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1.
Sci Rep ; 10(1): 8367, 2020 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-32433550

RESUMO

The majority of oligomeric proteins form clusters which have rotational or dihedral symmetry. Despite the many advantages of symmetric packing, protein oligomers are only nearly symmetric, and the origin of this phenomenon is still in need to be fully explored. Here we apply near-symmetry analyses by the Continuous Symmetry Measures methodology of protein homomers to their natural state, namely their structures in solution. NMR-derived structural data serves us for that purpose. We find that symmetry deviations of proteins are by far higher in solution, compared to the crystalline state; that much of the symmetry distortion is due to amino acids along the interface between the subunits; that the distortions are mainly due to hydrophilic amino acids; and that distortive oligomerization processes such as the swap-domain mechanism can be identified by the symmetry analysis. Most of the analyses were carried out on distorted C2-symmetry dimers, but C3 and D2 cases were analyzed as well. Our NMR analysis supports the idea that the crystallographic B-factor represents non-classical crystals, in which different conformers pack in the crystal, perhaps from the conformers which the NMR analysis provides.

2.
Angew Chem Int Ed Engl ; 59(12): 4698-4704, 2020 Mar 16.
Artigo em Inglês | MEDLINE | ID: mdl-31923344

RESUMO

An ultra-high increase in the WF of silver, from 4.26 to 7.42 eV, that is, an increase of up to circa 3.1 eV is reported. This is the highest WF increase on record for metals and is supported by recent computational studies which predict the potential ability to affect an increase of the WF of metals by more than 4 eV. We achieved the ultra-high increase by a new approach: Rather than using the common method of 2D adsorption of polar molecules layers on the metal surface, WF modifying components, l-cysteine and Zn(OH)2 , were incorporated within the metal, resulting in a 3D architecture. Detailed material characterization by a large array of analytical methods was carried out, the combination of which points to a WF enhancement mechanism which is based on directly affecting the charge transfer ability of the metal separately by cysteine and hydrolyzed zinc(II), and synergistically by the combination of the two through the known Zn-cysteine finger redox trap effect.

3.
ACS Nano ; 13(9): 10826-10834, 2019 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-31487452

RESUMO

We report a solution for the challenge of having luminescence and metal conductivity from the same material. The fabrication of a hybrid metal-conductive luminescent film that manifests this dual property is described: the conductivity arising from a continuous gold thin film structure and luminescence originating from the embedded fluorescent emitters (nanoparticles of silica-coated CdSe/CdS quantum dots (QD/SiO2 NPs)). The embedding of the QD/SiO2 NPs is performed via a self-templating gold electroless process. The presence of the insulating silica layer on the QDs avoids quenching and enables luminescence, while still allowing plasmonic coupling of the QDs, as observed by luminescence lifetime analysis and by surface-enhanced Raman scattering. The potential applications of this special dual functionality are demonstrated by its used as a temperature probe: Passing current (heating the gold thin film) affects the emission intensity and induces a spectral red-shift of the QD/SiO2 NPs. All properties of this metal-conductive luminescent film required the special embedding architecture and are not observed with simple adsorption of QD/SiO2 NPs on a continuous Au film.

4.
Sci Rep ; 9(1): 11215, 2019 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-31375700

RESUMO

The emergence of global antibiotic resistance necessitates the urgent need to develop new and effective antimicrobial agents. Combination of two antimicrobial agents can potentially improve antimicrobial potency and mitigate the development of resistance. Therefore, we have utilized metal molecular doping methodology whereby antimicrobial random peptides mixture (RPMs) are entrapped in a bactericidal copper metal matrix. The copper/RPM composite exhibits greater antimicrobial activity toward methicillin-resistant Staphylococcus aureus (MRSA) than either copper or RPMs alone. Our findings indicate that this bactericidal antimicrobial biomaterial could be utilized to efficiently eradicate antibiotic-resistant pathogenic bacteria for health, agricultural and environmental applications.

5.
Biochemistry ; 57(45): 6395-6403, 2018 11 13.
Artigo em Inglês | MEDLINE | ID: mdl-30346734

RESUMO

The degree of chirality of protein backbone residues is used to enrich the Ramachandran plot (RP) and create three-dimensional chiral RPs with much more structural information. Detailed comparative analysis of the four classical RPs (general, glycine, proline, and pre-proline) is provided, including statistical analysis of quantitative chirality distributions in the maps and in the secondary structures. Our results show that points with outlier chirality levels represent special transitional points in the folded protein such as α-helix kinks, twists of ß-strands, and transition points between secondary structures. A protein chirality spectrum in which the degree of chirality of each residue is plotted against the sequence number explores these special points. More than 65000 residues extracted from 200 high-quality proteins are used for this study, which shows that quantitative chirality is a general and useful structural parameter for protein conformational studies.


Assuntos
Glicina/química , Prolina/química , Conformação Proteica , Proteínas/química , Cristalografia por Raios X , Bases de Dados de Proteínas , Ligação de Hidrogênio , Modelos Moleculares , Dobramento de Proteína
6.
Chem Commun (Camb) ; 54(52): 7203-7206, 2018 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-29897057

RESUMO

A new approach for fine tuning of the metal work function (WF) in the range of 1 eV is described. WF control is achieved by 3D molecular doping of the metal rather than the classical 2D adsorption. Both small molecules (Congo red, thionine) and polymers (Nafion, poly(vinylbenzyltrimethylammonium)chloride) were shown to affect the work function of gold and silver. The in situ reaction of the dopants within the metallic matrix is a further tool for altering the WF, confirming that this effect is dopant-dependent. We attribute this effect to the charge transfer interactions between the dopant molecule and the surrounding 3D metallic cage.

7.
Adv Mater ; 30(41): e1706804, 2018 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-29529340

RESUMO

A unique materials' methodology enables the doping of metals with functional molecules, polymers, enzymes, and nanoparticles. The resulting materials have either the combined properties of the metal and the dopants, or new, sometimes synergetic properties that are not found in the separate components, emerge. Metals that have been doped so far include gold, silver, copper, iron, gallium, palladium, platinum, and several alloys. Numerous applications have been demonstrated including catalysis, biocatalysis, bioactivity, electrochemistry (including new type of batteries), corrosion resistance, induction of chirality, tailoring unconventional properties to metals, and more. Doping of metals and adsorption on them are completely different processes, doping being a 3D event, while adsorption is a 2D process. Thus, practically all special properties and functionalities that have been demonstrated are apparent only in the doped case. Here, progress made in this field in the past four years is reviewed, including methodologies for obtaining metallic doped thin films, enhancing corrosion resistance, biomedical applications, and the use of doped metals for complex catalytic network of reactions.


Assuntos
Metais/química , Animais , Materiais Biocompatíveis/química , Catálise , Humanos
8.
Biochemistry ; 56(42): 5635-5643, 2017 10 24.
Artigo em Inglês | MEDLINE | ID: mdl-28872841

RESUMO

Ramachandran plots (RPs) map the wealth of conformations of the polypeptide backbone and are widely used to characterize protein structures. A limitation of the RPs is that they are based solely on two dihedral angles for each amino acid residue and provide therefore only a partial picture of the conformational richness of the protein. Here we extend the structural RP analysis of proteins from a two-dimensional (2D) map to a three-dimensional map by adding the quantitative degree of chirality-the continuous chirality measure (CCM)-of the amino acid residue at each point in the RP. This measure encompasses all bond angles and bond lengths of an amino acid residue. We focus in this report on glycine (Gly) because, due to its flexibility, it occupies a large portion of the 2D map, thus allowing a detailed study of the chirality measure, and in order to evaluate the justification of classically labeling Gly as the only achiral amino acid. We have analyzed in detail 4366 Gly residues extracted from high resolution crystallographic data of 160 proteins. This analysis reveals not only that Gly is practically always conformationally chiral, but that upon comparing with the backbone of all amino acids, the quantitative chirality values of Gly are of similar magnitudes to those of the (chiral) amino acids. Structural trends and energetic considerations are discussed in detail. Generally we show that adding chirality to Ramachandran plots creates far more informative plots that highlight the sensitivity of the protein structure to minor conformational changes.


Assuntos
Bases de Dados de Proteínas , Glicina/química , Modelos Moleculares , Proteínas/química , Cristalografia por Raios X
9.
PLoS One ; 12(7): e0180030, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28708874

RESUMO

The majority of proteins form oligomers which have rotational symmetry. Literature has suggested many functional advantages that the symmetric packing offers. Yet, despite these advantages, the vast majority of protein oligomers are only nearly symmetric. A key question in the field of proteins structure is therefore, if symmetry is so advantageous, why do oligomers settle for aggregates that do not maximize that structural property? The answer to that question is apparently multi-parametric, and involves distortions at the interaction zones of the monomer units of the oligomer in order to minimize the free energy, the dynamics of the protein, the effects of surroundings parameters, and the mechanism of oligomerization. The study of this problem is in its infancy: Only the first parameter has been explored so far. Here we focus on the last parameter-the mechanism of formation. To test this effect we have selected to focus on the domain swapping mechanism of oligomerization, by which oligomers form in a mechanism that swaps identical portions of monomeric units, resulting in an interwoven oligomer. We are using continuous symmetry measures to analyze in detail the oligomer formed by this mechanism, and found, that without exception, in all analyzed cases, perfect symmetry is given away, and we are able to identify that the main burden of distortion lies in the hinge regions that connect the swapped portions. We show that the continuous symmetry analysis method clearly identifies the hinge region of swapped domain proteins-considered to be a non-trivial task. We corroborate our conclusion about the central role of the hinge region in affecting the symmetry of the oligomers, by a special probability analysis developed particularly for that purpose.


Assuntos
Modelos Moleculares , Proteínas/química , Proteínas/metabolismo , Bases de Dados de Proteínas , Domínios Proteicos , Estrutura Terciária de Proteína
10.
Sci Rep ; 7(1): 4161, 2017 06 23.
Artigo em Inglês | MEDLINE | ID: mdl-28646180

RESUMO

Matrices for sustained release of drugs have been based on polymers, biomaterials and oxides. The use of the major family of metals as matrices for sustained release is, to the best of our knowledge, unknown. In this context we describe a new family of bio-composites for sustained release of drugs, namely analgesic drugs entrapped within metallic silver. Synthetic methodologies were developed for the preparation of ibuprofen@Ag, naproxen@Ag, tramadol@Ag and bupivacaine@Ag composites. Detailed kinetic analysis of the release of the drugs from within the metal, is provided, demonstrating that metals can indeed serve as reservoirs for drug release. The metal in our case acts not only as a drug releasing source, but also as an antibacterial agent and this property of the composites was studied. Unexpectedly, it was found that the entrapment of the analgesics within silver, dramatically enhances the growth inhibition activity of wild type Pseudomonas aeruginosa, exceeding by far the inhibition activity of the separate components. A mechanism for this interesting observation is provided. The strong antimicrobial activity combined with the analgesic activity open the road for future applications of these materials as dual-purpose components in wound treatment.


Assuntos
Analgésicos/farmacologia , Desinfetantes/farmacologia , Liberação Controlada de Fármacos , Metais/química , Prata/farmacologia , Analgésicos/química , Preparações de Ação Retardada , Cinética , Testes de Sensibilidade Microbiana , Pseudomonas aeruginosa/efeitos dos fármacos , Temperatura
11.
J Colloid Interface Sci ; 505: 692-702, 2017 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-28658655

RESUMO

A successful methodology for obtaining hybrid films which allow thermal triggering and continuous, irreversible, control of their hydrophilicity/hydrophobicity nature was developed. Two types of poly(dimethylsiloxane)-silica (PDMS@SiO2) films were prepared for that purpose: A hydrophilic film in which the thermal treatment causes an irreversible gradual increase of hydrophobicity; and a hydrophobic film that turns more hydrophilic upon thermal treatment. The opposite directionality of the change is dictated by the film substrate, on which the same hybrid is deposited. In both cases the thermal treatment induced a phase separation which caused the change in hydrophobicity. The magnitude of change in hydrophilicity/hydrophobicity is continuously controllable in both types of films by either the temperature or heating time. The films were characterized before and after heating by a variety of methods, including contact angle (CA) measurements with the sessile drop and the tilting plate methods, and by X-ray photoelectron spectroscopy (XPS) analysis. A thorough kinetic study was carried out, following the progress of the changes in the wettability property of the surfaces. The kinetics analyses proved that the changes in the wettability in all cases are due to phase separation processes, the directionality of which is determined by the treatment of the substrate on which the films are deposited. By monitoring the change of wettability (ΔCA) at various temperatures, an Arrhenius plot was obtained from which the activation energy and Arrhenius pre-exponential factor for the phase separation were derived, corroborating the proposed mechanism. To the best of our knowledge, this is the first use of phase separation behavior of a hybrid film in order to apply irreversible, thermally controllable change of surface wettability, tailored to proceed in opposite directions, and the first kinetic study of such a process.

12.
Sci Rep ; 7(1): 1458, 2017 05 03.
Artigo em Inglês | MEDLINE | ID: mdl-28469182

RESUMO

We present a high-yield method for the renaturation of negatively charged enzymes. The approach is based on the use of alumina nanoparticles, which after electrostatic interaction with denatured protein molecules, prevent their aggregation and make the process of refolding controllable. The method, demonstrated by the renaturation of several enzymes, is efficient, rapid, employs a minimal amount of reagents and even can be applied to renature mixture of the denatured enzymes.


Assuntos
Fosfatase Ácida/química , Óxido de Alumínio/química , Anidrases Carbônicas/química , Peroxidase do Rábano Silvestre/química , Nanopartículas/química , Renaturação Proteica , Fosfatase Ácida/isolamento & purificação , Animais , Armoracia/química , Armoracia/enzimologia , Anidrases Carbônicas/isolamento & purificação , Bovinos , Ensaios Enzimáticos , Guanidina/química , Peroxidase do Rábano Silvestre/isolamento & purificação , Cinética , Conformação Proteica , Desnaturação Proteica , Dobramento de Proteína , Solanum tuberosum/química , Solanum tuberosum/enzimologia
13.
Colloids Surf B Biointerfaces ; 146: 731-6, 2016 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-27442952

RESUMO

Most enzymes are highly sensitive to UV-light in all of its ranges and their activity can irreversibly drop even after a short time of exposure. Here we report a solution of this problem by using sol-gel matrices as effective protectors against this route of enzyme inactivation and denaturation. The concept presented here utilizes several modes of action: First, the entrapment within the rigid ceramic sol-gel matrix, inhibits denaturation motions, and the hydration shell around the entrapped protein provides extra protection. Second, the matrix itself - alumina in this report - absorbs UV light. And third, sol-gel materials have been shown to be quite universal in their ability to entrap small molecules, and so co-entrapment with well documented sun-screening molecules (2-hydroxybenzophenone, 2,2'-dihydroxybenzophenone, and 2,2'-dihydroxy-4-methoxybenzophenone) is an additional key protective tool. Three different enzymes as models were chosen for the experiments: carbonic anhydrase, acid phosphatase and horseradish peroxidase. All showed greatly enhanced UV (regions UV-A, UV-B, and UV-C) stabilization after entrapment within the doped sol-gel alumina matrices.


Assuntos
Fosfatase Ácida/metabolismo , Óxido de Alumínio/química , Anidrases Carbônicas/metabolismo , Peroxidase do Rábano Silvestre/metabolismo , Transição de Fase , Proteólise/efeitos dos fármacos , Proteólise/efeitos da radiação , Fosfatase Ácida/química , Anidrases Carbônicas/química , Géis/química , Peroxidase do Rábano Silvestre/química , Humanos , Fotólise , Protetores Solares/química , Protetores Solares/farmacologia , Raios Ultravioleta
14.
J Colloid Interface Sci ; 468: 307-312, 2016 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-26852355

RESUMO

A facile method to produce highly stable magnetite magnetic fluid at neutral pH without any stabilizing agents, resulting in pure Fe3O4 nanoparticles dispersed in water is described. The hydrosol which consists of only two components - magnetite and water - behaves as a typical ferrofluid, that is, although it responds to a magnetic field, the magnetic particles cannot be phase-separated from the water by that field. No such pure magnetic fluid have been described before, making it a universal carrier which can be easily modified for any application in materials science and chemistry, and in particular for a range of applications where non-corrosivity, low viscosity, and mild conditions are needed, such as in most bioapplications and in nano electro-mechanical systems. Under optimal conditions the hydrosol is stable for at least three months.


Assuntos
Compostos Férricos/química , Nanopartículas de Magnetita/química , Nanopartículas/química , Coloides/química , Concentração de Íons de Hidrogênio , Tamanho da Partícula , Propriedades de Superfície
15.
Chemphyschem ; 17(1): 162-9, 2016 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-26494548

RESUMO

This work examines the concept of dispersing polymers in metals. Herein, this was mainly studied with molten gallium, in which 5-18 wt % of various short-chain polymers were incorporated and mixed. The nature of the solidified products was examined by using X-ray diffraction, electron microscopy, UV/Vis, differential scanning calorimetry, and thermal gravimetric analyses. It was found that some polymers can be dispersed as small domains within molten metals to form a heterogeneous solid. The ability to dope Ga with large polymers opens a new avenue to electronic materials.

16.
ACS Appl Mater Interfaces ; 7(48): 26461-9, 2015 Dec 09.
Artigo em Inglês | MEDLINE | ID: mdl-26571199

RESUMO

We present a methodology which by far extends the potential applications of thin conductive silver films achieved by an electroless molecular doping process of the metal with any of the endless functional molecules that the large library of organic molecules offer. The resulting metallic films within which the molecule is entrapped--molecule@Ag--carry both the classical chemical and physical properties of silver films, as well as the function of the entrapped molecule. Raman measurements of the organic molecules from within the silver films provide the first spectroscopic observations from within silver, and clearly show that entrapment, a three-dimensional process, and adsorption, a two-dimensional process, on silver films are distinctly different processes. Three organic molecules, the cationic Neutral red, the anionic Congo red, and the antibacterial agent chlorhexidine digluconate (CH), were used to demonstrate the generality of this method for various types of molecules. We studied the sensitivity of the film conductivity to the type of the molecule entrapped within the film, to its concentration, and to temperature. Dual functionality was demonstrated with CH@Ag films, which are both conductive and have prolonged and high antibacterial activity, a combination of properties that has been unknown so far.

17.
Sci Rep ; 5: 14411, 2015 Sep 23.
Artigo em Inglês | MEDLINE | ID: mdl-26394694

RESUMO

We describe a so-far unknown route for renaturing denatured enzymes, namely subjecting the denatured enzyme to an oxide sol-gel transition. The phenomenon was revealed in a detailed study of denatured carbonic anhydrase which was subjected to an alumina sol-gel transition, up to the thermally stabilizing entrapment in the final xerogel. Remarkably, not only that the killed enzyme regained its activity during the sol-gel process, but its activity increased to 180% of the native enzyme. To the best of our knowledge, this is the first report of enhanced activity following by renaturing (a "Phoenix effect"). Kinetic study which revealed a five-orders of magnitude (!) increase in the Arrhenius prefactor upon entrapment compared to solution. Circular dichroism analysis, differential scanning calorimetry, zeta potential analyses as well as synchronous fluorescence measurements, all of which were used to characterize the phenomenon, are consistent with a proposed mechanism which is based on the specific orienting interactions of the active site of the enzyme with respect to the alumina interface and its pores network.


Assuntos
Anidrases Carbônicas/metabolismo , Domínio Catalítico/fisiologia , Ativação Enzimática , Transição de Fase , Renaturação Proteica , Óxido de Alumínio/química , Animais , Varredura Diferencial de Calorimetria , Bovinos , Dicroísmo Circular , Reativadores Enzimáticos , Nanopartículas/química , Espectrometria de Fluorescência
18.
Sci Rep ; 5: 9555, 2015 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-25906433

RESUMO

We report a previously unrecognized mechanism for the prolonged action of biocidal agents, which we denote as the zombies effect: biocidally-killed bacteria are capable of killing living bacteria. The concept is demonstrated by first killing Pseudomonas aeruginosa PAO1 with silver nitrate and then challenging, with the dead bacteria, a viable culture of the same bacterium: Efficient antibacterial activity of the killed bacteria is observed. A mechanism is suggested in terms of the action of the dead bacteria as a reservoir of silver, which, due to Le-Chatelier's principle, is re-targeted to the living bacteria. Langmuirian behavior, as well as deviations from it, support the proposed mechanism.


Assuntos
Antibacterianos/farmacologia , Pseudomonas aeruginosa/efeitos dos fármacos , Nitrato de Prata/farmacologia , Antibacterianos/química , Espectrometria de Massas , Microscopia Eletrônica de Transmissão , Nitrato de Prata/química
19.
Proteins ; 83(4): 722-34, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25354765

RESUMO

The majority of protein oligomers form clusters which are nearly symmetric. Understanding of that imperfection, its origins, and perhaps also its advantages requires the conversion of the currently used vague qualitative descriptive language of the near-symmetry into an accurate quantitative measure that will allow to answer questions such as: "What is the degree of symmetry deviation of the protein?," "how do these deviations compare within a family of proteins?," and so on. We developed quantitative methods to answer this type of questions, which are capable of analyzing the whole protein, its backbone or selected portions of it, down to comparison of symmetry-related specific amino-acids, and which are capable of visualizing the various levels of symmetry deviations in the form of symmetry maps. We have applied these methods on an extensive list of homomers and heteromers and found that apparently all proteins never reach perfect symmetry. Strikingly, even homomeric protein clusters are never ideally symmetric. We also found that the main burden of symmetry distortion is on the amino-acids near the symmetry axis; that it is mainly the more hydrophilic amino-acids that take place in symmetry-distortive interactions; and more. The remarkable ability of heteromers to preserve near-symmetry, despite the different sequences, was also shown and analyzed. The comprehensive literature on the suggested advantages symmetric oligomerizations raises a yet-unsolved key question: If symmetry is so advantageous, why do proteins stop shy of perfect symmetry? Some tentative answers to be tested in further studies are suggested in a concluding outlook.


Assuntos
Conformação Proteica , Proteínas/química , Proteínas/metabolismo , Modelos Moleculares , Subunidades Proteicas/química , Subunidades Proteicas/metabolismo
20.
J Colloid Interface Sci ; 431: 157-64, 2014 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-24996025

RESUMO

Three-dimensional porous materials are routinely prepared from molecular precursors. We describe here a study of a much less explored route, namely of using of sub-micron particles as building blocks which are reacted with each other to form covalent porous materials. The motivation for such an approach is the expectation that shifting from molecules to particles is a potential source of new type of 3D-covalent porosity. This was indeed proven by employing two covalent linking reactions: Radical-initiated cross-linking of hybrid particles of polyethylene@silica (PE@silica), and the bridging of PE@aminosilica particles with the bi-functional suberoyl dichloride in a condensation-aggregation reaction. These resulted in the mesoporous materials (XPE@SiO2)n and (PE@amidosilica)n, respectively. The resulting mesoporous materials were investigated in detail, and the kinetics of their formation was followed by various methodologies. SEM shows that the geometry of the covalently aggregated particles is different from simple physical aggregation, and these stable structures could be achieved only through the strong covalent bonds. Real-time movies monitoring (links are provided) allowed the direct follow-up of the radical processes and condensation-polymerizations and identify their different routes. Applications in the fields of separation, supports for catalysis, and matrices for release, are envisaged.

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