Illumina short-read and MinION long-read WGS to characterize the molecular epidemiology of an NDM-1 Serratia marcescens outbreak in Romania

Background and Objectives

Serratia marcescens is an emerging nosocomial pathogen, and the carbapenemase bla_NDM has been reported in several surveys in Romania. We aimed to investigate the molecular epidemiology of S. marcescens in two Romanian hospitals over 2010–15, including a neonatal NDM-1 S. marcescens outbreak.

Methods

Isolates were sequenced using Illumina technology together with carbapenem-non-susceptible NDM-1-positive and NDM-1-negative Klebsiella pneumoniae and Enterobacter cloacae to provide genomic context. A subset was sequenced with MinION to fully resolve NDM-1 plasmid structures. Resistance genes, plasmid replicons and ISs were identified in silico for all isolates; an annotated phylogeny was reconstructed for S. marcescens. Fully resolved study NDM-1 plasmid sequences were compared with the most closely related publicly available NDM-1 plasmid reference.

Results

44/45 isolates were successfully sequenced (S. marcescens, n = 33; K. pneumoniae, n = 7; E. cloacae, n = 4); 10 with MinION. The S. marcescens phylogeny demonstrated several discrete clusters of NDM-1-positive and -negative isolates. All NDM-1-positive isolates across species harboured a pKOX_NDM1-like plasmid; more detailed comparisons of the plasmid structures demonstrated a number of differences, but highlighted the largely conserved plasmid backbones across species and hospital sites.

Conclusions

The molecular epidemiology is most consistent with the importation of a pKOX_NDM1-like plasmid into Romania and its dissemination amongst K. pneumoniae/E. cloacae and subsequently S. marcescens across hospitals. The data suggested multiple acquisitions of this plasmid by S. marcescens in the two hospitals studied; transmission events within centres, including a large outbreak on the Targu Mures neonatal unit; and sharing of the pKOX_NDM1-like plasmid between species within outbreaks.

Cervical vertebrae maturation: a blinded trial study

This blinded trial was conducted to analyze possible correlations between the cervical vertebrae maturation method (CVM) and the mineralization of mandibular teeth as described by Demirjian et al. (TMS). Panoramic and cephalometric radiographs of 500 orthodontic patients were analyzed by two blinded operators. TMS was utilized to analyze mineralization of second molar, second and first premolar and canine on the left side of the mandible; CVM stage was also evaluated. A blinded statistician performed statistical correlations and multiple regression analysis. Significant relations between CVM and TMS stages were identified for each tooth. Significant age differences resulted for CVM, second molar and second premolar (p<0.05). Significant correlations for second molar were observed between TMS D and CVM I-II, TMS G and CVM III, TMS H and CVM V-VI (p less than 0.01). Second molar stage G for both sexes indicates the ongoing of growth spurt. Stage G for boys and stage H for girls correlate significantly with the late part of PGS.

Assessment of Lung Ultrasound B-Lines in Dogs with Different Stages of Chronic Valvular Heart Disease

Background

In dogs with chronic valvular heart disease (CVHD), early recognition of pulmonary edema (PE) is of paramount importance. Recent studies in dogs showed that lung ultrasound examination (LUS) is a useful technique to diagnose cardiogenic PE.

Objectives

To describe LUS features in dogs with different stages of CVHD, and to determine its diagnostic accuracy in detecting PE using thoracic radiography as the reference standard.

Animals

Sixty‐three dogs with CVHD.

Methods

Prospective, multicenter, cross‐sectional study. Each dog underwent physical examination, echocardiography, thoracic radiography, and LUS. The LUS findings were classified as absent, rare, numerous, or confluent B‐lines. Sensitivity, specificity, and positive and negative predictive values of LUS B‐lines to identify PE were calculated using thoracic radiography as the reference standard.

Results

Dogs in stage B1 had absent or rare B‐lines in 14 of 15 cases (93.3%). Dogs in stage B2 had absent or rare B‐lines in 16 of 18 cases (88.9%). All dogs in stage C, without radiographic signs of PE, had absent or rare B‐lines. Dogs in stage C, with radiographic signs of PE, had numerous or confluent B‐lines in 18 of 20 cases (90%). Lung ultrasound examination detected PE with a sensitivity of 90%, specificity of 93%, and with positive and negative predictive values of 85.7 and 95.2%, respectively.

Conclusions and Clinical Importance

Lung ultrasound examination showed good diagnostic accuracy to identify cardiogenic PE and might be helpful in staging dogs with CVHD. Lung ultrasound examination should be considered as a new, noninvasive diagnostic tool for clinicians managing CVHD in dogs.

Species distribution and susceptibility profile to fluconazole, voriconazole and MXP-4509 of 551 clinical yeast isolates from a Romanian multi-centre study

This is the first multi-centre study regarding yeast infections in Romania. The aim was to determine the aetiological spectrum and susceptibility pattern to fluconazole, voriconazole and the novel compound MXP-4509. The 551 isolates were identified using routine laboratory methods, matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and DNA sequence analysis. Susceptibility testing was performed using the European Committee for Antimicrobial Susceptibility Testing (EUCAST) method and breakpoints. The yeasts originated from superficial infections (SUP, 51.5 %), bloodstream infections (BSI, 31.6 %) and deep-seated infections (DEEP, 16.9 %), from patients of all ages. Nine genera and 30 species were identified. The 20 Candida species accounted for 94.6 % of all isolates. C. albicans was the overall leading pathogen (50.5 %). Lodderomyces elongisporus is reported for the first time as a fungaemia cause in Europe. C. glabrata and Saccharomyces cerevisiae, as well as the non-Candida spp. and non-albicans Candida spp. groups, showed decreased fluconazole susceptibility (<75 %). The overall fluconazole resistance was 10.2 %. C. krusei accounted for 27 of the 56 fluconazole-resistant isolates. The overall voriconazole resistance was 2.5 % and was due mainly to C. glabrata and C. tropicalis isolates. Fluconazole resistance rates for the three categories of infection were similar to the overall value; voriconazole resistance rates differed: 4 % for BSI, 3.2 % for DEEP and 1.4 % for SUP. The antifungal activity of MXP-4509 was superior to voriconazole against C. glabrata and many fluconazole-resistant isolates. There was a large percentage of non-albicans Candida isolates. A large part of the high fluconazole resistance was not acquired but intrinsic, resulting from the high percentage of C. krusei.

The pathogenic L392V mutation of presenilin 1 decreases the affinity to glycogen synthase kinase-3 beta

Determination of the effects of presenilin 1 (PSEN1) mutations, involved in autosomal dominant early-onset Alzheimer's disease (ADEOAD), on the interaction between PSEN1 and binding proteins is essential to determine which interactions are involved in Alzheimer's disease (AD) pathogenesis. The PSEN1 binding protein glycogen synthase kinase-3 beta (GSK-3 beta) has been considered as a key protein in AD pathogenesis since GSK-3 beta phosphorylates tau and hyperphosphorylated tau is a main component of neurofibrillary tangles associated to AD. We show here, using surface plasmonic resonance, that the pathogenic L392V mutation, identified in a large French ADEOAD pedigree including 39 affected members, leads to a decreased affinity to GSK-3 beta. We conclude therefore that the increase of affinity of PSEN1 to GSK-3 beta reported in previous studies is not a common effect of pathogenic mutations associated to ADEOAD.

Measles epidemic in Romania, 1996-1998: assessment of vaccine effectiveness by case-control and cohort studies

A measles epidemic occurred in Romania with 32,915 cases and 21 deaths reported between November 1996 and June 1998, despite high vaccination coverage since the early 1980s. Most cases were unvaccinated children aged <2 years and vaccinated school-aged children. A case-control study among preschool children and a cohort study among primary-school children were conducted to estimate effectiveness of Romanian-produced measles vaccine, and to evaluate age at vaccination and waning immunity as risk factors for vaccine failure. Both studies indicated that measles vaccine was highly effective. One dose reduced the risk for measles by 89% (95% confidence interval (CI) 85, 91); two doses reduced the risk by 96% (95% CI 92, 98). Children vaccinated at <1 year of age were not at increased risk for measles compared with children vaccinated at > or =1 year. Waning immunity was not identified as a risk factor since vaccine effectiveness was similar for children vaccinated 6-8, 9-11, and 12-14 years in the past. Because specific groups were not at risk for vaccine failure, an immunization campaign that targets all school-aged children who lack two doses may be an effective strategy for preventing outbreaks. A mass campaign followed by increased first-dose coverage should provide the population immunity required to interrupt indigenous measles virus transmission in Romania.

The L392V mutation of presenilin 1 associated with autosomal dominant early-onset Alzheimer's disease alters the secondary structure of the hydrophilic loop

Autosomal dominant early-onset Alzheimer's disease results mainly from mutations of the presenilin 1 (PSEN1) gene, which codes for an integral membrane protein of 467 amino acids. The hydrophilic loop (amino acids 263-407) of PSEN1, in which many pathogenic mutations have been localized, appears to be crucial for the protein function since it includes the binding domains to different PSEN1 partners. Using circular dichroism (CD) we analyzed the structural effects of the pathogenic L392V mutation and compared them with those of the E318G substitution. This study revealed that, the L392V mutation, in a phospholipidic medium which mimics the in vivo membrane environment, reduces the alpha helix content of the PSEN1 loop, whereas the E318G substitution, considered as a polymorphism, does not. These results suggest that the pathogenic effect of some PSEN1 mutations within the hydrophilic loop could be the alteration of the interaction to the different binding proteins through a disruption of the secondary structure.

A survey on the vaccination practice for perinatal hepatitis B virus infection at a clinic in Okinawa, Japan

The prevalence of hepatitis B (HB) virus carrier mothers and the HB immunization rate at a clinic in Okinawa prefecture were investigated. The prevalence of HB virus carrier mothers during 1981-1985, 1986-1994 and 1995-1997 were 3.5%, 2.3% and 1.1% respectively. According to the national prevention program, passive-active immunoprophylaxis with HB immune globulin (HBIG) and HB vaccine was carried out for 12 infants born to HB virus carrier mothers positive for HBe antigen (high risk infants) and for 24 infants born to carrier mothers negative for HBe antigen (low risk infants) since 1986. The immunization rate of high risk infants and low risk infants were 100.0% and 91.7%, respectively. A follow up system for the prevention program and assessment of vaccination schedule will be necessary to improve HB immunization rate of low risk infants in the future.

Myb-DNA recognition: role of tryptophan residues and structural changes of the minimal DNA binding domain of c-Myb

The Myb oncoprotein specifically binds DNA by a domain composed of three imperfect repeats, R1, R2, and R3, each containing 3 tryptophans. The tryptophan fluorescence of the minimal binding domain, R2R3, of c-Myb was used to monitor structural flexibility changes occurring upon DNA binding to R2R3. The quenching of the Trp fluorescence by DNA titration shows that four out of the six tryptophans are involved in the formation of the specific R2R3-DNA complex and the environment of the tryptophan residues becomes more hydrophobic in the complex. The fluorescence intensity quenching of the tryptophans by binding of R2R3 to DNA is consistent with the decrease of the decay time: 1.46 ns for free R2R3 to 0.71 ns for the complexed protein. In the free R2R3, the six tryptophans are equally accessible to the iodide and acrylamide quenchers with a high collisional rate constant (4 x 10(9) and 3 x 10(9) M-1 s-1, respectively), indicating that R2R3 in solution is very flexible. In the R2R3-DNA complex, no Trp fluorescence quenching is observed with iodide whereas all tryptophan residues remain accessible to acrylamide with a collisional rate constant slightly slower than that in the free state. These results indicate that (i) a protein structural change occurs and (ii) the R2R3 molecule keeps a high mobility in the complex. The complex formation presents a two-step kinetics: a fast step corresponding to the R2R3-DNA association (7 x 10(5) M-1 s-1) and a slower one (0.004 s-1), which should correspond to a structural reorganization of the protein including a reordering of the water molecules at the protein-DNA interface.

[Nontuberculous mycobacteria in the hospital environment]

Mycobacteria other than tubercle (MOTT) are ubiquitous. Mycobacterial disease is most common at the extremes of age and at the patients with malignancy or HIV infection. In an attempt to establish effective measures to prevent nosocomial disease which has become increasingly important we investigated the presence of MOTT in hospital environment of oncological and pediatric units. Between 1994-1997, 21 strains of MOTT were isolated from 500 environmental specimens (4.2% positive samples). The sources of MOTT were tap water and dust. The most frequent species was Mycobacterium marinum.

Sequential and combined use of inactivated and oral poliovirus vaccines: Dolj District, Romania, 1992-1994

To determine the feasibility of a vaccination strategy that would reduce the risk of vaccine-associated paralysis while retaining a barrier against the spread of wild poliovirus, a 2-year project was undertaken using enhanced-potency inactivated poliovirus vaccine (IPV) administered at 2 and 3 months of age followed by doses of both IPV and oral poliovirus vaccine (OPV) administered at 4 and 9 months of age. Vaccination coverage by 12 months of age with three or more doses of IPV and two doses of OPV among 16,566 infants eligible for vaccination was > 95% and > 80%, respectively. Among 51 children from whom blood samples were obtained 45 days after their third dose of IPV and first dose of OPV, 100% had serum neutralizing antibodies (reciprocal titer > or = 10) to all three poliovirus types. No cases of paralytic poliomyelitis due to either wild or vaccine-related strains were reported. The project demonstrated the feasibility, safety, and high immunogenicity of sequential use of IPV followed by OPV in Romania.

Conformational changes upon binding of a receptor loop to lipid structures: possible role in signal transduction

The mas oncogene codes for a seven transmembrane helix protein. The amino acid sequence 253-266, from the third extracellular loop and beginning of helix 7, was synthesized either blocked or carrying an amino acid spin label at the N-terminus. Peptide binding to bilayers and micelles was monitored by ESR, fluorescence and circular dichroism. Binding induced tighter lipid packing, and caused an increase of peptide secondary structure. While binding to bilayers occurred only when peptide and phospholipid bore opposite charges, in micelles the interaction took place irrespective of charge. The results suggest that changes in lipid packing could modulate conformational changes in receptor loops related to the triggering of signal transduction.

Scorpion toxins as natural scaffolds for protein engineering

A compact, well-organized, and natural motif, stabilized by three disulfide bonds, is proposed as a basic scaffold for protein engineering. This motif contains 37 amino acids only and is formed by a short helix on one face and an antiparallel triple-stranded beta-sheet on the opposite face. It has been adopted by scorpions as a unique scaffold to express a wide variety of powerful toxic ligands with tuned specificity for different ion channels. We further tested the potential of this fold by engineering a metal binding site on it, taking the carbonic anhydrase site as a model. By chemical synthesis we introduced nine residues, including three histidines, as compared to the original amino acid sequence of the natural charybdotoxin and found that the new protein maintains the original fold, as revealed by CD and 1H NMR analysis. Cu2+ ions are bound with Kd = 4.2 x 10(-8) M and other metals are bound with affinities in an order mirroring that observed in carbonic anhydrase. The alpha/beta scorpion motif, small in size, easily amenable to chemical synthesis, highly stable, and tolerant for sequence mutations represents, therefore, an appropriate scaffold onto which polypeptide sequences may be introduced in a predetermined conformation, providing an additional means for design and engineering of small proteins.

Solution structure of a green mamba toxin that activates muscarinic acetylcholine receptors, as studied by nuclear magnetic resonance and molecular modeling

The three-dimensional solution structure of the MTX2 toxin (65 amino acids and 4 disulfides) from the green mamba venom (Dendroaspis angusticeps), a toxin that activates the pharmacological M1 muscarinic acetylcholine receptors, has been determined by nuclear magnetic resonance and molecular modeling. Seventeen structures were calculated from 810 distance and 68 dihedral angle restraints using DIANA and X-PLOR. The average rms deviation between the 17 refined structures and the energy-minimized average structure is 0.95 A for the backbone atoms. The overall folding of MTX2 consists of three loops stabilized by the four disulfides and forming a two- and a three-stranded beta-sheet. This structure appears to be very similar to that of other snake toxins, such as neurotoxins, fasciculins, and cardiotoxins, that also possess the same three-finger fold. For instance, the RMSd for the backbone atoms between MTX2 and the curaremimetic toxin alpha (from Naja nigricollis), the acetylcholinesterase inhibitor fasciculin 1 (from Dendroaspis angusticeps), and the cardiotoxic toxin gamma (from Naja nigricollis) are 1.86, 1.87, and 2.04 A, respectively. Local differences are observed between this toxin and the other structurally related toxins. Some of these differences could be relevant for the functional specificity of MTX2. In particular, this toxin presents a large twist at the tip of loop II due to a bulge (V31, T32; N35) that accommodates an inserted amino acid in the loop. This spatial arrangement brings the side chain of K34 in the beta-turn of the loop to be aligned with the beta-sheet. Hypotheses about a possible functional role of this lysine are described. Other characteristics in the side-chain distribution that could be related to the MTX2 function are presented.

Proton NMR studies of the structural and dynamical effect of chemical modification of a single aromatic side-chain in a snake cardiotoxin. Relation to the structure of the putative binding site and the cytolytic activity of the toxin

This paper presents the comparative comprehensive analysis of NMR structural parameters (NOEs, scalar coupling, chemical shifts) of toxin gamma, a cardiotoxin isolated from the venom of Naja nigricollis, and three chemical derivatives, i.e. the 2-nitrophenylsulphonyl (NPS)-Trp11, 3-nitro-Tyr22 and 3-nitro-Tyr51 derivatives. In previous work, the chemical modifications of single side chains have suggested that these aromatic residues, in association with several lysine residues, contributed to the cytotoxicity of toxin gamma. Analysis of these results based on the refined solution structure of the toxin has resulted in the proposal of a conserved phospholipid binding site through which cardiotoxins are likely to interact with the membrane of target cells. The present work shows that modifications of either the tryptophan residue or the tyrosine residues, which are within or near the proposed binding site, have no influence on the three-dimensional structure of the protein. On the other hand, the proton exchange study of the backbone amides indicates that the structural core of the protein is destabilized in the three derivatives. This corresponds to a decrease of the overall stability of the protein as indicated by the comparative solvent denaturation study of the unmodified toxin gamma and the Trp11 derivative. More specifically, the dynamics of the three-stranded beta sheet, a part of the structural core, are highly perturbed by the chemical modifications. This sheet was previously proposed as a part of the phospholipid binding site of cardiotoxins. The dynamical perturbation of this site appears to be correlated with the decrease in toxicity of the chemical derivatives.

Binding of peptide fragments from a seven helix membrane receptor to lipid bilayers and to micelles

Membrane proteins influence the organizational and motional properties of lipids, while the conformation and function of these proteins (receptors, channels, enzymes, pumps) are affected by the lipid environment. Model systems consisting of peptides and lipids can provide information at a molecular level about the interactions between proteins and lipids in biological membranes. We have synthesized peptides (residues 253-266 (EYWSTFGNLHHISL) from the seven-helix receptor expressed by the mas oncogene), having free or blocked N- and C-terminals. An analog was obtained by linking a spin-labeled amino acid to the N-terminal via a peptide bond. Several spectroscopic techniques were employed to study the interaction between the peptides and lipophilic systems (zwitterionic and negatively charged phospholipid bilayers, and negatively charged, positively charged, zwitterionic and nonionic micelles). Peptide conformational changes were monitored by circular dichroism (CD). The peptides acquired an increased secondary structure upon binding to the lipid systems. Additional evidence for peptide incorporation into micelles came from fluorescence measurements which indicated a blue shift of the tryptophan's emission wavelength, and from ESR spectra of the spin-labeled analog. While narrow lines were obtained in the aqueous phase, line broadening indicative of slower motion was observed in the presence of the lipophilic aggregates. The slow exchange between the two media allowed the evaluation of partition coefficients. The spectra in aqueous solution were also sensitive to conformational changes as a function of pH, allowing the determination of the N-terminal pK. ESR spectra of lipid spin probes incorporated into phospholipid bilayers indicated that the lipids became more immobilized upon binding of the peptides.

DNA and redox state induced conformational changes in the DNA-binding domain of the Myb oncoprotein

The DNA-binding domain of the oncoprotein Myb comprises three imperfect repeats, R1, R2 and R3. Only R2 and R3 are required for sequence-specific DNA-binding. Both are assumed to contain helix-turn-helix (HTH)-related motifs, but multidimensional heteronuclear NMR spectroscopy revealed a disordered structure in R2 where the second HTH helix was predicted [Jamin et al. (1993) Eur. J. Biochem., 216, 147-154]. We propose that the disordered region folds into a 'recognition' helix and generates a full HTH-related motif upon binding to DNA. This would move Cys43 into the hydrophobic core of R2. We observed that Cys43 was accessible to N-ethylmaleimide alkylation in the free protein, but inaccessible in the DNA complex. Mutant proteins with charged (C43D) or polar (C43S) side chains in position 43 bound DNA with reduced affinity, while hydrophobic replacements (C43A, C43V and C43I) gave unaltered or improved DNA-binding. Specific DNA-binding enhanced protease resistance dramatically. Fluorescence emission spectra and quenching experiments supported a DNA-induced conformational change. Moreover, reversible oxidation of Cys43 had an effect similar to the inactivating C43D mutation. The highly oxidizable Cys43 could function as a molecular sensor for a redox regulatory mechanism turning specific DNA-binding on or off by controlling the DNA-induced conformational change in R2.

Refined three-dimensional solution structure of a snake cardiotoxin: analysis of the side-chain organization suggests the existence of a possible phospholipid binding site

The solution structure of toxin gamma (60 residues, 4 disulfides) from Naja nigricollis was determined by proton nmr and molecular modeling with DIANA and X-PLOR. The structures were calculated using 489 distance and 81 dihedral angle constraints. The average atomic rms deviation between the nine refined structures and the average structure is 0.118 nm for the backbone atoms. Toxin gamma has an overall folding consisting of three loops stabilized by the four disulfides and forming a two- and a three-stranded beta-sheet (loop I and loops II, III, respectively). The same type of folding has been observed for two homologous cardiotoxins. The very close similarity of the solution structure of toxin gamma and the crystal structure of toxin VII4 includes details of the topological arrangement of numerous side chains. Among these are the conserved residues K12, K18, K35, and Y22, known to be critical for the cytolytic activity of toxin gamma. A cluster of hydrophobic side chains organized around Y22 is found on one side of the three-stranded beta-sheet and is spatially close to a group of three lysines (K12, K18, K35). The side chains of these lysines form a cationic site that can accommodate the binding of a phosphate ion as found in the crystal structure of toxin VII4. The hydrophobic cluster constitutes a possible binding site for the hydrophobic moiety of phospholipids. Together with the complementary cationic site, this hydrophobic surface can form a conserved site by which cardiotoxins bind to membrane phospholipids.

Synthesis of charybdotoxin and of two N-terminal truncated analogues. Structural and functional characterisation

Charybdotoxin and two N-terminal truncated peptides, corresponding to the 2-37 and 7-37 sequences, were obtained by stepwise solid-phase synthesis using N alpha-t-butyloxycarbonyl and benzyltype side-chain protection. While this strategy was generally useful, the S-acetamidomethyl protecting group used for the six cysteines was not completely stable under HF treatment and its subsequent removal by mercury(II) treatment was neither complete nor devoid of side reactions. The completely deprotected native and truncated sequences were folded efficiently in the presence of glutathione and were finally purified by high-pressure liquid chromatography with overall yields of 4.0-5.0%. Each protein was characterised chemically, structurally and functionally. 1H-NMR spectroscopy was used and a complete assignment of all the protons of the three synthetic proteins was achieved. NMR data show that synthetic charybdotoxin is indistinguishable from the natural protein. The two truncated proteins contain the same elements of secondary structure and a similar overall three-dimensional structure, in agreement with circular dichroic measurements. The shortest analogue, however, may have local structural perturbations and/or higher flexibility. Biological activity on dog epithelial Ca(2+)-activated K+ channels and on rat brain synaptosomal voltage-dependent K+ channels show that synthetic charybdotoxin was as potent as the natural toxin on both channels. For both channels, deletion of the first amino acid, 5-oxoproline (pyroglutamic acid) decreased only slightly the potency of the inhibitor, while deletion of the entire 1-6 segment reduced potency much more. We conclude that the N-terminal region of charybdotoxin plays a functional role in tuning the toxin's biological activity but is not essential for the folding and stability of the structure. The structure of the shortest analogue represents an interesting example of how a well organised and stable alpha/beta fold can be engineered with only 31 amino acid residues.

Secondary structure of the DNA-binding domain of the c-Myb oncoprotein in solution. A multidimensional double and triple heteronuclear NMR study

The DNA-binding domain of the c-Myb oncoprotein contains two repeats, R2 and R3, both of which have been proposed to be related to the helix-turn-helix (HTH) motif. As a first step towards determination of the three-dimensional structure of this domain and of the mode of interaction with the DNA, we have undertaken multidimensional heteronuclear NMR studies using uniformly 15N-labeled and 13C, 15N double-labeled R2R3 and, a selectively 15N-enriched sample on all lysine, histidine and leucine residues of R2R3. We present almost complete assignments of the backbone 1H, 15N and 13C" atoms and determine the secondary structure of R2R3 in solution. The R3 repeat is composed of three helices (residues 62-75, 78-85 and 91-100) while for the R2 repeat only two helices are found (residues 10-23 and 28-34). The remaining C-terminal part of the R2 repeat, predicted to be helical and part of the HTH motif, undergoes intermediate conformational exchange processes. Stabilization of this segment might occur upon binding to DNA.

Mapping of two "neutralizing" epitopes of a snake curaremimetic toxin by proton nuclear magnetic resonance spectroscopy

Two monoclonal antibodies, called M alpha 1 and M alpha 2,3, have been previously shown to neutralize the toxic activity of the curaremimetic toxin alpha from Naja nigricollis. In this paper, we report the mapping of the two corresponding epitopes, using affinity chromatography and proton 2D-NMR spectroscopy. The H-D exchange rates of labile amide hydrogens have been measured in toxin alpha bound to each antibody and in toxin alpha alone. Analysis of the exchange data revealed two regions containing amide hydrogens with decreased exchange rates in the bound toxin compared to the free toxin. These two regions correspond to the sites of interaction with M alpha 1 and M alpha 2,3, respectively. They are consistent with prior biochemical mapping studies, and they include several residues that were not previously identified. Thus, the two antigenic sites are found to be centered on two different loops of toxin alpha. Comparison of these antigenic sites with the active site of toxin alpha allows us to delineate the molecular events associated with the two neutralization processes.

Three-dimensional solution structure of a curaremimetic toxin from Naja nigricollis venom: a proton NMR and molecular modeling study

The solution conformation of toxin alpha from Naja nigricollis (61 amino acids and four disulfides), a snake toxin which specifically blocks the activity of the nicotinic acetylcholine receptor (AcChoR), has been determined using nuclear magnetic resonance spectroscopy and molecular modeling. The solution structures were calculated using 409 distance and 73 dihedral angle restraints. The average atomic rms deviation between the eight refined structures and the mean structure is approximately 0.5 A for the backbone atoms. The overall folding of toxin alpha consists of three major loops which are stabilized by three disulfide bridges and one short C terminal loop stabilized by a fourth disulfide bridge. All the disulfides are grouped in the same region of the molecule, forming a highly constrained structure from which the loops protrude. As predicted, this structure appears to be very similar to the 1.4-A resolution crystal structure of another snake neurotoxin, namely, erabutoxin b from Laticauda semifasciata. The atomic rms deviation for the backbone atoms between the solution and crystal structures is approximately 1.7 A. The minor differences which are observed between the two structures are partly related to the deletion of one residue from the chain of toxin alpha. It is notable that, although the two toxins differ from each other by 16 amino acid substitutions, their side chains have an essentially similar spatial organization. However, most of the side chains which constitute the presumed AcChoR binding site for the curaremimetic toxins are poorly resolved in toxin alpha.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of side-chain organization on a refined model of charybdotoxin: structural and functional implications

The spatial organization of side chains on a refined model of charybdotoxin is presented. First, the structural role of two groups of well-defined, low-accessible side chains (Thr3, Val5, Val16, Leu20, Cys33 and Leu20, His21, Thr23, Cys17, Cys35) is discussed. These side chains are conserved in three out of the five known scorpion toxins acting on K+ channels. Interestingly, they are not conserved in scyllatoxin which presents a slightly different secondary structure organization. Second, the spatial organization of all positively charged residues is analyzed. Comparison with the results presented by Park and Miller [(1992) Biochemistry (preceding paper in this issue)] shows that all functionally important positive residues are located on the beta-sheet side of the toxin. These results are different from those obtained by Auguste et al. [(1992) Biochemistry 31, 648-654] on scyllatoxin, which blocks a different type of K+ channel. This study shows, in fact, that functionally important positive residues are located on the helix side of the toxin. Thus, charybdotoxin and scyllatoxin, which present the same global fold, interact with two different classes of K+ channels by two different parts of the motif.

Peptide inhibitors of E. collagenolyticum bacterial collagenase--effect of N-methylation. Consequences on biological activity and conformational properties

Peptide inhibitors of E. collagenolyticum bacterial collagenase, HS-CH2-CH2-CO-Pro-Yaa (Yaa = Ala, Leu, Nle), have been N-methylated at the Yaa position. The N-methylation slightly increases the inhibitory potency of the modified peptides as compared to the parent compounds. The conformational effects of the N-methylation have been investigated by both 1H 2D-NMR and molecular mechanics energy minimization. Three low-energy conformers have been predicted for the unmethylated parent compounds (Yaa = Ala, Leu, Nle). They are characterized by the psi value of the central proline residue: psi Pro = 150 degrees (trans' conformation), psi Pro = 70 degrees (C7 conformation) and psi Pro = -50 degrees (cis' conformation). The N-methylation has been found to strongly increase the energy of the C7 conformer and to a less extent the energy of the cis' conformer. This leaves the trans' conformation as the only low-energy conformer. The ROESY experiments have established that both the N-methyl peptides and the parent compounds adopt the same preferred backbone conformation in water solution, i.e. the trans' conformation. Based on these results, the activities of the N-methyl peptides are discussed and a possible conformation of the inhibitor in the bound state is proposed.

Refined structure of charybdotoxin: common motifs in scorpion toxins and insect defensins

Conflicting three-dimensional structures of charybdotoxin (Chtx), a blocker of K+ channels, have been previously reported. A high-resolution model depicting the tertiary structure of Chtx has been obtained by DIANA and X-PLOR calculations from new proton nuclear magnetic resonance (NMR) data. The protein possesses a small triple-stranded antiparallel beta sheet linked to a short helix by two disulfides and to an extended fragment by one disulfide, respectively. This motif also exists in all known structures of scorpion toxins, irrespective of their size, sequence, and function. Strikingly, antibacterial insect defensins also adopt this folding pattern.

Three-dimensional structure of natural charybdotoxin in aqueous solution by 1H-NMR. Charybdotoxin possesses a structural motif found in other scorpion toxins

A 600-MHz proton NMR study of natural charybdotoxin, a toxin acting on K+ channels, is reported. The unambiguous sequential assignment of all the protons of the toxin was achieved. The analysis of NOEs and of backbone coupling constants showed the existence of an alpha-helix (residues 10-19) and of an antiparallel beta-sheet in the 26-35 part. Three-dimensional structures were generated by distance geometry, using a set of 114 interresidual calibrated constraints (63 sequential, 47 medium and long range, 4 hydrogen bonds) and 29 phi angles. These structures show that charybdotoxin is composed of a beta-sheet linked to an alpha-helix by two disulphide bridges and to an extended fragment by the third disulphide bridge. Comparison with the other known structures of long and short scorpion toxins shows that this structural motif is common to all these proteins.

Proton and tritium NMR relaxation studies of peptide inhibitor binding to bacterial collagenase: conformation and dynamics

The interaction of succinyl-Pro-Ala, a competitive inhibitor of Achromobacter iophagus collagenase, with the enzyme was studied by longitudinal proton and tritium relaxation. Specific deuterium and tritium labeling of the succinyl part at vicinal positions allowed the measurement of the cross-relaxation rates of individual proton or tritium spin pairs in the inhibitor-enzyme complex as well as in the free inhibitor. Overall correlation times, internuclear distances, and qualitative information on the internal mobility in Suc1 (as provided by the generalized order parameter S2) could be deduced by the comparison of proton and tritium cross-relaxation of spin pairs at complementary positions in the -CH2- CH2- moiety as analyzed in terms of the model-free approach by Lipari and Szabo. The conformational and motional parameters of the inhibitor in the free and enzyme-bound state were directly compared by this method. The measurement of proton cross-relaxation in the Ala residue provided additional information on the inhibitor binding. The determination of the order parameter in different parts of the inhibitor molecule in the bound state indicates that the succinyl and alanyl residues are primarily involved in the interaction with the enzyme activity site. The succinyl moiety, characterized in solution by the conformational equilibrium among the three staggered rotamers--i.e., trans: 50%; g+: 20%; g-: 30%--adopted in the bound state the unique trans conformation.

Inhibition of Clostridium histolyticum collagenases by phosphonamide peptide inhibitors

Several phosphonamide peptides having the general structure R-PO(OH)-Xaa-Yaa-Zaa were synthesized and tested for inhibition of Clostridium histolyticum collagenase. Inhibition was found to depend on the nature of R, Xaa, Yaa and Zaa such that the maximal affinity (Ki = 5 nM) was observed when R = p-nitrophenylethyl, Xaa = Gly, Yaa = Pro and Zaa = 2-aminohexanoic acid; this represents the tightest binding of inhibitor reported to date for any bacterial collagenase. Substitution of the p-nitrophenylethyl by a methyl group led to a 500-fold decrease of the potency, highlighting the existence of optimal interaction between the nitrophenylethyl side chain and one subsite of the enzyme. Replacement of the NH group in glycine residue (Xaa position) by -O- or -N-CH3 produces significantly less potent inhibitors, presumably due in part to the loss of a hydrogen bond between the inhibitor and collagenase active site. These phosphonamidates are thought to be acting as transition-state analogues of the peptide substrate.

Do cardiotoxins possess a functional site? Structural and chemical modification studies reveal the functional site of the cardiotoxin from Naja nigricollis

Examination of the literature has revealed that regarding the amino acid sequences, cardiotoxins constitute a family of homogeneous compounds. In contrast, cardiotoxins appear heterogeneous as far as their biological and spectroscopic properties are concerned. As a result, comparison between these molecules with a view to establishing structure-activity correlations is complicated. We have therefore reviewed recent works aiming at identifying the functional site of a defined cardiotoxin, ie toxin gamma from the venom of the spitting cobra Naja nigricollis. The biological and structural properties of toxin gamma are first described. In particular, a model depicting the 3-dimensional structure of the toxin studied by NMR spectroscopy is proposed. The toxin polypeptide chain is folded into 3 adjacent loops rich in beta-sheet structure connected to a small globular core containing the 4 disulfide bonds. A number of derivatives chemically modified at a single aromatic or amino group have been prepared. The structure of each derivative was probed by emission fluorescence, circular dichroism and NMR spectroscopy. Also tested was the ability of the derivatives to kill mice, depolarize excitable cell membranes and lyse epithelial cells. Modification of some residues in the first loop, in particular Lys-12 and at the base of the second loop substantially affected biological properties, with no sign of concomitant structural modifications other than local changes. Modifications in other regions much less affected the biological properties of the toxin. A plausible functional site for toxin gamma involving loop I and the base of loop II is presented. It is stressed that the functional site of other cardiotoxins may be different.

Local interactions in peptides. 1H-1H, 13C-H coupling constants and calculations for the conformational analysis of N-acetyl-N'-methylamides of aliphatic amino acids

We report the results of a joint NMR and theoretical investigation devoted to the conformational properties of N-acetyl-N'-methylamides of aliphatic amino acids with side chains of increasing bulkiness: Gly, Ala, Leu, Ile, and tert.Leu. In this series, determination of the coupling constants 3JHNC alpha H together with the coupling constants 3JC'NC alpha H (thanks to specific carbon-13 labeling of the N-acetyl carbonyl group) led to the derivation of alternative A, B, and C parameters in a Karplus-type relation expressing the dependence of 3JC'NC alpha H upon the phi dihedral angle. The value of the latter is found to increase regularly following the increase of the side-chain bulkiness. The theoretical conformational analysis is performed by applying the SIBFA procedure, which uses empirical formulas based on ab initio SCF computations. The conformational energy maps illustrate the progressive distortion of the backbone conformation incurred in the series Gly to tert.Leu. Theoretical values computed for 3JHNC alpha H and 3JC'NC alpha H are found to be in a good quantitative agreement with the experimental ones.

Delineation of chicken cathepsin L secondary structure; relationship between pH dependence activity and helix content

The secondary structure of the recently sequenced chicken liver cathepsin L (EC 3.4.22.15) has been studied both by circular dichroism and a predictive method. The structural data provided by these approaches allow us to underline the extent of the structural similarities between cathepsin L and papain, one of the best known proteins in the cysteine proteinase family. The predictive method of Garnier et al. (J. Mol. Biol. 120 (1978) 97-120) is used to locate alpha-helix and beta-sheet segments in the cathepsin L sequence. An optimization of decision constants has been performed, using circular dichroism data, to improve good predictions. The combination of these approaches lead us to suggest that the location of ordered structures observed in papain is maintained in cathepsin L, but with an additional alpha-helix in the middle region (residues 85-108) of cathepsin L. Furthermore, we show that cathepsin L inactivation at neutral pH is correlated to the lost of alpha-helix content (40% at pH 5.8 and 17% at pH 7.0) in this protein. It appears that such an effect can be related to the change in the ionization state of histidine side-chains which are shown to be mainly located in the predicted alpha-helix regions.

New thiol inhibitors of Clostridium histolyticum collagenase. Importance of the P3' position

An extensive series of synthetic mercaptotripeptides (HS-CH2-CH2-CO-Pro-Yaa) was prepared, and the inhibitory constants were determined on the Clostridium histolyticum collagenase. Among the factors which control the optimal binding of these inhibitors, we found that the presence of a free C-terminal carboxylate group in the position P3' of the compounds is of primary importance. In general, the esterification of this carboxylate group decreased the potency of the inhibitors by two orders of magnitude. We observed also that the enzyme favored the inhibitors having a long linear apolar or basic side-chain at the position P3'. The present data suggest a large S3' subsite of the C. histolyticum collagenase. The compound which contains a homoarginine residue at the P3' position with a Ki of 0.2 microM proved to be the most potent synthetic inhibitor known to date for the C. histolyticum collagenase.

Role of tyrosine and tryptophan residues in the structure-activity relationships of a cardiotoxin from Naja nigricollis venom

This paper is an attempt to localize the critical area determining toxicity in a snake cardiotoxin. Toxin gamma is a single-chain polypeptide of 60 amino acids, which has been isolated from the venom of the African spitting cobra, Naja nigricollis. Three aromatic residues, namely, Trp-11, Tyr-22, and Tyr-51, have been individually modified by chemical means. The structure of the native toxin and of each derivative has been carefully investigated by circular dichroism, fluorescence, proton magnetic resonance spectroscopy, and two specific monoclonal antibodies. None of the chemical modifications alters the overall structure of the toxin, which in all cases remains folded into three adjacent loops (I, II, and III) rich in beta-pleated sheet emerging from a small globular region containing four disulfide bridges. A number of subtle changes, however, have been detected in the structure of each derivative compared with that of the native toxin. In particular, nitration of Tyr-51 provoked a structural perturbation in the globular region. Nitration of Tyr-22 induces a more substantial change in the beta-sheet area of the molecule. Thus, the strong inter-ring NOE that is observed in the native toxin between Tyr-22 and Tyr-51 vanishes in the Tyr-22 derivative, and significant changes are observed in the globular region. In contrast, no alteration of the beta-sheet structure of loops II and III has been detected after modification of Trp-11. All changes observed for this derivative remain located in the vicinity of the indole side chain of Trp-11 in loop I. The biological consequences of the modifications were measured: the lethal potency in vivo in mice and the cytotoxic activities in vitro on FL-cells. Lethal activities correlate with cytotoxicity: Tyr-51 modified toxin is equally potent as native toxin, whereas Tyr-22 and Trp-11 derivatized toxins are characterized by substantially lesser activities, the Trp-11 derivatized toxin being the least potent. We conclude that (1) Tyr-51 is not involved in the functional site of the toxin, although it is in interaction with the core of the molecule, (2) Tyr-22 may play a dual structural and functional role, and (3) Trp-11 is in, or in close proximity to, the functional site of the toxin. These data indicate the importance of loop I in determining toxicity of the cardiotoxin.

A proton NMR investigation of proline-24 cis-trans isomerism in corticotropin 1-32 and related peptides

250 MHz 1H-NMR studies performed on aqueous solutions of corticotropin1-32, corticotropin1-24, corticotropin15-32, corticotropin20-32 and corticotropin15-24 have allowed the location and the subsequent assignment of the signals of Tyrosine-23 aromatic protons and valine-22 methyl protons. These signals are sensitive to the geometry of proline-24, clearly transcribe its isomerism and yield the ratio of the cis-trans conformers. It is concluded that for large peptides in specific cases, the proton signals of side chains can be used to probe the backbone conformation.

Influence of hydrogen bonding on the rotamer distribution of the histidine side chain in peptides: 1H NMR and CD studies

Both 1H NMR and circular dichroism pH titration studies on histidine, His-Gly, Gly-His and Gly-His-Gly indicate that the side-chain spatial orientation depends strongly on the vicinal charges. The arrangement of the imidazole side-chain (rotamer population) is shown by the histidine beta and beta' and the glycine methylene proton chemical shifts as well as the vicinal 1H-1H coupling constants 3JCalpha-H-beta-H, beta'-H. For His-Gly and Gly-His-Gly a good correlation can be found between the ionization of the glycine COOH group and the increase of rotamer III (g-g) which is also visualized by circular dichroism through an enhancement of the ellipticity at 212 nm. In these two peptides a hydrogen bond between the imidazolium and the carboxylate group is supposed to stabilize rotamer III at pH 4-5.

Conformational studies of corticotropin1-32 and constitutive peptides by circular dichroism

Circular dichroism spectra on corticotropin1-32 and its constitutive N-, and C-terminal peptides are determined in water and trifluoroethanol under several conditions in the aromatic and peptide spectral regions. Furthermore, the effects of pH and varied mixtures of water-trifluoroethanol are examined on the corticotropin1-32 molecule. The results show that the N- and C-terminal series have a different behaviour in both aqueous and organic media. Corticotropin and the former peptides display "random" spectra in water, and alpha-helix type spectra in trifluoroethanol, while the latter have "random" spectra in both solvents. In the holopeptide corticotropin, the side chain-side chain effects, as reflected by the titration curves obtained from variations in the aromatic region, support the idea of an helical organization of part of the backbone even in aqueous solution. When going from water to trifluoroethanol corticotropin1-32 undergoes a conformational change which leads to an alpha-helix, following a linear pathway. These results, together with other observations, indicate the possible role of the conformation of corticotropin molecules in their biological life.

Le couplage phosphore-phosphore dans l'adenosine di- et triphosphate

The pH dependence of spin-spin coupling constants J (P-O-P) of ADP and ATP has been determined from the phosphorus NMR spectra at 0 degrees. The variation curves have been interpreted as titration curves. These give different pK values. Comparison with the tripolyphosphate shows the existence of triphosphate chain structural deformation in the nucleotides.