Biomedical subjects
J F O'Connell
Publications and source records attributed to J F O'Connell.
Male strategies and Plio-Pleistocene archaeology.
Archaeological data are frequently cited in support of the idea that big game hunting drove the evolution of early Homo, mainly through its role in offspring provisioning. This argument has been disputed on two grounds: (1) ethnographic observations on modern foragers show that although hunting may contribute a large fraction of the overall diet, it is an unreliable day-to-day food source, pursued more for status than subsistence; (2) archaeological evidence from the Plio-Pleistocene, coincident with the emergence of Homo can be read to reflect low-yield scavenging, not hunting. Our review of the archaeology yields results consistent with these critiques: (1) early humans acquired large-bodied ungulates primarily by aggressive scavenging, not hunting; (2) meat was consumed at or near the point of acquisition, not at home bases, as the hunting hypothesis requires; (3) carcasses were taken at highly variable rates and in varying degrees of completeness, making meat from big game an even less reliable food source than it is among modern foragers. Collectively, Plio-Pleistocene site location and assemblage composition are consistent with the hypothesis that large carcasses were taken not for purposes of provisioning, but in the context of competitive male displays. Even if meat were acquired more reliably than the archaeology indicates, its consumption cannot account for the significant changes in life history now seen to distinguish early humans from ancestral australopiths. The coincidence between the earliest dates for Homo ergaster and an increase in the archaeological visibility of meat eating that many find so provocative instead reflects: (1) changes in the structure of the environment that concentrated scavenging opportunities in space, making evidence of their pursuit more obvious to archaeologists; (2) H. ergaster's larger body size (itself a consequence of other factors), which improved its ability at interference competition.
Genetics, archaeology, and holocene hunter-gatherers.
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Peptide aldehyde inhibitors of bacterial peptide deformylases.
Bacterial peptide deformylases (PDF, EC 3.5.1.27) are metalloenzymes that cleave the N-formyl groups from N-blocked methionine polypeptides. Peptide aldehydes containing a methional or norleucinal inhibited recombinant peptide deformylase from gram-negative Escherichia coli and gram-positive Bacillus subtilis. The most potent inhibitor was calpeptin, N-CBZ-Leu-norleucinal, which was a competitive inhibitor of the zinc-containing metalloenzymes, E. coli and B. subtilis PDF with Ki values of 26.0 and 55.6 microM, respectively. Cobalt-substituted E. coli and B. subtilis deformylases were also inhibited by these aldehydes with Ki values for calpeptin of 9.5 and 12.4 microM, respectively. Distinct spectral changes were observed upon binding of calpeptin to the Co(II)-deformylases, consistent with the noncovalent binding of the inhibitor rather than the formation of a covalent complex. In contrast, the chelator 1,10-phenanthroline caused the time-dependent inhibition of B. subtilis Co(II)-PDF activity with the loss of the active site metal. The fact that calpeptin was nearly equipotent against deformylases from both gram-negative and gram-positive bacterial sources lends further support to the idea that a single deformylase inhibitor might have broad-spectrum antibacterial activity.
A high quality nuclear magnetic resonance solution structure of peptide deformylase from Escherichia coli: application of an automated assignment strategy using GARANT.
The NMR structure of the peptide deformylase (PDF) (1-150) from Escherichia coli, which is an essential enzyme that removes the formyl group from nascent polypeptides and represents a potential target for drug discovery, was determined using 15N/13C doubly labeled protein. Nearly completely automated assignment routines were employed to assign three-dimensional triple resonance, 15N-resolved and 13C-resolved NOESY spectra using the program GARANT. This assignment strategy, demonstrated on a 17 kDa protein, is a significant advance in the automation of NMR data assignment and structure determination that will accelerate future work. A total of 2302 conformational constraints were collected as input for the distance geometry program DYANA. After restrained energy minimization with the program X-PLOR the 20 best conformers characterize a high quality structure with an average of 0.43 A for the root-mean-square deviation calculated from the backbone atoms N, C alpha and C', and 0.81 A for all heavy atoms of the individual conformers relative to the mean coordinates for residues 1 to 150. The globular fold of PDF contains two alpha-helices comprising residues 25-40, 125-138, six beta-strands 57-60, 70-77, 85-88, 98-101, 105-111, 117-123 and one 3(10) helix comprising residues 49-51. The C-terminal helix contains the HEXXH motif positioning a zinc ligand in a similar fashion to other metalloproteases, with the third ligand being cysteine and the fourth presumably a water. The three-dimensional structure of PDF affords insight into the substrate recognition and specificity for N-formylated over N-acetylated substrates and is compared to other PDF structures.
Predictable deuteration of recombinant proteins expressed in Escherichia coli.
Random deuteration of recombinant proteins in Escherichia coli is widely used for protein structure determination by nuclear magnetic resonance (NMR). It is desirable to predict accurately the degree of deuteration because each NMR experiment benefits from a different level of deuteration. The method described here which uses [2H]2O and glucose as the sole carbon and deuterium sources is an alternative for a previously published procedure using acetate and [2H]2O (Venter et al., J. Biomol. NMR 5, 339-344, 1995) and it is of advantage for proteins that do not express well using acetate. While the deuteration degree with acetate is approximately linear with the [2H]2O content in the medium, the use of glucose leads to deviations up to 19%, which is analyzed systematically here. With [2H]2O as the sole deuterium source 0-86% of the chemically nonexchangeable hydrogen atoms can be deuterated. Higher levels of deuteration require perdeuterated glucose in combination with [2H]2O. As an example, recombinant peptide deformylase from Bacillus subtilis was overexpressed, deuterated to various degrees, purified, and analyzed by mass spectrometry and NMR.
Grandmothering, menopause, and the evolution of human life histories.
Long postmenopausal lifespans distinguish humans from all other primates. This pattern may have evolved with mother-child food sharing, a practice that allowed aging females to enhance their daughters' fertility, thereby increasing selection against senescence. Combined with Charnov's dimensionless assembly rules for mammalian life histories, this hypothesis also accounts for our late maturity, small size at weaning, and high fertility. It has implications for past human habitat choice and social organization and for ideas about the importance of extended learning and paternal provisioning in human evolution.
Treatment of human enterovirus infections.
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SCH 43478 and analogs: in vitro activity and in vivo efficacy of novel agents for herpesvirus type 2.
SCH 43478 and analogs are a class of non-nucleoside antiviral agents that have potent and selective activity against herpes simplex virus type 2 (HSV-2). The IC50 for these compounds in plaque reduction analysis using Vero cells ranges from 0.8 to 2.0 microg/ml. All compounds have a LC50 > 100 microg/ml in cytotoxicity analysis. Mechanism of action studies suggest that these molecules have an effect on the transactivation of viral immediate early (alpha) gene expression. Time of addition studies indicate that antiviral activity of these analogs is limited to the initial 2-3 h after infection and is not due to inhibition of viral adsorption or penetration. Analysis of HSV protein expression demonstrates that SCH 49286 inhibits the accumulation of viral immediate early (alpha) gene products. SCH 43478 demonstrates statistically significant efficacy (P < 0.05) in the guinea pig genital model of HSV infection. Following subcutaneous administration in a therapeutic treatment regimen, SCH 43478 (90 mg/kg/day) is efficacious in reducing the number and severity of lesions and the neurological complications of acute HSV infection. Thus, SCH 43478 and analogs are anti-herpesvirus agents with a unique mechanism of action.
Diagnosis of enterovirus infection by polymerase chain reaction of multiple specimen types.
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SCH 48973: a potent, broad-spectrum, antienterovirus compound.
SCH 48973 is a novel molecule with potent, selective, antienterovirus activity. In assays of the cytopathic effect against five picornaviruses, SCH 48973 had antiviral activity (50% inhibitory concentrations [IC50s]) of 0.02 to 0.11 microg/ml, with no detectable cytotoxicity at 50 microg/ml. SCH 48973 inhibited 80% of 154 recent human enterovirus isolates at an IC50 of 0.9 microg/ml. The antiviral activity of SCH 48973 is derived from its specific interaction with viral capsid, as confirmed by competition binding studies. The affinity constant (Ki) for SCH 48973 binding to poliovirus was 8.85 x 10(-8) M. In kinetic studies, a maximum of approximately 44 molecules of SCH 48973 were bound to poliovirus capsid. SCH 48973 demonstrated efficacy in a murine poliovirus model of enterovirus disease. SCH 48973 increased the survival of infected mice when it was administered orally at dosages of 3 to 20 mg/kg of body weight/day. Oral administration of SCH 48973 also reduced viral titers in the brains of infected mice. On the basis of its in vitro and in vivo profiles, SCH 48973 represents a potential candidate for therapeutic intervention against enterovirus infections.
Comparison of the structure of human recombinant short form stromelysin by multidimensional heteronuclear NMR and X-ray crystallography.
Stromelysin-1 is a matrix metalloprotease that has been implicated in a number of degenerative diseases. Here we present the refined NMR solution structure of the catalytic domain of stromelysin-1 complexed with a small inhibitor and compare it to the X-ray crystal structure of the same complex. The structures are similar in global fold and show an unusual bottomless S1' subsite. There are differences, however, in the least well defined regions, Phe83-Ile89, His224-Phe232 and Pro249- Pro250, reflecting the lack of NOE data and large B-factors. The region His224-Phe232 contains residues of the S1' subsite and, consequently, small differences are observed in this subsite. Hydrogen-bond data show that, in contrast to the crystal structure, the solution structure lacks a hydrogen bond between the amide of Tyr223 and the carbonyl of the P3' residue. Analysis of bound water shows two tightly bound water molecules both in the solution and the crystal structure; neither of these waters are in the inhibitor binding site.
Antipicornavirus activity of SCH 47802 and analogs: in vitro and in vivo studies.
SCH 47802 and its derivatives are potent inhibitors of enteroviruses in vitro. The IC50 for SCH 47802 ranges from 0.03 to 10 micrograms/ml when tested against a spectrum of enteroviruses in plaque reduction assays. The compounds have in vitro therapeutic indices of at least 81 based on viral cytopathic effect (CPE) assays. The in vitro activity of SCH 47802 translates into in vivo activity in the murine model of poliovirus encephalitis. In an oral dosing regimen, SCH 47802 protects mice from mortality at 60 mg/kg per day. Consistent with the in vivo efficacy, pharmacokinetic analyses after oral dosing with SCH 47802 demonstrate serum levels of the compound above the in vitro IC50 for poliovirus for at least 4 h. SCH 47802 and its active analogs stabilize poliovirus to thermal inactivation indicating that the compounds bind to the virus capsid. Mechanistic studies with poliovirus indicate that SCH 47802 acts early in viral infection. This series of molecules represents potential candidates for the treatment of human enterovirus infections.
The nuclear-magnetic-resonance solution structure of the mutant alpha-amylase inhibitor [R19L] Tendamistat and comparison with wild-type Tendamistat.
The recombinant mutant alpha-amylase inhibitor [R19L]Tendamistat, with Arg19 replaced by Leu, was prepared and its NMR solution structure determined. Based on complete sequence-specific 1H-NMR assignments, 845 nuclear Overhauser effect upper-distance constraints and 156 dihedral angle constraints were collected using two-dimensional homonuclear 1H-NMR experiments. The structure was calculated with the program DIANA, using the redundant dihedral angle constraints strategy for improved convergence. For restrained energy minimization, the programs FANTOM and AMBER were used. The wild-type NMR solution structure was similarly recalculated from the previously published input of conformational constraints [Kline, A., Braun, W. & Wüthrich, K. (1988) J. Mol. Biol. 204, 675-724]. For each protein a group of 20 conformers represents a well-defined solution structure, with average root-mean-square-distance values for the backbone atoms of the individual conformers relative to the mean coordinates of 50 pm. The two structures are nearly identical to each other and to the previously published Tendamistat structures in solution and in crystals. The only significant difference is strictly localized near the single amino acid substitution in the presumed active site -Trp18-Arg(Leu)-Tyr-, i.e. Leu19 and Tyr20 are more precisely defined in the solution structure of [R19L]Tendamistat than the corresponding residues Arg19 and Tyr20 in wild-type Tendamistat.
The NMR structure of the inhibited catalytic domain of human stromelysin-1.
The three-dimensional structure of the catalytic domain of stromelysin-1 complexed with an N-carboxyl alkyl inhibitor has been determined by NMR methods. The global fold consists of three helices, a five stranded beta-sheet and a methionine located in a turn near the catalytic histidines, classifying stromelysin-1 as a metzincin. Stromelysin-1 is unique in having two independent zinc binding sites: a catalytic site and a structural site. The inhibitor binds in an extended conformation. The S1' subsite is a deep hydrophobic pocket, whereas S2' appears shallow and S3' open.
Determination of the nuclear-magnetic-resonance solution structure of cardiotoxin CTX IIb from Naja mossambica mossambica.
The NMR structure of cardiotoxin CTX IIb from Naja mossambica mossambica in aqueous solution was determined from a total of 593 nuclear Overhauser enhancement distance constraints and 135 dihedral angle constraints, which were collected using two-dimensional homonuclear 1H-NMR experiments. Structure calculations were performed with the program DIANA, using the redundant dihedral angle constraints strategy for improved convergence, followed by restrained energy minimization with the program FANTOM and a modified version of the program AMBER. The CTX IIb structure is represented by a group of 20 conformers with an average root-mean-square deviation relative to the mean solution structure of 0.072 nm for the backbone atoms, and 0.116 nm for all heavy atoms. The molecular structure of CTX IIb is characterized by a three-stranded beta-sheet made up of residues 20-26, 32-39 and 48-54, and a two-stranded beta-sheet composed of residues 1-5 and 10-14. A cluster of four disulfide bonds, 3-21, 14-38, 42-53 and 54-59, form the core of the molecule and crosslink the individual polypeptide strands. The NMR structure is similar to the previously reported X-ray crystal structure of the cardiotoxin CTX VII4 from the same species. Differences between the two structures were noted in the tips of the two loops formed by residues 6-9 and 27-31, which connect the beta-strand 1-5 with 10-14, and 20-26 with 32-39, respectively. For these loops the NMR data also indicate significantly increased dynamic disorder in the solution structure. These observations are discussed with respect to earlier suggestions by others that these two loops are essential structural elements for function and specificity of a wide variety of homologous toxins.
Demography of the Hadza, an increasing and high density population of Savanna foragers.
This is a report on the demography of the Hadza, a population of East African hunter-gatherers. In it, we describe the results of a census, and our estimation of age structure, survivorship, mean age of women at childbearing, number of live children, total population size and density, and rate of change since 1967. We show that relevant measures fit closely the stable population model North 6 chosen by Dyson to represent Hadza demography in the 1960s. We compare aspects of Hadza demography with surrounding non-Hadza and with the !Kung. Among other things, we find that the Hadza have a higher population density, higher fertility, and a faster population growth rate than do the !Kung. These demographic differences are consistent with our expectations, which were based on differences in the costs and benefits of foraging in the two regions. We also show that Hadza demographic parameters display remarkable consistency over the past 20 years. Since neighboring populations have been encroaching on the area used by the Hadza, and Hadza foragers have been subject to interludes of externally imposed settlement, this consistency is surprising. We discuss some of the implications.
Hunting income patterns among the Hadza: big game, common goods, foraging goals and the evolution of the human diet.
The assumption that large mammal hunting and scavenging are economically advantageous to hominid foragers is examined in the light of data collected among the Hadza of northern Tanzania. Hadza hunters disregard small prey in favour of larger forms (mean adult mass greater than or equal to 40 kg). Here we report experimental data showing that hunters would reduce their mean rates if they included small animals in the array they target. Still, daily variance in large animal hunting returns is high, and the risk of failure correspondingly great, significantly greater than that associated with small game hunting and trapping. Sharing large kills reduces the risk of meatless days for big game hunters, and obviates the problem of storing large amounts of meat. It may be unavoidable if large carcasses cannot be defended economically against the demands of other consumers. If so, then large prey are common goods. A hunter may gain no consumption advantage from his own big game acquisition efforts. We use Hadza data to model this 'collective action' problem, and find that an exclusive focus on large game with extensive sharing is not the optimal strategy for hunters concerned with maximizing their own chances of eating meat. Other explanations for the emergence and persistence of this practice must be considered.