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1.
Appl Spectrosc ; : 37028241239977, 2024 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-38646777

RESUMO

Circular dichroism (CD) spectroscopy is an analytical technique that measures the wavelength-dependent differential absorbance of circularly polarized light and is applicable to most biologically important macromolecules, such as proteins, nucleic acids, and carbohydrates. It serves to characterize the secondary structure composition of proteins, including intrinsically disordered proteins, by analyzing their recorded spectra. Several computational tools have been developed to interpret protein CD spectra. These methods have been calibrated and tested mostly on globular proteins with well-defined structures, mainly due to the lack of reliable reference structures for disordered proteins. It is therefore still largely unclear how accurately these computational methods can determine the secondary structure composition of disordered proteins. Here, we provide such a required reference data set consisting of model structural ensembles and matching CD spectra for eight intrinsically disordered proteins. Using this set of data, we have assessed the accuracy of several published CD prediction and secondary structure estimation tools, including our own CD analysis package, SESCA. Our results show that for most of the tested methods, their accuracy for disordered proteins is generally lower than for globular proteins. In contrast, SESCA, which was developed using globular reference proteins, but was designed to be applicable to disordered proteins as well, performs similarly well for both classes of proteins. The new reference data set for disordered proteins should allow for further improvement of all published methods.

2.
Chirality ; 36(4): e23667, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38607651

RESUMO

Fluorescence-detected linear dichroism (FD-LD) enables one to collect linear dichroism spectra for oriented fluorophores in the presence of other absorbing species and light scattering. The experiment proceeds by scanning the excitation wavelength and using a filter to collect only emitted photons from the fluorophore. Thus, it has the potential to give data with enhanced selectivity and quality. By using a synchrotron radiation light source and fluorescence-detection, we show data for a range of fluorophores in different orienting environments. Film and flow-oriented FD-LD spectra were collected down to 170 nm. Even for flow-oriented liposomes, we have data collected down to 210 nm. For strongly scattering samples, for example, liposomes, FD-LD has the clear advantage that scattering is absent for the longer wavelength fluorescence photons. The collimated and smaller beam size of the synchrotron radiation also gives rise to sharper and more well-defined features in the spectra.

3.
J Chem Phys ; 160(5)2024 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-38341687

RESUMO

A synchrotron based vacuum ultraviolet absorption spectrum for γ-pyrone has been interpreted in terms of singlet excited electronic states using a variety of coupled cluster, configuration interaction, and density functional calculations. The extremely weak spectral onset at 3.557 eV shows eight vibrational peaks, which following previous analyses, are attributed to a forbidden 1A2 state. A contrasting broad peak with a maximum at 5.381 eV has a relatively high cross-section of 30 Mb; this arises from three overlapping states, where a 1A1 state dominates over progressively weaker 1B2 and 1B1 states. After fitting the second band to a polynomial Gaussian function and plotting the regular residuals over 20 vibrational peaks, we have had limited success in analyzing this fine structure. However, the small separation between these three states clearly shows that their vibrational satellites must overlap. Singlet valence and Rydberg state vibrational profiles were determined by configuration interaction using the CAM-B3LYP density functional. Vibrational analysis using both the Franck-Condon and Herzberg-Teller procedures showed that both procedures contributed to the profiles. Theoretical Rydberg states were evaluated by a highly focused CI procedure. The superposition of the lowest photoelectron spectral band on the vacuum ultraviolet spectrum near 6.4 eV shows that the 3s and 3p Rydberg states based on the 2B2 ionic state are present; those based on the other low-lying ionic state (X2B1) are destroyed by broadening; this is a dramatic extension of the broadening previously witnessed in our studies of halogenobenzenes.

4.
Chirality ; 36(3): e23654, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38419414

RESUMO

Glycerophospholipid membranes are one of the key cellular components. Still, their species-dependent composition and homochirality remain an elusive subject. In the context of the astrophysical circularly polarized light scenario likely involved in the generation of a chiral bias in meteoritic amino and sugar acids in space, and consequently in the origin of life's homochirality on Earth, this study reports the first measurements of circular dichroism and anisotropy spectra of a selection of glycerophospholipids, their chiral backbones and their analogs. The rather low asymmetry in the interaction of UV/VUV circularly polarized light with sn-glycerol-1/3-phosphate indicates that chiral photons would have been unlikely to directly induce symmetry breaking to membrane lipids. In contrast, the anisotropy spectra of d-3-phosphoglyceric acid and d-glyceraldehyde-3-phosphate unveil up to 20 and 100 times higher maximum anisotropy factor values, respectively. This first experimental report, targeted on investigating the origins of phospholipid symmetry breaking, opens up new avenues of research to explore alternative mechanisms leading to membrane lipid homochirality, while providing important clues for the search for chiral biosignatures of extant and/or extinct life in space, in particular for the ExoMars 2028 mission.


Assuntos
Aminoácidos , Glicerofosfolipídeos , Estereoisomerismo , Raios Ultravioleta , Fosfatos
5.
Biophys Chem ; 303: 107113, 2023 12.
Artigo em Inglês | MEDLINE | ID: mdl-37778197

RESUMO

The mitochondrial outer membrane creates a diffusion barrier between the cytosol and the mitochondrial intermembrane space, allowing the exchange of metabolic products, important for efficient mitochondrial function in neurons. The ganglioside-induced differentiation-associated protein 1 (GDAP1) is a mitochondrial outer membrane protein with a critical role in mitochondrial dynamics and metabolic balance in neurons. Missense mutations in the GDAP1 gene are linked to the most common human peripheral neuropathy, Charcot-Marie-Tooth disease (CMT). GDAP1 is a distant member of the glutathione-S-transferase (GST) superfamily, with unknown enzymatic properties or functions at the molecular level. The structure of the cytosol-facing GST-like domain has been described, but there is no consensus on how the protein interacts with the mitochondrial outer membrane. Here, we describe a model for GDAP1 assembly on the membrane using peptides vicinal to the GDAP1 transmembrane domain. We used oriented circular dichroism spectroscopy (OCD) with synchrotron radiation to study the secondary structure and orientation of GDAP1 segments at the outer and inner surfaces of the outer mitochondrial membrane. These experiments were complemented by small-angle X-ray scattering, providing the first experimental structural models for full-length human GDAP1. The results indicate that GDAP1 is bound into the membrane via a single transmembrane helix, flanked by two peripheral helices interacting with the outer and inner leaflets of the mitochondrial outer membrane in different orientations. Impairment of these interactions could be a mechanism for CMT in the case of missense mutations affecting these segments instead of the GST-like domain.


Assuntos
Doença de Charcot-Marie-Tooth , Membranas Mitocondriais , Humanos , Membranas Mitocondriais/metabolismo , Síncrotrons , Mitocôndrias/metabolismo , Neurônios/metabolismo , Mutação de Sentido Incorreto , Doença de Charcot-Marie-Tooth/genética , Doença de Charcot-Marie-Tooth/metabolismo , Proteínas de Membrana/metabolismo
6.
Nat Commun ; 14(1): 3381, 2023 Jun 08.
Artigo em Inglês | MEDLINE | ID: mdl-37291172

RESUMO

Systematic enrichments of L-amino acids in meteorites is a strong indication that biological homochirality originated beyond Earth. Although still unresolved, stellar UV circularly polarized light (CPL) is the leading hypothesis to have caused the symmetry breaking in space. This involves the differential absorption of left- and right-CPL, a phenomenon called circular dichroism, which enables chiral discrimination. Here we unveil coherent chiroptical spectra of thin films of isovaline enantiomers, the first step towards asymmetric photolysis experiments using a tunable laser set-up. As analogues to amino acids adsorbed on interstellar dust grains, CPL-helicity dependent enantiomeric excesses of up to 2% were generated in isotropic racemic films of isovaline. The low efficiency of chirality transfer from broadband CPL to isovaline could explain why its enantiomeric excess is not detected in the most pristine chondrites. Notwithstanding, small, yet consistent L-biases induced by stellar CPL would have been crucial for its amplification during aqueous alteration of meteorite parent bodies.


Assuntos
Meteoroides , Fotoquímica , Aminoácidos/química , Valina
7.
J Chem Phys ; 158(23)2023 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-37318170

RESUMO

A synchrotron-based vacuum ultraviolet absorption spectrum (VUV) of quadricyclane (QC) is reported with energies up to 10.8 eV. Extensive vibrational structure has been extracted from the broad maxima by fitting short energy ranges of the VUV spectrum to high level polynomial functions and processing the regular residuals. Comparison of these data with our recent high-resolution photoelectron spectral of QC showed that this structure must be attributed to Rydberg states (RS). Several of these appear before the valence states at higher energies. Both types of states have been calculated by configuration interaction, including symmetry-adapted cluster studies (SAC-CI) and time dependent density functional theoretical methods (TDDFT). There is a close correlation between the SAC-CI vertical excitation energies (VEE) and both Becke 3-parameter hybrid functional (B3LYP), especially Coulomb-attenuating method-B3LYP determined ones. The VEE for several low-lying s-, p, d-, and f-RS have been determined by SAC-CI and adiabatic excitation energies by TDDFT methods. Searches for equilibrium structures for 11,3A2 and 11B1 states for QC led to rearrangement to a norbornadiene structure. Determination of the experimental 00 band positions, which show extremely low cross-sections, has been assisted by matching features in the spectra with Franck-Condon (FC) fits. Herzberg-Teller (HT) vibrational profiles for the RS are more intense than the FC ones, but only at high energy, and are attributed to up to ten quanta. The vibrational fine structure of the RS calculated by both FC and HT procedures gives an easy route to generating HT profiles for ionic states, which usually require non-standard procedures.

8.
Rev Sci Instrum ; 94(5)2023 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-37166246

RESUMO

We describe the commissioning of a new electron-ion coincidence spectrometer used to diagnose the photon beam from a plane grating monochromator beamline at the ASTRID2 synchrotron radiation facility. The spectrometer allows determination of the absolute photon intensity by calibration to the photoabsorption cross sections of known gases, such as the rare gases Ar, Kr, and Xe presented here. The spectrometer operates at very low pressure (∼10-8-10-9 mbar) and-due to the coincidence electron-ion detection scheme-the detector efficiencies can be determined routinely; hence, the spectrometer can be recalibrated swiftly. By variation of a single potential of the spectrometer, the content of higher order radiation in the monochromatized synchrotron radiation can be analyzed. The layout and operation of the synchrotron radiation beamline at ASTRID2 and its additional photon diagnostic units are additionally described.

9.
Adv Mater ; 35(36): e2301907, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37204117

RESUMO

Modification of the electronic structure of quantum matter by ad atom deposition allows for directed fundamental design of electronic and magnetic properties. This concept is utilized in the present study in order to tune the surface electronic structure of magnetic topological insulators based on MnBi2 Te4 . The topological bands of these systems are typically strongly electron-doped and hybridized with a manifold of surface states that place the salient topological states out of reach of electron transport and practical applications. In this study, micro-focused angle-resolved photoemission spectroscopy (microARPES) provides direct access to the termination-dependent dispersion of MnBi2 Te4 and MnBi4 Te7 during in situ deposition of rubidium atoms. The resulting band structure changes are found to be highly complex, encompassing coverage-dependent ambipolar doping effects, removal of surface state hybridization, and the collapse of a surface state band gap. In addition, doping-dependent band bending is found to give rise to tunable quantum well states. This wide range of observed electronic structure modifications can provide new ways to exploit the topological states and the rich surface electronic structures of manganese bismuth tellurides.

10.
J Phys Chem A ; 127(6): 1445-1457, 2023 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-36730450

RESUMO

High-resolution photoabsorption cross-sections in the 3.7-10.8 eV energy range are reinvestigated for nitromethane (CH3NO2), while for nitroethane (C2H5NO2), they are reported for the first time. New absorption features are observed for both molecules which have been assigned to vibronic excitations of valence, Rydberg, and mixed valence-Rydberg characters. In comparison with nitromethane, nitroethane shows mainly broad absorption bands with diffuse structures, which can be interpreted as a result of the side-chain effect contributing to an increased number of internal degrees of freedom. New theoretical quantum chemical calculations performed at the time-dependent density functional theory (TD-DFT) level were used to qualitatively help interpret the recorded photoabsorption spectra. From the photoabsorption cross-sections, photolysis lifetimes in the terrestrial atmosphere have been obtained for both compounds. Relevant internal conversion from Rydberg to valence character is noted for both molecules, while the nuclear dynamics of CH3NO2 and C2H5NO2 along the C-N reaction coordinate have been evaluated through potential energy curves at the TD-DFT level of theory, showing that the pre-dissociative character is more prevalent in nitromethane than in nitroethane.

11.
J Chem Phys ; 158(1): 014303, 2023 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-36610949

RESUMO

C4F7N is a promising candidate for the replacement of sulfur hexafluoride as an insulating medium, and it is important to understand the chemical changes initiated in the molecule by collision with free electrons, specifically the formation of neutral fragments. The first step of neutral fragmentation is electronic excitation, yet neither the absorption spectrum in the vacuum ultraviolet (VUV) region nor the electron energy loss spectrum have previously been reported. Here, we experimentally probed the excited states by VUV photoabsorption spectroscopy and electron energy loss spectroscopy (EELS). We found that the distribution of states populated upon electron impact with low-energy electrons is significantly different from that following photoabsorption. This difference was confirmed and interpreted with ab initio modeling of both VUV and EELS spectra. We propose here a new computational protocol for the simulation of EELS spectra combining the Born approximation with approximate forms of correlated wave functions, which allows us to calculate the (usually very expensive) scattering cross sections at a cost similar to the calculation of oscillator strengths. Finally, we perform semi-classical non-adiabatic dynamics simulations to investigate the possible neutral fragments of the molecule formed through electron-induced neutral dissociation. We show that the product distribution is highly non-statistical.

12.
J Chem Phys ; 158(1): 014304, 2023 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-36610975

RESUMO

A synchrotron-based photoionization spectrum up to 27 eV represents a considerable improvement in resolution over early He(I) and He(II) spectra. Symmetry-adapted coupled cluster calculations of the ionic state sequence give the sequence of state vertical ionization energies (VIE) as 12B2 < 12B1 < 12A2 < 22B1 < 12A1. Generally, these symmetry-adapted cluster configuration interactions VIE match reasonably well with the experimental spectrum over this wide energy range. Density functional calculations of the corresponding adiabatic terms (AIE) were also performed. Higher energy ionic states were determined by complete active space self-consistent field methods; these include all π-ionizations and some σ-ionic states. These were analyzed by Franck-Condon (FC) procedures and compared with an experiment. The spectral onset is complex, where two states, later shown to be the 12B2 and 12B1 states, are strongly overlapping. The superposition of the FC vibrational structure in the 12B2 and 12B1 states accounts for most of the peaks arising at the onset of the photoelectron spectra. However, the small separation between these two ionic states makes vibronic interaction fairly inevitable. In the absence of Herzberg-Teller analyses for ionic states, we have sought and determined a transition state between the 12B2 and 12B1 states, showing that vibronic coupling does occur. The lack of degradation in the vibrational envelope of the higher of the two states contrasts with our previous work on the halogenobenzenes, where overlapping state envelopes led to considerable widening of the line width at half-height of the higher energy states.

13.
Protein Sci ; 32(2): e4567, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-36658780

RESUMO

DNA-binding proteins from starved cells (Dps) are small multifunctional nanocages expressed by prokaryotes in acute oxidative stress conditions or during the starvation-induced stationary phase, as a bacterial defense mechanism. Dps proteins protect bacterial DNA from damage by either direct binding or by removing precursors of reactive oxygen species from solution. The DNA-binding properties of most Dps proteins studied so far are related to their unordered, flexible, N- and C-terminal extensions. In a previous work, we revealed that the N-terminal tails of Deinoccocus grandis Dps shift from an extended to a compact conformation depending on the ionic strength of the buffer and detected a novel high-spin ferrous iron center in the proximal ends of those tails. In this work, we further explore the conformational dynamics of the protein by probing the effect of divalent metals binding to the tail by comparing the metal-binding properties of the wild-type protein with a binding site-impaired D34A variant using size exclusion chromatography, dynamic light scattering, synchrotron radiation circular dichroism, and small-angle X-ray scattering. The N-terminal ferrous species was also characterized by Mössbauer spectroscopy. The results herein presented reveal that the conformation of the N-terminal tails is altered upon metal binding in a gradual, reversible, and specific manner. These observations may point towards the existence of a regulatory process for the DNA-binding properties of Dps proteins through metal binding to their N- and/or C-terminal extensions.


Assuntos
Proteínas de Bactérias , Deinococcus , Sequência de Aminoácidos , Proteínas de Bactérias/química , Deinococcus/química , Deinococcus/genética , Deinococcus/metabolismo , DNA Bacteriano/metabolismo
14.
Spectrochim Acta A Mol Biomol Spectrosc ; 286: 122019, 2023 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-36308827

RESUMO

The UV absorbance bands of 1,4-distyrylbenzene (1,4-Bis[(E)-2-phenylethenyl]benzene, DSB) are investigated by Synchrotron Radiation Linear Dichroism (SRLD) spectroscopy using stretched polyethylene as an anisotropic solvent. The observed polarization data provide information on the transition moment directions of the observed spectral features. The investigation covers the range 15,000-58,000 cm-1 (667-172 nm), thereby providing new information on the transitions of DSB in the vacuum UV region. The observed spectrum is characterized by four main band systems centered at 27,600, 41,000, 49,800, and 57,500 cm-1 (362, 244, 201, and 174 nm). In general, the observed bands and their polarization directions are well predicted by the results of quantum chemical calculations using Time-Dependent Density Functional Theory (TD-DFT) with the functional CAM-B3LYP, and with the semiempirical all-valence-electrons method LCOAO.

15.
Sci Adv ; 8(46): eadd4614, 2022 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-36399555

RESUMO

Propylene oxide, the first chiral molecule recently detected in the interstellar medium, has once again raised the question whether biomolecular chirality might have cosmic origins. However, accurate chiroptical properties of propylene oxide in the ultraviolet spectral range necessary to suggest possible asymmetric synthetic routes in the gas phase are scarce. Here, we report on the first experimental measurements of the anisotropy spectra of gas-phase propylene oxide in the vacuum ultraviolet spectral range. Our experimental results provide novel insights into the handedness of interstellar circular polarization at the dawn of molecular evolution of our star- and planet-forming region. Besides the fundamental importance of this new investigation for understanding the origin and evolution of homochirality on Earth, our high-resolution experimental electronic circular dichroism data will inspire new efforts in quantum computational spectroscopy.

16.
J Chem Phys ; 157(15): 154307, 2022 Oct 21.
Artigo em Inglês | MEDLINE | ID: mdl-36272785

RESUMO

A new vacuum ultraviolet absorption (VUV) spectrum of azulene vapor has been obtained by using a synchrotron radiation source. The onset of the ultraviolet spectrum, previously reported by Sidman et al., has been analyzed in detail by Franck-Condon (FC) and Herzberg-Teller (HT) methods. The photoelectron spectral profile identifies the 3px-Rydberg state 00 band to be 131 cm-1 from the VUV maximum. Excited state energy levels were calculated by three independent methods: the wide scan VUV spectrum was correlated with symmetry adapted cluster configuration interaction calculations. The low energy portion of the spectrum was studied by both time dependent density functional theoretical methods (TDDFT) and multi-reference multi-root CI (MRD-CI). Equilibrium structures were determined for valence states at the TDDFT level. Rydberg states were determined by both TDDFT and MRD-CI. The FC + HT analyses were performed on the TDDFT wave-functions. The HT intensity profiles are generally low in intensity, relative to the FC ones; however, HT is dominant in the second singlet state (S2, 11A1). As a result, numerous non-symmetric modes, their overtones, and combination bands show considerable intensity in that band. Energies obtained from use of extremely diffuse s-, p-, d-, or f-character functions enabled realistic extrapolation to the IE1 for many Rydberg states (RS). The lowest RS (3b13s) based on IE2 lies at 4.804 eV with a quantum defect of 0.714. Differentiation between valence and RS is readily made using the second moments of the charge distribution.

17.
Adv Sci (Weinh) ; 9(32): e2202359, 2022 11.
Artigo em Inglês | MEDLINE | ID: mdl-35988154

RESUMO

The surface of a carboxylate-enriched octuple mutant of Bacillus subtilis lipase A (8M) is chemically anionized to produce core (8M)-shell (cationic polymer surfactants) bionanoconjugates in protein liquid form, which are termed anion-type biofluids. The resultant lipase biofluids exhibit a 2.5-fold increase in hydrolytic activity when compared with analogous lipase biofluids based on anionic polymer surfactants. In addition, the applicability of the anion-type biofluid using Myoglobin (Mb) that is well studied in anion-type solvent-free liquid proteins is evaluated. Although anionization resulted in the complete unfolding of Mb, the active α-helix level is partially recovered in the anion-type biofluids, and the effect is accentuated in the cation-type Mb biofluids. These highly active anion-type solvent-free liquid enzymes exhibit increased thermal stability and provide a new direction in solvent-free liquid protein research.


Assuntos
Lipase , Tensoativos , Solventes/química , Lipase/química , Lipase/metabolismo , Tensoativos/química , Hidrólise , Polímeros/química , Mioglobina/química
18.
Rev Sci Instrum ; 93(7): 075110, 2022 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-35922303

RESUMO

In this work, we present a new endstation for the AMOLine of the ASTRID2 synchrotron at Aarhus University, which combines a cluster and nanodroplet beam source with a velocity map imaging and time-of-flight spectrometer for coincidence imaging spectroscopy. Extreme-ultraviolet spectroscopy of free nanoparticles is a powerful tool for studying the photophysics and photochemistry of resonantly excited or ionized nanometer-sized condensed-phase systems. Here, we demonstrate this capability by performing photoelectron-photoion coincidence experiments with pure and doped superfluid helium nanodroplets. Different doping options and beam sources provide a versatile platform to generate various van der Waals clusters as well as He nanodroplets. We present a detailed characterization of the new setup and show examples of its use for measuring high-resolution yield spectra of charged particles, time-of-flight ion mass spectra, anion-cation coincidence spectra, multi-coincidence electron spectra, and angular distributions. A particular focus of the research with this new endstation is on intermolecular charge and energy-transfer processes in heterogeneous nanosystems induced by valence-shell excitation and ionization.

19.
Int J Mol Sci ; 23(14)2022 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-35887179

RESUMO

Encapsulins are protein nanocages capable of harboring smaller proteins (cargo proteins) within their cavity. The function of the encapsulin systems is related to the encapsulated cargo proteins. The Myxococcus xanthus encapsulin (EncA) naturally encapsulates ferritin-like proteins EncB and EncC as cargo, resulting in a large iron storage nanocompartment, able to accommodate up to 30,000 iron atoms per shell. In the present manuscript we describe the binding and protection of circular double stranded DNA (pUC19) by EncA using electrophoretic mobility shift assays (EMSA), atomic force microscopy (AFM), and DNase protection assays. EncA binds pUC19 with an apparent dissociation constant of 0.3 ± 0.1 µM and a Hill coefficient of 1.4 ± 0.1, while EncC alone showed no interaction with DNA. Accordingly, the EncAC complex displayed a similar DNA binding capacity as the EncA protein. The data suggest that initially, EncA converts the plasmid DNA from a supercoiled to a more relaxed form with a beads-on-a-string morphology. At higher concentrations, EncA self-aggregates, condensing the DNA. This process physically protects DNA from enzymatic digestion by DNase I. The secondary structure and thermal stability of EncA and the EncA-pUC19 complex were evaluated using synchrotron radiation circular dichroism (SRCD) spectroscopy. The overall secondary structure of EncA is maintained upon interaction with pUC19 while the melting temperature of the protein (Tm) slightly increased from 76 ± 1 °C to 79 ± 1 °C. Our work reports, for the first time, the in vitro capacity of an encapsulin shell to interact and protect plasmid DNA similarly to other protein nanocages that may be relevant in vivo.


Assuntos
Myxococcus xanthus , Proteínas de Bactérias/metabolismo , DNA/metabolismo , Ferritinas/metabolismo , Ferro/metabolismo , Myxococcus xanthus/genética , Myxococcus xanthus/metabolismo
20.
Front Microbiol ; 13: 872306, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35783412

RESUMO

Microbially-produced ice nucleating proteins (INpro) are unique molecular structures with the highest known catalytic efficiency for ice formation. Airborne microorganisms utilize these proteins to enhance their survival by reducing their atmospheric residence times. INpro also have critical environmental effects including impacts on the atmospheric water cycle, through their role in cloud and precipitation formation, as well as frost damage on crops. INpro are ubiquitously present in the atmosphere where they are emitted from diverse terrestrial and marine environments. Even though bacterial genes encoding INpro have been discovered and sequenced decades ago, the details of how the INpro molecular structure and oligomerization foster their unique ice-nucleation activity remain elusive. Using machine-learning based software AlphaFold 2 and trRosetta, we obtained and analysed the first ab initio structural models of full length and truncated versions of bacterial INpro. The modeling revealed a novel beta-helix structure of the INpro central repeat domain responsible for ice nucleation activity. This domain consists of repeated stacks of two beta strands connected by two sharp turns. One beta-strand is decorated with a TxT amino acid sequence motif and the other strand has an SxL[T/I] motif. The core formed between the stacked beta helix-pairs is unusually polar and very distinct from previous INpro models. Using synchrotron radiation circular dichroism, we validated the ß-strand content of the central repeat domain in the model. Combining the structural model with functional studies of purified recombinant INpro, electron microscopy and modeling, we further demonstrate that the formation of dimers and higher-order oligomers is key to INpro activity. Using computational docking of the new INpro model based on rigid-body algorithms we could reproduce a previously proposed homodimer structure of the INpro CRD with an interface along a highly conserved tyrosine ladder and show that the dimer model agrees with our functional data. The parallel dimer structure creates a surface where the TxT motif of one monomer aligns with the SxL[T/I] motif of the other monomer widening the surface that interacts with water molecules and therefore enhancing the ice nucleation activity. This work presents a major advance in understanding the molecular foundation for bacterial ice-nucleation activity.

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