Massively parallel approximate Bayesian computation for estimating nanoparticle diffusion coefficients, sizes and concentrations using confocal laser scanning microscopy

We implement a massively parallel population Monte Carlo approximate Bayesian computation (PMC-ABC) method for estimating diffusion coefficients, sizes and concentrations of diffusing nanoparticles in liquid suspension using confocal laser scanning microscopy and particle tracking. The method is based on the joint probability distribution of diffusion coefficients and the time spent by a particle inside a detection region where particles are tracked. We present freely available central processing unit (CPU) and graphics processing unit (GPU) versions of the analysis software, and we apply the method to characterize mono- and bidisperse samples of fluorescent polystyrene beads.

Vancomycin therapeutic guidelines: a summary of consensus recommendations from the infectious diseases Society of America, the American Society of Health-System Pharmacists, and the Society of Infectious Diseases Pharmacists

Practice guidelines for therapeutic monitoring of vancomycin treatment for Staphylococcus aureus infection in adult patients were reviewed by an expert panel of the Infectious Diseases Society of America, the American Society of Health-System Pharmacists, and the Society of Infectious Diseases Pharmacists. A literature review of existing evidence regarding vancomycin dosing and monitoring of serum concentrations, in addition to patient outcomes combined with expert opinion regarding the drug's pharmacokinetic, pharmacodynamic, and safety record, resulted in new recommendations for targeting and adjustment of vancomycin therapy.

ASHP Therapeutic Position Statement on Strategies for Identifying and Preventing Pneumococcal Resistance

The incidence of drug-resistant S. pneumoniae continues to increase, causing significant morbidity and mortality. Health care providers should seize the opportunity to promote the judicious use of antimicrobials and aggressive vaccination with the pneumococcal vaccines as a means to lessen this significant health problem.

MUNIN: application of three-way decomposition to the analysis of heteronuclear NMR relaxation data

MUNIN (Multidimensional NMR Spectra Interpretation), a recently introduced approach exploiting the mathematical concept of three-way decomposition, is proposed for separation and quantitative relaxation measurements of strongly overlapped resonances in sets of heteronuclear two-dimensional spectra that result from typical relaxation experiments. The approach is general and may also be applied to sets of two-dimensional spectra with arbitrary modulation along the third dimension (e.g., J-coupling, diffusion). Here, the method is applied for the analysis of 15N rotating frame relaxation data.

MUNIN: a new approach to multi-dimensional NMR spectra interpretation

A new method, MUNIN (Multi-dimensional NMR spectra interpretation), is introduced for the automated interpretation of three-dimensional NMR spectra. It is based on a mathematical concept referred to as three-way decomposition. An NMR spectrum is decomposed into a sum of components, with each component corresponding to one or a group of peaks. Each component is defined as the direct product of three one-dimensional shapes. A consequence is reduction in dimensionality of the spectral data used in further analysis. The decomposition may be applied to frequency-domain or time-domain data, or to a mixture of these. Features of MUNIN include good resolution in crowded regions and the absence of assumptions about line shapes. Uniform sampling of time-domain data, a prerequisite for discrete Fourier transform, is not required. This opens an avenue for the processing of NMR data that do not follow oscillating behaviour, e.g. from relaxation measurements. The application of MUNIN is illustrated for a 1H-15N-NOESY-HSQC, where each component is defined as the set of all NOE peaks formed by a given amide group. As a result, the extraction of structural information simply consists of one-dimensional peak picking of the shape along the NOE-axis obtained for each amide group.

Backbone dynamics of the channel-forming antibiotic zervamicin IIB studied by 15N NMR relaxation

The backbone dynamics of the channel-forming peptide antibiotic zervamicin IIB (Zrv-IIB) in methanol were studied by 15N nuclear magnetic resonance relaxation measurements at 11.7, 14.1 and 18.8 T magnetic fields. The anisotropic overall rotation of the peptide was characterized based on 15N relaxation data and by hydrodynamic calculations. 'Model-free' analysis of the relaxation data showed that the peptide is fairly rigid on a sub-nanosecond time-scale. The residues from the polar side of Zrv-IIB helix are involved in micro-millisecond time-scale conformational exchange. The conformational exchange observed might indicate intramolecular processes or specific intermolecular interactions of potential relevance to Zrv-IIB ion channel formation.

The prion protein globular domain and disease-related mutants studied by molecular dynamics simulations

In humans, familial forms of transmissible spongiform encephalopathies (TSE; "prion diseases") have been shown to segregate with the exchange of individual amino acids in the prion protein (PrP) sequence. We used the NMR structure of the globular domain of mouse PrP in the cellular form (PrP(C)) as a starting point for investigations by long-time molecular dynamics (MD) simulations at ambient temperature of likely impacts of such mutations on the PrP(C) structure, making use of the fact that species-related amino acid replacements between mouse PrP and human PrP are spatially well separated from the disease-related mutations in human PrP. In the MD simulations these amino acid substitutions were found to have a variety of different effects on the protein structure, with some species showing altered packing of regular secondary structure elements, while other mutants showed no or only strictly localized changes of the structure near the variant amino acid. The fact that some of the disease-related amino acid exchanges cause no measurable change of the PrP(C) structure indicates that their influence on the conformational transition to the scrapie form of PrP may be due to modified intermolecular interactions during the aggregation process.

[Zolmitriptan in treatment of migraine attack--the ARES Study]

In an open-label Swiss multicentre trial to assess patient acceptance, efficacy and safety of zolmitriptan 2.5 mg tablets in the acute treatment of migraine, 112 patients were enrolled and 281 migraine attacks evaluated. Patients completed a specially designed protocol during and after each attack. Special attention was given to the patients' subjective comparison of the study drug with previously used abortive treatments. On this matter, zolmitriptan performed clearly better than analgesics and NSAIDS (78% "better"). Compared with sumatriptan, zolmitriptan was narrowly preferred (45% "better", 36% "worse"). Headache intensity was reduced from moderate or severe to mild or none after one hour in 51% and after 2 hours in 70%. Median time to efficacy was 50 minutes. Autonomic symptoms such as nausea and photo- and phonophobia were improved in 45 to 55%. A subjectively significant improvement in general condition (functionality) was reported in 51% after one hour and in 72% after 2 hours. Headache recurrence was reported by 25% of the responders after a median time lapse of 14 hours. Adverse effects were reported by 22%, and were all short lasting and spontaneously reversible. Rapid efficacy, high and persistent response rate, improvement of headache, autonomic symptoms and general condition, and excellent tolerability are thus the reasons for the patients' preference of zolmitriptan over traditional abortive drugs.

Local effects of mifepristone on the nonhuman primate endometrium

OBJECTIVE

To determine the effects of a low-dose mifepristone regimen on endometrium in the rhesus monkey by endometrial staging and analysis of molecular markers of endometrial receptivity.

DESIGN

A prospective, randomized comparative study.

SETTING

Academic research environment.

ANIMAL(S)

Normally cycling rhesus (Macaca mulatta) monkeys.

INTERVENTION(S)

Monkeys (5 per control or treatment group) received 0.03 mg of mifepristone in vehicle (sesame oil) per kilogram of body weight or vehicle daily from day 2 of the menstrual cycle to 7 days after the midcycle E2 surge.

MAIN OUTCOME MEASURE(S)

Serum estradiol (E2) and progesterone (P) levels; endometrial staging and immunoreactivity of leukemia inhibitory factor and interleukin-6 performed on fixed endometrial tissues; and relative abundance of endometrial estrogen and P receptor mRNA evaluated with semiquantitative reverse transcriptase polymerase chain reaction in which cyclophilin mRNA, a housekeeping gene product, was coamplified as the reference standard.

RESULT(S)

Mifepristone at 0.03 mg/kg/d induced a delay in the endometrial cycle with a shift from the late to midsecretory phase. This treatment regimen did not suppress the midcycle gonadotropin surge or, presumably, ovulation because P levels were normal during the midluteal phase. The staining intensity of leukemia inhibitory factor and interleukin-6 was dependent upon the endometrial stage and was decreased in treated monkeys. E and P receptor mRNAs increased significantly with mifepristone treatment compared with controls, another indication of delayed uterine staging.

CONCLUSION(S)

Mifepristone at 0.03 mg/kg/d had no antiovulatory effect but delayed development of the endometrium from the late to midsecretory phase. This study provides further evidence that endometrial maturation can be altered without affecting ovarian cyclicity.

NMR solution structure of the human prion protein

The NMR structures of the recombinant human prion protein, hPrP(23-230), and two C-terminal fragments, hPrP(90-230) and hPrP(121-230), include a globular domain extending from residues 125-228, for which a detailed structure was obtained, and an N-terminal flexibly disordered "tail." The globular domain contains three alpha-helices comprising the residues 144-154, 173-194, and 200-228 and a short anti-parallel beta-sheet comprising the residues 128-131 and 161-164. Within the globular domain, three polypeptide segments show increased structural disorder: i.e., a loop of residues 167-171, the residues 187-194 at the end of helix 2, and the residues 219-228 in the C-terminal part of helix 3. The local conformational state of the polypeptide segments 187-193 in helix 2 and 219-226 in helix 3 is measurably influenced by the length of the N-terminal tail, with the helical states being most highly populated in hPrP(23-230). When compared with the previously reported structures of the murine and Syrian hamster prion proteins, the length of helix 3 coincides more closely with that in the Syrian hamster protein whereas the disordered loop 167-171 is shared with murine PrP. These species variations of local structure are in a surface area of the cellular form of PrP that has previously been implicated in intermolecular interactions related both to the species barrier for infectious transmission of prion disease and to immune reactions.

Conformational changes of the BS2 operator DNA upon complex formation with the Antennapedia homeodomain studied by NMR with 13C/15N-labeled DNA

The NMR structures have been determined for a 13C/15N doubly labeled 14 base-pair DNA duplex comprising the BS2 operator sequence both free in solution and in the complex with the Antennapedia homeodomain. The impact of the DNA labeling is assessed from comparison with a previous structure of the same complex that was determined using isotope labeling only for the protein. Differences between the two structure determinations are nearly completely limited to the DNA, which retains the global B -conformation of the free DNA also in the complex. Local protein-induced conformational changes are a narrowing of the minor groove due to the interaction with the N-terminal arm of the homeodomain, and changes of the sugar puckers of the deoxyriboses G5 and C6, which are apparently induced by van der Waals interactions with Tyr25, and with Gln50 and Arg53, respectively. The high conservation of these amino acid residues in homeodomains suggests that protein-induced shifts in some sugar puckers contribute to the affinity of homeodomains to their cognate DNA. The data obtained here with the Antennapedia homeodomain-DNA complex clearly show that nucleic acid isotope-labeling can support detailed conformational characterization of DNA in complexes with proteins, which will be indispensable for structure determinations of complexes containing globally distorted DNA conformations.

NMR structure of the chimeric hybrid duplex r(gcaguggc).r(gcca)d(CTGC) comprising the tRNA-DNA junction formed during initiation of HIV-1 reverse transcription

A high-quality NMR solution structure of the chimeric hybrid duplex r(gcaguggc).r(gcca)d(CTGC) was determined using the program DYANA with its recently implemented new module FOUND, which performs exhaustive conformational grid searches for dinucleotides. To ensure conservative data interpretation, the use of 1H-1H lower distance limit constraints was avoided. The duplex comprises the tRNA-DNA junction formed during the initiation of HIV-1 reverse transcription. It forms an A-type double helix that exhibits distinct structural deviations from a standard A-conformation. In particular, the minor groove is remarkably narrow, and its width decreases from about 7.5 A in the RNA/RNA stem to about 4.5 A in the RNA/DNA segment. This is unexpected, since minor groove widths for A-RNA and RNA/DNA hybrid duplexes of approximately 11 A and approximately 8.5 A, respectively, were previously reported. The present, new structure supports that reverse transcriptase-associated RNaseH specificity is related primarily to conformational adaptability of the nucleic acid in 'induced-fit'-type interactions, rather than the minor groove width of a predominantly static nucleic acid duplex.

Nonstructural C protein is required for efficient measles virus replication in human peripheral blood cells

The P gene of measles virus (MV) encodes the phosphoprotein, a component of the virus ribonucleoprotein complex, and two nonstructural proteins, C and V, with unknown functions. Growth of recombinant MV, defective in C or V expression, was explored in human peripheral blood mononuclear cells (PBMC). The production of infectious recombinant MV V- was comparable to that of parental MV tag in simian Vero fibroblasts and in PBMC. In contrast, MV C- progeny was strongly reduced in PBMC but not in Vero cells. Consistently, the expression of both hemagglutinin and fusion proteins, as well as that of nucleoprotein mRNA, was lower in MV C--infected PBMC. Thus, efficient replication of MV in natural host cells requires the expression of the nonstructural C protein. The immunosuppression that accompanies MV infection is associated with a decrease in the in vitro lymphoproliferative response to mitogens. MV C- was as potent as MV tag or MV V- in inhibiting the phytohemagglutinin-induced proliferation of PBMC, indicating that neither the C protein nor the V protein is directly involved in this effect.

Attitudes and practices of pharmacy managers regarding needle sales to injection drug users

OBJECTIVE

To determine Louisiana pharmacy managers' attitudes and practices regarding needle and syringe sales to suspected injection drug users (IDUs) without prescriptions, and to assess which factors affect their decisions to sell nonprescription needles and syringes.

DESIGN

Cross-sectional mail survey.

SETTING

The six most populous cities of Louisiana.

PARTICIPANTS

Pharmacy managers with active permits not affiliated with large hospitals or institutions.

MAIN OUTCOME MEASURES

Selling nonprescription needles to suspected IDUs, willingness to sell nonprescription needles to suspected IDUs, and reasons for not selling nonprescription needles to suspected IDUs.

RESULTS

Approximately one-fourth of the respondents reported that they had sold needles and syringes to suspected IDUs without a prescription. The most frequently cited reason for not selling was fear of increasing drug use; however, many of these pharmacists reported that they would conduct a sale if the customer had a referral from an agency or clinic.

CONCLUSION

Pharmacists can assist in the prevention of HIV transmission through nonprescription needle sales to IDUs. This role can be promoted through education of pharmacists and development of referral systems for IDUs.

Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY

A new approach for automated peak picking of multidimensional protein NMR spectra with strong overlap is introduced, which makes use of the program AUTOPSY (automated peak picking for NMR spectroscopy). The main elements of this program are a novel function for local noise level calculation, the use of symmetry considerations, and the use of lineshapes extracted from well-separated peaks for resolving groups of strongly overlapping peaks. The algorithm generates peak lists with precise chemical shift and integral intensities, and a reliability measure for the recognition of each peak. The results of automated peak picking of NOESY spectra with AUTOPSY were tested in combination with the combined automated NOESY cross peak assignment and structure calculation routine NOAH implemented in the program DYANA. The quality of the resulting structures was found to be comparable with those from corresponding data obtained with manual peak picking.

Conformational analysis of protein and nucleic acid fragments with the new grid search algorithm FOUND

The new computer algorithm FOUND, which is implemented as an integrated module of the DYANA structure calculation program, is capable of performing systematic local conformation analyses by exhaustive grid searches for arbitrary contiguous fragments of proteins and nucleic acids. It uses torsion angles as the only degrees of freedom to identify all conformations that fulfill the steric and NMR-derived conformational restraints within a contiguous molecular fragment, as defined either by limits on the maximal restraint violations or by the fragment-based DYANA target function value. Sets of mutually dependent torsion angles, for example in ribose rings, are treated as a single degree of freedom. The results of the local conformation analysis include allowed torsion angle ranges and stereospecific assignments for diastereotopic substituents, which are then included in the input of a subsequent structure calculation. FOUND can be used for grid searches comprising up to 13 torsion angles, such as the backbone of a complete alpha-helical turn or dinucleotide fragments in nucleic acids, and yields a significantly higher number of stereospecific assignments than the precursor grid search algorithm HABAS.

Prion protein NMR structure and familial human spongiform encephalopathies

The refined NMR structure of the mouse prion protein domain mPrP(121-231) and the recently reported NMR structure of the complete 208-residue polypeptide chain of mPrP are used to investigate the structural basis of inherited human transmissible spongiform encephalopathies. In the cellular form of mPrP no spatial clustering of mutation sites is observed that would indicate the existence of disease-specific subdomains. A hydrogen bond between residues 128 and 178 provides a structural basis for the observed highly specific influence of a polymorphism in position 129 in human PrP on the disease phenotype that segregates with the mutation Asp-178-Asn. Overall, the NMR structure implies that only part of the disease-related amino acid replacements lead to reduced stability of the cellular form of PrP, indicating that subtle structural differences in the mutant proteins may affect intermolecular signaling in a variety of different ways.

Regional distribution of 5alpha-reductase type 1 and type 2 mRNA along the human epididymis

OBJECTIVE

To determine the regional distribution and relative expression of 5alpha-reductase type 1 and type 2 mRNA within the human testis and regions of the epididymis.

DESIGN

Prospective observational study.

SETTING

University academic medical center.

PATIENT(S)

Two young adult male organ donors.

INTERVENTION(S)

None

MAIN OUTCOME MEASURE(S)

The distribution of 5alpha-reductase type 1 and type 2 mRNA in the testis and regions of the epididymis was detected by Northern blot analysis. The relative abundance of each 5alpha-reductase mRNA was evaluated using semiquantitative reverse transcriptase-polymerase chain reaction (RT-PCR) in which cyclophilin mRNA, a house-keeping gene product, was coamplified as the reference standard.

RESULT(S)

Northern blot analysis revealed the 5alpha-reductase type 2 transcript in the midcaput, distal caput, corpus, and proximal cauda of the epididymis, but the transcript was undetectable in the testis, proximal caput, and distal cauda region. No transcript for the type 1 isozyme was detected by Northern blot. The more sensitive RT-PCR showed low levels of type 1 mRNA in the testis and epididymis, with the highest abundance in the proximal caput. Type 2 mRNA of 5alpha-reductase was most abundant in the midcaput, was decreased in the more distal regions, and was more abundant than type 1 mRNA in all epididymal regions except for the proximal caput.

CONCLUSION(S)

Both 5alpha-reductase type 1 and type 2 mRNAs are present in the human epididymis. The type 2 isozyme mRNA is predominant, being more highly expressed than the low-abundance type 1 mRNA.

Prion protein structural features indicate possible relations to signal peptidases

Transmissible spongiform encephalopathies (TSEs) in mammalian species are believed to be caused by an oligomeric isoform, PrP(Sc), of the cellular prion protein, PrP(C). One of the key questions in TSE research is how the observed accumulation of PrP(Sc), or possibly the concomitant depletion of PrP(C) can cause fatal brain damage. Elucidation of the so far unknown function of PrP(C) is therefore of crucial importance. PrP(C) is a membrane-anchored cell surface protein that possesses a so far unique three-dimensional structure. While the N-terminal segment 23-120 of PrP(C) is flexibly disordered, its C-terminal residues 121-231 form a globular domain with three alpha-helices and a two-stranded beta-sheet. Here we report the observation of structural similarities between the domain of PrP(121-231) and the soluble domains of membrane-anchored signal peptidases. At the level of the primary structure we find 23% identity and 41% similarity between residues 121-217 of the C-terminal domain of murine PrP and a catalytic domain of the rat signal peptidase. The invariant PrP residues Tyr-128 and His-177 align with the two presumed active-site residues of signal peptidases and are in close spatial proximity in the three-dimensional structure of PrP(121-231).

Prion (PrPSc)-specific epitope defined by a monoclonal antibody

Prions are infectious particles causing transmissible spongiform encephalopathies (TSEs). They consist, at least in part, of an isoform (PrPSc) of the ubiquitous cellular prion protein (PrPC). Conformational differences between PrPC and PrPSc are evident from increased beta-sheet content and protease resistance in PrPSc. Here we describe a monoclonal antibody, 15B3, that can discriminate between the normal and disease-specific forms of PrP. Such an antibody has been long sought as it should be invaluable for characterizing the infectious particle as well as for diagnosis of TSEs such as bovine spongiform encephalopathy (BSE) or Creutzfeldt-Jakob disease (CJD) in humans. 15B3 specifically precipitates bovine, murine or human PrPSc, but not PrPC, suggesting that it recognizes an epitope common to prions from different species. Using immobilized synthetic peptides, we mapped three polypeptide segments in PrP as the 15B3 epitope. In the NMR structure of recombinant mouse PrP, segments 2 and 3 of the 15B3 epitope are near neighbours in space, and segment 1 is located in a different part of the molecule. We discuss models for the PrPSc-specific epitope that ensure close spatial proximity of all three 15B3 segments, either by intermolecular contacts in oligomeric forms of the prion protein or by intramolecular rearrangement.

Prion protein NMR structure and species barrier for prion diseases

The structural basis of species specificity of transmissible spongiform encephalopathies, such as bovine spongiform encephalopathy or "mad cow disease" and Creutzfeldt-Jakob disease in humans, has been investigated using the refined NMR structure of the C-terminal domain of the mouse prion protein with residues 121-231. A database search for mammalian prion proteins yielded 23 different sequences for the fragment 124-226, which display a high degree of sequence identity and show relevant amino acid substitutions in only 18 of the 103 positions. Except for a unique isolated negative surface charge in the bovine protein, the amino acid differences are clustered in three distinct regions of the three-dimensional structure of the cellular form of the prion protein. Two of these regions represent potential species-dependent surface recognition sites for protein-protein interactions, which have independently been implicated from in vitro and in vivo studies of prion protein transformation. The third region consists of a cluster of interior hydrophobic side chains that may affect prion protein transformation at later stages, after initial conformational changes in the cellular protein.

The NMR solution structure of the non-classical homeodomain from the rat liver LFB1/HNF1 transcription factor

The nuclear magnetic resonance (NMR) solution structure of the non-classical homeodomain from the rat liver LFB1/HNF1 transcription factor was determined with the program DIANA from an input of 1356 nuclear Overhauser enhancement (NOE) upper distance constraints and 228 dihedral angle constraints collected using experiments with the unlabelled, the uniformly 15N-labelled and the uniformly 13C-labelled protein. Out of a group of 50 independently calculated conformers the 20 conformers with the smallest residual DIANA target function values were refined by energy minimization with the program OPAL and are used to represent the NMR structure. The average of the pairwise root-mean-square deviations (r.m.s.d.) of these 20 individual NMR conformers relative to the mean coordinates is 0.73 A (1 A = 0.1 nm) for the backbone atoms N, C(alpha) and C' of residues 15 to 82. The chain-terminal polypeptide segments 1-14 and 90-99 are disordered in solution. The globular fold contains three well-defined helices comprising the residues 19 to 29, 37 to 53 and 71 to 81, and the third helix is extended by a less well-ordered fourth helix with residues 82 to 89, which coincides with corresponding observations in "classical" homeodomains. Side-chain analysis resulted in 33 "best-defined" side-chains, with global displacements smaller than 1.1 A, and addition of these side-chains to the global superposition of residues 15 to 82 resulted in a r.m.s.d of 0.81 A. The protein contains two hydrophobic cores, one of which corresponds to the helical packing seen in classical homeodomains, while the other one stabilizes the conformation of the 21-residue insertion between helices II and III. The individual helices and their relative spatial arrangements are stabilized by a variety of structural motifs, which include medium-range and long-range hydrogen bonds and salt bridges. Detailed comparison with the Antennapedia homeodomain, and studies of the complex formation with an operator DNA half-site provided initial information on the DNA-binding mode of the LFB1/HNF1 homeodomain.

Comparison between clinical examination, cw-Doppler ultrasound and colour-duplex sonography in the diagnosis of incompetent perforating veins

OBJECTIVES

This study was conducted to investigate the accuracy and agreement between clinical examination, continuous wave (cw)-Doppler ultrasound and colour-duplex sonography (CDS) in diagnosing incompetent perforating veins (ICPV).

DESIGN

Observational cohort study.

MATERIAL AND METHODS

Nineteen patients with chronic venous insufficiency (CVI) were examined clinically, by hand-held cw-Doppler ultrasound in combination with tourniquet compression and CDS.

RESULTS

The low accuracy of the clinical examination and the diagnosis of ICPV by cw-Doppler were surprising. The specificity was 15% and sensitivity 29%, when CDS was taken as the "gold standard". Furthermore the results show clearly that the application of a tourniquet cannot provide reliable results.

CONCLUSIONS

In patients with CVI, clinical and cw-Doppler cannot accurately diagnose ICPV when compared to CDS.

Structural role of a buried salt bridge in the 434 repressor DNA-binding domain

The independently folding 63-residue N-terminal DNA-binding domain of the 434 repressor, 434(1-63), contains a buried Arg10-Glu35 salt bridge. A corresponding salt bridge is found in a variety of prokaryotic and eukaryotic DNA-binding proteins with helix-turn-helix motifs. Here, the NMR solution structures of 434(1-63) and the mutant protein 434[R10M](1-63) were determined to investigate the structural role of this salt bridge. Both proteins contain the same type of global fold, with five alpha-helices and a helix-turn-helix motif formed by the helices II and III. The primary structural difference caused by the Arg10 --> Met mutation is a translation of helix I along its axis relative to the helix II-turn-helix III motif. This limited conformational change is paralleled by a 9 kJ M(-1) decrease of the stability of the folded mutant protein in aqueous solution at pH 4.8. It affects the pKa value of Glu19 as well as the population of a hydrogen bond between the backbone amide proton of Asn16 and the side-chain carboxylate group of Glu19. Using the crystal structure of the 434 repressor dimer complexed with the operator DNA as a basis, model building of the DNA complex with the NMR structure of 434[R10M](1-63) shows that Asn16, which is located on the protein surface, makes direct contact with the DNA and indicates that the point mutation Arg10 --> Met should also lead to modifications of the protein-protein contacts in the complex.

The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules

A new program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for the analysis of MD trajectories, OPAL affords high efficiency and flexibility for work with different force fields, and offers a user-friendly interface and extensive trajectory analysis capabilities. Salient features are computational speeds of up to 1.5 GFlops on vector supercomputers such as the NEC SX-3, ellipsoidal boundaries to reduce the system size for studies in explicit solvents, and natural treatment of the hydrostatic pressure. Practical applications of OPAL are illustrated with MD simulations of pure water, energy minimization of the NMR structure of the mixed disulfide of a mutant E. coli glutaredoxin with glutathione in different solvent models, and MD simulations of a small protein, pheromone Er-2, using either instantaneous or time-averaged NMR restraints, or no restraints.

NMR structure of the mouse prion protein domain PrP(121-231)

The 'protein only' hypothesis states that a modified form of normal prion protein triggers infectious neurodegenerative diseases, such as bovine spongiform encephalopathy (BSE), or Creutzfeldt-Jakob disease (CJD) in humans. Prion proteins are thought to exist in two different conformations: the 'benign' PrPcform, and the infectious 'scrapie form', PrPsc. Knowledge of the three-dimensional structure of PrPc is essential for understanding the transition to PrPsc. The nuclear magnetic resonance (NMR) structure of the autonomously folding PrP domain comprising residues 121-231 (ref. 6) contains a two-stranded antiparallel beta-sheet and three alpha-helices. This domain contains most of the point-mutation sites that have been linked, in human PrP, to the occurrence of familial prion diseases. The NMR structure shows that these mutations occur within, or directly adjacent to, regular secondary structures. The presence of a beta-sheet in PrP(121-231) is in contrast with model predictions of an all-helical structure of PrPc (ref. 8), and may be important for the initiation of the transition from PrPc to PrPsc.

Hydration and DNA recognition by homeodomains

A 2-nanosecond molecular dynamics (MD) simulation of an Antennapedia homeodomain-DNA complex in explicit solvent water at ambient temperature and pressure was performed to supplement experimental nuclear magnetic resonance (NMR) data on the structure and dynamics of this complex. In addition to direct protein-DNA contacts, the MD trajectory attributes an essential role for specific DNA recognition to hydration water molecules that mediate intermolecular contacts. The simulation provides a detailed description of the pathways of hydration water molecules exchanging in and out of the protein-DNA interface and indicates that the residence times of these "interior" waters are on the nanosecond time scale, near the lower end of the range determined by NMR.

Automated sequence-specific NMR assignment of homologous proteins using the program GARANT

The program GARANT (General Algorithm for Resonance AssignmeNT) for automated sequence-specific NMR assignment of proteins is based on the mapping of peaks predicted from the amino acid sequence onto the peaks observed in multidimensional spectra [C. Bartels, P. Güntert, M. Billeter and K. Wüthrich (1996) J. Comput. Chem., manuscript submitted for publication]. In this paper we demonstrate the potential of GARANT for the assignment of homologous proteins when either the three-dimensional structure or the chemical shifts of the parent protein are known. In these applications, GARANT utilizes supplementary information either in the form of interatomic distances derived from the three-dimensional structure, in order to add nuclear Overhauser effects reflecting the tertiary structure to the list of expected peaks, or in the form of the chemical shifts of the parent protein, in order to obtain a better estimate of the positions of the expected peaks. The procedure is illustrated with three different proteins: (i) a mutant form of Tendamistat (74 residues), using homonuclear 2D (1)H NMR spectra and either the three-dimensional structure or the chemical shifts of the wild-type protein; (ii) the mutant Antp(C39S, W56S) homeodomain (68 residues), using homonuclear 2D (1)H NMR spectra and the three-dimensional structure of the Antp(C39S) homeodomain; and (iii) free cyclophilin A (165 residues), using heteronuclear 3D NMR spectra and the three-dimensional structure of a cyclophilin A-cyclosporin A complex. In these three systems nearly complete assignment of the polypeptide backbone resonances and assignment of over 80% of the amino acid side-chain resonances was obtained without manual intervention.

Messenger ribonucleic acid kinetics in human oocytes--effects of in vitro culture and nuclear maturational status

OBJECTIVE

To study the effects of different nuclear maturational status (prophase I [PI] versus metaphase II [MII]) and in vitro culture on the kinetics of maternal messenger ribonucleic acid (mRNA) in human oocytes.

DESIGN

Molecular biology on excess oocytes obtained from our clinical IVF program.

INTERVENTIONS

The oocytes, classified as either PI or MII at collection, were used as such or cultured in vitro for an additional 24 hours. The relative levels of c-mos and cyclin-B1 were measured using semiquantitative reverse transcriptase polymerase chain reaction (RT-PCR).

RESULTS

The mean levels of c-mos and cyclin-B1 transcripts were indistinguishable between the PI, MII, PI oocytes matured in vitro, PI oocytes failing to mature, and MII oocytes cultured for additional 24 hours. The variability in the levels of these transcripts increased during the vitro culture.

CONCLUSIONS

The level of c-mos and cyclin-B1 transcripts were not different in PI versus MII oocytes, therefore, differences seen in the clinical outcome of PI and MII oocytes may be unrelated to levels of these gene products. C-mos and cyclin B1 mRNA were maintained in vitro, thus degradation of maternal RNA is not activated in excess during the 24-hour culture.

[Color duplex ultrasonography in the diagnosis of deficient perforating veins in comparison to cw-Doppler ultrasonography and clinical examination]

The study was conducted to investigate the accuracy and agreement between clinical examination, cw-Doppler ultrasound and color-duplex sonography in diagnosing incompetent perforating veins. Nineteen patients with chronic venous insufficiency (CVI) were examined clinically, by hand-held cw-Doppler ultrasound in combination with tourniquet compression and color-coded duplex sonography CDS. The accuracy of the clinical examination and the diagnosis of ICPV by cw-Doppler were surprisingly low. The specificity was 15% and sensitivity 29%, when CDS was taken as gold standard. Furthermore the results show clearly that the application of a tourniquet cannot provide reliable results. It is concluded that in patients with CVI clinical and cw-Doppler examinations are not sufficient for an accurate diagnosis of incompetent perforating veins. Color-duplex provides a new noninvasive approach for accurate anatomical and functional diagnosis, which is of great importance prior to surgical interventions and/or sclerotherapy.

Domains of the measles virus N protein required for binding to P protein and self-assembly

The nucleocapsid protein (N, 525 amino acids) of measles virus plays a central role in the replication of the viral genomic RNA. Its functions require interactions with itself and with other viral components. The N protein encapsidates genomic RNA, a function reflected in its ability to self-assemble into nucleocapsid-like particles in the absence of other viral proteins. The substrate for the packaging of nascent RNA during RNA replication is a complex between the N and phosphoprotein (P). The domains on the N protein that promote binding to P protein and self-assembly have been identified utilizing a series of N protein deletions. Two noncontiguous regions, amino acids 4-188 and 304-373 of N protein, are required for the formation of the soluble N-P complex, while deletion of amino acids 189-239 did not affect N-P binding. Amino acids 240-303 appear to be necessary for the stability of the protein. The N-terminal 398 amino acids are all required for the formation of organized nucleocapsid-like particles, since deletion of the central region from amino acids 189-373 completely abolished N-N interaction, and deletion of amino acids 4-188 and 374-492 caused the formation of unstructured aggregates.

MOLMOL: a program for display and analysis of macromolecular structures

MOLMOL is a molecular graphics program for display, analysis, and manipulation of three-dimensional structures of biological macromolecules, with special emphasis on nuclear magnetic resonance (NMR) solution structures of proteins and nucleic acids. MOLMOL has a graphical user interface with menus, dialog boxes, and on-line help. The display possibilities include conventional presentation, as well as novel schematic drawings, with the option of combining different presentations in one view of a molecule. Covalent molecular structures can be modified by addition or removal of individual atoms and bonds, and three-dimensional structures can be manipulated by interactive rotation about individual bonds. Special efforts were made to allow for appropriate display and analysis of the sets of typically 20-40 conformers that are conventionally used to represent the result of an NMR structure determination, using functions for superimposing sets of conformers, calculation of root mean square distance (RMSD) values, identification of hydrogen bonds, checking and displaying violations of NMR constraints, and identification and listing of short distances between pairs of hydrogen atoms.

NMR studies of DNA duplexes singly cross-linked by different synthetic linkers

Molecular modelling studies resulted in the design of a variety of non-nucleotidic covalent linkers to bridge the 3'-end of the (+)-strand and the 5'-end of the (-)-strand in DNA duplexes. Three of these linkers were synthesized and used to prepare singly cross-linked duplexes d(GTGGAATTC)-linker-d(GAATTCCAC). Linker I is an assembly of a propylene-, a phosphate- and a second propylene-group and is thought to mimic the backbone of two nucleotides. Linkers II and III consist of five and six ethyleneglycol units, respectively. The melting temperatures of the cross-linked duplexes are 65 degrees C for I and 73 degrees C for II and III, as compared with 36 degrees C for the corresponding non-linked nonadeoxynucleotide duplex. The three cross-linked duplexes were structurally characterized by nuclear magnetic resonance spectroscopy. The 1H and 31P resonance assignments in the DNA stem were obtained using standard methods. For the resonance assignment of the linker protons, two-dimensional 1H-31P heteronuclear COSY and two-quantum-experiments were used. Distance geometry calculations with NOE-derived distance constraints were performed and the resulting structures were energy-minimized. In duplex I, the nucleotides flanking the propylene-phosphate-propylene-linker do not form a Watson-Crick base pair, whereas in duplexes II and III the entire DNA stem is in a B-type double helix conformation.

The program XEASY for computer-supported NMR spectral analysis of biological macromolecules

A new program package, XEASY, was written for interactive computer support of the analysis of NMR spectra for three-dimensional structure determination of biological macromolecules. XEASY was developed for work with 2D, 3D and 4D NMR data sets. It includes all the functions performed by the precursor program EASY, which was designed for the analysis of 2D NMR spectra, i.e., peak picking and support of sequence-specific resonance assignments, cross-peak assignments, cross-peak integration and rate constant determination for dynamic processes. Since the program utilizes the X-window system and the Motif widget set, it is portable on a wide range of UNIX workstations. The design objective was to provide maximal computer support for the analysis of spectra, while providing the user with complete control over the final resonance assignments. Technically important features of XEASY are the use and flexible visual display of 'strips', i.e., two-dimensional spectral regions that contain the relevant parts of 3D or 4D NMR spectra, automated sorting routines to narrow down the selection of strips that need to be interactively considered in a particular assignment step, a protocol of resonance assignments that can be used for reliable bookkeeping, independent of the assignment strategy used, and capabilities for proper treatment of spectral folding and efficient transfer of resonance assignments between spectra of different types and different dimensionality, including projected, reduced-dimensionality triple-resonance experiments.

The sequence and conformation of human pancreatic procarboxypeptidase A2. cDNA cloning, sequence analysis, and three-dimensional model

A full-length cDNA clone coding for human pancreatic preprocarboxypeptidase A2 has been isolated from a lambda gt 11 human pancreatic library. Expression clones were identified by specific interaction with antisera raised against the native protein. The open reading frame of the polynucleotide sequence is 1254 base pairs in length and encodes a protein of 417 amino acids. This cDNA includes a short leader signal peptide of 16 amino acids and a 94-amino acid-long activation segment. The amino acid sequence shows 89% identity to that of rat procarboxypeptidase A2, the only A2 form sequenced so far, and 64% identity to that of human procarboxypeptidase A1. The newly determined sequence was modeled to the three-dimensional crystal structures of both bovine carboxypeptidase A and porcine procarboxypeptidase A1 by a novel distance geometry approach. Biases in the modeling were avoided by relying exclusively on automatic procedures and by using random structures as starting points. Information taken from the known homologous structures refers only to the backbone since no explicit data describing the conformation of side chains were transferred. Ten structures of human carboxypeptidase A2 were determined on the basis of each of the two known crystal structures. The root-mean-square distance for the backbone atoms between the 10 structures and their mean for 237 selected residues is 0.7 A when starting from the bovine protein and 0.8 A for 251 selected residues when starting from the porcine protein. The 94 residue-long activation segment was also determined in the modeling based on the porcine zymogen; its structure is well defined but not its orientation with respect to the enzyme moiety. The model obtained for human procarboxypeptidase A2 is discussed with respect to the specificity and activation of the enzyme.

Rationale and experience in treating suspected hospital-based mixed infections

Ochsner Foundation Hospital of the Ochsner Medical Institutions (OMI), a 532-bed tertiary care facility in New Orleans, uses a formulary review process common to many institutions. Considered in the selection of antimicrobial therapy are efficacy, safety, and cost. At OMI, ticarcillin-clavulanate plus gentamicin are the standard broad-spectrum antimicrobial agents for initial treatment of suspected mixed infections. The pharmacy department provides an aminoglycoside-monitoring program and convenient dosing guidelines. The regimen has resulted in good therapeutic outcomes and few adverse effects. Bacterial resistance has not been detected. Future plans include a large-scale concurrent review of patient outcomes, resistance patterns, and rates of fungal overgrowth associated with these agents.