Anti-Inflammatory Cytokines in Peri-Implant Soft Tissues: A Preliminary Study on Humans Using CDNA Microarray Technology

The mucosa around implants and the gingiva around teeth respond to plaque formation with the development of an inflammatory lesion which has similar magnitude and histological features. Different cell types in inflamed and healthy periodontal and peri-implant tissues are capable of producing a variety of important pro-inflammatory and anti-inflammatory cytokines and growth factors which mediate the host response. The aim of this study is to compare the expression levels of anti-inflammatory cytokines detectable in the peri-implant soft tissue of two single-implant crowns supported either by zirconia or titanium abutments. Two frozen samples of peri-implant soft tissue of two single-implant crowns supported either by zirconia or titanium abutments were treated to obtain mRNA. The mRNA extracted from these specimens was converted in cDNA and analyzed with “SuperArray GEArray Q Series Human Inflammatory Cytokine/Receptor Gene Array kit”, planned for studying 96 genes involved in inflammatory response. Data showed that gene expression levels of anti-inflammatory cytokines were higher in specimens sampled from the zirconia abutment compared with those from the titanium abutment. It was considered important to detect the mRNA levels of the anti-inflammatory mediators in healthy peri-implant tissues to verify the biological tolerability of zirconia compared with titanium abutments. The difference detected in cytokine expression could be due to the intrinsic biological tolerability of zirconia ceramics or to a lesser bacterial accumulation.

Targeting the BH3-interacting domain death agonist to develop mechanistically unique antidepressants

The BH3-interacting domain death agonist (Bid) is a pro-apoptotic member of the B-cell lymphoma-2 (Bcl-2) protein family. Previous studies have shown that stress reduces levels of Bcl-2 in brain regions implicated in the pathophysiology of mood disorders, whereas antidepressants and mood stabilizers increase Bcl-2 levels. The Bcl-2 protein family has an essential role in cellular resilience as well as synaptic and neuronal plasticity and may influence mood and affective behaviors. This study inhibited Bid in mice using two pharmacological antagonists (BI-11A7 and BI-2A7); the selective serotonin reuptake inhibitor citalopram was used as a positive control. These agents were studied in several well-known rodent models of depression-the forced swim test (FST), the tail suspension test (TST), and the learned helplessness (LH) paradigm-as well as in the female urine sniffing test (FUST), a measure of sex-related reward-seeking behavior. Citalopram and BI-11A7 both significantly reduced immobility time in the FST and TST and attenuated escape latencies in mice that underwent the LH paradigm. In the FUST, both agents significantly improved duration of female urine sniffing in mice that had developed helplessness. LH induction increased the activation of apoptosis-inducing factor (AIF), a caspase-independent cell death constituent activated by Bid, and mitochondrial AIF expression was attenuated by chronic BI-11A7 infusion. Taken together, the results suggest that functional perturbation of apoptotic proteins such as Bid and, alternatively, enhancement of Bcl-2 function, is a putative strategy for developing novel therapeutics for mood disorders.

A survey of the anti-apoptotic Bcl-2 subfamily expression in cancer types provides a platform to predict the efficacy of Bcl-2 antagonists in cancer therapy

We investigated the mRNA expression levels of all six antiapoptotic Bcl-2 subfamily members in 68 human cancer cell lines using qPCR techniques and measured the ability of known Bcl-2 inhibitors to induce cell death in 36 of the studied tumor cell lines. Our study reveals that Mcl-1 represents the anti-apoptotic Bcl-2 subfamily member with the highest mRNA levels in the lung, prostate, breast, ovarian, renal, and glioma cancer cell lines. In leukemia/lymphoma and melanoma cancer cell lines, Bcl-2 and Bfl-1 had the highest levels of mRNA, respectively. The observed correlation between the cell killing properties of known Bcl-2 inhibitors and the relative mRNA expression levels of anti-apoptotic Bcl-2 proteins provide critical insights into apoptosis-based anticancer strategies that target Bcl-2 proteins. Our data may explain current challenges of selective Bcl-2 inhibitors in the clinic, given that severe expression of Bcl-2 seems to be limited to leukemia cell lines. Furthermore, our data suggest that in most cancer types a strategy targeted to Mcl-1 inhibition, or combination of Bfl-1 and Mcl-1 inhibition for melanoma, may prove to be more successful than therapies targeting only Bcl-2.

Bid-induced release of AIF from mitochondria causes immediate neuronal cell death

Mitochondrial dysfunction and release of pro-apoptotic factors such as cytochrome c or apoptosis-inducing factor (AIF) from mitochondria are key features of neuronal cell death. The precise mechanisms of how these proteins are released from mitochondria and their particular role in neuronal cell death signaling are however largely unknown. Here, we demonstrate by fluorescence video microscopy that 8-10 h after induction of glutamate toxicity, AIF rapidly translocates from mitochondria to the nucleus and induces nuclear fragmentation and cell death within only a few minutes. This markedly fast translocation of AIF to the nucleus is preceded by increasing translocation of the pro-apoptotic bcl-2 family member Bid (BH3-interacting domain death agonist) to mitochondria, perinuclear accumulation of Bid-loaded mitochondria, and loss of mitochondrial membrane integrity. A small molecule Bid inhibitor preserved mitochondrial membrane potential, prevented nuclear translocation of AIF, and abrogated glutamate-induced neuronal cell death, as shown by experiments using Bid small interfering RNA (siRNA). Cell death induced by truncated Bid was inhibited by AIF siRNA, indicating that caspase-independent AIF signaling is the main pathway through which Bid mediates cell death. This was further supported by experiments showing that although caspase-3 was activated, specific caspase-3 inhibition did not protect neuronal cells against glutamate toxicity. In conclusion, Bid-mediated mitochondrial release of AIF followed by rapid nuclear translocation is a major mechanism of glutamate-induced neuronal death.

Breed assignment of Italian cattle using biallelic AFLP markers

The verification of the breed origin of animal products is relevant for food safety and authenticity. We assessed the suitability of AFLP molecular markers in the assignment of cattle individuals to their breed of origin. Three hundred and ninety-six animals belonging to 16 cattle breeds genotyped with 141 AFLP markers were used as reference data set. Assignment was performed with likelihood (aflpop) and Bayesian (structure) methods. The Bayesian approach was superior to the likelihood algorithm with respect to (i) the correct assignment of simulated individuals to their breed of origin (93% vs. 81% respectively), (ii) the correct assignment of 44 sampled Romagnola animals (91% vs. 45% respectively) and (iii) the correct classification of animals belonging to a breed that was not included within the reference dataset. Thus, AFLP profiling in combination with the Bayesian approach seems a useful tool for breed assignment.

Feminizing Wolbachia in Zyginidia pullula (Insecta, Hemiptera), a leafhopper with an XX/X0 sex-determination system

Zyginidia pullula is a grass-dwelling leafhopper characterized by a bisexual reproduction mode. In this species, some females collected in Northern Italy, when mated with males, gave origin to an exclusively female brood. Here, we demonstrated that in these lineages an infection by a new strain of Wolbachia pipientis-designated as wZygpul-was detected by amplifying and sequencing the wsp and 16S rRNA genes. About half of the female progeny were characterized by intersexual phenotypes, i.e. showing upper pygofer appendages, a typical male secondary sexual feature. The karyological analysis proved that while phenotypically normal females had a female genotype, those with upper pygofer appendages had a male genotype and were thus feminized males. The complete removal of W. pipientis after tetracycline treatment of morphologically normal females, and the consequent re-appearance of males in the brood, permitted us to connect the feminizing effect with the presence of the bacterium. This is the first case of feminization by W. pipientis in an XX/X0 sex-determination system, and is the second case reported in insects.

Quantitative determination of apogossypol, a pro-apoptotic analog of gossypol, in mouse plasma using LC/MS/MS

A simple and selective liquid chromatography/tandem mass spectrometry (LC/MS/MS) method based on internal standard quantitation using apigenin as the internal standard has been developed and validated for the analysis of the gossypol analog apogossypol, a pro-apoptotic compound, in mouse plasma. The methodology involves protein precipitation of plasma samples followed by LC/MS/MS analysis. Ascorbic acid was added to the spiking solutions and plasma samples to stabilize the easily oxidized compound. Separation of apogossypol and the internal standard from the plasma matrix was achieved using a C18 column with a gradient elution profile consisting of 5mM ammonium acetate and methanol. The validated range of the method extended from 10 to 2000 ng/mL with accuracies of 85-115% and precision of <15%. The average recovery of apogossypol at three concentrations (50, 200 and 1000 ng/mL) assayed in triplicate using this methodology was determined to be 90.8+/-12.9%. Recovery for the internal standard (apigenin) at a concentration of 500 ng/mL was found to be 99.9+/-6.41%. Apogossypol concentrations of 50 ng/mL and above were found to be stable in extracted plasma for 24h when stored at 25 degrees C. This method has been applied to the determination of apogossypol concentrations in plasma collected from mice given an IV dose of apogossypol.

Tuscany autochthonous cattle breeds: an original genetic resource investigated by AFLP markers

The aim of this study was to assess the genetic diversity of four autochthonous cattle breeds of Tuscany and their relationships in comparison with Italian Friesian and Italian Brown, using amplified fragment length polymorphism markers. A total of 212 individuals were genotyped with three primer combinations generating 102 polymorphic markers. Average expected heterozygosity ranged from 0.23 in Mucca Pisana to 0.26 in Chianina, Italian Friesian, Italian Brown and Maremmana. The differences resulted not significant (Kruskall-Wallis test, p = 0.416). Gst-B index revealed that 86% of the total genetic variance is retained within population and only 14% is accounted by the between populations component. Multivariate analysis at individual and population level indicated that: (i) Calvana and Chianina are quite separate from the other breeds as an effect of the bottleneck experienced or as a signature of different origin; (ii) Podolian, Maremmana and Italian Brown clustered with the double purpose Mucca Pisana, revealing their contribution to its admixed genetic make up; (iii) Italian Friesian behaved always as out group. The 'analysis of molecular variance' recovered a significant subdivision clustering the six populations into three groups: Italian Friesian and Italian Brown versus Maremmana and Mucca Pisana versus Chianina and Calvana (6% of the total variance).

Traditional Chinese medicines with caspase-inhibitory activity

Clinical evidence indicates that traditional Chinese medicine (TCM) drugs can reduce stroke-inflicted brain damage. To date, the molecular basis of the apparent neuroprotective effects of these TCM drugs remains largely obscure. Several lines of evidence indicate that the activation of cell death programs leads to the loss of neurons during the reperfusion phase of ischemic stroke. In particular, activation of caspases (cysteinyl aspartate-specific proteinases) is a critical step in neuronal apoptosis. Using nuclear magnetic resonance (NMR) and fluorescence assays, we screened a collection of 58 TCM drugs that are commonly used in stroke therapy for caspase inhibitory activity. We found that aqueous extracts of Lianqiao (Fructus Forsythiae) and Shouwuteng (Caulis Polygoni multiflori) blocked the activity of the initiator caspase-8 as well as the effector caspase-3 and caspase-7 in a dose-dependent manner with an IC(50)10 microg/ml. Identification of caspase inhibitory activity of these TCM drugs, allows the formulation of testable hypotheses and design of further investigations aimed at the elucidation of the molecular basis of TCM stroke therapy.

Comparative analysis of direct and indirect implant impression techniques an in vitro study. An in vitro study

Implant impression and transfer of the implant position to a working cast for rehabilitative purposes not always represent a predictable reconstructive step. The variable results depend on the transfer technique utilized and on the accuracy of the impression materials. The aim of this study was to compare the accuracy of the direct and indirect impression techniques and to analyze the distortion of different impression materials. An edentulous acrylic resin mandible was used as reference model: in the cuspid position 2 laboratory analogs were inserted perpendicularly to the occlusal plane and fastened with resin. Two impressions for each indirect and direct recording techniques with 4 different impression materials were made. Polyvinyl siloxanes were used for the repositioning implant level method. Polyethers were used for the ''pick up'' impression technique. Analysis of cast distortion was measured computing the inter-implant position on the developed models compared to that of the master model. Measurements were recorded by a digital caliper. The results of this in vitro study demonstrate that the direct impression technique is preferable to the indirect one and that the Impregum polyether impression material is the most precise when used in association with a direct technique.

Comparative analysis of deformation of two implant/abutment connection systems during implant insertion. An in vitro study

AIM

The implant/abutment interface represents a crucial element to maintain the structural stability of the implant restoration and to prevent mechanical problems that can compromise the long-term success of the implant treatment.

METHODS

In this study deformation of the external hexagonal and internal octagonal extension of 2 implants after applying different values of insertion torque has been tested. The implants were secured in a customized resin baseplate, with the implant neck exposed, then different values of insertion torque were applied by an electronic torque controller.

RESULTS

Five internal octagonal implants were tested for 60 seconds to different torque magnitudes (12 Ncm, 21 Ncm, 27 Ncm, 36 Ncm, 42 Ncm). Two external hexagonal implants were tested for 60 seconds to a torque value of 27 Ncm and of 36 Ncm.

CONCLUSIONS

After torquing tests, each implant was examined by a scanning electron microscope (SEM) medium and high magnification to evaluate the deformation of the 2 different antirotational systems. The SEM analysis of the internal octagonal and external hexagonal antirotational systems of the TBR implant showed a deformation proportional to the magnitude of the applied torque during implant insertion. The geometric deformation of the antirotational extension is capable of compromising its function after a torque magnitude of 36 Ncm or superior to this value. Moreover it was demonstrated a more evident alteration of the external hexagonal extension in comparison with the octagonal system after applying a torque value of 27 Ncm.

[Development of a multiple PCR method for the identification of Ureaplasma parvum and Ureaplasma urealyticum]

Ureaplasma parvum and Ureaplasma urealyticum, also known as biovar parvum and biovar T960, respectively, could be associated with several disorders in men, women, and mainly, in newborn children with under weight. Several methods have been developed in order to identify the species or biovars of ureaplasmas. We developed a Multiplex-PCR method using the UPS-UPSA and UUS2-UUA2 primers, specific for U. parvum and U. urealyticum, respectively. This Multiplex-PCR method was used to identify cultures of clinical positive samples to Ureaplasma spp. by the "MYCOFAST Evolution-2" Kit. Of 56 positive cultures to Ureaplasma spp. from newborn children, 70% were U. parvum and 30% U. urealyticum; in 76 positive samples in women, 83% corresponded to U. parvum and 17% to U. urealyticum, while in 63 positive samples of men, 76% identified U. parvum and 24% U. urealyticum. The PCR-multiplex method showed specificity for the identification of the biovars or species of ureaplasmas of clinical interest.

[Influence of biphosphonates on the integration process of endosseous implants evaluated using single photon emission computerized tomography (SPECT)]

Biphosphonates are a large class of drugs which inhibits the resorbing activity of osteoclasts. The aim of this study was to evaluate the influence of topical application of the biphosphonate alendronate on the integration process of endosseus implants placed in a partially edentulous patient. After incision and elevation of a mucoperiosteal flap and carrying out the osteotomy, 2 SLA implants 10 mm long and 3.5 mm wide were inserted in the area of # 4.5 and 4.6. Before placement of # 4.5, a paste made of grinded tablets of alendronate and Rifocin was applied in the osteotomy. Fifteen days after stage I, an evaluation of the osteoblastic peri-implant activity was carried out using single photon emission computerized tomography. Healing was within normal limits. Four months after stage I, the 2 implants were uncovered and considered clinically and radiographically integrated. The osteoblastic activity was judged similar bet-ween the 2 implants in terms of quality of biological response. Osseous scintigraphy and the achievement of implant osseointegration demonstrate the lack of toxicity of the topical application of the biphosphonate alendronate during the initial osseous healing. However, new experimental studies and clinical trials are necessary to confirm the results obtained.

[Vertical ridge augmentation using a microplate in conjunction with a Gore-Tex membrane. A case report]

Oral implantology is considered an acceptable treatment modality to replace missing teeth when a recipient site with a sufficient horizontal and vertical bone volume exists. Guided bone regeneration is based on the principle of selective exclusion of non osteogenic cells from the bony defect by a barrier membrane. Several supporting systems of the barrier membrane have been successfully used to treat non space-mantaining de-fects. A 35-year-old female affected by a partial edentulism in the molar area of the right mandible showed 8 mm of bone height of the residual ridge above the alveolar canal. A vertical ridge augmentation was performed using a Gore-Tex membrane in conjunction with a microplate and an irradiated freeze-dried cortico-cancellous allograft. Six months after the surgical procedure a 11.5 mm by 5 mm threaded implant was placed into the regenerated bone. After three months of healing, the implant was uncovered and considered integrated. Before the implant placement, a biopsy of the regenerated bone was arried out by a triphine. The histological examination of the bony core showed the attainment of biological goals of guided bone regeneration. The surgical technique followes in this case report has been effective in regenerating a vertical bone volume sufficient for implant treatment.

NMR in the acceleration of drug discovery

The field of NMR spectroscopy has grown beyond expectations from the first historic observation of nuclear magnetic resonance in 1946 by Bloch and Purcell, to the first generation of protein structures 20 years ago, to the present where NMR structures now represent 15 to 20% of those submitted to the Protein Data Bank (PDB). However, the applications of NMR go far beyond structure determination. Since NMR is a non-invasive technique that provides a wealth of information about structure and dynamics, it is an ideal analytical method that is now being used in every step of the drug discovery and development process. Indeed, NMR is undergoing a renaissance in the pharmaceutical industry as a plethora of new applications have been developed, ranging from in vitro screening methods in early stage discovery to in vivo magnetic resonance imaging techniques used to assess drug efficacy in clinical trials. In this review, we will present an overview of the role of NMR in these areas, with a special focus on how NMR is poised to revolutionize the high-throughput structural characterization of protein-ligand interactions.

Distal extension mandibular removable partial denture connected to an anterior fixed implant-supported prosthesis: a clinical report

This clinical report demonstrates the possibility of achieving positive results with a removable prosthesis connected to an implant-supported fixed prosthesis. Bone quality and quantity at the implant sites are essential requirements for the success of the treatment. The support of the RPD and its connection with the fixed prosthesis creates stability during chewing activity and allows a functional activity similar to that involving an overdenture. The adoption of an occlusal scheme with subocclusion of the fixed prosthesis contacts compared with those of the removable prosthesis, together with the stress-director system of the RPD can be effective factors that decrease the risk of loss of implant integration. Further long-term follow-up studies with a larger patient population are needed to confirm the clinical and biomechanical validity of the prosthetic solution described in this clinical report.

Structural insights into substrate binding by the molecular chaperone DnaK

How substrate affinity is modulated by nucleotide binding remains a fundamental, unanswered question in the study of 70 kDa heat shock protein (Hsp70) molecular chaperones. We find here that the Escherichia coli Hsp70, DnaK, lacking the entire alpha-helical domain, DnaK(1-507), retains the ability to support lambda phage replication in vivo and to pass information from the nucleotide binding domain to the substrate binding domain, and vice versa, in vitro. We determined the NMR solution structure of the corresponding substrate binding domain, DnaK(393-507), without substrate, and assessed the impact of substrate binding. Without bound substrate, loop L3,4 and strand beta3 are in significantly different conformations than observed in previous structures of the bound DnaK substrate binding domain, leading to occlusion of the substrate binding site. Upon substrate binding, the beta-domain shifts towards the structure seen in earlier X-ray and NMR structures. Taken together, our results suggest that conformational changes in the beta-domain itself contribute to the mechanism by which nucleotide binding modulates substrate binding affinity.

Magnetization transfer via residual dipolar couplings: application to proton-proton correlations in partially aligned proteins

A novel three-dimensional NMR experiment is reported that allows the observation of correlations between amide and other protons via residual dipolar couplings in partially oriented proteins. The experiment is designed to permit quantitative measurement of the magnitude of proton-proton residual dipolar couplings in larger molecules and at higher degree of alignments. The observed couplings contain data valuable for protein resonance assignment, local protein structure refinement, and determination of low-resolution protein folds.

Line narrowing in spectra of proteins dissolved in a dilute liquid crystalline phase by band-selective adiabatic decoupling: application to 1HN-15N residual dipolar coupling measurements

Residual heteronuclear dipolar couplings obtained from partially oriented protein samples can provide unique NMR constraints for protein structure determination. However, partial orientation of protein samples also causes severe 1H line broadening resulting from residual 1H-1H dipolar couplings. In this communication we show that band-selective 1H homonuclear decoupling during data acquisition is an efficient way to suppress residual 1H-1H dipolar couplings, resulting in spectra that are still amenable to solution NMR analysis, even with high degrees of alignment. As an example, we present a novel experiment with improved sensitivity for the measurement of one-bond 1HN-15N residual dipolar couplings in a protein sample dissolved in magnetically aligned liquid crystalline bicelles.

NMR structure of the human oncofoetal fibronectin ED-B domain, a specific marker for angiogenesis

BACKGROUND

The process of angiogenesis (i.e. the formation of new blood vessels from pre-existing ones) is fundamental to physiological processes such as reproduction, development and repair, as well as to pathological conditions such as tumor progression, rheumathoid arthritis and ocular disorders. The oncofoetal ED-B domain, a specific marker of angiogenesis, consists of 91 amino acid residues that are inserted by alternative splicing into the fibronectin (FN) molecule.

RESULTS

The NMR structure of the ED-B domain is reported and reveals important differences from other FN type III domains. A comparison of the ED-B domain with the crystal structure of a four-domain FN fragment shows the novel features of ED-B to be located in loop regions that are buried at interdomain interfaces, and which therefore largely determine the global shape of the FN molecule. The negatively charged amino acids in this highly acidic protein are uniformly distributed over the molecular surface, with the sole exception of a solvent-exposed hydrophobic patch that represents a potential specific recognition site. Epitope mapping with 82 decapeptides that span the ED-B sequence revealed that three ED-B-specific monoclonal antibodies, which selectively target newly forming blood vessels in tumor-bearing mice, bind to adjacent regions on the ED-B surface.

CONCLUSIONS

The NMR structure enables the identification of a large surface area of the ED-B domain that appears to be accessible in vivo, opening up new diagnostic and therapeutic opportunities. Furthermore, the mapping of specific monoclonal antibodies to the three-dimensional structure of the ED-B domain, and their use in angiogenesis inhibition experiments, provides a basis for further investigation of the role of the ED-B domain in the formation of new blood vessels.

Pilus chaperone FimC-adhesin FimH interactions mapped by TROSY-NMR

The 23 kDa two-domain periplasmic chaperone FimC from Escherichia coli is required for the assembly of type-1 pili, which are filamentous, highly oligomeric protein complexes anchored to the outer bacterial membrane that mediate adhesion of pathogenic E. coli strains to host cell surfaces. Here we identified the contact sites on the surface of the NMR structure of FimC that are responsible for the binding of the 28 kDa mannose-binding type-1 pilus subunit FimH by 15N and 1H NMR chemical shift mapping, using transverse relaxation-optimized spectroscopy (TROSY). The FimH-binding surface of FimC is formed nearly entirely by the N-terminal domain, and its extent and shape indicate that FimC binds a folded form of the pilus subunits.

NMR solution structure of the periplasmic chaperone FimC

The NMR structure of the 205-residue periplasmic chaperone FimC is presented. This protein consists of two globular domains with immunoglobulin-like folds connected by a 15-residue linker peptide. The relative orientation of the two domains is defined by hydrophobic contacts and an interdomain salt bridge. FimC mediates the assembly of type-1 pili, which are filamentous surface organelles of uropathogenic Escherichia coli strains that enable the bacteria to attach to host cell surfaces and persist in macrophages. The availability of the NMR structure of FimC provides a new basis for rational design of drugs against infections by uropathogenic bacteria.

NMR structure of the J-domain and the Gly/Phe-rich region of the Escherichia coli DnaJ chaperone

The recombinant N-terminal 107-amino acid polypeptide fragment 2-108 of the DnaJ molecular chaperone of Escherichia coli, which contains the J-domain (residues 2 to 76) and the Gly/Phe-rich region (residues 77 to 108), was uniformly labeled with nitrogen-15 and carbon-13. The complete NMR solution structure of the J-domain was determined with the program DIANA on the basis of 682 nuclear Overhauser enhancement (NOE) upper distance limits and 180 dihedral angle constraints. It contains three well-defined helices comprising residues 6 to 10, 18 to 32 and 41 to 57, and a fourth helix, consisting of residues 61 to 68, which is well defined as a regular secondary structure but for which the location relative to the remainder of the molecule is not precisely determined. The helices II and III form an antiparallel helical coiled-coil. Helix I is approximately parallel to the plane defined by the helices II and III and runs from the carboxy-terminal end of the helix III to the center of helix II. Helix IV is positioned near the carboxy-terminal end of helix III and is on the same side of the coiled coil as helix I, but it is oriented approximately perpendicular to the plane of the helices II and III. This novel alpha-protein topology leads to formation of a hydrophobic core involving side-chains of all four helices. A strong correlation is seen between the extent of sequence-conservation of hydrophobic residues in the family of J-domain homologues, and the structural organization of the hydrophobic core in these proteins. The residues which have key roles for the specificity of the interaction of DnaJ-like proteins with their corresponding Hsp70 counterparts are located on the outer surfaces of the helices II and III, and in the loop connecting these two helices. Measurements of backbone amide proton exchange rates, 15N spin relaxation times and heteronuclear 15N {1H} NOEs provided additional insights into local conformational equilibria and internal rate processes in DnaJ(2-108). In the Gly/Phe-rich region, which is poorly ordered in the NMR solution structure and does not form a globular core, the polypeptide segment 90 to 103 differs from the segments 77 to 89 and 104 to 108 by reduced local flexibility. Considering that this same segment shows sequence conservation with corresponding segments in the Gly/Phe-rich regions of other DnaJ-like proteins, its reduced flexibility may be directly linked to the formation of the ternary DnaJ-DnaK-polypeptide complex.

NMR structure determination of the Escherichia coli DnaJ molecular chaperone: secondary structure and backbone fold of the N-terminal region (residues 2-108) containing the highly conserved J domain

DnaJ from Escherichia coli is a 376-amino acid protein that functions in conjunction with DnaK and GrpE as a chaperone machine. The N-terminal fragment of residues 2-108, DnaJ-(2-108), retains many of the activities of the full-length protein and contains a structural motif, the J domain of residues 2-72, which is highly conserved in a superfamily of proteins. In this paper, NMR spectroscopy was used to determine the secondary structure and the three-dimensional polypeptide backbone fold of DnaJ-(2-108). By using 13C/15N doubly labeled DnaJ-(2-108), nearly complete sequence-specific assignments were obtained for 1H, 15N, 13C alpha, and 13C beta, and about 40% of the peripheral aliphatic carbon resonances were also assigned. Four alpha-helices in polypeptide segments of residues 6-11, 18-31, 41-55, and 61-68 in the J domain were identified by sequential and medium-range nuclear Overhauser effects. For the J domain, the three-dimensional structure was calculated with the program DIANA from an input of 536 nuclear Overhauser effect upper-distance constraints and 52 spin-spin coupling constants. The polypeptide backbone fold is characterized by the formation of an antiparallel bundle of two long helices, residues 18-31 and 41-55, which is stabilized by a hydrophobic core of side chains that are highly conserved in homologous J domain sequences. The Gly/Phe-rich region from residues 77 to 108 is flexibly disordered in solution.

Effects of variable selection on CoMFA coefficient contour maps in a set of triazines inhibiting DHFR

An example of a CoMFA study is described with the aim to discuss one of the major problems of this 3D QSAR method: lack of variable selection. It is shown that the use of nonrelevant energy parameters might produce CoMFA contour maps which poorly reflect the actual nature of the binding site and are in part statistical artefacts. The data set employed in our analysis comprises triazine inhibitors of dihydrofolate reductase (DHFR), isolated from chicken liver, which have already been the object of a QSAR study by other authors. Since three-dimensional structures of triazine-DHFR complexes are known, it was possible not only to reduce ambiguities in the superimposition of the ligands, but also to compare the resulting CoMFA contour maps with the enzyme active site.