Dynamic properties of ions in models of ion channels studied by molecular dynamics simulation.
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Computer Simulation↗
Biomedical subjects
G R Smith
Publications and source records attributed to G R Smith.
Electrostatics of ligand-gated ion channels.
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Amino Acid Sequence↗
Molecular dynamics of ion/channel interactions.
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Electric Conductivity↗
Long-term renal function in patients with irradiated bilateral Wilms tumor. National Wilms' Tumor Study Group.
The treatment of bilateral Wilms tumor (BWT) involves a multidisciplinary approach including surgery, chemotherapy, and radiation therapy. The long-term renal function in patients receiving all three treatment modalities has not been evaluated. Long-term renal function was evaluated in 81 children with synchronous BWT who received radiation therapy as part of their treatment. Renal function was assessed by measuring blood urea nitrogen (BUN) and serum creatinine (Cr). The normal range for the BUN was defined as 10-24 mg/dl, and the Cr was considered normal at levels of <1.5 mg/dl. Moderate elevations were defined as a BUN of 25-50 mg/dl and/or a Cr of 1.6-2.5 mg/dl and marked elevations as a BUN of >50 mg/dl and/or a Cr of >2.5 mg/dl. BUN and Cr levels were measured prior to treatment and at the following intervals: 6 months after treatment, 1 year after treatment, 2 years after treatment, and at last follow-up. Any elevation during the posttreatment follow-up period was considered abnormal. A total of 28 children (34.6%) had elevated BUN and/or Cr levels, and 18 had moderate and 10 had marked renal insufficiency. No dose-response relationship was established when comparing the radiation doses of those with elevated values to those with normal values. The renal complication rate was moderate, and other factors including surgery, extent and nature of chemotherapy, and recurrent tumor must also be taken into account. The elevations present in several children could be attributed to tumor recurrence and in one case to gentamicin toxicity. The management of children with BWT should consider all of these risks, and attempts to preserve renal parenchyma are warranted.
Antineoplastic Combined Chemotherapy Protocols↗
Rural-urban differences in depression treatment and suicidality.
OBJECTIVES: Because there are fewer per capita providers trained to deliver mental health services in rural areas, the authors hypothesized that depressed rural individuals would receive less outpatient treatment and report higher rates of hospital admittance and suicide attempts than their urban counterparts. METHODS: The authors recruited 74% of eligible participants (n = 470) from a 1992 telephone survey and followed up 95% of subjects for 1 year. The authors collected data from subjects on psychiatric problems and service use and from insurers/providers on treatment and expenditures. RESULTS: Although there were no rural-urban differences in the rate, type, or quality of outpatient depression treatment, rural subjects made significantly fewer specialty care visits for depression. Depressed rural individuals had 3.05 times the odds of being admitted to the hospital for physical problems (P = 0.02) and 3.06 times the odds of being admitted for mental health problems (P = 0.08) during the year. Elevated rates of hospital admittance disappear in models controlling for number of specialty care depression visits in the previous month. Rural subjects reported significantly more suicide attempts during the period of 1 year (P = 0.05). CONCLUSIONS: Additional work is warranted to determine how to alter barriers to outpatient specialty care if the rural health care delivery system is to provide cost-effective depression care.
Adolescent↗
Molecular characterization of Fiji disease fijivirus genome segment 9.
This is the first report of sequence from Fiji disease fijivirus (FDV), the type member of the genus Fijivirus of the family Reoviridae. FDV genome segment (S9) comprised 1843 nt and contained two non-overlapping ORFs, separated by a 57 nt intergenic region. S9 ORF 1 comprised 1008 nt and encoded a 335-amino-acid polypeptide (predicted molecular mass 38.6 kDa), while ORF 2 comprised 627 nt and encoded a 208-amino-acid polypeptide (predicted molecular mass 23.8 kDa). The 5' and 3' non-coding regions were 49 and 102 nt, respectively. The S9 terminal sequences were 5' AAGUUUUU------UGUC 3', and located immediately adjacent to these sequences were 12 bp imperfect inverted repeats. The entire S9 ORF 1 and the hydrophilic regions of S9 ORF 2 were each expressed as a fusion protein with the maltose-binding protein in Escherichia coli. Antibodies produced against the ORF 1 fusion protein reacted strongly with a protein of approximately 39 kDa present in both crude extracts of FDV-infected sugarcane and partially purified FDV preparations. In contrast, antibodies raised against the modified ORF 2 fusion protein did not react with any proteins in the same samples. Further, polyclonal antibodies produced against partially purified FDV reacted with the ORF 1, but not the modified ORF 2, fusion protein. These results indicate that FDV S9 ORF 1 encodes a major structural protein, while ORF 2 probably encodes a non-structural protein.
Amino Acid Sequence↗
Expenditures for the treatment of major depression.
OBJECTIVE: Health policy makers lack accurate information about per capita spending for the treatment of major depression, the distribution of those expenditures, and the proportion of the health care dollar consumed by depression treatment. METHOD: The authors recruited and followed a community cohort of individuals with major depression; the 298 subjects were either enrolled in fee-for-service insurance plans or self-insured. Charges for all health care services received during the year following baseline were abstracted from medical and insurance records. RESULTS: Over the course of 1 year, 48.1% of the subjects received depression treatment. The per capita total expenditure for inpatient and outpatient depression treatment averaged $631, with a median of $152, for the treated subjects. Just 4.9% of the treated subjects consumed 45.0% of the outpatient expenditures. Depression treatment consumed only 8 cents of every health care dollar spent on the patients treated for depression. CONCLUSIONS: Studies are needed to examine how the level and distribution of expenditures for depression treatment change under managed care and to determine whether and how any differences affect outcomes in the afflicted population. Managed care attempts to contain costs by limiting outpatient care may not affect total health care expenditures dramatically, since depression treatment consumes such a minuscule portion of the health care dollar spent on this population.
Adolescent↗
Implementing a statewide outcomes management system for consumers of public mental health services.
The authors describe the development and implementation of an outcomes management system designed to measure outcomes and processes of care for public mental health consumers in Arkansas. The public-academic project was implemented in 1995 and is based on the Shewhart-Deming model of continuous quality improvement. All 15 community mental health centers (CMHCs) in the state participate in the project, which prospectively measures longitudinal outcomes of care for the tracer conditions of major depression and schizophrenia. Multiperspective measurement tools are used to measure patients' psychiatric status and general health status at periodic intervals; information is gathered on functioning, symptoms, severity of illness, social factors, demographic characteristics, and quality of life. A problem encountered during implementation was the relatively low rate of referral of patients with the tracer conditions for monitoring. Voluntary rather than mandatory participation in the outcomes management system by the CMHCs as well as clinicians' misperceptions about the system's purpose and concerns about confidentiality may have partly accounted for the low rate.
Arkansas↗
Glenohumeral deformity secondary to brachial plexus birth palsy.
Ninety-four patients who had brachial plexus birth palsy were entered into a prospective study to evaluate the association between persistent palsy, age-related musculoskeletal deformity, and functional limitations. Of these patients, forty-two had either computerized tomography or magnetic resonance imaging to assess the presence and degree of incongruity of the glenohumeral joint, deformity of the humeral head, and hypoplasia of the glenoid as part of the preoperative planning for a reconstructive operation. Functional ability was rated with use of the classification of Mallet, on a scale of 1 to 5. The mean glenoscapular angle (the degree of retroversion of the glenoid) on the affected side was -25.7 degrees compared with -5.5 degrees on the unaffected side. Twenty-six (62 per cent) of the forty-two shoulders had evidence of posterior subluxation of the humeral head, with a mean of only 25 per cent (range, 0 to 50 per cent) of the head being intersected by the scapular line. Progressive deformity was found with increasing age (p < 0.001). The natural history of untreated brachial plexus birth palsy with residual weakness is progressive glenohumeral deformity due to persistent muscle imbalance. The status of the glenohumeral joint must be addressed when the choice between tendon transfer and humeral derotation osteotomy for reconstruction of the shoulder is considered for these patients.
Adolescent↗
An extensive and diverse gene family of nicotinic acetylcholine receptor alpha subunits in Caenorhabditis elegans.
Using reverse transcription-polymerase chain reactions the transcription of eight novel candidate nicotinic acetylcholine receptor (nAChR) alpha subunit genes has been demonstrated in the nematode Caenorhabditis elegans. Together with five other alpha subunit genes described elsewhere by ourselves (unc-38) and other workers (deg-3, acr-4, Ce21 and acr-6), this is now the largest known family of nAChR alpha subunit genes in a single species. By homology we have identified four groups of alpha subunits: DEG-3-like; ACR-16[Ce21]-like; UNC-38-like and ACR-8-like. Five C. elegans nAChR alpha subunits contain a modification in loop C of the ACh binding site in which the normally conserved Tyr-x-Cys-Cys, is replaced by a distinct motif (Tyr-x-x-Cys-Cys). Variation is also found in the channel lining M2 regions, including the replacement in four subunits of the highly conserved leucine at the 9' position by valine and most notably, the replacement in all ACR-8-like subunits of the highly conserved glutamic acid at the -1' position by histidine. Restrained molecular dynamics simulations have been used to generate homo-pentameric M2 helix bundle models for alpha subunits and possible functional implications examined. The calculated electrostatic potential energy profile for the M2 region of ACR-8 differs strikingly from that of ACR-16[Ce21] largely due to the presence of histidine at the -1' position, suggesting a possible perturbation of nAChR channel action permeability in the presence of this subunit type.
Amino Acid Sequence↗
Transcription factor Mts1/Mts2 (Atf1/Pcr1, Gad7/Pcr1) activates the M26 meiotic recombination hotspot in Schizosaccharomyces pombe.
Homologous recombination hotspots increase the frequency of recombination in nearby DNA. The M26 hotspot in the ade6 gene of Schizosaccharomyces pombe is a meiotic hotspot with a discrete, cis-acting nucleotide sequence (5'-ATGACGT-3') defined by extensive mutagenesis. A heterodimeric M26 DNA binding protein, composed of subunits Mts1 and Mts2, has been identified and purified 40,000-fold. Cloning, disruption, and genetic analyses of the mts genes demonstrate that the Mts1/Mts2 heterodimer is essential for hotspot activity. This provides direct evidence that a specific trans-acting factor, binding to a cis-acting site with a unique nucleotide sequence, is required to activate this meiotic hotspot. Intriguingly, the Mts1/Mts2 protein subunits are identical to the recently described transcription factors Atf1 (Gad7) and Pcr1, which are required for a variety of stress responses. However, we report differential dependence on the Mts proteins for hotspot activation and stress response, suggesting that these proteins are multifunctional and have distinct activities. Furthermore, ade6 mRNA levels are equivalent in hotspot and nonhotspot meioses and do not change in mts mutants, indicating that hotspot activation is not a consequence of elevated transcription levels. These findings suggest an intimate but separable link between the regulation of transcription and meiotic recombination. Other studies have recently shown that the Mts1/Mts2 protein and M26 sites are involved in meiotic recombination elsewhere in the S. pombe genome, suggesting that these factors help regulate the timing and distribution of homologous recombination.
Activating Transcription Factor 1↗
Channels formed by the transmembrane helix of phospholamban: a simulation study.
Phospholamban is a small membrane protein which can form cation selective ion channels in lipid bilayers. Each subunit contains a single, largely hydrophobic transmembrane helix. The helices are thought to assemble as a pentameric and approximately parallel bundle surrounding a central pore. A model of this assembly (PDB code IPSL) has been used as the starting point for molecular dynamics (MD) simulations of a system consisting of the pentameric helix bundle, plus 217 water molecules located within and at either mouth of the pore. Interhelix distance restraints were employed to maintain the integrity of the helix bundle during a 500 ps MD simulation. Water molecules within the pore exhibited reduced diffusional and rotational mobility. Interactions between the alpha-helix dipoles and the water dipoles, the latter aligned anti-parallel to the former, contribute to the stability of the system. Analysis of the potential energy of interaction of a K+ ion as it was moved through the pore suggested that unfavourable interactions of the cation with the aligned helix dipoles at the N-terminal mouth were overcome by favourable ion-water interactions. Comparable analysis for a Cl ion revealed that the ion-(pore + water) interactions were unfavourable along the whole of the pore, increasingly so from the N- to the C-terminal mouth. Overall, the interaction energy profiles were consistent with a pore selective for cations over anions. Pore radius profiles were used to predict a channel conductance of 50 to 70 ps in 0.2 M KCl, which compares well with an experimental value of 100 ps.
Calcium-Binding Proteins↗
Class III antiarrhythmic activity in vivo by selective blockade of the slowly activating cardiac delayed rectifier potassium current IKs by (R)-2-(2,4-trifluoromethyl)-N-[2-oxo-5-phenyl-1-(2,2,2-trifluoroethyl)- 2, 3-dihydro-1H-benzo[e][1,4]diazepin-3-yl]acetamide.
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Acetamides↗
The RecBCD enzyme initiation complex for DNA unwinding: enzyme positioning and DNA opening.
The Escherichia coli RecBCD enzyme unwinds DNA from a free double-stranded DNA end to produce single-stranded DNA intermediates of homologous recombination. In the absence of ATP RecBCD binds to a free DNA end to form an initiation complex for DNA unwinding. We studied the structure of these complexes formed with blunt-ended, 5'-extended, and 3'-extended DNA. Reactivity to the single-stranded DNA-specific reagents KMnO4 and dimethyl sulfate indicated that RecBCD opened, in a Mg(2+)-dependent manner, the terminal five or six base-pairs in each substrate. Thymine residues located four to six nucleotides from the 5' end were only partially reactive to KMnO4, suggesting that part of the 5'-terminated strand was partially shielded by the enzyme. DNase I footprinting indicated that the enzyme positions itself relative to the end of the longer of the two strands, although an exception was noted. These results imply flexibility in the ability of RecBCD to open the DNA and position itself for unwinding on DNA with different types of ends. They also imply conformational differences of RecBCD enzyme bound to different types of ends; these conformational differences may be related to those occurring during the unwinding cycle.
Adenosine Triphosphate↗
Position- and orientation-independent activity of the Schizosaccharomyces pombe meiotic recombination hot spot M26.
The activity of the M26 meiotic recombination hot spot of Schizosaccharomyces pombe depends on the presence of the heptamer 5'-ATGACGT-3'. Transplacement of DNA fragments containing the ade6-M26 gene to other chromosomal loci has previously demonstrated that the heptamer functions in some, but not all, transplacements, suggesting that hot spot activity depends on chromosomal context. In this study, hot spot activity was tested in the absence of gross DNA changes by using site-directed mutagenesis to create the heptamer sequence at novel locations in the genome. When created by mutagenesis of 1-4 bp in the ade6 and ura4 genes, the heptamer was active as a recombination hot spot, in an orientation-independent manner, at all locations tested. Thus, the heptamer sequence can create an active hot spot in other chromosomal contexts, provided that the gross chromosomal structure is not altered; this result is consistent with the hypothesis that a specific higher-order chromatin structure is required for M26 hot spot activity.
DNA, Fungal↗
The influenza A virus M2 channel: a molecular modeling and simulation study.
The M2 protein of influenza virus forms ion channels activated by low pH which are proton permeable and play a key role in the life cycle of the virus. M2 is a 97-residue integral membrane protein containing a single transmembrane (TM) helix. M2 is present as disulfide-linked homotetramers. The TM domain of M2 has been modeled as a bundle of four parallel M2 helices. The helix bundle forms a left-handed supercoil surrounding a central pore. Residue H37 has been implicated in the mechanism of low-pH activation of the channel. Models generated with H37 in a fully deprotonated state exhibit a pore occluded by a ring of H37 side chains oriented toward the lumen of the pore. Models with H37 in a fully protonated state no longer exhibit such occlusion of the pore, as the H37 side chains adopt a more interfacial location. Extended molecular dynamics simulations with water molecules within and at the mouths of the pores support this distinction between the H37-deprotonated and H37-protonated models. These simulations suggest that only in the H37-protonated model is there a continuous column of water extending the entire length of the central pore. A mechanism for activation of M2 by low pH is presented in which the H37-deprotonated model corresponds to the "closed" form of the channel, while the H37-protonated model corresponds to the "open" form. A switch from the closed to the open form of the channel occurs if H37 is protonated midway through a simulation. The open channel is suggested to contain a wire of H-bonded water molecules which enables proton permeability.
Computer Simulation↗
Molecular dynamics study of water and Na+ ions in models of the pore region of the nicotinic acetylcholine receptor.
The nicotinic acetylcholine receptor (nAChR) is an integral membrane protein that forms ligand-gated and cation-selective channels. The central pore is lined by a bundle of five approximately parallel M2 helices, one from each subunit. Candidate model structures of the solvated pore region of a homopentameric (alpha7)5 nAChR channel in the open state, and in two possible forms of the closed state, have been studied using molecular dynamics simulations with restraining potentials. It is found that the mobility of the water is substantially lower within the pore than in bulk, and the water molecules become aligned with the M2 helix dipoles. Hydrogen-bonding patterns in the pore, especially around pore-lining charged and hydrophilic residues, and around exposed regions of the helix backbone, have been determined. Initial studies of systems containing both water and sodium ions together within the pore region have also been conducted. A sodium ion has been introduced into the solvated models at various points along the pore axis and its energy profile evaluated. It is found that the ion causes only a local perturbation of the water structure. The results of these calculations have been used to examine the effectiveness of the central ring of leucines as a component of a gate in the closed-channel model.
Amino Acid Sequence↗
The dielectric properties of water within model transbilayer pores.
Ion channels contain extended columns of water molecules within their transbilayer pores. The dynamic properties of such intrapore water have been shown to differ from those of water in its bulk state. In previous molecular dynamics simulations of two classes of model pore (parallel bundles of Ala20 alpha-helices and antiparallel barrels of Ala10 beta-strands), a substantially reduced translational and rotational mobility of waters was observed within the pore relative to bulk water. Molecular dynamics simulations in the presence of a transpore electrostatic field (i.e., a voltage drop along the pore axis) have been used to estimate the resultant polarization (due to reorientation) of the intrapore water, and hence to determine the local dielectric behavior within the pore. It is shown that the local dielectric constant of water within a pore is reduced for models formed by parallel alpha-helix bundles, but not by those formed by beta-barrels. This result is discussed in the context of electrostatics calculations of ion permeation through channels, and the effect of the local dielectric of water within a helix bundle pore is illustrated with a simple Poisson-Boltzmann calculation.
Computer Simulation↗