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1.
Science ; 369(6510): 1432-1433, 2020 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-32943513
2.
Science ; 369(6507): 1054-1055, 2020 08 28.
Artigo em Inglês | MEDLINE | ID: mdl-32855324
3.
Nat Commun ; 11(1): 4348, 2020 08 28.
Artigo em Inglês | MEDLINE | ID: mdl-32859910

RESUMO

The interpretation of molecular vibrational spectroscopic signals in terms of atomic motion is essential to understand molecular mechanisms and for chemical characterization. The signals are usually assigned after harmonic normal mode analysis, even if molecular vibrations are known to be anharmonic. Here we obtain the quantum anharmonic vibrational eigenfunctions of the 11-atom protonated glycine molecule and we calculate the density distribution of its nuclei and its geometry parameters, for both the ground and the O-H stretch excited states, using our semiclassical method based on ab initio molecular dynamics trajectories. Our quantum mechanical results describe a molecule elongated and more flexible with respect to what previously thought. More importantly, our method is able to assign each spectral peak in vibrational spectroscopy by showing quantitatively how normal modes involving different functional groups cooperate to originate that spectroscopic signal. The method will possibly allow for a better rationalization of experimental spectroscopy.


Assuntos
Glicina/química , Simulação de Dinâmica Molecular , Vibração , Estrutura Molecular , Teoria Quântica , Espectrofotometria Infravermelho , Termodinâmica
4.
Nature ; 583(7814): 31-32, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32612218

Assuntos
Teoria Quântica
6.
J Mol Graph Model ; 100: 107695, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32702590

RESUMO

COVID-19, a disease caused by a new strain of coronavirus (SARS-CoV-2) originating from Wuhan, China, has now spread around the world, triggering a global pandemic, leaving the public eagerly awaiting the development of a specific medicine and vaccine. In response, aggressive efforts are underway around the world to overcome COVID-19. In this study, referencing the data published on the Protein Data Bank (PDB ID: 7BV2) on April 22, we conducted a detailed analysis of the interaction between the complex structures of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 and Remdesivir, an antiviral drug, from the quantum chemical perspective based on the fragment molecular orbital (FMO) method. In addition to the hydrogen bonding and intra-strand stacking between complementary strands as seen in normal base pairs, Remdesivir bound to the terminus of an primer-RNA strand was further stabilized by diagonal π-π stacking with the -1A' base of the complementary strand and an additional hydrogen bond with an intra-strand base, due to the effect of chemically modified functional group. Moreover, stable OH/π interaction is also formed with Thr687 of the RdRp. We quantitatively revealed the exhaustive interaction within the complex among Remdesivir, template-primer-RNA, RdRp and co-factors, and published the results in the FMODB database.


Assuntos
Monofosfato de Adenosina/análogos & derivados , Alanina/análogos & derivados , Antivirais/química , Betacoronavirus/química , RNA Replicase/química , RNA Viral/química , Proteínas Virais/química , Monofosfato de Adenosina/química , Alanina/química , Motivos de Aminoácidos , Betacoronavirus/enzimologia , Sítios de Ligação , Bases de Dados de Proteínas , Ligação de Hidrogênio , Simulação de Acoplamento Molecular , Conformação de Ácido Nucleico , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Estrutura Secundária de Proteína , Teoria Quântica , RNA Replicase/antagonistas & inibidores , RNA Viral/antagonistas & inibidores , Termodinâmica , Proteínas Virais/antagonistas & inibidores
7.
PLoS One ; 15(7): e0236188, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32701995

RESUMO

Microalgae and cyanobacteria are considered as important model organisms to investigate the biology of photosynthesis; moreover, they are valuable sources of biomolecules for several biotechnological applications. Understanding the species-specific traits of photosynthetic electron transport is extremely important, because it contributes to the regulation of ATP/NADPH ratio, which has direct/indirect links to carbon fixation and other metabolic pathways and thus overall growth and biomass production. In the present work, a cuvette-based setup is developed, in which a combination of measurements of dissolved oxygen, pH, chlorophyll fluorescence and NADPH kinetics can be performed without disturbing the physiological status of the sample. The suitability of the system is demonstrated using a model cyanobacterium Synechocystis sp. PCC6803, as well as biofuel-candidate microalgae species, such as Chlorella sorokiniana, Dunaliella salina and Nannochloropsis limnetica undergoing inorganic carbon (Ci) limitation. Inorganic carbon limitation, induced by photosynthetic Ci uptake under continuous illumination, caused a decrease in the effective quantum yield of PSII (Y(II)) and loss of oxygen-evolving capacity in all species investigated here; these effects were largely recovered by the addition of NaHCO3. Detailed analysis of the dark-light and light-dark transitions of NADPH production/uptake and changes in chlorophyll fluorescence kinetics revealed species- and condition-specific responses. These responses indicate that the impact of decreased Calvin-Benson cycle activity on photosynthetic electron transport pathways involving several sections of the electron transport chain (such as electron transfer via the QA-QB-plastoquinone pool, the redox state of the plastoquinone pool) can be analyzed with high sensitivity in a comparative manner. Therefore, the integrated system presented here can be applied for screening for specific traits in several significant species at different stages of inorganic carbon limitation, a condition that strongly impacts primary productivity.


Assuntos
Carbono/farmacologia , Cianobactérias/fisiologia , Compostos Inorgânicos/farmacologia , Microalgas/fisiologia , Fotossíntese , Chlorella/efeitos dos fármacos , Chlorella/fisiologia , Clorofila/metabolismo , Cianobactérias/efeitos dos fármacos , Transporte de Elétrons/efeitos dos fármacos , Fluorescência , Cinética , Microalgas/efeitos dos fármacos , NADP/metabolismo , Oxigênio/metabolismo , Fotossíntese/efeitos dos fármacos , Complexo de Proteína do Fotossistema II/metabolismo , Teoria Quântica , Synechocystis/efeitos dos fármacos , Synechocystis/fisiologia
10.
Nature ; 582(7811): 186-187, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32528088
11.
Nature ; 583(7815): 314-318, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32499654

RESUMO

Light-driven sodium pumps actively transport small cations across cellular membranes1. These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience. Although the resting state structures of the prototypical sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) have been solved2,3, it is unclear how structural alterations over time allow sodium to be translocated against a concentration gradient. Here, using the Swiss X-ray Free Electron Laser4, we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds. Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds. Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion binds transiently close to the retinal within one millisecond. In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit. These results provide direct molecular insight into the dynamics of active cation transport across biological membranes.


Assuntos
Flavobacteriaceae/química , Rodopsinas Microbianas/química , Rodopsinas Microbianas/efeitos da radiação , ATPase Trocadora de Sódio-Potássio/química , ATPase Trocadora de Sódio-Potássio/efeitos da radiação , Sítios de Ligação , Cristalografia , Elétrons , Transporte de Íons , Isomerismo , Lasers , Prótons , Teoria Quântica , Retinaldeído/química , Retinaldeído/metabolismo , Bases de Schiff/química , Sódio/metabolismo , Análise Espectral , Eletricidade Estática , Fatores de Tempo
12.
Proc Natl Acad Sci U S A ; 117(26): 14682-14687, 2020 06 30.
Artigo em Inglês | MEDLINE | ID: mdl-32546523

RESUMO

We predict and experimentally verify an entoptic phenomenon through which humans are able to perceive and discriminate optical spin-orbit states. Direct perception and discrimination of these particular states of light with polarization-coupled spatial modes is possible through the observation of distinct profiles induced by the interaction between polarization topologies and the radially symmetric dichroic elements that are centered on the foveola in the macula of the human eye. A psychophysical study was conducted where optical states with a superposition of right and left circular polarization coupled to two different orbital angular momentum (OAM) values ([Formula: see text] and [Formula: see text]) were directed onto the retina of participants. The number of azimuthal fringes that a human sees when viewing the spin-orbit states is shown to be equal to the number (N) of radial lines in the corresponding polarization profile of the beam, where [Formula: see text] The participants were able to correctly discriminate between two states carrying OAM [Formula: see text] and differentiated by [Formula: see text] and [Formula: see text], with an average success probability of 77.6% (average sensitivity [Formula: see text], [Formula: see text], [Formula: see text]). These results enable methods of robustly characterizing the structure of the macula, probing retina signaling pathways, and conducting experiments with human detectors and optical states with nonseparable modes.


Assuntos
Fenômenos Fisiológicos Oculares , Retina/fisiologia , Percepção Visual/fisiologia , Humanos , Luz , Estimulação Luminosa , Teoria Quântica
14.
Science ; 368(6491): 582-583, 2020 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-32381705
15.
J Phys Chem Lett ; 11(12): 4785-4790, 2020 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-32463239

RESUMO

The severe acute respiratory syndrome coronavirus (SARS-CoV-2) pandemic is setting the global health crisis of our time, causing a devastating societal and economic burden. An idiosyncratic trait of coronaviruses is the presence of spike glycoproteins on the viral envelope, which mediate the virus binding to specific host receptor, enabling its entry into the human cells. In spite of the high sequence identity of SARS-CoV-2 with its closely related SARS-CoV emerged in 2002, the atomic-level determinants underlining the molecular recognition of SARS-CoV-2 to the angiotensin-converting enzyme 2 (ACE2) receptor and, thus, the rapid virus spread into human body, remain unresolved. Here, multi-microsecond-long molecular dynamics simulations enabled us to unprecedentedly dissect the key molecular traits liable of the higher affinity/specificity of SARS-CoV-2 toward ACE2 as compared to SARS-CoV. This supplies a minute per-residue contact map underlining its stunningly high infectivity. Harnessing this knowledge is pivotal for urgently developing effective medical countermeasures to face the ongoing global health crisis.


Assuntos
Betacoronavirus/metabolismo , Glicoproteínas/metabolismo , Simulação de Dinâmica Molecular , Proteínas Virais/metabolismo , Motivos de Aminoácidos , Infecções por Coronavirus/patologia , Infecções por Coronavirus/virologia , Glicoproteínas/química , Humanos , Ligação de Hidrogênio , Pandemias , Peptidil Dipeptidase A/química , Peptidil Dipeptidase A/metabolismo , Pneumonia Viral/patologia , Pneumonia Viral/virologia , Ligação Proteica , Estrutura Quaternária de Proteína , Estrutura Terciária de Proteína , Teoria Quântica , Vírus da SARS/metabolismo , Proteínas Virais/química , Ligação Viral
16.
Food Chem ; 326: 126988, 2020 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-32447162

RESUMO

In this study, a simple and quick ionic liquid- based ultrasonic-assisted microextraction (IL-UA-ME) procedure has been improved for extraction of melamine in dairy productsfollowed by UV-VIS spectrometry. For the analysis of stability and reactivity of melamine and its some metal complexes, quantum chemical parameters like frontier orbital energy-HOMO-LUMO energy gap, hardness and softness were calculated using computational chemistry tools. The results regarding to stability analysis made considering density functional theory showed that theoretical data obtained are compatible with experimentally obtained results, and Fe-melamine complex is more stable compared to others. Under optimum conditions, the linearity was in the range of 0.05-400 ng mL-1 with detection limit of 0.015 ng mL-1. Following the validation studies, recovery and relative standard deviation were obtained in range of 92.5-104.3% and 1.4-2.1%, respectively. The first research article in which experimental and theoretical studies are used together for the determination of melamine in dairy products.


Assuntos
Laticínios/análise , Líquidos Iônicos/química , Triazinas/análise , Complexos de Coordenação/química , Concentração de Íons de Hidrogênio , Limite de Detecção , Teoria Quântica , Microextração em Fase Sólida , Sonicação , Temperatura , Triazinas/química , Triazinas/isolamento & purificação
17.
Adv Exp Med Biol ; 1194: 253-261, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32468541

RESUMO

The applications of game theory in biology are numerous and include the comparison and modeling situations between bacteria, viruses, etc. This work provides insights about the connection between biology and evolving populations with classical and quantum evolutionary game theory and explains the benefits of unconventional computing methods in the study of such phenomena. In particular, the introduction of automata brings new possibilities into the decision-making process.


Assuntos
Evolução Biológica , Teoria do Jogo , Modelos Biológicos , Animais , Tomada de Decisões , Humanos , Teoria Quântica , Inquéritos e Questionários
18.
Nucleic Acids Res ; 48(11): 5825-5838, 2020 06 19.
Artigo em Inglês | MEDLINE | ID: mdl-32392301

RESUMO

We identified over 1000 instances of water-nucleobase stacking contacts in a variety of RNA molecules from a non-redundant set of crystal structures with resolution ≤3.0 Å. Such contacts may be of either the lone pair-π (lp-π) or the OH-π type, in nature. The distribution of the distances of the water oxygen from the nucleobase plane peaks at 3.5 Å for A, G and C, and approximately at 3.1-3.2 Å for U. Quantum mechanics (QM) calculations confirm, as expected, that the optimal energy is reached at a shorter distance for the lp-π interaction as compared to the OH-π one (3.0 versus 3.5 Å). The preference of each nucleobase for either type of interaction closely correlates with its electrostatic potential map. Furthermore, QM calculations show that for all the nucleobases a favorable interaction, of either the lp-π or the OH-π type, can be established at virtually any position of the water molecule above the nucleobase skeleton, which is consistent with the uniform projection of the OW atoms over the nucleobases ring we observed in the experimental occurrences. Finally, molecular dynamics simulations of a model system for the characterization of water-nucleobase stacking contacts confirm the stability of these interactions also under dynamic conditions.


Assuntos
Simulação de Dinâmica Molecular , RNA/química , Água/química , Oxigênio/química , Teoria Quântica , Termodinâmica
19.
Sci Total Environ ; 726: 138432, 2020 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-32344249

RESUMO

Tetracycline is a type of broad-spectrum, naturally occurring antibiotic that leads to several side effects, such as affecting intestinal flora and increase in bacterial resistance. The affinity of tetracycline for abiotic and biotic surfaces and metal ions is closely related to its deprotonation state and charge distribution; however, its deprotonation-protonation property remains unclear. In this study, the hydrolysis of tetracycline was investigated by combining experiments with quantum-chemical calculations. The molecular structure of the probable deprotonation states were optimized by quantum-chemical calculations, and the corresponding absorbance spectra were predicted based on frontier molecular orbital (FMO) theory. The absorbance spectra showed structure-specific features at the different deprotonation states. In addition, changes in tetracycline absorbance spectra in the pH range of 2.00-12.00 was examined by spectroscopic titration. The deprotonation was found to proceed in the order of site 3, 4, 12, and 10, which was identified by comparing the quantum-chemical calculations and experimental differential absorbance spectra (DAS). The results in this study are of great significance for further studies of the transport and fate of tetracycline in the environment.


Assuntos
Teoria Quântica , Análise Espectral Raman , Antibacterianos , Modelos Moleculares , Espectrofotometria Ultravioleta , Espectroscopia de Infravermelho com Transformada de Fourier , Tetraciclina
20.
J Vis Exp ; (158)2020 04 08.
Artigo em Inglês | MEDLINE | ID: mdl-32338653

RESUMO

The computational study of the formation and growth of atmospheric aerosols requires an accurate Gibbs free energy surface, which can be obtained from gas phase electronic structure and vibrational frequency calculations. These quantities are valid for those atmospheric clusters whose geometries correspond to a minimum on their potential energy surfaces. The Gibbs free energy of the minimum energy structure can be used to predict atmospheric concentrations of the cluster under a variety of conditions such as temperature and pressure. We present a computationally inexpensive procedure built on a genetic algorithm-based configurational sampling followed by a series of increasingly accurate screening calculations. The procedure starts by generating and evolving the geometries of a large set of configurations using semi-empirical models then refines the resulting unique structures at a series of high-level ab initio levels of theory. Finally, thermodynamic corrections are computed for the resulting set of minimum-energy structures and used to compute the Gibbs free energies of formation, equilibrium constants, and atmospheric concentrations. We present the application of this procedure to the study of hydrated glycine clusters under ambient conditions.


Assuntos
Atmosfera/química , Modelos Químicos , Pressão , Teoria Quântica , Eletricidade Estática , Temperatura , Termodinâmica , Vibração
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