Probing conformational changes in orphan nuclear receptor: The NGFI-B intermediate is a partially unfolded dimer

Human nerve growth factor-induced B (NGFI-B) is a member of the NR4A subfamily of orphan nuclear receptors (NRs). Lacking identified ligands, orphan NRs show particular co-regulator proteins binding properties, different from other NRs, and they might have a non-classical quaternary organization. A body of evidence suggests that NRs recognition of and binding to ligands, DNA, homo- and heterodimerization partners and co-regulator proteins involve significant conformational changes of the NR ligand-binding domains (LBDs). To shed light on largely unknown biophysical properties of NGFI-B, here we studied structural organization and unfolding properties of NGFI-B ligand (like)-binding domain induced by chemical perturbation. Our results show that NGFI-B LBD undergoes a two-state guanidine hydrochloride (GndHCl) induced denaturation, as judged by changes in the a-helical content of the protein monitored by circular dichroism spectroscopy (CD). In contrast, changes in the tertiary structure of NGFI-B LBD, reported by intrinsic fluorescence, reveal a clear intermediate state. Additionally, SAXS results demonstrate that the intermediate observed by intrinsic fluorescence is a partially folded homodimeric structure, which further unfolds without dissociation at higher GndHCl concentrations. This partially unfolded dimeric assembly of NGFI-B LBD might resemble an intermediate that this domain access momentarily in the native state upon interactions with functional partners. (C) 2008 Elsevier B.V. All rights reserved.

Mutagenicity of paepalantine dimer and glycoside derivatives from Paepalanthus bromelioides

The first isocoumarin isolated from the methylene chloride extract of Paepalanthus bromelioides, named paepalantine (isocoumarin 1), was found to have antimicrobial activity; but, it is mutagenic clastogenic and cytotoxic. Two other isocoumarins, paepalantine-9-O-beta-D-glucopyranoside (isocoumarin 2) and paepalantine-9-O-beta-D-allopyranosyl(1-->6) glucopyranoside (isocoumarin 3) were isolated from the ethanolic extract. A fourth new isocoumarin, also isolated from the methylene chloride extract of the capitula of P. bromelioides, was characterized as an 8-8' dimer of paepalantine and denominated isocoumarin 4. The abilities of isocoumarins 2, 3 and 4 to induce mutations in Salmonella typhimurium strains TA97a, TA98, TA100 and TA102 were investigated. Mutagenic activity was observed in strain TA97a treated with isocoumarin 2 in the presence of S9 mixture. The substitution of H at position 9 by glucose or glucose-allose caused reductions in the mutagenic activities of paepalantine, indicating this to be an important site for these properties. (C) 2003 Elsevier Ltd. All rights reserved.

Mutagenic and cytotoxic effect of planifolin: A naphthopyranone dimer isolated from Paepalanthus planifolius

A naphthopyranone dimer, named planifolin, was isolated from a methylene chloride extract of the capitula of Paepalanthus planifolius Koern. The molecule (C31H26O10) appeared to be made up of two monomeric portions, semi-vioxanthin and paepalantine (an isocoumarin), linked by an ether bond, and it may possess several kinds of biological activity that can be related to its polyphenolic structure. Short-term tests that detect genetic damage can afford the information needed to evaluate carcinogenic risks of chemicals to humans. The Ames test, recommended for testing the mutagenicity of chemical compounds with potential pharmacological application, was used in the present study. The mutagenic activity was evaluated in Salmonella typhimurium strains TA100, TA98, TA102 and TA97a and the cytotoxic effect in McCoy cells. The in vitro cytotoxicity of planifolin to McCoy cells, tested in microculture with neutral red, showed a significant cytotoxic index (CI50) of 12.83 mu g/mL. Planifolin showed mutagenic activity for TA100, TA98 and TA97a. The results indicate that this new naphthopyranone dimer causes mutations by substitution and by addition and deletion of bases in the sequence of DNA. Moreover, its mutagenic potential was increased by metabolic activation. (c) 2005 Elsevier Ltd. All rights reserved.

Electronic correlations for a two-level dimer: dynamical susceptibilities

The exact solution for the full electronic Hamiltonian for a two-level dimer is obtained. The parameter constellation (20) is reparametrized via orthogonal Slater atomic orbitals, yielding a three-parameter model. With the dimer embedded in a thermal bath, several temperature-dependent dynamical susceptibilities are computed. (C) 2002 Elsevier B.V. B.V. All rights reserved.

Planifolin, a new naphthopyranone dimer and flavonoids from Paepalanthus planifolius

A new naphthopyranone dimer (I) named planifolin was isolated from a methylene chloride extract of the capitula of Paepalanthus planifolius. The structure of 1 has been determined by chemical and spectroscopic means. In addition, a known dihydronaphthopyranone glycoside and seven known flavonoids were isolated from an ethanolic extract of the leaves of P. planifolius.

A new cytotoxic naphthopyrone dimer from Paepalanthus bromelioides

A new naphthopyrone dimer was isolated from the capitula of Paepalanthus bromelioides by chromatographic procedures. Its structure was deduced from spectrometric data. On colorimetric assay for cytotoxicity the new dimer showed IC50 of 55.9 μM. (C) 2000 Elsevier Science B.V.

Electronic correlations in a two-level dimer

The exact solution for the full electronic Hamiltonian for a two-level dimer is obtained. The parameter constellation (roughly 20) is reparametrized via orthogonal Gaussian atomic orbitals, yielding a five-parameter model. With the dimer embedded in a thermal bath, the specific heat and several temperature-dependent dynamical susceptibilities are computed. © 2001 Elsevier Science B.V. All rights reserved.

Interaction between the antimicrobial peptide Aurein 1.2 dimer and mannans

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

How pH Modulates the Dimer-Decamer Interconversion of 2-Cys Peroxiredoxins from the Prx1 Subfamily

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Identification of Regions Involved in Substrate Binding and Dimer Stabilization within the Central Domains of Yeast Hsp40 Sis1

Protein folding, refolding and degradation are essential for cellular life and are regulated by protein homeostatic processes such those that involve the molecular chaperone DnaK/Hsp70 and its co-chaperone DnaJ. Hsp70 action is initiated when proteins from the DnaJ family bind an unfolded protein for delivery purposes. In eukaryotes, the DnaJ family can be divided into two main groups, Type I and Type II, represented by yeast cytosolic Ydj1 and Sis1, respectively. Although sharing some unique features both members of the DnaJ family, Ydj1 and Sis1 are structurally and functionally distinct as deemed by previous studies, including the observation that their central domains carry the structural and functional information even in switched chimeras. In this study, we combined several biophysical tools for evaluating the stability of Sis1 and mutants that had the central domains (named Gly/Met rich domain and C-terminal Domain I) deleted or switched to those of Ydj1 to gain insight into the role of these regions in the structure and function of Sis1. The mutants retained some functions similar to full length wild-type Sis1, however they were defective in others. We found that: 1) Sis1 unfolds in at least two steps as follows: folded dimer to partially folded monomer and then to an unfolded monomer. 2) The Gly/Met rich domain had intrinsically disordered characteristics and its deletion had no effect on the conformational stability of the protein. 3) The deletion of the C-terminal Domain I perturbed the stability of the dimer. 4) Exchanging the central domains perturbed the conformational stability of the protein. Altogether, our results suggest the existence of two similar subdomains in the C-terminal domain of DnaJ that could be important for stabilizing each other in order to maintain a folded substrate-binding site as well as the dimeric state of the protein.

Statistical Mechanics of Monomer-Dimer Models on Complete and Erdös-Rényi Graphs

Nella tesi sono trattate due famiglie di modelli meccanico statistici su vari grafi: i modelli di spin ferromagnetici (o di Ising) e i modelli di monomero-dimero. Il primo capitolo è dedicato principalmente allo studio del lavoro di Dembo e Montanari, in cui viene risolto il modello di Ising su grafi aleatori. Nel secondo capitolo vengono studiati i modelli di monomero-dimero, a partire dal lavoro di Heilemann e Lieb,con l'intento di dare contributi nuovi alla teoria. I principali temi trattati sono disuguaglianze di correlazione, soluzioni esatte su alcuni grafi ad albero e sul grafo completo, la concentrazione dell'energia libera intorno al proprio valor medio sul grafo aleatorio diluito di Erdös-Rényi.

Rigorous results in Spin Glasses and Monomer-Dimer systems

In this work I reported recent results in the field of Statistical Mechanics of Equilibrium, and in particular in Spin Glass models and Monomer Dimer models . We start giving the mathematical background and the general formalism for Spin (Disordered) Models with some of their applications to physical and mathematical problems. Next we move on general aspects of the theory of spin glasses, in particular to the Sherrington-Kirkpatrick model which is of fundamental interest for the work. In Chapter 3, we introduce the Multi-species Sherrington-Kirkpatrick model (MSK), we prove the existence of the thermodynamical limit and the Guerra's Bound for the quenched pressure together with a detailed analysis of the annealed and the replica symmetric regime. The result is a multidimensional generalization of the Parisi's theory. Finally we brie y illustrate the strategy of the Panchenko's proof of the lower bound. In Chapter 4 we discuss the Aizenmann-Contucci and the Ghirlanda-Guerra identities for a wide class of Spin Glass models. As an example of application, we discuss the role of these identities in the proof of the lower bound. In Chapter 5 we introduce the basic mathematical formalism of Monomer Dimer models. We introduce a Gaussian representation of the partition function that will be fundamental in the rest of the work. In Chapter 6, we introduce an interacting Monomer-Dimer model. Its exact solution is derived and a detailed study of its analytical properties and related physical quantities is performed. In Chapter 7, we introduce a quenched randomness in the Monomer Dimer model and show that, under suitable conditions the pressure is a self averaging quantity. The main result is that, if we consider randomness only in the monomer activity, the model is exactly solvable.