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1.
J Photochem Photobiol B ; 243: 112713, 2023 Jun.
Article in English | MEDLINE | ID: mdl-37086566

ABSTRACT

Ultraviolet C (UVC) light has long been used as a sterilizing agent, primarily through devices that emit at 254 nm. Depending on the dose and duration of exposure, UV 254 nm can cause erythema and photokeratitis and potentially cause skin cancer since it directly modifies nitrogenated nucleic acid bases. Filtered KrCl excimer lamps (emitting mainly at 222 nm) have emerged as safer germicidal tools and have even been proposed as devices to sterilize surgical wounds. All the studies that showed the safety of 222 nm analyzed cell number and viability, erythema generation, epidermal thickening, the formation of genetic lesions such as cyclobutane pyrimidine dimers (CPDs) and pyrimidine-(6-4)-pyrimidone photoproducts (6-4PPs) and cancer-inducing potential. Although nucleic acids can absorb and be modified by both UV 254 nm and UV 222 nm equally, compared to UV 254 nm, UV 222 nm is more intensely absorbed by proteins (especially aromatic side chains), causing photooxidation and cross-linking. Here, in addition to analyzing DNA lesion formation, for the first time, we evaluated changes in the proteome and cellular pathways, reactive oxygen species formation, and metalloproteinase (MMP) levels and activity in full-thickness in vitro reconstructed human skin (RHS) exposed to UV 222 nm. We also performed the longest (40 days) in vivo study of UV 222 nm exposure in the HRS/J mouse model at the occupational threshold limit value (TLV) for indirect exposure (25 mJ/cm2) and evaluated overall skin morphology, cellular pathological alterations, CPD and 6-4PP formation and MMP-9 activity. Our study showed that processes related to reactive oxygen species and inflammatory responses were more altered by UV 254 nm than by UV 222 nm. Our chronic in vivo exposure assay using the TLV confirmed that UV 222 nm causes minor damage to the skin. However, alterations in pathways related to skin regeneration raise concerns about direct exposure to UV 222 nm.


Subject(s)
DNA Damage , Nucleic Acids , Mice , Animals , Humans , Reactive Oxygen Species/metabolism , Pyrimidine Dimers/metabolism , Skin/radiation effects , Ultraviolet Rays , Nucleic Acids/metabolism , Erythema
2.
J Neurochem ; 166(1): 58-75, 2023 Jul.
Article in English | MEDLINE | ID: mdl-35149997

ABSTRACT

Abnormal phase transitions have been implicated in the occurrence of proteinopathies. Disordered proteins with nucleic acidbinding ability drive the formation of reversible micron-sized condensates capable of controlling nucleic acid processing/transport. This mechanism, achieved via liquid-liquid phase separation (LLPS), underlies the formation of long-studied membraneless organelles (e.g., nucleolus) and various transient condensates formed by driver proteins. The prion protein (PrP) is not a classical nucleic acid-binding protein. However, it binds nucleic acids with high affinity, undergoes nucleocytoplasmic shuttling, contains a long intrinsically disordered region rich in glycines and evenly spaced aromatic residues, among other biochemical/biophysical properties of bona fide drivers of phase transitions. Because of this, our group and others have characterized LLPS of recombinant PrP. In vitro phase separation of PrP is modulated by nucleic acid aptamers, and depending on the aptamer conformation, the liquid droplets evolve to solid-like species. Herein, we discuss recent studies and previous evidence supporting PrP phase transitions. We focus on the central role of LLPS related to PrP physiology and pathology, with a special emphasis on the interaction of PrP with different ligands, such as proteins and nucleic acids, which can play a role in prion disease pathogenesis. Finally, we comment on therapeutic strategies directed at the non-functional phase separation that could potentially tackle prion diseases or other protein misfolding disorders.


Subject(s)
Nucleic Acids , Prion Diseases , Prions , Animals , Prion Proteins/metabolism , Prions/metabolism , Mammals/metabolism , Nucleic Acids/metabolism
3.
Biochim Biophys Acta Gen Subj ; 1865(11): 129996, 2021 11.
Article in English | MEDLINE | ID: mdl-34474118

ABSTRACT

BACKGROUND: Cellular nucleic acid binding protein (CNBP) is a conserved single-stranded nucleic acid binding protein present in most eukaryotes, but not in plants. Expansions in the CNBP gene cause myotonic dystrophy type 2. Initially reported as a transcriptional regulator, CNBP was then also identified acting as a translational regulator. SCOPE OF REVIEW: The focus of this review was to link the CNBP structural features and newly reported biochemical activities with the recently described biological functions, in the context of its pathological significance. MAJOR CONCLUSIONS: Several post-translational modifications affect CNBP subcellular localization and activity. CNBP participates in the transcriptional and translational regulation of a wide range of genes by remodeling single-stranded nucleic acid secondary structures and/or by modulating the activity of trans-acting factors. CNBP is required for proper neural crest and heart development, and plays a role in cell proliferation control. Besides, CNBP has been linked with neurodegenerative, inflammatory, and congenital diseases, as well as with tumor processes. GENERAL SIGNIFICANCE: This review provides an insight into the growing functions of CNBP in cell biology. A unique and robust mechanistic or biochemical connection among these roles has yet not been elucidated. However, the ability of CNBP to dynamically integrate signaling pathways and to act as nucleic acid chaperone may explain most of the roles and functions identified so far.


Subject(s)
DNA-Binding Proteins/metabolism , RNA-Binding Proteins/metabolism , Animals , DNA-Binding Proteins/genetics , Humans , Nucleic Acids/metabolism , RNA-Binding Proteins/genetics
4.
ACS Appl Bio Mater ; 4(8): 6404-6416, 2021 08 16.
Article in English | MEDLINE | ID: mdl-35006917

ABSTRACT

Cell-penetrating peptides (CPPs) are a topical subject potentially exploitable for creating nanotherapeutics for the delivery of bioactive loads. These compounds are often classified into three major categories according to their physicochemical characteristics: cationic, amphiphilic, and hydrophobic. Among them, the group of hydrophobic CPPs has received increasing attention in recent years due to toxicity concerns posed by highly cationic CPPs. The hexapeptide PFVYLI (P, proline; F, phenylalanine; V, valine; Y, tyrosine; L, leucine; and I, isoleucine), a fragment derived from the C-terminal portion of α1-antitrypsin, is a prototypal example of hydrophobic CPP. This sequence shows reduced cytotoxicity and a capacity of nuclear localization, and its small size readily hints at its suitability as a building block to construct nanostructured materials. In this study, we examine the self-assembling properties of PFVYLI and investigate its ability to form noncovalent complexes with nucleic acids. By using a combination of biophysical tools including synchrotron small-angle X-ray scattering and atomic force microscopy-based infrared spectroscopy, we discovered that this CPP self-assembles into discrete nanofibrils with remarkable amyloidogenic features. Over the course of days, these fibrils coalesce into rodlike crystals that easily reach the micrometer range. Despite lacking cationic residues in the composition, PFVYLI forms noncovalent complexes with nucleic acids that retain ß-sheet pairing found in amyloid aggregates. In vitro vectorization experiments performed with double-stranded DNA fragments indicate that complexes promote the internalization of nucleic acids, revealing that tropism toward cell membranes is preserved upon complexation. On the other hand, transfection assays with splice-correction oligonucleotides (SCOs) for luciferase expression show limited bioactivity across a narrow concentration window, suggesting that the propensity to form amyloidogenic aggregates may trigger endosomal entrapment. We anticipate that the findings presented here open perspectives for using this archetypical hydrophobic CPP in the fabrication of nanostructured scaffolds, which potentially integrate properties of amyloids and translocation capabilities of CPPs.


Subject(s)
Cell-Penetrating Peptides , Nucleic Acids , Amyloidogenic Proteins/genetics , Cell-Penetrating Peptides/chemistry , Hydrophobic and Hydrophilic Interactions , Nucleic Acids/metabolism , Oligonucleotides/genetics , Transfection
5.
Cells ; 9(12)2020 12 11.
Article in English | MEDLINE | ID: mdl-33322404

ABSTRACT

The aging population has contributed to the rapid rise in the global incidence of neurodegenerative diseases. Despite the medical advances, there are no effective treatments for these disorders. Therefore, there is an urgent need for new treatments for these diseases. In this sense, cell therapy has been recognized as the best candidate for treating incurable diseases, such as neurodegenerative disorders. However, the therapeutic use of these cells can be limited by several factors. Thus, there has been a rediscovery that extracellular vesicles, including exosomes, can be alternatively explored in the treatment of these diseases, overcoming the limits of cell-based therapy. In this sense, this review aims to revisit all areas from biology, including biogenesis and the content of exosomes, to biotechnology, proposing the minimal information required to isolate, characterize, and study the content of these vesicles for scientific and/or clinical purposes.


Subject(s)
Exosomes/metabolism , Neurodegenerative Diseases/therapy , Biotechnology , Culture Media, Conditioned/chemistry , Endosomal Sorting Complexes Required for Transport/genetics , Exosomes/transplantation , Humans , Mesenchymal Stem Cells/cytology , Mesenchymal Stem Cells/metabolism , Metalloproteases/metabolism , Neurodegenerative Diseases/pathology , Nucleic Acids/metabolism , Vascular Endothelial Growth Factor A/metabolism
6.
Sci Rep ; 10(1): 5470, 2020 03 25.
Article in English | MEDLINE | ID: mdl-32214181

ABSTRACT

Capsid proteins often present a positively charged arginine-rich sequence at their terminal regions, which has a fundamental role in genome packaging and particle stability for some icosahedral viruses. These sequences show little to no conservation and are structurally dynamic such that they cannot be easily detected by common sequence or structure comparisons. As a result, the occurrence and distribution of positively charged domains across the viral universe are unknown. Based on the net charge calculation of discrete protein segments, we identified proteins containing amino acid stretches with a notably high net charge (Q > + 17), which are enriched in icosahedral viruses with a distinctive bias towards arginine over lysine. We used viral particle structural data to calculate the total electrostatic charge derived from the most positively charged protein segment of capsid proteins and correlated these values with genome charges arising from the phosphates of each nucleotide. We obtained a positive correlation (r = 0.91, p-value <0001) for a group of 17 viral families, corresponding to 40% of all families with icosahedral structures described to date. These data indicated that unrelated viruses with diverse genome types adopt a common underlying mechanism for capsid assembly based on R-arms.


Subject(s)
Capsid Proteins/metabolism , Genome, Viral , Nucleic Acids/metabolism , Viral Proteins/metabolism , Viruses/genetics , Viruses/metabolism , Amino Acid Sequence , Nucleotides/metabolism , Phosphates/metabolism , Protein Domains , Static Electricity , Virion/metabolism , Virus Assembly/genetics
7.
Adv Neurobiol ; 18: 267-286, 2017.
Article in English | MEDLINE | ID: mdl-28889272

ABSTRACT

Methylmercury (MeHg) is a highly neurotoxic environmental pollutant. Even though molecular mechanisms mediating MeHg toxicity are not completely understood, several lines of evidence indicate that the neurotoxic effects resultant from MeHg exposure represent a consequence of its pro-oxidative properties. In this regard, MeHg is a soft electrophile that preferentially interacts with (and oxidize) nucleophilic groups (mainly thiols and selenols) from biomolecules, including proteins and low-molecular-weight molecules. Such interaction contributes to the occurrence of oxidative stress and impaired function of several molecules [proteins (receptors, transporters, enzymes, structural proteins), lipids (i.e., membrane constituents and intracellular messengers), and nucleic acids (i.e., DNA)], culminating in neurotoxicity.In this chapter, an initial background on the general aspects regarding the neurotoxicology of MeHg, with a particular focus on its pro-oxidative properties and its interaction with nucleophilic thiol- and selenol-containing molecules, is provided. Even though experimental evidence indicates that symptoms (i.e., motor impairment) resultant from MeHg exposure are linked to its pro-oxidative properties, as well as to their molecular consequences (lipid peroxidation, disruption of glutamate and/or calcium homeostasis, etc.), data concerning the relationship between molecular parameters and behavioral impairment others that those related to the motor function (i.e., visual impairment, cognitive skills, etc.) are scarce. Thus, even though scientific research has provided a significant amount of knowledge concerning the mechanisms mediating MeHg-induced neurotoxicity in the last decades, the whole scenario is far from being completely understood, and further research in this area is well warranted.


Subject(s)
Mercury Poisoning, Nervous System/metabolism , Methylmercury Compounds/poisoning , Neurons/metabolism , Oxidative Stress , Reactive Oxygen Species/metabolism , Glutamic Acid/metabolism , Humans , Lipid Metabolism , Mercury Poisoning, Nervous System/physiopathology , Nucleic Acids/metabolism , Oxidation-Reduction , Selenium Compounds/metabolism , Sulfhydryl Compounds/metabolism , Synaptic Transmission
8.
Int J Mol Sci ; 18(5)2017 May 17.
Article in English | MEDLINE | ID: mdl-28513534

ABSTRACT

Transmissible spongiform encephalopathies (TSEs) are a group of neurodegenerative disorders that affect humans and other mammals. The etiologic agents common to these diseases are misfolded conformations of the prion protein (PrP). The molecular mechanisms that trigger the structural conversion of the normal cellular PrP (PrPC) into the pathogenic conformer (PrPSc) are still poorly understood. It is proposed that a molecular cofactor would act as a catalyst, lowering the activation energy of the conversion process, therefore favoring the transition of PrPC to PrPSc. Several in vitro studies have described physical interactions between PrP and different classes of molecules, which might play a role in either PrP physiology or pathology. Among these molecules, nucleic acids (NAs) are highlighted as potential PrP molecular partners. In this context, the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) methodology has proven extremely valuable to investigate PrP-NA interactions, due to its ability to select small nucleic acids, also termed aptamers, that bind PrP with high affinity and specificity. Aptamers are single-stranded DNA or RNA oligonucleotides that can be folded into a wide range of structures (from harpins to G-quadruplexes). They are selected from a nucleic acid pool containing a large number (1014-1016) of random sequences of the same size (~20-100 bases). Aptamers stand out because of their potential ability to bind with different affinities to distinct conformations of the same protein target. Therefore, the identification of high-affinity and selective PrP ligands may aid the development of new therapies and diagnostic tools for TSEs. This review will focus on the selection of aptamers targeted against either full-length or truncated forms of PrP, discussing the implications that result from interactions of PrP with NAs, and their potential advances in the studies of prions. We will also provide a critical evaluation, assuming the advantages and drawbacks of the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) technique in the general field of amyloidogenic proteins.


Subject(s)
Aptamers, Nucleotide/metabolism , Carrier Proteins/metabolism , Prion Proteins/metabolism , Amyloidogenic Proteins/metabolism , Animals , DNA, Single-Stranded/metabolism , Humans , Nucleic Acids/metabolism , Prion Diseases/metabolism , Prion Proteins/antagonists & inhibitors , Protein Binding , SELEX Aptamer Technique
9.
Rapid Commun Mass Spectrom ; 30(1): 209-20, 2016 Jan 15.
Article in English | MEDLINE | ID: mdl-26661988

ABSTRACT

RATIONALE: A full understanding of the biological impact of nanomaterials demands analytical procedures suitable for the detection/quantification of epigenetic changes that occur in the exposed organisms. Here, the effect of CuO nanoparticles (NPs) on global methylation of nucleic acids in Lepidium sativum was evaluated by liquid chromatography/ion trap mass spectrometry. Enhanced selectivity toward cytosine-containing nucleosides was achieved by using their proton-bound dimers formed in positive electrospray ionization (ESI(+)) as precursor ions for multiple reaction monitoring (MRM) quantification based on one or two ion transitions. METHODS: Plants were exposed to CuO NPs (0-1000 mg L(-1)); nucleic acid extracts were washed with bathocuproine disulfate; nucleosides were separated on a Luna C18 column coupled via ESI(+) to an AmaZon SL mass spectrometer (Bruker Daltonics). Cytidine, 2´-deoxycytidine, 5-methylcytidine, 5-methyl-2´-deoxycytidine and 5-hydroxymethyl-2´-deoxycytidine were quantified by MRM based on MS(3) ([2M+H](+)/[M+H](+)/[M+H-132](+) or [M+H-116](+)) and MS(2) ([2M+H](+)/[M+H](+) ). RESULTS: Bathocuproine disulfate, added as Cu(I) complexing agent, allowed for elimination of [2M+Cu](+) adducts from the mass spectra. Poorer instrumental detection limits were obtained for MS(3) (20-120 fmol) as compared to MS(2) (9.0-41 fmol); however, two ion transitions helped to eliminate matrix effects in plant extracts. The procedure was tested by analyzing salmon sperm DNA (Sigma) and applied for the evaluation of DNA and RNA methylation in plants; in the absence of NPs, 13.03% and 0.92% methylated cytosines were found in DNA and RNA, respectively; for NPs concentration >50 mg L(-1), DNA hypomethylation was observed with respect to unexposed plants. RNA methylation did not present significant changes upon plant exposure; 5-hydroxymethyl-2´-deoxycytidine was not detected in any sample. CONCLUSIONS: The MRM quantification proposed here of cytosine-containing nucleosides using their proton-bound homo-dimers as precursor ions proved its utility for the assessment of global methylation of DNA and RNA in plants under stress imposed by CuO NPs. Detection of copper adducts with cytosine-containing ions, and their elimination by washing extracts with Cu(I) chelator, calls for further investigation.


Subject(s)
Chromatography, Liquid/methods , Copper/toxicity , Lepidium sativum/drug effects , Nucleic Acids/analysis , Spectrometry, Mass, Electrospray Ionization/methods , DNA Methylation/drug effects , Nucleic Acids/chemistry , Nucleic Acids/metabolism , Plant Extracts/chemistry , Tandem Mass Spectrometry/methods
10.
Biochem Biophys Res Commun ; 445(1): 196-202, 2014 Feb 28.
Article in English | MEDLINE | ID: mdl-24508256

ABSTRACT

SET and hnRNPK are proteins involved in gene expression and regulation of cellular signaling. We previously demonstrated that SET accumulates in head and neck squamous cell carcinoma (HNSCC); hnRNPK is a prognostic marker in cancer. Here, we postulate that SET and hnRNPK proteins interact to promote tumorigenesis. We performed studies in HEK293 and HNSCC (HN6, HN12, and HN13) cell lines with SET/hnRNPK overexpression and knockdown, respectively. We found that SET and/or hnRNPK protein accumulation increased cellular proliferation. SET accumulation up-regulated hnRNPK mRNA and total/phosphorylated protein, promoted hnRNPK nuclear location, and reduced Bcl-x mRNA levels. SET protein directly interacted with hnRNPK, increasing both its binding to nucleic acids and Bcl-xS repression. We propose that hnRNPK should be a new target of SET and that SET-hnRNPK interaction, in turn, has potential implications in cell survival and malignant transformation.


Subject(s)
Cell Proliferation , Histone Chaperones/metabolism , Nucleic Acids/metabolism , Ribonucleoproteins/metabolism , Transcription Factors/metabolism , bcl-X Protein/metabolism , Carcinoma, Squamous Cell/genetics , Carcinoma, Squamous Cell/metabolism , Carcinoma, Squamous Cell/pathology , Cell Line, Tumor , Cell Nucleus/metabolism , DNA-Binding Proteins , Gene Expression Regulation , HEK293 Cells , Head and Neck Neoplasms/genetics , Head and Neck Neoplasms/metabolism , Head and Neck Neoplasms/pathology , Heterogeneous-Nuclear Ribonucleoprotein K , Histone Chaperones/genetics , Humans , Immunoblotting , Microscopy, Confocal , Nucleic Acids/genetics , Phosphorylation , Protein Binding , RNA Interference , RNA, Messenger/genetics , RNA, Messenger/metabolism , Reverse Transcriptase Polymerase Chain Reaction , Ribonucleoproteins/genetics , Transcription Factors/genetics , Up-Regulation , bcl-X Protein/genetics
11.
Photochem Photobiol Sci ; 12(5): 930-5, 2013 May.
Article in English | MEDLINE | ID: mdl-23483124

ABSTRACT

A low-intensity laser is used in treating herpes labialis based on the biostimulative effect, albeit the photobiological basis is not well understood. In this work experimental models based on Escherichia coli cultures and plasmids were used to evaluate effects of low-intensity red laser on DNA at fluences for treatment of herpes labialis. To this end, survival and transformation efficiency of plasmids in E. coli AB1157 (wild type), BH20 (fpg/mutM(-)) and BW9091 (xthA(-)), content of the supercoiled form of plasmid DNA, as well as nucleic acids and protein content from bacterial cultures exposed to the laser, were evaluated. The data indicate low-intensity red laser: (i) alters the survival of plasmids in wild type, fpg/mutM(-) and xthA(-)E. coli cultures depending of growth phase, (ii) alters the content of the supercoiled form of plasmids in the wild type and fpg/mutM(-)E. coli cells, (iii) alters the content of nucleic acids and proteins in wild type E. coli cells, (iv) alters the transformation efficiency of plasmids in wild type and fpg/mutM(-)E. coli competent cells. These data could be used to understand positive effects of low-intensity lasers on herpes labialis treatment.


Subject(s)
Escherichia coli/radiation effects , Herpes Labialis/genetics , Lasers , Plasmids/metabolism , Escherichia coli/growth & development , Escherichia coli/metabolism , Escherichia coli Proteins/metabolism , Nucleic Acids/metabolism , Plasmids/chemistry , Transformation, Bacterial/radiation effects
12.
Proc Natl Acad Sci U S A ; 108(9): 3689-94, 2011 Mar 01.
Article in English | MEDLINE | ID: mdl-21303985

ABSTRACT

Excessive release of proinflammatory cytokines by innate immune cells is an important component of the pathogenic basis of malaria. Proinflammatory cytokines are a direct output of Toll-like receptor (TLR) activation during microbial infection. Thus, interference with TLR function is likely to render a better clinical outcome by preventing their aberrant activation and the excessive release of inflammatory mediators. Herein, we describe the protective effect and mechanism of action of E6446, a synthetic antagonist of nucleic acid-sensing TLRs, on experimental cerebral malaria (ECM) induced by Plasmodium berghei ANKA. We show that in vitro, low doses of E6446 specifically inhibited the activation of human and mouse TLR9. Tenfold higher concentrations of this compound also inhibited the human TLR8 response to single-stranded RNA. In vivo, therapy with E6446 diminished the activation of TLR9 and prevented the exacerbated cytokine response observed during acute Plasmodium infection. Furthermore, severe signs of ECM, such as limb paralysis, brain vascular leak, and death, were all prevented by oral treatment with E6446. Hence, we provide evidence that supports the involvement of nucleic acid-sensing TLRs in malaria pathogenesis and that interference with the activation of these receptors is a promising strategy to prevent deleterious inflammatory responses that mediate pathogenesis and severity of malaria.


Subject(s)
Hydrocarbons, Aromatic/pharmacology , Malaria, Cerebral/prevention & control , Malaria, Cerebral/therapy , Nucleic Acids/metabolism , Toll-Like Receptors/antagonists & inhibitors , Animals , Blood-Brain Barrier/drug effects , Blood-Brain Barrier/pathology , Humans , Hydrocarbons, Aromatic/chemistry , Inflammation/complications , Inflammation/pathology , Lipopolysaccharides/pharmacology , Malaria, Cerebral/chemically induced , Malaria, Cerebral/parasitology , Mice , Mice, Inbred C57BL , Plasmodium chabaudi/drug effects , Plasmodium chabaudi/physiology , Shock, Septic/chemically induced , Shock, Septic/complications , Toll-Like Receptors/metabolism
13.
Front Biosci (Landmark Ed) ; 15(1): 132-50, 2010 01 01.
Article in English | MEDLINE | ID: mdl-20036811

ABSTRACT

Since the first description of prion diseases, great effort has been made toward comprehending this new paradigm in biology. Despite large advances in the field, many questions remain unanswered, especially concerning the conversion of PrP(C) into PrP(Sc). How this conformational transition evolves is a crucial problem that must be solved in order to attain further progress in therapeutics and prevention. Recent developments have indicated the requirement for partners of the prion protein in triggering the conversion. In the present review, we will explore the interaction of PrP with some of its most intriguing partners, such as sulfated glycans and nucleic acids. These molecules seem to play a dual role in prion biology and could be fundamental to explaining how prion diseases arise, as well as in the development of effective therapeutic approaches.


Subject(s)
Glycosaminoglycans/metabolism , Nucleic Acids/metabolism , Prion Diseases/metabolism , Prions/metabolism , Animals , Humans , Models, Molecular , PrPC Proteins/chemistry , PrPC Proteins/metabolism , PrPSc Proteins/chemistry , PrPSc Proteins/metabolism , Prions/chemistry , Protein Binding , Protein Conformation
14.
Acc Chem Res ; 43(2): 271-9, 2010 Feb 16.
Article in English | MEDLINE | ID: mdl-19817406

ABSTRACT

Protein misfolding has been implicated in a large number of diseases termed protein- folding disorders (PFDs), which include Alzheimer's disease, Parkinson's disease, transmissible spongiform encephalopathies, familial amyloid polyneuropathy, Huntington's disease, and type II diabetes. In these diseases, large quantities of incorrectly folded proteins undergo aggregation, destroying brain cells and other tissues. The interplay between ligand binding and hydration is an important component of the formation of misfolded protein species. Hydration drives various biological processes, including protein folding, ligand binding, macromolecular assembly, enzyme kinetics, and signal transduction. The changes in hydration and packing, both when proteins fold correctly or when folding goes wrong, leading to PFDs, are examined through several biochemical, biophysical, and structural approaches. Although in many cases the binding of a ligand such as a nucleic acid helps to prevent misfolding and aggregation, there are several examples in which ligands induce misfolding and assembly into amyloids. This occurs simply because the formation of structured aggregates (such as protofibrillar and fibrillar amyloids) involves decreases in hydration, formation of a hydrogen-bond network in the secondary structure, and burying of nonpolar amino acid residues, processes that also occur in the normal folding landscape. In this Account, we describe the present knowledge of the folding and misfolding of different proteins, with a detailed emphasis on mammalian prion protein (PrP) and tumoral suppressor protein p53; we also explore how ligand binding and hydration together influence the fate of the proteins. Anfinsen's paradigm that the structure of a protein is determined by its amino acid sequence is to some extent contradicted by the observation that there are two isoforms of the prion protein with the same sequence: the cellular and the misfolded isoform. The cellular isoform of PrP has a disordered N-terminal domain and a highly flexible, not-well-packed C-terminal domain, which might account for its significant hydration. When PrP binds to biological molecules, such as glycosaminoglycans and nucleic acids, the disordered segments appear to fold and become less hydrated. Formation of the PrP-nucleic acid complex seems to accelerate the conversion of the cellular form of the protein into the disease-causing isoform. For p53, binding to some ligands, including nucleic acids, would prevent misfolding of the protein. Recently, several groups have begun to analyze the folding-misfolding of the individual domains of p53, but several questions remain unanswered. We discuss the implications of these findings for understanding the productive and incorrect folding pathways of these proteins in normal physiological states and in human disease, such as prion disorders and cancer. These studies are shown to lay the groundwork for the development of new drugs.


Subject(s)
Prions/chemistry , Prions/metabolism , Protein Folding , Tumor Suppressor Protein p53/chemistry , Tumor Suppressor Protein p53/metabolism , Water/chemistry , Humans , Ligands , Nucleic Acids/chemistry , Nucleic Acids/metabolism
15.
Trends Biochem Sci ; 33(3): 132-40, 2008 Mar.
Article in English | MEDLINE | ID: mdl-18243708

ABSTRACT

In transmissible spongiform encephalopathies, the infectious material consists chiefly of a protein, the scrapie prion protein PrP(Sc), that carries no genetic coding material; however, prions are likely to have accomplices that chaperone their activity and promote the conversion of the cellular prion protein PrP(C) into the disease-causing isoform (PrP(Sc)). Recent studies from several laboratories indicate that PrP(C) recognizes many nucleic acids (NAs) with high affinities, and we correlate these findings with a possible pathophysiological role for this interaction. Thus, of the chaperones, NA is the most likely candidate for prions. The participation of NAs in prion propagation opens new avenues for developing new diagnostic tools and therapeutics to target prion diseases, as well as for understanding the function of PrP(C), probably as a NA chaperone.


Subject(s)
Nucleic Acids/metabolism , Prions/metabolism , Animals , Humans , Models, Biological , Prions/chemistry , Protein Binding , Protein Conformation
16.
Planta ; 225(6): 1339-51, 2007 May.
Article in English | MEDLINE | ID: mdl-17123099

ABSTRACT

The glycine-rich protein AtGRP2 is one of the four members of the cold-shock domain (CSD) protein family in Arabidopsis. It is characterized by the presence of a nucleic acid-binding CSD domain, two glycine-rich domains and two CCHC zinc-fingers present in nucleic acid-binding proteins. In an attempt to further understand the role of CSD/GRP proteins in plants, we have proceeded to the functional characterization of the AtGRP2 gene. Here, we demonstrate that AtGRP2 is a nucleo-cytoplasmic protein involved in Arabidopsis development with a possible function in cold-response. Expression analysis revealed that the AtGRP2 gene is active in meristematic tissues, being modulated during flower development. Down-regulation of AtGRP2 gene, using gene-silencing techniques resulted in early flowering, altered stamen number and affected seed development. A possible role of AtGRP2 as an RNA chaperone is discussed.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/growth & development , Arabidopsis/metabolism , Flowers/growth & development , RNA-Binding Proteins/metabolism , Seeds/growth & development , Cold Temperature , Flowers/metabolism , Gene Expression Regulation, Plant , Meristem/metabolism , Nucleic Acids/chemistry , Nucleic Acids/metabolism , Protein Binding , Protein Transport , Seeds/metabolism
17.
BMC Mol Biol ; 6: 9, 2005 Apr 15.
Article in English | MEDLINE | ID: mdl-15833107

ABSTRACT

BACKGROUND: Preparation of RNA free from DNA is a critical step before performing RT-PCR assay. Total RNA isolated from several sources, including those obtained from Saccharomyces cerevisiae, using routine methodologies are frequently contaminated with DNA, which can give rise to amplification products that mimic the amplicons expected from the RNA target. RESULTS: We investigated the efficiency of two DNase I based protocols for eliminating DNA contaminations from RNA samples obtained from yeast cells. Both procedures are very efficient in eliminating DNA contamination from RNA samples and entail three main steps, which involve treating of RNA samples with DNase I, inhibition of the enzyme by EDTA and its subsequent inactivation at 65 degrees C. The DNase I treated samples were further purified with phenol: chloroform followed by precipitation with ice-cold ethanol (protocol I) or, alternatively, they were directly used in RT-PCR reactions (protocol II). Transcripts from ACT1, PDA1, CNA1, CNA2, TPS1 and TPS2 analyzed after each treatment showed that all mRNAs tested can be amplified if total RNA was extracted and purified after DNase I treatment, however, only TPS1, TPS2 and ACT1 mRNAs were amplified without extraction/purification step. CONCLUSION: Although more laborious and requiring a higher initial amount of material, the inclusion of an extraction and purification step allows to prepare RNA samples that are free from DNA and from low molecular contaminants and can be applied to amplify any Saccharomyces cerevisiae mRNA by RT-PCR.


Subject(s)
Deoxyribonuclease I/drug effects , Nucleic Acids/metabolism , RNA, Fungal/isolation & purification , Reverse Transcriptase Polymerase Chain Reaction/methods , Actins/analysis , DNA Primers , Edetic Acid , Electrophoresis, Agar Gel/methods , Saccharomyces cerevisiae/chemistry , Saccharomyces cerevisiae Proteins/analysis
18.
Eur J Pharmacol ; 510(1-2): 17-24, 2005 Mar 07.
Article in English | MEDLINE | ID: mdl-15740720

ABSTRACT

Trans-dehydrocrotonin has antiulcerogenic and antitumor activities. A complex of beta-cyclodextrin with dehydrocrotonin was developed to improve the delivery of dehydrocrotonin. Complex in solid state was evaluated using X-ray diffraction (XRD), differential scanning calorimetry (DSC), thermal gravimetric analysis (TGA) and scanning electron microscopy (SEM). X-ray diffraction and scanning electron microscopy studies showed that dehydrocrotonin exists in a semicrystalline state in the complexed form with beta-cyclodextrin. Differential scanning calorimetry studies showed the existence of a complex of dehydrocrotonin with beta-cyclodextrin. The thermal gravimetric analysis studies confirmed the differential scanning calorimetry results of the complex. Free dehydrocrotonin and the dehydrocrotonin/beta-cyclodextrin inclusion complex were assayed in freshly isolated rat hepatocytes and in V79 cells. Cytotoxicity was determined using nucleic acid content, methylthiazoletetrazolium (MTT) reduction and neutral red uptake assays. In all assays, there was a large reduction (3.5-16.1-fold) in the cytotoxicity of dehydrocrotonin in hepatocytes when complexed with beta-cyclodextrin, whereas for V79 cells the decrease in cytotoxicity was 1.7- and 1.87-fold for MTT reduction and nucleic acid content assays, respectively. The lower cytotoxicity of the dehydrocrotonin/beta-cyclodextrin complex compared to free dehydrocrotonin in rat hepatocytes and V79 cells suggests that such a complex may be useful for the administration of dehydrocrotonin in vivo.


Subject(s)
Diterpenes, Clerodane/pharmacology , Fibroblasts/drug effects , Hepatocytes/drug effects , beta-Cyclodextrins/pharmacology , Animals , Calorimetry, Differential Scanning , Cell Line , Cell Survival/drug effects , Cells, Cultured , Diterpenes, Clerodane/chemistry , Dose-Response Relationship, Drug , Fibroblasts/cytology , Fibroblasts/metabolism , Hepatocytes/cytology , Hepatocytes/metabolism , Inhibitory Concentration 50 , Male , Microscopy, Electron, Scanning , Nucleic Acids/metabolism , Rats , Rats, Wistar , Thermogravimetry , X-Ray Diffraction , beta-Cyclodextrins/chemistry
19.
Protein Pept Lett ; 12(3): 251-5, 2005 Apr.
Article in English | MEDLINE | ID: mdl-15777274

ABSTRACT

The main hypothesis for prion diseases proposes that the cellular protein (PrP(c)) can be altered into a misfolded, beta-sheet-rich isoform (PrP(Sc)). We describe here that host nucleic acid may catalyze the conversion between PrP(c) and PrP(Sc) isoforms, by reducing the protein mobility and by making the protein-protein interactions more likely. We summarize the findings, focusing in the biological relevance of the catalytic action of nucleic acid.


Subject(s)
Nucleic Acids , PrPC Proteins , Protein Conformation , DNA/chemistry , DNA/metabolism , Nucleic Acids/chemistry , Nucleic Acids/metabolism , PrPC Proteins/chemistry , PrPC Proteins/metabolism , PrPSc Proteins/chemistry , PrPSc Proteins/metabolism , Protein Folding , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism
20.
Bioresour Technol ; 96(3): 383-7, 2005 Feb.
Article in English | MEDLINE | ID: mdl-15474942

ABSTRACT

A highly soluble fish protein hydrolysates (FPH) with an 80% protein (peptide size between 1.5 and 20 kDa) and a low free amino acid content was obtained from hake (Merluccius hubssi) filleting waste [Lat. Am. Appl. Res. 30 (2000) 241]. Assays with Halobacterium salinarum, Escherichia coli, Bacillus subtilis and Staphylococcus epidermidis were performed in order to test that FPH as nutrient source for archaea and eubacteria culture media. Cell growth was evaluated by plate count, and by monitoring turbidity and nucleic acids content in liquid cultures. Neither cell growth nor generation times resulting from control and FPH cultures exhibited statistically significant differences at alpha: 0.05 suggesting that FPH can be used as an alternative substrate for microorganism cultural purposes.


Subject(s)
Archaea/growth & development , Bacteria/growth & development , Culture Media/metabolism , Gadiformes/metabolism , Protein Hydrolysates/metabolism , Analysis of Variance , Animals , Colony Count, Microbial , Fisheries , Nephelometry and Turbidimetry , Nucleic Acids/metabolism , Protein Hydrolysates/isolation & purification , Waste Products
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