Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry

Disordered or unstructured regions of proteins, while often very important biologically, can pose significant challenges for resonance assignment and three‐dimensional structure determination of the ordered regions of proteins by NMR methods. In this article, we demonstrate the application of ¹H/²H exchange mass spectrometry (DXMS) for the rapid identification of disordered segments of proteins and design of protein constructs that are more suitable for structural analysis by NMR. In this benchmark study, DXMS is applied to five NMR protein targets chosen from the Northeast Structural Genomics project. These data were then used to design optimized constructs for three partially disordered proteins. Truncated proteins obtained by deletion of disordered N‐ and C‐terminal tails were evaluated using ¹H‐¹⁵N HSQC and ¹H‐¹⁵N heteronuclear NOE NMR experiments to assess their structural integrity. These constructs provide significantly improved NMR spectra, with minimal structural perturbations to the ordered regions of the protein structure. As a representative example, we compare the solution structures of the full length and DXMS‐based truncated construct for a 77‐residue partially disordered DUF896 family protein YnzC from Bacillus subtilis, where deletion of the disordered residues (ca. 40% of the protein) does not affect the native structure. In addition, we demonstrate that throughput of the DXMS process can be increased by analyzing mixtures of up to four proteins without reducing the sequence coverage for each protein. Our results demonstrate that DXMS can serve as a central component of a process for optimizing protein constructs for NMR structure determination. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Micronuclei, genetic polymorphisms and cardiovascular disease mortality in a nested case-control study in Italy

AIM: To validate the predictive value of micronuclei (MN) in peripheral blood lymphocytes (PBL) and glutathione-S-transferases (GSTs) polymorphisms (GSTM1 and GSTT1) for mortality risk (MR) of cardiovascular diseases (CVD). METHODS: Blood samples from 1650 healthy subjects selected from the general population were collected between June 1991 and November 1993, and slides were immediately prepared for MN assessment. The vital status, or the cause of death, was monitored for all subjects until January 2005. At the end of the follow-up, 111 deaths were recorded and 39 CVD cases were observed (age range=42-88 years). Two thousand binucleated (BN) cells/subject were scored for the MN assay and GSTs genotypes were assessed on the DNA extracted from the blood or serum samples. RESULTS: A significantly higher MN frequency was recorded for the case group in comparison with the control group (n=67, Kruskall-Wallis test, p=0.006) and GSTT1 null genotype was significantly less frequent in CVD patients (chi(2)-test, p=0.036). The influence of other factors were evaluated using a unconditional logistic regression that confirmed a significant association of GSTT1 positive genotype with an increased OR for CVD (OR=6.29, 95% CI 1.32-29.95) beside a significant effect of age (OR=1.13, 95% CI 1.03-1.26 year(-1)). Finally, subjects with an higher MN frequency showed a higher MR for CVD (Log-rank test, p=0.001). CONCLUSIONS: MN confirmed to be a suitable cytogenetic biomarker for early prediction of CVD death. The GSTT1 positive genotype is associated with an increased MR for CVD.     

On the mechanisms involved in biological heme crystallization

Blood-feeding organisms digest hemoglobin, releasing large quantities of heme inside their digestive tracts. Free heme is very toxic, and these organisms have evolved several mechanisms to protect against its deleterious effects. One of these adaptations is the crystallization of heme into the dark-brown pigment hemozoin (Hz). Here we review the process of Hz formation, focusing on organisms other than Plasmodium that have contributed to a better understanding of heme crystallization. Hemozoin has been found in several distinct classes of organisms including protozoa, helminths and insects and Hz formation is the predominant form of heme detoxification. The available evidence indicates that amphiphilic structures such as phospholipid membranes and lipid droplets accompanied by specific proteins play a major role in heme crystallization. Because this process is specific to a number of blood-feeding organisms and absent in their hosts, Hz formation is an attractive target for the development of novel drugs to control illnesses associated with these hematophagous organisms.     

A study of the scutellum in eight Chagas disease vector species from genus Triatoma (Hemiptera, Reduviidae) using optical and scanning electron microscopy

The aim of this study was to analyze the external morphology of the scutellum through optical microscopy and scanning electron microscopy (SEM) in male specimens of Triatoma costalimai, T. delpontei, T. eratyrusiformis, T. matogrossensis, T. infestans melanosoma, T. sherlocki, T. tibiamaculata, and T. vandae. A total of 30 photographs of the scutellum were made. Magnification varied from 50X to 750X. Regarding depth and forms of the central depression, the heart-shaped form was predominant, with some exceptions, so that this shape appears to be a common characteristic for species of genus Triatoma Laporte, 1832. In T. eratyrusiformis, a kind of sensillum with important taxonomic value was observed. The different sizes and shapes of the designs found on the posterior process of the scutellum were also of important taxonomic interest. The study of the scutellum based on SEM showed valuable characteristics, allowing the use of this structure to aid the diagnosis of triatomine species. Thus, more specimens in subsequent studies and analyses of morphometric parameters should contribute to agreement on phylogenetic aspects in this genus. A Key to eight species of Triatoma based on male scutellar morphology is presented.     

An Imported Case of Blastomyces Dermatitidis Infection in Mexico

Blastomycosis is an acute or chronic primary infection of the respiratory system, endemic in North America (United States of America and Canada), Africa and Asia. We report a case in Mexico, in a three years old child who had been born in California and lived in Chicago, U.S.A. The patient presented pulmonary symptoms prior to development of a skin ulcer. Blastomyces dermatitidis was identified by mycological and molecular procedures. The patient was successfully treated with amphotericin B, oral ketoconazole and itraconazole.     

Nucleus-independent chemical shift criterion for aromaticity in π-extended tetraoxa[8]circulenes

Recently synthesized π-extended symmetrical tetraoxa[8]circulenes that exhibit electroluminescent properties were calculated at the density functional theory (DFT) level using the quantum theory of atoms in molecules (QTAIM) approach to electron density distribution analysis. Nucleus-independent chemical shift (NICS) indices were used to characterize the aromaticity of the studied molecules. The tetraoxa[8]circulene molecules were found to consist of two antiaromatic perimeters (according to the Hückel “4n” antiaromaticity rule) that include 8 and 24 π-electrons. Conversely, NICS calculations demonstrated the existence of a common π-extended system (distributed like a flat ribbon) in the studied tetraoxa[8]circulene molecules. Thus, these symmetrical tetraoxa[8]circulene molecules provide examples of diatropic systems characterized by the presence of induced diatropic ring currents.

Synthesis of the beta anomer of the spacer-equipped tetrasaccharide side chain of the major glycoprotein of the Bacillus anthracis exosporium

The beta glycoside of the tetrasaccharide sequence beta-Ant-(1-->3)-alpha-l-Rhap-(1-->3)-alpha-l-Rhap-(1-->2)-l-Rhap, whose aglycon allows conjugation to proteins, was synthesized for the first time. A stepwise synthetic approach was applied with thioglycosides as glycosyl donors, and the beta anomer of the compound was obtained equipped with a spacer group whose further transformation allows conjugation to suitable carriers. To synthesize the beta-anthrosyl linkage with high stereoselectivity, a linker-equipped rhamnotriose derivative was glycosylated with ethyl 4-azido-3-O-benzyl-2-O-bromoacetyl-4,6-dideoxy-1-thio-beta-d-glucopyranoside. Further functionalization of the tetrasaccharide thus obtained, followed by deprotection, gave the target substance.     

Enhanced cytotoxicity without internuclear spread of adenovirus upon cell fusion by measles virus glycoproteins

The efficiency of viruses in cancer therapy is enhanced by proteins that mediate the fusion of infected cells with their neighbors. It was reported that replication-competent adenovirus particles can spread between nuclei within fusion-generated syncytia. To assess this conjecture, we generated fusogenic adenoviruses that express a balanced ratio of the F and H glycoproteins of measles virus. The viruses displayed enhanced cytotoxicity but largely unchanged replication efficiencies compared to a nonfusogenic virus. Most notably, the virus genomes did not spread through fusion-generated multinuclear cells. Hence, adenovirus replication in syncytia remains largely restricted to initially transduced nuclei.     

Synthesis, characterization, X-ray molecular structure and catalase-like activity of a non-heme iron complex: Dichloro[N-propanoate-N,N-bis-(2-pyridylmethyl)amine]iron(III)

In this work we present the synthesis and characterization of the complex dichloro[N-propanoate-N,N-bis-(2-pyridylmethyl)amine]iron(III) [Fe^III(PBMPA)Cl₂]. The ligand LiPBMPA was synthesized through the Michael reaction of BMPA with methylacrylate, followed by alkaline hydrolysis. The complex [Fe^III(PBMPA)Cl₂] has been synthesized by the reaction of the ligand with FeCl₃ · H₂O and was mainly characterized by cyclic voltammetry, conductivimetry, and electronic, infrared and Mössbauer spectroscopies, and by X-ray structural analysis, which showed an iron center coordinated by one carboxylate oxygen in a monodentate way, one tertiary amine, two pyridine groups and two chloride ions. It has been proposed that in water the chloride ligands are shifted by the solvent molecules and the species [Fe^III(PBMPA)(H₂O)₂]Cl₂ is predominant. The catalase-like activity of the complex was tested in water, and it proved to be active in the hydrogen peroxide dismutation. Kinetics studies were conducted following the initial rates method. The reaction is first order in relation to both the complex and the hydrogen peroxide. Based on the presence of a lag phase that depends on the initial complex concentration, we propose that the active species that shows in situ catalase-like activity, is a binuclear complex.