesses), multiple abscesses, abscesses with enteric fistulas or whose drainage routes traversed normal organs, as well as complicated abscesses (appendiceal, splenic, interloop, and pelvic). Using these expanded criteria, cure was achieved nonoperatively in 92 (73.6%) of 125 abscesses with ten deaths (9%), and 11 complications (9%). Cure was achieved in 82% of simple abscesses, but only 45% of complex abscesses. There was no correlation between size, depth, drainage route, or etiology of the abscess (spontaneous v postoperative) with either cure or complications. We recommend a trial of percutaneous drainage in all simple abscesses and most complex abscesses with clinical response as the key determinant of the need for operative intervention.

Abscess↗
PubMed1985

Venous stasis ulceration. Effectiveness of subfascial ligation.

Forty-seven extremities with recurrent venous ulceration were treated by subfascial ligation of incompetent perforating veins. The limbs were observed for an average of 8.5 years (range, 0.5 to 13 years). The risk for recurrence was 22%, 41%, and 51% at 1, 3, and 5 years, respectively. Patients with bilateral ulceration or prior venous ligation were at the highest risk for recurrence, while those with prior excision of prominent varicose veins had a reduced risk. There has been no loss of limbs or life secondary to this venous problem during the 398 cumulative years of observation.

Adult↗