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Biomedical subjects

W C Johnson

Publications and source records attributed to W C Johnson.

At least 19 recordsLinked to original sources
PubMed1992

Circular dichroism and molecular modeling yield a structure for the complex of human immunodeficiency virus type 1 trans-activation response RNA and the binding region of Tat, the trans-acting transcriptional activator.

Transcription in the human immunodeficiency virus type 1 (HIV-1) retrovirus is regulated by binding the viral Tat protein (trans-acting transcriptional activator) to the trans-activation response (TAR) RNA sequence. Here, vacuum UV circular dichroism (VUV-CD) is used to study the structure of TAR and its complex with two peptide fragments that are important for Tat binding to TAR. The VUV-CD spectrum of TAR is typical of A-form RNA and is minimally perturbed when bound to either the short or the long Tat peptide. The CD spectra of the complexes indicate an extended structure in the arginine-rich region of Tat from amino acid residue 47 through residue 58 and a short alpha-helix within the adjacent 59-72 region. Models of TAR and its peptide complexes are constructed to integrate these spectroscopic results with current biochemical data. The model suggests that (i) the arginine-rich 49-58 region is primarily responsible for electrostatic interactions with the phosphates of the RNA, (ii) the arginine side chains can additionally interact with substituent groups of the nucleotide bases to confer base recognition in the complex, (iii) the recognition of uracil-23 in TAR is facilitated by the peptide backbone, and (iv) the glutamine-rich face of an alpha-helix within the 59-72 region pairs to bases UGG at nucleotide positions 31-33 in the TAR loop and thus provides an additional motif in the Tat trans-activating protein to recognize TAR RNA.

Amino Acid Sequence↗
PubMed1992

Intrinsic pigment cell stimulating activity in the skin of the leopard frog, Rana pipiens.

Consistent with the concept that specific pigment patterns of amphibians might result from the highly localized distribution of stimulators and inhibitors of pigment cell expression in the skin, the spot pattern of the leopard frog, Rana pipiens, was examined through the use of the Xenopus neural tube explant assay system (Fukuzawa and Ide, 1988). Media conditioned with pieces of skin from dorsal black spotted areas promoted melanization of neural crest cells at a significantly higher level than did media conditioned with dorsal interspot skin in the absence of extra tyrosine. All conditioned media contained exceedingly low concentrations of tyrosine. With the addition of supplemental tyrosine, the melanization capacity of conditioned media from the interspot areas was elevated to that of the spotted skin. Control media conditioned with ventral frog skin inhibited melanization, as usual, because of the presumed presence of melanization inhibiting factor (MIF). It is considered that dorsal skin contains a melanization stimulating factor (MSF) which is present in significantly higher levels in spotted skin than in interspot areas and that expression of the particular pigmentary pattern of this leopard frog is regulated by the relative distribution of MIF, MSF, and possibly other intrinsic substances present in the skin.

Animals↗
PubMed1992

Environment affects amino acid preference for secondary structure.

Three equivocal amino acid sequences were synthesized that are predicted to be alpha-helical from amino acid preference but are found to be primarily beta-strand from x-ray diffraction of their respective proteins. In some solvent systems we recover the alpha-helical structure predicted by amino acid preference, whereas in other systems we mimic the interior of the protein and produce a beta-strand. These results are experimental proof that the environment is important in determining the secondary structure formed by an amino acid sequence; therefore schemes that predict secondary structure from amino acid sequence alone can never be totally successful.

Amino Acid Sequence↗
PubMed1992

Structural properties of arrestin studied by chemical modification and circular dichroism.

A unique conformation of arrestin is crucial for its interaction with phosphorylated photolyzed rhodopsin. Conformational changes in arrestin were investigated using chemical modification and circular dichroism. We studied the kinetics of sulfhydryl modification of bovine arrestin in order to determine whether its conformation is altered by the presence of ligands or salts at different ionic strengths. We found that all three cysteines (stoichiometry was 2.7 +/- 0.06 3-carboxy-4-nitrophenyl sulfide (NbS)/arrestin) are accessible for modification by NbS2. Under pseudo-first-order conditions (30-100-fold excess of NbS2 over arrestin), the modifications of the 3 cysteines are indistinguishable. At higher concentrations of NbS2 (150-300-fold excess), the pseudo-first-order plot is not linear, and the reaction can be resolved into two processes that involve two classes of sulfhydryl groups. Addition of CaCl2, MgCl2, inorganic phosphate, MgATP, or MgGTP had little effect on the rate of modification of the cysteine residues; however, heparin and inositol hexakisphosphate, which have been shown to induce conformational changes in arrestin, block modification of one sulfhydryl group of arrestin and accelerate the modification of the remaining two. Analysis of CD spectra revealed that arrestin has virtually no alpha-helical structure, about 40% beta-structure, about 18% beta-turns, and about 40% other structure. The CD spectrum for arrestin did not change in the presence of heparin. These studies suggest that arrestin exists in equilibrium between two or more conformational states. However, it is proposed that conversion between these conformations occur without altering significantly the secondary structure of arrestin.

Adenosine Triphosphate↗
PubMed1992

Extending CD spectra of proteins to 168 nm improves the analysis for secondary structures.

The CD spectra for 10 proteins with known secondary structure have been extended from 178 to 168 nm. Combined with the data for 6 other proteins investigated previously, this produces a basis set of 16 proteins, which can be used to analyze CD spectra for secondary structure. Extending the spectra adds another CD band to the data and increases the information content from the equivalent of five to six. Analyzing the CD for each of the 16 proteins in the basis set with the 15 other proteins shows a modest improvement in the prediction of secondary structure with the extended CD spectra.

Circular Dichroism↗
PubMed1992

Multivalent ions are necessary for poly[d(AC).d(GT)] to assume the Z form: a CD study.

In previous work, it was shown that poly[d(AC).d(GT)] could be forced into the Z form by strong dehydrating conditions, provided EDTA was not present. Presumably multivalent impurities were also necessary for the transition. In order to gain control over the B to Z transition for this DNA, we carefully removed all divalent contaminants from the sample and asked the obvious question: What ions are necessary for the transition under dehydrating conditions? We systemically investigated the effect of various multivalent ions. The common contaminants Ca2+, Mg2+, and Fe3+ will not cause the transition, but Co2+ and Ni2+ facilitate the transition, undoubtedly because of their well-known propensity to bind to purine N7. Since the transition also depends on the synergistic dehydrating action of sodium perchlorate and ethanol, we include CD spectra for the independent variations of these two factors. In addition, vacuum-uv CD spectra for the A form and various B forms of poly[d(AC).d(GT)] are presented for the first time.

Circular Dichroism↗
PubMed1992

Stacking interactions of ApA analogues with modified backbones.

CD spectra have been measured as a function of temperature for a number of ApA analogues with modified backbones. Oligonucleotides with these modified backbones are being used as antisense agents having potential as viral therapeutics. Results of these studies show that when a carbonyl is substituted for the phosphate to produce an uncharged backbone, the analogues that have either sugar or morpholino substitution do not stack. In contrast, when a morpholino group is substituted for the sugar and the phosphate is modified so as to be uncharged, there is strong base stacking. Stacking interactions in the phosphorus-linked morpholino analogues are at least as strong as those found in d(ApA). The stacking interactions in ApA are weak by comparison. Singular value decomposition demonstrates that the stacking is two state, and Taylor series decomposition yields a coefficient that measures base stacking interactions. The van't Hoff equation is applied to the base stacking coefficient from the Taylor series fitting to give thermodynamic parameters.

Circular Dichroism↗
PubMed1992

Preliminary biological characterization of a melanization stimulating factor (MSF) from the dorsal skin of the channel catfish, Ictalurus punctatus.

A two step fractionation of conditioned media made from the darkly pigmented dorsal skin of the channel catfish, Ictalurus punctatus, has produced fractions that contain a melanization stimulating factor (MSF). Isolated neural tubes of Xenopus laevis embryos exposed to conditioned media and to specific fractions exhibit greater melanization (increased numbers of melanized cells and elevated percentages of melanized cells), a greater number of dendrites per melanized cell, and a greater number of emigrated neural crest cells than control neural tubes. The presence of MSF activity in the darkly pigmented dorsal integument suggests a role for a molecule or molecules in the development and maintenance of the dorsal/ventral pigment pattern of this piscine species and possibly of other vertebrates.

Animals↗
PubMed1992

Pleomorphic lipoma. Case report and discussion of "atypical" lipomatous tumors.

A case of pleomorphic lipoma is described. Pleomorphic lipoma is included in the "atypical" lipoma classification. Because of its atypical microscopic appearance, it must be differentiated from liposarcoma. We will discuss pleomorphic lipoma and its position in the classification of atypical fatty tumors.

Glycosaminoglycans↗
PubMed1992

Intrinsic pigment-cell stimulating activity in the catfish integument.

In keeping with the concept that local factors in the vertebrate integument affect the expression of pigment cells, the present study was directed toward demonstrating the existence of such factors in the skin of the channel catfish, Ictalurus punctatus. This species has a dark dorsal surface in marked contrast to an almost white midventral surface. Pieces of skin from these two surfaces were used to condition culture media, which were in turn bioassayed using the Xenopus neural tube explant system (Fukuzawa and Ide, 1988, Dev. Biol. 129:25). A certain number of neural crest cells grow out from the explant, and many of these are melanized in a culture medium of Steinberg's basic salt solution (BSS). When the BSS was conditioned with either dorsal or ventral skin, a profound increase in both the number of crest cells emigrated from the neural tubes and the percentage of melanized cells was observed. The effects of dorsal skin were stronger than those of ventral skin and were evident on a dose/response basis. Initial fractionation of conditioned BSS with DEAE ion exchange chromatography produced fractions of particular potency in the stimulation of melanogenesis. A similarly conditioned medium based upon Leibovitz's L-15 was used in the primary culture of mature chromatophores, namely, melanophores, iridophores, and xanthophores from tadpoles of Rana pipiens. Both dorsal and ventral conditioned media stimulated iridophores and xanthophores, but seemed to have little or no effect on tadpole melanophores. A melanization inhibiting factor (MIF) from the ventral surface of adult frogs has been suggested as the basis for the light colored ventrum of amphibians, and although the present experiments were not designed to study catfish MIF, the possible existence of such a factor in this species was supported by the results. The total results of this investigation are discussed in the light of the possible presence of a melanization inhibiting factor (MIF) of greater prevalence in the ventrum and a melanization stimulatory factor (MSF) of greater prevalence in the dorsal integument. It is suggested that the light-colored ventral surface of the catfish and other poikilotherms may result from the presence of higher levels of MIF than MSF. Thus, the expression of melanophores is inhibited while that of iridophores is enhanced. In contrast, higher levels of MSF over MIF in the dark dorsal surface would result in melanophore stimulation and inhibition of iridophore expression.

Animals↗
PubMed1991

A search for protein structural changes accompanying the contractile interaction.

It appears that small movements (detected hitherto only by fluorescence resonance energy transfer measurements and crosslinking studies) in a region of the myosin S-1 particle may mediate chemomechanical energy transduction in the contractile system. Here we find under conditions of high precision at 10 degrees C and 20 degrees C that ATP binding to S-1 causes small (0.4%) changes in CD signal, delta epsilon 222, as do temperature changes in the regime below 16 degrees C. ATP binding perturbs tryptophan residues that we now think are in the mobile region, and we find here that temperature affects tryptophan fluorescence in much the same way that it affects the CD signal, so we believe that the CD signal reports transduction-related movements in S-1. If S-1 is exposed to the range 16-30 degrees C, CD signal falls with temperature; ATP counteracts this fall. Analysis of vacuum-UV CD spectra yields 42% alpha-helix, 9% antiparallel beta-sheet, 7% parallel beta-sheet, 14% beta-turns, and 29% other structures.

Adenosine Triphosphate↗
PubMed1991

Activating region of HIV-1 Tat protein: vacuum UV circular dichroism and energy minimization.

Tat protein is a trans-acting transcriptional activator of the human immunodeficiency virus type 1 and is essential for viral transcription. By homology with other transcriptional activators, Tat is expected to possess a nucleic acid binding region and a separate adjacent activating region. In order to localize the activating region of Tat, we have synthesized the sequences 2-23 and 38-60 of the protein. These two peptides contain the two candidates for the activating regions proposed from mutation experiments in previous studies: sequence 1-13 and sequence 38-45. The argument advanced to justify the location of the activating region within the sequence 1-13 was the periodicity of acidic, polar, and hydrophobic residues consistent with that of an amphipathic alpha-helix, similar to the activating region of many eukaryotic transcriptional activators. We have monitored by vacuum UV circular dichroism the ability of each peptide to adopt an alpha-helical conformation under conditions that strongly favor the formation of secondary structures. Only peptide 38-60 adopts an alpha-helical conformation in these conditions, in keeping with Chou-Fasman prediction. Energy minimization and molecular dynamics were carried out for several possible conformations of sequences 1-14 and 38-60. Our results indicate that only the sequence 38-45 is able to form an alpha-helix with amphipathic characteristics.

Amino Acid Sequence↗
PubMed1991

The circular dichroism of tumor necrosis factor-alpha: measurement into the vacuum UV and analysis for secondary structure.

The circular dichroism (CD) spectrum of tumor necrosis factor-alpha has been measured into the vacuum UV to 168 nm. Analysis of the CD for secondary structure is in good agreement with X-ray diffraction results, but the analysis is somewhat unstable. Adding the CD of this protein together with its X-ray determined secondary structure to the basis set should improve subsequent analyses of CD spectra for other all-beta proteins.

Circular Dichroism↗
PubMed1991

Cerebrovascular hemodynamic changes associated with carotid endarterectomy.

To evaluate the effect of carotid surgery on the cerebral circulation, transcranial Doppler sonography and ocular pneumoplethysmography were performed on 36 patients who underwent unilateral carotid endarterectomy. Ocular pneumoplethysmography and transcranial Doppler sonography tests were performed within a week before and after operation, and transcranial Doppler sonography was repeated greater than or equal to 30 days after operation. Middle and anterior cerebral arteries were insonated bilaterally, and flow velocities ipsilateral (iMCAFV or iACAFV) and contralateral (cMCAFV or cACAFV) to the side of surgery were recorded. The iMCAFV and iACAFV increased significantly in the immediate postoperative period, and the iMCAFV remained elevated on the second follow-up study. Patients with greater than or equal to 75% ipsilateral carotid stenosis (N = 23) had increased iMCAFV, iACAFV, and decreased cACAFV after operation, whereas those with less than 75% stenosis (N = 13) had no significant transcranial Doppler sonography changes. Those with greater than or equal to 75% contralateral carotid stenosis (N = 17) had significant increases in iMCAFV, cMCAFV, and iACAFV after operation, whereas those with less than 75% contralateral carotid stenosis had no significant transcranial Doppler sonography changes. A subset of patients (N = 13) did not increase iMCAFV after surgery. The ocular pneumoplethysmography changes were significantly different in both groups when preoperative and postoperative values were compared. We conclude that carotid endarterectomy can cause lasting cerebral hemodynamic changes, but that its effects are not uniform among all patients.

Aged↗
PubMed1991

Hyalohyphomycosis masquerading as squamous cell carcinoma.

A case of primary cutaneous hyalohyphomycosis in a healthy individual is presented. The initial clinical impression was keratoacanthoma or squamous cell carcinoma. Upon excision, the lesion proved to be an example of cutaneous hyalohyphomycosis due to an unidentified, non-pigmented fungal organism. The lesion was completely excised, and the patient was treated with saturated solution of potassium iodide. To date, there has been no evidence of recurrence. The clinical, histologic and mycologic aspects of hyalophyphomycosis are discussed.

Aged↗
PubMed1990

Stabilization of the Z' form of poly(dGdC):poly(dGdC) in solution by multivalent ions relates to the ZII form in crystals.

Both multivalent ions and 85% ethanol are required to produce the original Z' form of poly(dGdC):poly(dGdC) in solution. When multivalent impurities are removed by dialysis against 0.5 M NaCl and 1 mM EDTA, the circular dichroism retains features of the standard Z form. Addition of Ca+2 nearly reverses this effect. Analysis by singular value decomposition of near-ultraviolet circular dichroism spectra collected during titrations of polynucleotide in 60% ethanol with multivalent ions reveal that, at concentrations below .5 per nucleotide, they stabilize Z'-like forms in a two-state equilibrium with the Z form. Differences among the Z' spectra produced by the different ions suggest that at least three families of Z' structures exist. Furthermore, comparison with crystal data indicates that the Z' form in solution is related to the ZII form in crystals.

Calcium↗