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1.
Mult Scler ; : 1352458519845287, 2019 May 13.
Artigo em Inglês | MEDLINE | ID: mdl-31079539

RESUMO

BACKGROUND: Somatosensory temporal discrimination threshold (STDT) is altered in multiple sclerosis (MS). In healthy subjects (HS), voluntary movement modulates the STDT through mechanisms of subcortical sensory gating. OBJECTIVE: With neurophysiological and magnetic resonance imaging (MRI) techniques, we investigated sensory gating and sensorimotor integration in MS. METHODS: We recruited 38 relapsing-remitting multiple sclerosis (RR-MS) patients with no-to-mild disability and 33 HS. We tested STDT at rest and during index finger abductions and recorded the movement kinematics. Participants underwent a 3T MRI protocol. RESULTS: Patients exhibited higher STDT values and performed slower finger movements than HS. During voluntary movement, STDT values increased in both groups, albeit to a lesser extent in patients, while the mean angular velocity of finger movements decreased in patients alone. Patients had a smaller volume of the thalamus, pallidum and caudate nucleus, and displayed higher mean diffusivity in the putamen, pallidum and thalamus. STDT correlated with thalamic volume while mean angular velocity correlated with putaminal volume. Changes in mean angular velocity during sensorimotor integration inversely correlated with mean diffusivity in the thalamus and pallidum. Changes in STDT and velocity were associated with fatigue score. CONCLUSION: Altered STDT and sensorimotor integration are related to structural damage in the thalamus and basal ganglia in MS and likely to affect motor performance.

2.
Phys Chem Chem Phys ; 20(25): 17132-17140, 2018 Jun 27.
Artigo em Inglês | MEDLINE | ID: mdl-29897359

RESUMO

Furan derivatives, potentially carcinogenic to humans, can be formed, in addition to carbohydrates and other sources, from the degradation of ascorbic acid (AA). At present, the mechanisms involved in the ascorbic acid degradation are not yet fully understood. In this study, we reported a gas-phase investigation, performed using Triple Quadrupole (TQ/MS) and Ion Trap Mass Spectrometry (QIT/MS) together with quantum mechanical calculations at the B3LYP/6-31+G(d,p) level of theory, on the non-oxidative degradation mechanism of l-ascorbic acid (AA) to furan derivatives. Gaseous protonated ascorbic acid ions, the AAH+ ionic reagents, were generated by Electrospray Ionization (ESI) of an aqueous AA solution added with a mild protonation reagent. The Collisionally Induced Dissociation (CID) mass spectra of the AAH+ ions displayed gaseous fragment ions corresponding to the degradation intermediates and reaction products, which were structurally characterized and identified. Precise mechanistic insights were achieved by using l-[1-13C]-AA. On the basis of experimental and computational results, the gas phase non-oxidative acid catalyzed degradation mechanism of ascorbic acid is proposed, a benchmark point for the comprehension of the mechanism in the condensed phase.

3.
Mar Drugs ; 15(11)2017 Nov 02.
Artigo em Inglês | MEDLINE | ID: mdl-29099042

RESUMO

The electrochemical response of four natural cytotoxic thiazinoquinones isolated from the Aplidium species was studied using conventional solution-phase and solid-state techniques, based on the voltammetry of immobilized particles methodology. The interaction with O2 and electrochemically generated reactive oxygen species (ROS) was electrochemically monitored. At the same time, a molecular modeling study including density functional theory (DFT) calculations was performed in order to analyze the conformational and electronic properties of the natural thiazinoquinones, as well as those of their reduced intermediates. The obtained electrochemical and computational results were analyzed and correlated to cytotoxic activity of these compounds, highlighting some features possibly related to their mechanism of action.


Assuntos
Organismos Aquáticos , Quinonas/química , Espécies Reativas de Oxigênio/química , Urocordados , Animais , Eletroquímica
4.
J Mass Spectrom ; 51(12): 1146-1151, 2016 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-27600482

RESUMO

In order to investigate the gas-phase mechanisms of the acid catalyzed degradation of ascorbic acid (AA) to furan, we undertook a mass spectrometric (ESI/TQ/MS) and theoretical investigation at the B3LYP/6-31 + G(d,p) level of theory. The gaseous reactant species, the protonated AA, [C6 H8 O6 ]H+ , were generated by electrospray ionization of a 10-3 M H2 O/CH3 OH (1 : 1) AA solution. In order to structurally characterize the gaseous [C6 H8 O6 ]H+ ionic reactants, we estimated the proton affinity and the gas-phase basicity of AA by the extended Cooks's kinetic method and by computational methods at the B3LYP/6-31 + G(d,p) level of theory. As expected, computational results identify the carbonyl oxygen atom (O2) of AA as the preferred protonation site. From the experimental proton affinity of 875.0 ± 12 kJ mol-1 and protonation entropy ΔSp 108.9 ± 2 J mol-1 K-1 , a gas-phase basicity value of AA of 842.5 ± 12 kJ mol-1 at 298 K was obtained, which is in agreement with the value issuing from quantum mechanical computations. Copyright © 2016 John Wiley & Sons, Ltd.


Assuntos
Ácido Ascórbico/análise , Ácido Ascórbico/química , Gases/análise , Gases/química , Íons/análise , Íons/química , Cinética , Espectrometria de Massas , Modelos Moleculares
5.
Mol Inform ; 35(8-9): 309-25, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-27546035

RESUMO

Computer-aided drug discovery plays a strategic role in the development of new potential therapeutic agents. Nevertheless, the modeling of biological systems still represents a challenge for computational chemists and at present a single computational method able to face such challenge is not available. This prompted us, as computational medicinal chemists, to develop in-house methodologies by mixing various bioinformatics and computational tools. Importantly, thanks to multi-disciplinary collaborations, our computational studies were integrated and validated by experimental data in an iterative process. In this review, we describe some recent applications of such integrated approaches and how they were successfully applied in i) the search of new allosteric inhibitors of protein-protein interactions and ii) the development of new redox-active antimalarials from natural leads.


Assuntos
Antimaláricos/química , Animais , Antimaláricos/farmacologia , Antimaláricos/uso terapêutico , Biologia Computacional/métodos , Desenho Assistido por Computador , Desenho de Fármacos , Descoberta de Drogas/métodos , Humanos , Oxirredução/efeitos dos fármacos , Mapas de Interação de Proteínas/efeitos dos fármacos
6.
J Chem Theory Comput ; 12(10): 4925-4933, 2016 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-27571168

RESUMO

We simulated the intrinsic reaction path of the Green Fluorescent Protein (GFP) proton shuttle in both the ground state (S0) and first singlet excited state (S1), accounting for the main energetic and steric effects of the protein in a convenient model including the chromophore, the crystallographic water, and the residues directly involved in the proton transfer event. We adopted density functional theory (DFT) and time-dependent density functional theory (TD-DFT) levels to define the potential energy surfaces of the two electronic states, and we compared results obtained by the Damped Velocity Verlet and the Hessian-based Predictor-Corrector integrators of the intrinsic reaction coordinate, which gave a comparable and consistent picture of the mechanism. We show that, at S1, the GFP proton transfer becomes favored, with respect to S0, as suggested by the experimental evidence. As an important finding, this change is strictly related to the rearrangement of the hydrogen bond network composing the reaction path, which, in S1, relaxes to a tighter and planar configuration, as a consequence of the photoinduced relaxation in the GFP chromophore structure, thus prompting more effectively for the proton shuttle. Therefore, we give an unprecedented direct proof of the key role played by the photoinduced structural relaxation of the GFP on the chromophore photoacidity, validating, in particular, the hypothesis of Fang and co-workers [Nature 2009, 462, 200].


Assuntos
Proteínas de Fluorescência Verde/química , Proteínas de Fluorescência Verde/metabolismo , Ligação de Hidrogênio , Modelos Moleculares , Prótons , Teoria Quântica , Termodinâmica , Água/química
7.
J Chem Theory Comput ; 11(9): 4364-9, 2015 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-26575929

RESUMO

Herein, we report a comprehensive benchmark of C≡N stretching vibrations computed at harmonic and anharmonic levels with the aim of proposing and validating a reliable computational strategy to get accurate results for this puzzling vibrational mode without any ad hoc scaling factor. Anharmonic calculations employing second-order vibrational perturbation theory provide very good results when performed using the B2PLYP double-hybrid functional, in conjunction with an extended basis set and supplemented by semiempirical dispersion contributions. For larger systems, B2PLYP harmonic frequencies, together with B3LYP anharmonic corrections, offer a very good compromise between accuracy and computational cost without the need of any empirical scaling factor.


Assuntos
Nitrilos/química , Teoria Quântica , Estrutura Molecular , Espectrofotometria Infravermelho , Vibração
8.
J Chem Theory Comput ; 11(9): 4342-63, 2015 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-26575928

RESUMO

The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC calculations.


Assuntos
Ácido Pirúvico/química , Teoria Quântica , Estrutura Molecular , Espectrofotometria Infravermelho
9.
Phys Chem Chem Phys ; 12(37): 11697-709, 2010 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-20714476

RESUMO

The popular AMBER force-field has been extended to provide an accurate description of large and flexible nitroxide free-radicals in condensed phases. New atom types have been included, and relevant parameters have been fitted based on geometries, vibrational frequencies and potential energy surfaces computed at the DFT level for several different classes of nitroxides, both in vacuo and in different solvents. The resulting computational tool is capable of providing reliable structures, vibrational frequencies, relative energies and spectroscopic observables for large and flexible nitroxide systems, including those typically used as spin labels. The modified force field has been employed in the context of an integrated approach, based on classical molecular dynamics and discrete-continuum solvent models, for the investigation of environmental and short-time dynamic effects on the hyperfine and gyromagnetic tensors of PROXYL, TEMPO and INDCO spin probes. The computed magnetic parameters are in very good agreement with the available experimental values, and the procedure allows for an unbiased evaluation of the role of different effects in tuning the overall EPR observables.


Assuntos
Óxidos de Nitrogênio/química , Espectroscopia de Ressonância de Spin Eletrônica , Hidrocarbonetos Aromáticos/química , Modelos Moleculares , Solventes , Marcadores de Spin
10.
Magn Reson Chem ; 48 Suppl 1: S11-22, 2010 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-20625984

RESUMO

Magnetic spectroscopic techniques such as electron paramagnetic resonance (EPR) and paramagnetic NMR (PNMR) are valuable tools for understanding the structure and dynamics of complex systems such as, for example, biomolecules or nanomaterials labeled with suitable free radicals. Unfortunately, such spectra do not give direct access to the radical structure because of the subtle interplay between several different effects not easily separable and evaluable by experimentalists alone. In this respect, computational spectroscopy is becoming an essential and versatile tool for the assignment and interpretation of experimental spectra. In this article, the new integrated computational approaches developed in the recent years in our research group are reviewed. Such approaches have been applied to two widely used spin probes showing that proper account of stereo-electronic, environmental and dynamical effects leads to magnetic properties in remarkable agreement with experimental results.


Assuntos
Simulação por Computador , Óxidos N-Cíclicos/química , Espectroscopia de Ressonância de Spin Eletrônica , Radicais Livres/química , Espectroscopia de Ressonância Magnética , Soluções , Integração de Sistemas
11.
Chemistry ; 16(21): 6234-42, 2010 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-20411542

RESUMO

The room-temperature C-H activation of ethane by metal-free SO(2)(*+) radical cations has been investigated under different pressure regimes by mass spectrometric techniques. The major reaction channel is the conversion of ethane to ethylene accompanied by the formation of H(2)SO(2)(*+), the radical cation of sulfoxylic acid. The mechanism of the double C-H activation, in the absence of the single activation product HSO(2)(+), is elucidated by kinetic studies and quantum chemical calculations. Under near single-collision conditions the reaction occurs with rate constant k=1.0 x 10(-9) (+/-30%) cm(3) s(-1) molecule(-1), efficiency=90%, kinetic isotope effect k(H)/k(D)=1.1, and partial H/D scrambling. The theoretical analysis shows that the interaction of SO(2)(*+) with ethane through an oxygen atom directly leads to the C-H activation intermediate. The interaction through sulfur leads to an encounter complex that rapidly converts to the same intermediate. The double C-H activation occurs by a reaction path that lies below the reactants and involves intermediates separated by very low energy barriers, which include a complex of the ethyl cation suitable to undergo H/D scrambling. Key issues in the observed reactivity are electron-transfer processes, in which a crucial role is played by geometrical constraints. The work shows how mechanistic details disclosed by the reactions of metal-free electrophiles may contribute to the current understanding of the C-H activation of ethane.


Assuntos
Carbono/química , Cátions/química , Etano/química , Hidrogênio/química , Dióxido de Enxofre/química , Metais/química , Teoria Quântica , Temperatura
12.
Phys Chem Chem Phys ; 12(15): 3741-6, 2010 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-20358068

RESUMO

An integrated computational strategy for the evaluation of reliable structures and magnetic properties of spin probes and spin labels has been extended to aromatic species. From an electronic point of view, delocalization of the unpaired electron density over aromatic moieties reduces significantly the computed nitrogen isotropic hyperfine coupling constant (A(N)) with respect to values characteristic of aliphatic nitroxides. Solvent effects in not too high polarity media are quite small, but not negligible. At this stage computed A(N) are lower than their experimental counterparts by more than 1 G. Inclusion of vibrational averaging effects by molecular dynamics simulations with a new reliable force field restores full agreement with experiment pointing out the limits of static approaches irrespective of the sophistication of the electronic quantum mechanical method. The generality and computational effectiveness of the proposed integrated approach paves the route toward a reliable analysis of the interplay of stereo-electronic, environmental, and dynamical effects in tuning the properties of large flexible magnetic systems of biological and technological interest.


Assuntos
Óxidos N-Cíclicos/química , Elétrons , Marcadores de Spin , Espectroscopia de Ressonância de Spin Eletrônica , Simulação de Dinâmica Molecular , Teoria Quântica , Solventes/química , Estereoisomerismo
13.
Org Biomol Chem ; 8(4): 846-56, 2010 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-20135043

RESUMO

A multidisciplinary approach, based on molecular dynamics/mechanics, ab initio calculations, dynamic docking studies, and chemical reactions, has been employed to gain insight into the mechanism of the antimalarial action of plakortin and dihydroplakortin, simple 1,2-dioxanes isolated from the sponge Plakortis simplex. Our results show that these molecules, after interaction of the endoperoxide bond with Fe(ii), likely coming from the heme molecule, give rise to the formation of an oxygen radical, followed by rearrangement to give a carbon radical centered on the "western" alkyl side-chain. The carbon radicals generated on the side-chain, amenable for intermolecular reactions, should represent the toxic intermediates responsible for subsequent reactions leading to plasmodium death. The minimal structural requirements necessary for the activity of this class of antimalarial agents have been identified and discussed throughout the paper.


Assuntos
Antimaláricos/farmacologia , Plasmodium falciparum/efeitos dos fármacos , Poríferos/química , Animais , Dioxanos/química , Dioxanos/farmacologia , Dioxinas/química , Dioxinas/toxicidade , Modelos Químicos , Testes de Sensibilidade Parasitária , Plakortis/química , Relação Quantitativa Estrutura-Atividade , Relação Estrutura-Atividade
14.
J Phys Chem A ; 113(52): 15150-5, 2009 Dec 31.
Artigo em Inglês | MEDLINE | ID: mdl-19711967

RESUMO

In the present paper we report the key results of a comprehensive computational study aimed at investigating the dependence of the singlet-triplet energy gap in phenyl-bridged bis-nitroxide diradicals, on the basis set and on soft structural parameters like torsion and pyramidalization. We have compared the BS-DFT technique with the post-Hartree-Fock DDCI2 multireference approach. With this latter method we have also studied the different role that sigma and pi core and virtual orbitals have in the resulting singlet-triplet energy gap.The results obtained represent one step forward in the definition of a protocol for an efficient and reliable computation of spin-spin coupling in diradical systems.


Assuntos
Magnetismo , Conformação Molecular , Óxidos de Nitrogênio/química , Teoria Quântica , Modelos Moleculares , Padrões de Referência , Termodinâmica
15.
J Phys Chem B ; 113(26): 9026-34, 2009 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-19507811

RESUMO

An integrated experimental and computational approach was used to compare the properties of representative molecules containing intrabridgehead nitrogen atoms with those of the corresponding radical cations issuing from one-electron oxidation with the aim of unraveling the characteristics of the three-electron sigma-bonds formed in the open-shell species. From a quantitative point of view, last-generation density functional methods coupled with proper basis sets and, when needed, continuum models for describing bulk solvent effects confirm their reliability for the computation of structures and magnetic properties of organic free radicals. From an interpretative point of view, different hybridizations of nitrogen atoms tuned by their chemical environment lead to markedly different magnetic properties that represent reliable and sensitive probes of structural and electronic characteristics.


Assuntos
Magnetismo , Nitrogênio/química , Piridinas/química , Teoria Quântica , Dimerização , Eletroquímica , Espectroscopia de Ressonância de Spin Eletrônica , Radicais Livres/química , Oxirredução
16.
J Chem Theory Comput ; 5(1): 192-9, 2009 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-26609832

RESUMO

Calculations on a large set of free radicals containing atoms of the second and third row show that the computational model defined by the new N07D basis set and hybrid density functionals (B3LYP and PBE0) provides remarkably accurate g-tensor values at reasonable computational costs. Since in previous works it has been shown that the same computational model delivers reliable results also for structural parameters and hyperfine couplings, the route seems paved toward full a priori computation of EPR spectra of large free radicals both in vacuo and in condensed phases.

17.
Org Biomol Chem ; 6(18): 3300-5, 2008 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-18802636

RESUMO

The role of local geometric and stereo-electronic effects in tuning the preference for different cross-linked adducts between thymine and purinic bases has been analyzed by a computational approach rooted in density functional theory. Our study points out that G--T and T--G tandem lesions are produced according to the same mechanism as A--T and T--A intrastrand adducts, and in both cases purine--T adducts are preferred rather than the opposite sequences. Moreover, use of conceptual DFT tools allows the rationalization of the preferential occurrence of G--T and T--G tandem lesions in place of their A--T and T--A counterparts.


Assuntos
Elétrons , Guanina/química , Radical Hidroxila/química , Timina/química , Gases/química , Cinética , Modelos Moleculares , Estrutura Molecular , Oxirredução , Termodinâmica
18.
J Chem Phys ; 128(2): 024501, 2008 Jan 14.
Artigo em Inglês | MEDLINE | ID: mdl-18205453

RESUMO

Electron spin resonance (ESR) measurements are highly informative on the dynamic behavior of molecules, which is of fundamental importance to understand their stability, biological functions and activities, and catalytic action. The wealth of dynamic information which can be extracted from a continuous wave electron spin resonance (cw-ESR) spectrum can be inferred by a basic theoretical approach defined within the stochastic Liouville equation formalism, i.e., the direct inclusion of motional dynamics in the form of stochastic (Fokker-Planck/diffusive) operators in the super Hamiltonian H governing the time evolution of the system. Modeling requires the characterization of magnetic parameters (e.g., hyperfine and Zeeman tensors) and the calculation of ESR observables in terms of spectral densities. The magnetic observables can be pursued by the employment of density functional theory which is apt, provided that hybrid functionals are employed, for the accurate computation of structural properties of molecular systems. Recently, an ab initio integrated computational approach to the in silico interpretation of cw-ESR spectra of multilabeled systems in isotropic fluids has been discussed. In this work we present the extension to the case of nematic liquid crystalline environments by performing simulations of the ESR spectra of the prototypical nitroxide probe 4-(hexadecanoyloxy)-2,2,6,6-tetramethylpiperidine-1-oxy in isotropic and nematic phases of 5-cyanobiphenyl. We first discuss the basic ingredients of the integrated approach, i.e., (1) determination of geometric and local magnetic parameters by quantum-mechanical calculations, taking into account the solvent and, when needed, the vibrational averaging contributions; (2) numerical solution of a stochastic Liouville equation in the presence of diffusive rotational dynamics, based on (3) parameterization of diffusion rotational tensor provided by a hydrodynamic model. Next we present simulated spectra with minimal resorting to fitting procedures, proving that the combination of sensitive ESR spectroscopy and sophisticated modeling can be highly helpful in providing three-dimensional structural and dynamic information on molecular systems in anisotropic environments.


Assuntos
Compostos de Bifenilo/química , Nitrilos/química , Piperidinas/química , Espectroscopia de Ressonância de Spin Eletrônica/métodos , Conformação Molecular
19.
J Chem Theory Comput ; 4(5): 751-64, 2008 May.
Artigo em Inglês | MEDLINE | ID: mdl-26621090

RESUMO

Extensive calculations on a large set of free radicals containing atoms of the second and third row show that the B3LYP/N07D computational model provides remarkably accurate structural parameters and magnetic tensors at reasonable computational costs. The key of this success is the optimization of core-valence s functions for hyperfine coupling constants, while retaining (and even improving) the good performances of the parent 6-31+G(d,p) basis set for valence properties through reoptimization of polarization and diffuse p functions.

20.
J Am Chem Soc ; 129(36): 11248-58, 2007 Sep 12.
Artigo em Inglês | MEDLINE | ID: mdl-17705490

RESUMO

In this work we present an effective and flexible computational approach, which is the result of an ongoing development in our groups, allowing the complete a priori simulation of the ESR spectra of complex systems in solution. The usefulness and reliability of the method are demonstrated on the very demanding playground represented by the tuning of the equilibrium between 3(10)- and alpha-helices of polypeptides by different solvents. The starting point is the good agreement between computed and X-ray diffraction structures for the 3(10)-helix adopted by the double spin-labelled heptapeptide Fmoc-(Aib-Aib-TOAC)2-Aib-OMe. Next, density functional computations, including dispersion interactions and bulk solvent effects, suggest another energy minimum corresponding to an alpha-helix in polar solvents, which, eventually, becomes the most stable structure. Computation of magnetic and diffusion tensors provides the basic ingredients for the building of complete spectra by methods rooted in the Stochastic Liouville Equation (SLE). The remarkable agreement between computed and experimental spectra at different temperatures allowed us to identify helical structures in the various solvents. The generality of the computational strategy and its implementation in effective and user-friendly computer codes pave the route toward systematic applications in the field of biomolecules and other complex systems.


Assuntos
Simulação por Computador , Peptídeos/química , Marcadores de Spin , Modelos Moleculares , Estrutura Secundária de Proteína
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