Conformational study of a collagen peptide by 1H NMR spectroscopy: observation of the 14N-1H spin-spin coupling of the Arg guanidinium moiety in the triple-helix structure

AbstractCB2, a CNBr peptide of 36 residues from type I collagen α1(I) chain has been studied by NMR spectroscopy as a function of temperature. At low temperature, the guanidinium protons of Arg9 showed sharp 1:1:1 NMR triplets around 6.95 ppm, characteristic of 14N coupled protons (1JNH=52 Hz) when the quadrupolar relaxation rate is drastically reduced. These spectral characteristics and the low temperature coefficient of the 1:1:1 triplets (Δδ/ΔT of −3.6 ppb/°C) suggest that the H atoms of the protonated guanidinium moiety of Arg9 in the triple helix are slowly exchanging with bulk water, most likely involved in hydrogen bonds. On the basis of conformational energy computations on a model segment of type I collagen (Vitagliano, L., Némethy, G., Zagari, A. and Scheraga, H.A. (1993) Biochemistry 32, 7354–7359), similar to CB2, our data could indicate that the guanidinium group of Arg9 form hydrogen bonds with a backbone carbonyl of an adjacent chain probably by using the Nϵ hydrogen, leaving the four Nη hydrogens bound to water molecules that must be in slow exchange with bulk water and that could therefore be considered structural elements of the trimeric α1(I) CB2 triple helix. The behaviour of Arg9 has been investigated also in terms of equilibrium between random monomer and helical trimer conformations controlled by temperature. The thermal unfolding process was found to be reversible and the melting point resulted to be 17°C

A QSTR-based expert system to predict sweetness of molecules

This work describes a novel approach based on advanced molecular similarity to predict the sweetness of chemicals. The proposed Quantitative Structure-Taste Relationship (QSTR) model is an expert system developed keeping in mind the five principles defined by the Organization for Economic Co-operation and Development (OECD) for the validation of (Q)SARs. The 649 sweet and non-sweet molecules were described by both conformation-independent extended-connectivity fingerprints (ECFPs) and molecular descriptors. In particular, the molecular similarity in the ECFPs space showed a clear association with molecular taste and it was exploited for model development. Molecules laying in the subspaces where the taste assignation was more difficult were modeled trough a consensus between linear and local approaches (Partial Least Squares-Discriminant Analysis and N-nearest-neighbor classifier). The expert system, which was thoroughly validated through a Monte Carlo procedure and an external set, gave satisfactory results in comparison with the state-of-the-art models. Moreover, the QSTR model can be leveraged into a greater understanding of the relationship between molecular structure and sweetness, and into the design of novel sweeteners.Instituto de Investigaciones Fisicoquímicas Teóricas y AplicadasFacultad de Ciencias Exacta

Hydration studies on the archaeal protein Sso7d using NMR measurements and MD simulations

<p>Abstract</p> <p>Background</p> <p>How proteins approach surrounding molecules is fundamental to our understanding of the specific interactions that occur at the surface of proteins. The enhanced surface accessibility of small molecules such as organic solvents and paramagnetic probes to protein binding sites has been observed; however, the molecular basis of this finding has not been fully established. Recently, it has been suggested that hydration dynamics play a predominant role in controlling the distribution of hot spots on surface of proteins.</p> <p>Results</p> <p>In the present study, the hydration of the archaeal multifunctional protein Sso7d from <it>Solfolobus solfataricus </it>was investigated using a combination of computational and experimental data derived from molecular dynamics simulations and ePHOGSY NMR spectroscopy.</p> <p>Conclusions</p> <p>We obtained a convergent protein hydration landscape that indicated how the shape and stability of the Sso7d hydration shell could modulate the function of the protein. The DNA binding domain overlaps with the protein region involved in chaperon activity and this domain is hydrated only in a very small central region. This localized hydration seems to favor intermolecular approaches from a large variety of ligands. Conversely, high water density was found in surface regions of the protein where the ATP binding site is located, suggesting that surface water molecules play a role in protecting the protein from unspecific interactions.</p

A New Similarity/Diversity Measure for the Characterization of DNA Sequences

In this paper, a new similarity/diversity measure is proposed as a new approach to the analysis of sequential data, where useful information can be also obtained by the ordering relationships between the sequence elements. This methodology has been applied to characterize DNA sequences, evaluating their similarity/diversity. The new proposed distance (weighted standardized Hasse distance) is evaluated between pairs of Hasse matrices derived from the classical partial ordering rules. It can be naturally standardized, thus allowing the interpretation of these distances as absolute values (e.g. percentage) and deriving simple similarity and correlation indices. DNA sequences taken from the first exons of the beta-globins for eight different species have been analyzed. Sensitivity analysis has been also performed, showing the high capability of this measure to take into account small modifications of the DNA sequences. Finally, a comparison with results obtained from literature is given

Publisher Correction: Scaffold hopping from natural products to synthetic mimetics by holistic molecular similarity

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The p50 NF-\u3baB subunit is a prognostic regulator of colorectal cancer-associated inflammation

In most tumors, tumor associated macrophages (TAMs) express an M2-skewed phenotype and are therefore associated with unfavorable prognosis. However, the impact of TAMs in colorectal cancer (CRC) development and outcome is still controversial. We first demonstrate, by parallel studies in colitis-associated cancer (CAC) and in genetically driven ApcMin mouse models, that p50 NF-\u3baB is essential for CRC development by restraining M1-dependent antitumor response. In absence of p50 mice developed fewer and smaller CRC lesions which express enhanced levels of M1/Th1 cytokines/chemokines including IL-12 and CXCL10, whose administration restrained CAC development in vivo. Moreover colons from p50-/- tumor bearers showed a reduced number of TAMs, as opposed to increased NK, NKT, CD8+ T cells and apoptotic cancer cells. Consistently, in CRC patients, high burden of p50+ TAMs was associated with decreased M1/Th1 inflammation and worse outcome indicating p50 as a new candidate for prognostic and target therapeutic intervention

Comparative in vitro toxicity of a graphene oxide-silver nanocomposite and the pristine counterparts toward macrophages

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Graphene oxide (GO) is a highly oxidized graphene form with oxygen functional groups on its surface. GO is an excellent platform to support and stabilize silver nanoparticles (AgNP), which gives rise to the graphene oxide-silver nanoparticle (GOAg) nanocomposite. Understanding how this nanocomposite interacts with cells is a toxicological challenge of great importance for future biomedical applications, and macrophage cells can provide information concerning the biocompatibility of these nanomaterials. The cytotoxicity of the GOAg nanocomposite, pristine GO, and pristine AgNP was compared toward two representative murine macrophages: a tumoral lineage (J774) and peritoneal macrophages collected from Balb/c mouse. The production of reactive oxygen species (ROS) by J774 macrophages was also monitored. We investigated the internalization of nanomaterials by transmission electron microscopy (TEM). The quantification of internalized silver was carried out by inductively coupled plasma mass spectrometry (ICP-MS). Nanomaterial stability in the cell media was investigated overtime by visual observation, inductively coupled plasma optical emission spectrometry (ICP OES), and dynamic light scattering (DLS). Results: The GOAg nanocomposite was more toxic than pristine GO and pristine AgNP for both macrophages, and it significantly induced more ROS production compared to pristine AgNP. TEM analysis showed that GOAg was internalized by tumoral J774 macrophages. However, macrophages internalized approximately 60 % less GOAg than did pristine AgNP. The images also showed the degradation of nanocomposite inside cells. Conclusions: Although the GOAg nanocomposite was less internalized by the macrophage cells, it was more toxic than the pristine counterparts and induced remarkable oxidative stress. Our findings strongly reveal a synergistic toxicity effect of the GOAg nanocomposite. The toxicity and fate of nanocomposites in cells are some of the major concerns in the development of novel biocompatible materials and must be carefully evaluated.Graphene oxide (GO) is a highly oxidized graphene form with oxygen functional groups on its surface. GO is an excellent platform to support and stabilize silver nanoparticles (AgNP), which gives rise to the graphene oxide-silver nanoparticle (GOAg) nanoco14CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)140560/2014-9The authors thank the National Council for Technological and Scientific Development (CNPq) for the PhD student scholarship (140560/2014-9) and the financial support. The authors also acknowledge Dr. Daniel Ruiz Abanádes for suggestions, Renata Magueta fo

Immediate Occlusal Loading of One-Piece Zirconia Implants: Five-Year Radiographic and Clinical Evaluation

PURPOSE: To evaluate radiographic and clinical outcomes of immediate occlusally loaded one-piece zirconia implants after 5 years of follow-up. MATERIALS AND METHODS: This longitudinal clinical investigation included patients older than 18 years, in need of implant-supported single-unit dental rehabilitations. One-piece zirconia in healed and postextraction sites and immediately restored with provisional crowns in light occlusal contact. Definitive zirconia-ceramic restorations were delivered 3 to 4 months after surgery. Primary estimated outcomes were implant survival and success. Periapical radiographs were taken at implant insertion (T0), after 1 year (T1), and after 5 years (T2) to assess marginal bone loss (MBL). Probing depth (PD), modified Bleeding Index (mBI), modified Plaque Index (mPI), and gingival recession (REC) were also measured repeatedly for implants and reference teeth. Changes in parameters over time were assessed using the Wilcoxon signed rank test. In addition, multilevel mixed effects linear and logistic regression models were fitted to take into account within-subject correlations and baseline values. RESULTS: Thirty-two implants were inserted in postextraction and healed sites (n = 16 of each) in 17 patients. One immediate implant was lost after 3 months, and one patient with one implant dropped out after T1. Therefore, the cumulative survival rates were 96.9% at T1 and 96.8% at T2 (4.3 to 6 years). No significant differences were observed in mean MBL between immediate and delayed implants at either T1 or T2. Moreover, different baseline parameters (sex, arch, implant location, smoking habits, grafting) did not show any influence on MBL at either time. In general, for all clinical parameters (PD, mBI, mPI, REC), implants seemed to perform similar to if not better than natural teeth. CONCLUSION: Radiographic and clinical evaluations after 5 years showed satisfactory amounts of MBL and acceptable soft tissue health

Multisystem autoimmune disease caused by increased STAT3 phosphorylation, and dysregulated gene expression

Signal transducer and activator of transcription (STAT) 3 is a member of the STAT family, and plays a major role in various immunological mechanisms.1 Mutations in STAT3 are associated with a broad spectrum of manifestations, including immunodeficiency, autoimmunity, and malignancy.2 In particular, heterozygous germline loss-of-function (LOF) mutations cause Hyper-IgE syndrome (HIES),3–5 while heterozygous germline gain-of-function (GOF) mutations have recently been associated to multi-organ autoimmune manifestations (i.e. type 1 diabetes, enteropathy, cytopenia, interstitial lung disease, hypothyroidism), lymphoproliferation, short stature, and recurrent infections (OMIM #615952).6–8 We report a 7-year-old boy who presented with early-onset severe enteropathy, and diffuse eczematous dermatitis since birth. During the first weeks of life, Hirschsprung disease was also suspected and surgically treated. Gastrointestinal and cutaneous manifestations were first ascribed to food allergy with quite a good response to amino acid-based formula. In the following months, the patient failed to thrive, and developed respiratory tract infections. At two years, the patient presented with progressive interstitial lung disease characterized by lymphocytic interstitial infiltration leading to pulmonary hypertension, tricuspid insufficiency, and right ventricular heart failure with hepatomegaly. Because of the increased risk of infections, he received intravenous (IV) immunoglobulin infusions (400 mg/kg), prophylaxis with cotrimoxazole and fluconazole. Methylprednisolone at 0.3 mg/kg/day was also given to treat autoimmune manifestations