Conformational and helicoidal analysis of the molecular dynamics of proteins: "curves," dials and windows for a 50 psec dynamic trajectory of BPTI

A new procedure for the graphic analysis of molecular dynamics (MD) simulations on proteins is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the conformational and helicoidal parameters for each structure entering the analysis via the method "Curves," developed for proteins by Sklenar, Etchebest, and Lavery (Proteins: Structure, Function Genet. 6:46-60, 1989) followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels ("dials") for each torsional parameter and "windows" on the range values assumed by the linear and angular helicoidal parameters, and is present in a form isomorphous with the primary structure per se. The complete time evolution of dynamic structure can then be depicted in a set of four composite figures. Dynamic aspects of secondary and tertiary structure are also provided. The procedure is illustrated with an analysis of a 50 psec in vacuo simulation on the 58 residue protein, bovine pancreatic trypsin inhibitor (BPTI), in the vicinity of the local minimum on the energy surface corresponding to a high resolution crystal structure. The time evolution of 272 conformational and 788 helicoidal parameters for BPTI is analyzed. A number of interesting features can be discerned in the analysis, including the dynamic range of conformational and helicoidal motions, the dynamic extent of 2 degrees structure motifs, and the calculated fluctuations in the helix axis. This approach is expected to be useful for a critical analysis of the effects of various assumptions about force field parameters, truncation of potentials, solvation, and electrostatic effects, and can thus contribute to the development of more reliable simulation protocols for proteins. Extensions of the analysis to present differential changes in conformational and helicoidal parameters is expected to be valuable in MD studies of protein complexes with substrates, inhibitors, and effectors and in determining the nature of structural changes in protein-protein interactions.

Abnormal control of ventilation in adolescents with myelodysplasia

Infants with myelomeningocele have abnormalities in ventilatory control. To determine whether these persist into later life, we studied 14 patients with myelomeningocele and Arnold-Chiari malformation (age 18.0 +/- 0.8 (SE) years), and compared them with 14 control subjects (age 24.0 +/- 0.9 years). Pulmonary function and ventilatory muscle strength did not differ between patients with myelomeningocele and control subjects. Hypercapnic ventilatory responses were significantly lower in the group with myelomeningocele (1.98 L/min/mm Hg) compared with control values (3.33 L/min/mm Hg; p less than 0.01). Hypoxic ventilatory responses (-1.4 L/min/%oxygen saturation of hemoglobin in arterial blood) were not significantly different from control values (-2.14 L/min/%oxygen saturation). In control subjects the hypercapnic and hypoxic ventilatory responses were highly correlated with each other within subjects (r = 0.84; p less than 0.002) but not in those with myelomeningocele (r = 0.34; not significant). We concluded that adolescents and young adults with myelomeningocele have abnormalities in control of ventilation during sleep and wakefulness. We speculate that the Arnold-Chiari malformation interferes with central chemosensitivity (hypercapnic ventilatory response) and central integration of chemoreceptor output.

Hypoxic and hypercapnic ventilatory responses in awake children with congenital central hypoventilation syndrome

Congenital central hypoventilation syndrome (CCHS) has been thought to be a disorder of central chemoreceptor responsiveness. Previous studies in CCHS have shown decreased or absent ventilatory responsiveness to both hypercarbia and hypoxia. However, hypoxic responsiveness during wakefulness has not been systematically studied. We studied hypoxic and hypercapnic ventilatory responses during wakefulness in five children with CCHS (6 to 11 yr of age). To measure the hypercapnic response, the children rebreathed a hyperoxic hypercapnic mixture until PaCO2 reached 56 to 69 mm Hg. For the hypoxic response, the children rebreathed a hypoxic gas mixture, at mixed venous PCO2, until SaO2 had fallen to less than 78%. We found that the ventilatory responses to hypercapnia and hypoxia were very variable (linear correlation coefficients ranging from -0.44 to +0.63 for hypercapnic responses and from -0.15 to +0.77 for hypoxic responses), with no significant change from baseline in response to either stimulus. There was no evidence of progressive ventilatory stimulation despite increasing stimulus. Additionally, these children had no subjective sensation of dyspnea or discomfort. This establishes that hypoxic and hypercapnic ventilatory control is absent during wakefulness. Chemoreceptor control (peripheral and central) is, therefore, defective in all states in children with CCHS. We speculate that the defect in CCHS lies in central integration of the central and peripheral chemoreceptor signals.

Congenital central hypoventilation syndrome associated with multiple ganglioneuromas

A five-year-old girl had congenital central hypoventilation syndrome and mediastinal and adrenal tumors. The mediastinal mass was though to be present, retrospectively, for at least four years prior to surgery. Pathology of the excised tumors revealed benign ganglioneuromas. This is the first case reported of an association between CCHS and multiple ganglioneuromas. This suggests that CCHS, like neural crest tumors, may result from maldevelopment of the embryonic neural crest.

Long-term pulmonary sequelae of meconium aspiration syndrome

To determine the incidence of long-term sequelae after meconium aspiration syndrome (MAS), we studied 11 children who had MAS at age 8.2 +/- 0.2 years (mean +/- SD) and nine healthy control subjects with pulmonary function and exercise stress tests. The MAS children had evidence of mild airway obstruction, hyperinflation, and increased closing volumes in comparison with control values. During graded exercise stress tests on a treadmill, MAS children achieved normal maximal oxygen consumption and anaerobic threshold without a significant fall in arterial oxygen saturation or increase in CO2 tension. Exercise-induced bronchospasm occurred in four (36%) MAS subjects but in none of the control subjects. We conclude that children surviving MAS have long-term pulmonary sequelae, including airway obstruction, hyperinflation, elevated closing volumes, and airway hyperreactivity; yet they achieve normal aerobic capacity. These findings are similar, although less severe, than those after prematurity and bronchopulmonary dysplasia.

Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows

A new procedure for the analysis of the structure and molecular dynamics of duplex DNA is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the values of the conformational and helicoidal parameters for each structure entering the analysis using the method "Curves" developed by Lavery and Sklenar, J. Biomol. Str. Dyn. 6, 63 (1988), followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels, or "dials", for each IUPAC torsional parameter and "windows" on the range of values assumed by the linear and angular helicoidal parameters, and is presented in a form isomorphous with the structure per se. The complete time evolution of the conformational and helicoidal parameters of a DNA double helix can then be depicted in a set of six composite figures. Dynamical aspects of helix bending are also subsumed in this analysis. The procedure is illustrated with an analysis of the structures of canonical A and B forms of DNA and the 300 degrees K native dodecamer duplex d(CGCGAATTCGCG). The "dials and windows" are then used for a comprehensive analysis of 30 psec of molecular dynamics on the dodecamer in the vicinity of a canonical B-DNA energy minimum. This involves presentation of the time evolution of 206 conformational and 230 helicoidal parameters for the dodecamer. A number of interesting structural features can be recognized in the analysis, including crankshaft motions, BI - BII transitions, sugar repuckerings, and a description of spontaneous helix bending at what corresponds to the 1 degrees and 2 degrees "hinge points" indicated in the crystal structure. Our approach is expected to be directly useful for critical analysis of the effects of various assumptions about force field parameters, hydration and electrostatic effects and thus contribute to the development of reliable simulation protocols for nucleic acid systems. Extension of the method to present differential changes in conformational and helicoidal parameters is expected to be valuable for the analysis of structural and molecular dynamics studies of the reorganization and adaptation of DNA on complexation with various drugs and regulatory proteins.

Thermal vibrations and electrostatic properties of parabanic acid at 123 and 298 K

The crystal structure of parabanic acid (1H,3H-imidazoletrione, C3H2N2O3, Mr = 114.1) at 123 K [monoclinic, P2(1)/n, Z = 4, a = 10.704 (2), b = 8.187 (2), c = 4.969 (1) A, beta = 92.32 (1)o] has been determined by neutron and X-ray diffraction. Neutron reflections [1658, (sin theta)/lambda less than or equal to 0.78 A-1, lambda = 1.0470 (1) A, mu = 0.75 cm-1] in full-matrix least-squares refinement (wR = 0.055) gave nuclear parameters with bond lengths having estimated standard deviations (e.s.d.'s) of 0.001 A. X-ray reflections [3150 with magnitude of F magnitude of greater than or equal to 3 sigma and (sin theta)/lambda less than or equal to 1.3 A-1, Mo Ka, lambda = 0.7093 (1) A, mu = 1.708 cm-1] were used in full-matrix least-squares refinement (R = 0.022) assuming Stewart's rigid pseudoatom model, so as to determine the charge-density distribution. Sharp features near the O nuclei in the residual electron density map noted by Craven & McMullan (CM) [Acta Cryst. (1979), B35, 934-945] in their 298 K study were absent at 123 K. New refinements using CM's 298 K data give significant third-order thermal parameters for O atoms due to anharmonic molecular stretching, with good agreement between probability density functions, (p.d.f.'s) from X-ray and neutron diffraction. When deconvoluted from the thermal vibrations in the crystal, deformation charge densities derived at 298 and 123 K are in satisfactory agreement and conform closely to the 2 mm symmetry of the isolated molecule. The molecular dipole moment is 2.3 (3) D [7.7 (10) x 10(-30) C m]. A map of molecular electrostatic potential indicates that the carbonyl O atoms in parabanic acid are weakly electronegative. This is confirmed by calculation of the electrostatic energy of interaction for the two distinct H-bonded pairs of molecules isolated from the crystal. Energy values are weakly attractive [-7 (3) and 5 (2) kJ mol-1]. Similar calculations are less reliable for pairs of molecules forming intermolecular C....O distances as short as 2.75 A. However, depending on the model, energy values are repulsive or negligibly small. Thus the high stability of parabanic acid crystals (m.p. 516 K with decomposition) cannot be explained.

Phase I study of taxol administered as a short i.v. infusion daily for 5 days

Taxol inhibits cell division by promoting the assembly and stabilization of microtubules. This report describes the results of a phase I trial of taxol administered as a short iv infusion daily for 5 days every 4 weeks. Sixteen patients with refractory malignancy received 21 courses of taxol at five doses between 5 and 40 mg/m2/day X 5. The first nine patients received taxol as a 60-minute infusion. Two patients experienced anaphylactoid reactions, one at the 5-mg/m2/day and the second at the 15-mg/m2/day X 5 dose levels. These reactions were characterized by facial flushing, tachypnea, and hypotension within several minutes of drug administration. These anaphylactoid reactions occurred on the first day of treatment in the first patient and on the first day of the second course in the second patient. These reactions may be related to the rapid administration of the polyoxyethylated castor oil (Cremophor EL) vehicle in which taxol is formulated. No anaphylactoid reactions were observed in the seven patients who received taxol as a 6-hour infusion with antihistamine and prednisone premedication. Dose-related myelosuppression was seen; leukopenia (wbc count less than 1000/mm3) and granulocytopenia (granulocytes less than or equal to 200/mm3) occurred on Days 8 and 9 in two of two patients treated at the 40 mg/m2/day X 5 level. Thrombocytopenia was mild, with a platelet nadir of 87,000-95,000/mm3 at the highest dose level. Premedication with glucocorticoids and antihistamines coupled with a prolonged 6-hour infusion permitted taxol to be administered at 30 mg/m2/day X 5 safely without immediate life-threatening reactions.

Further studies on elastase and trypsin inhibitory activities in mammalian lenses

Elastase and trypsin inhibitory capacities increased significantly on heat treatment of the lens extract for 15 min at 60 degrees C in human infant (mean increase 290 and 335%), human adult (130 and 245%), ovine (90 and 140%), and bovine (70 and 90%) lenses. No increase was observed in human cataractous lenses. Preincubation with target enzymes in the absence of substrate abolished the antitryptic activity in lenses whereas antielastase activity was more resistant. No decrease in antielastase activity in human adult and cataractous lenses was observed on 15-min preincubation whereas about 50% of activity was abolished in human infant lenses. The differences were attributed to the changes in the levels of endogenous proteinases and proenzymes during cataractogenesis and aging.

Xanthine oxidase-mediated mutagenicity of the bladder carcinogen 4-nitrobiphenyl

Xanthine oxidase catalyzed mutagenicity of 4-nitrobiphenyl (NBP), a dog-bladder carcinogen, was tested in Ames assay using Salmonella typhimurium TA98 strains. NBP was active as a mutagen in the parent strain TA98 which is proficient in nitroreductase, while it was inactive in the strain TA98NR which is deficient in nitroreductase. However, preincubation of NBP at 37 degrees C with NADH and commercial preparations of xanthine oxidase for 30 min resulted in a dose-dependent increase in the mutagenic activity in TA98NR. Allopurinol blocked the xanthine oxidase catalyzed mutagenicity of NBP in TA98NR and the extent of inhibition was dependent upon the concentration of the inhibitor. Rat-liver and dog-bladder cytosol preparations also enhanced the mutagenic activity of NBP in TA98NR in a dose-dependent manner. In addition, the cytosol-mediated activity was also inhibited by allopurinol, implying that the cytosolic enzyme activity might be due to xanthine oxidase. In vitro enzymatic reduction of NBP using bacterial cell lysates of TA98 and TA98NR revealed the major product of reduction to be 4-aminobiphenyl. The transient intermediates of reduction were not detected during the in vitro incubation. The reduction intermediate N-hydroxylaminobiphenyl showed direct and equal mutagenic activity in both TA98 and TA98NR, in contrast to NBP. These results suggest that N-hydroxylaminobiphenyl is generated during the preincubation of NBP with xanthine oxidase or cytosolic preparations and the former might account for the mutagenicity of NBP. Furthermore, the occurrence of such enzyme(s) in the target tissue for NBP carcinogenesis, support the hypothesis that metabolic activation of the bladder carcinogen NBP could occur within the target organ by virtue of its intrinsic metabolic potential.

Quantitative assessments of the cytotoxicity of bladder carcinogens towards cultured normal human uroepithelial cells

Chemical carcinogens are known to exert cytotoxic effects on cells. The survival of cultured human uroepithelial cells (HUC) after exposure to several important classes of human and experimental animal bladder carcinogens has been quantitatively assessed in vitro using reduction in cell number and/or colony forming efficiency as the endpoint(s). Cells were treated with different carcinogens or various metabolites of a procarcinogen and the responses were analyzed with respect to the cell type used and to the donor source of the cells. The cytotoxic responses of HUC to the stable bladder procarcinogens tested [4-aminobiphenyl (ABP), 4-nitrobiphenyl, N-[4-(5-nitro-2-furyl)-2-thiazole]formamide and 2-amino-4-(5-nitro-2-furyl)thiazole] were dependent on both the concentration of chemical used and the duration of exposure. The survival of HUC after exposure to several metabolites of ABP differed. The N-hydroxylated derivatives of ABP (N-hydroxy-4-amino-biphenyl and N-hydroxy-4-acetylaminobiphenyl) were considerably more cytotoxic toward HUC than ABP or 4-acetylaminobiphenyl. The survival of HUC from different individuals after treatment with the direct acting carcinogen N-nitro-N-methylurea was very similar. In contrast, the survival of HUC from different donors varied considerably after treatment with the procarcinogen 3-methylcholanthrene which requires metabolic activation. However, significant heterogeneity in the survival of HUC from five donors after exposure to the human bladder procarcinogen ABP was not observed in this study. Cultures of normal human fibroblasts from four donors showed an unexpected heterogeneous response to the cytotoxic effects of ABP. These results demonstrate that many variables affect the cytotoxic response of normal cells to bladder carcinogens.

Mutagenicity of 3,4-diphenyl-5-nitrofuran analogs in Salmonella typhimurium

A new series of chemicals comprising eight different 3,4-diphenyl-substituted furan analogs, namely, methyl-3,4-diphenyl-2-furoate, methyl-3,4-diphenyl-5-nitro-2-furoate, 3,4-diphenyl-5-nitro-2-furoic acid, 3,4-diphenyl-5-nitro-2-acetylfuran, 3,4-diphenyl-5-nitro-2-bromoacetylfuran, 2-amino-4-(3,4-diphenyl-5-nitro-2-furyl)thiazole, 2-acetyl-amino-4-(3,4-diphenyl-5-nitro-2-furyl)thiazole and 2-formyl-amino-4-(3,4-diphenyl-5-nitro-2-furyl)thiazole were synthesized and their mutagenic activities tested in Salmonella typhimurium. The structure--activity relationship studies revealed that for mutagenic activity the nitro group is essential and that the potency of activity is greatly altered by the nature of the substituent at the 2-position of the furan ring. The mutagenic activities of these chemicals were generally much higher in TA100 compared to TA98. The relative order of activities for 2-substituted, 3,4-diphenyl-5-nitrofurans were COOCH3 greater than COCH2BR greater than COCH3 greater than COOH in S. typhimurium TA100. 3,4-Diphenyl-5-nitro-2-bromoacetylfuran was equally active in nitroreductase-proficient (TA98, TA100) and in nitroreductase-deficient (TA98NR, TA100NR) strains. In contrast, the acetyl and carboxymethyl ester analogs were relatively less active in nitroreductase-deficient strains. Mutagenic activities of 3,4-diphenyl-substituted furylthiazoles in comparison with the unsubstituted analogs of N-[4-(5-nitro-2-furyl)-2-thiazolyl]-formamide, N-[4-(5-nitro-2-furyl)-2-thiazolyl]-acetamide and 2-amino-4-(5-nitro-2-furyl)thiazole revealed that the phenyl groups drastically reduced their mutagenic activities. However, the relative order of activities formylamino greater than or equal to acetylamino greater than amino were the were the same between phenyl-substituted and unsubstituted analogs.

Identification of 4-(5-amino-2-furyl)thiazole (AFT) as a reductive metabolite of the carcinogen 4-(5-nitro-2-furyl)thiazole (NFT)

The chemical synthesis of 4-(5-amino-2-furyl)thiazole (AFT) and its formation during the in vitro reductive metabolism of 4-(5-nitro-2-furyl)thiazole (NFT) by rat liver tissues on anaerobic incubation with NADPH were examined. AFT was synthesized by catalytic reduction of NFT with 5% palladium on activated carbon. Purified AFT, a pale yellow powder, melted at 105 degrees C and had an extinction coefficient of 16.3 mM-1 cm-1 at 297 nm in methanol. The proton n.m.r. spectrum, i.r. and mass spectra were consistent with the assigned structure. Analysis of the ethyl acetate extract, following incubation of NFT with rat liver tissue preparations, revealed a metabolite whose chromatographic and mass spectral characteristics were the same as those obtained with synthetic AFT, thus establishing the structural identity of the metabolite as AFT. These data show that AFT is formed on reduction and could act as a precursor for the formation of 1-(4-thiazolyl)-3-cyano-1-propanone as postulated earlier.

Proteases and protease inhibitory activities in normal mammalian lenses and human cataractous lenses

Trypsin inhibition (reduction in benzoyl arginine p-nitroanilide hydrolysis), elastase inhibition (reduction in succinyl trialanyl p-nitroanilide hydrolysis), and chymotrypsin inhibition (reduction in acetyl tyrosine ethyl ester hydrolysis) by neutral extracts of mammalian lenses were estimated. The activities were found to be markedly elevated in human cortical cataract lenses compared to normal adult lenses (antielastase 7.21 +/- 3.90 units (mean +/- SD) in cataract compared to 1.46 +/- 0.57 in normals; antitryptic, 0.54 +/- 0.38 and 0.12 +/- 0.04; antichymotryptic, 1.03 +/- 0.61 and 0.297 +/- 0.055). Antielastase activity was distinctly higher in adult normal human lenses compared to infant lenses (0.159 +/- 0.068). Elastase- and trypsin-like activities were detected at low levels in all mammalian lenses. Chymotrypsin-like activity could not be observed in the lenses. The cataractous lenses had lower trypsin- and elastase-like activities compared to normal human lenses (elastase 1.20 +/- 0.643 in normal compared to 0.062 +/- 0.035 in cataract; trypsin, 0.367 +/- 0.154 and 0.069 +/- 0.038). The role of protease: inhibitor complexes in the expression of the individual activities and their role in cataractogenesis are discussed.

Prevalence of respiratory diseases and their association with growth rate and space in randomly selected swine herds

The prevalence and extent of respiratory tract lesions were measured in 1425 pigs from 27 randomly selected herds in the summer of 1982 and winter of 1983. About 75% of pigs had lesions of enzootic pneumonia, approximately 60% had atrophic rhinitis and approximately 11% had pleuropneumonia and/or pleuritis. Individual pig growth rate was recorded on two of the farms, and it was found that the correlations between growth rate and severity of enzootic pneumonia lesions were positive on one farm and negative on the other. Negative correlations between severity of turbinate atrophy and growth rate existed in one of the two herds. Extent of pneumonia and severity of turbinate atrophy were poorly related in individual pigs but herd averages were moderately and positively correlated. Prevalence of diffuse pleuritis and of pleuropneumonia were positively related, as were the extent of pneumonia and prevalence of localized pleuritis. Prevalence of pleuropneumonia was strongly correlated with increased days-to-market. A method of estimating the average days-to-market using weekly herd data (inventory) was developed.