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1.
Protein Sci ; 33(3): e4906, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38358120

RESUMEN

Proteins, especially of eukaryotes, often have disordered domains and may contain multiple folded domains whose relative spatial arrangement is distributed. The MMMx ensemble modeling and analysis toolbox (https://github.com/gjeschke/MMMx) can support the design of experiments to characterize the distributed structure of such proteins, starting from AlphaFold2 predictions or folded domain structures. Weak order can be analyzed with reference to a random coil model or to peptide chains that match the residue-specific Ramachandran angle distribution of the loop regions and are otherwise unrestrained. The deviation of the mean square end-to-end distance of chain sections from their average over sections of the same sequence length reveals localized compaction or expansion of the chain. The shape sampled by disordered chains is visualized by superposition in the principal axes frame of their inertia tensor. Ensembles of different sizes and with weighted conformers can be compared based on a similarity parameter that abstracts from the ensemble width.


Asunto(s)
Proteínas , Modelos Moleculares , Proteínas/química , Conformación Proteica
2.
Protein Sci ; 33(3): e4908, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38358133

RESUMEN

Interactions between membrane proteins (MPs) and lipid bilayers are critical for many cellular functions. In the Rosetta molecular modeling suite, the implicit membrane energy function is based on a "slab" model, which represent the membrane as a flat bilayer. However, in nature membranes often have a curvature that is important for function and/or stability. Even more prevalent, in structural biology research MPs are reconstituted in model membrane systems such as micelles, bicelles, nanodiscs, or liposomes. Thus, we have modified the existing membrane energy potentials within the RosettaMP framework to allow users to model MPs in different membrane geometries. We show that these modifications can be utilized in core applications within Rosetta such as structure refinement, protein-protein docking, and protein design. For MP structures found in curved membranes, refining these structures in curved, implicit membranes produces higher quality models with structures closer to experimentally determined structures. For MP systems embedded in multiple membranes, representing both membranes results in more favorable scores compared to only representing one of the membranes. Modeling MPs in geometries mimicking the membrane model system used in structure determination can improve model quality and model discrimination.


Asunto(s)
Liposomas , Proteínas de la Membrana , Proteínas de la Membrana/química , Membrana Dobles de Lípidos/química , Modelos Moleculares , Micelas
3.
Molecules ; 29(4)2024 Feb 13.
Artículo en Inglés | MEDLINE | ID: mdl-38398585

RESUMEN

The prediction of three-dimensional (3D) protein structure from amino acid sequences has stood as a significant challenge in computational and structural bioinformatics for decades. Recently, the widespread integration of artificial intelligence (AI) algorithms has substantially expedited advancements in protein structure prediction, yielding numerous significant milestones. In particular, the end-to-end deep learning method AlphaFold2 has facilitated the rise of structure prediction performance to new heights, regularly competitive with experimental structures in the 14th Critical Assessment of Protein Structure Prediction (CASP14). To provide a comprehensive understanding and guide future research in the field of protein structure prediction for researchers, this review describes various methodologies, assessments, and databases in protein structure prediction, including traditionally used protein structure prediction methods, such as template-based modeling (TBM) and template-free modeling (FM) approaches; recently developed deep learning-based methods, such as contact/distance-guided methods, end-to-end folding methods, and protein language model (PLM)-based methods; multi-domain protein structure prediction methods; the CASP experiments and related assessments; and the recently released AlphaFold Protein Structure Database (AlphaFold DB). We discuss their advantages, disadvantages, and application scopes, aiming to provide researchers with insights through which to understand the limitations, contexts, and effective selections of protein structure prediction methods in protein-related fields.


Asunto(s)
Inteligencia Artificial , Proteínas , Conformación Proteica , Modelos Moleculares , Proteínas/química , Algoritmos , Biología Computacional/métodos , Bases de Datos de Proteínas , Programas Informáticos , Pliegue de Proteína
4.
SAR QSAR Environ Res ; 35(2): 157-179, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38346125

RESUMEN

A Disintegrin and Metalloproteinase 17 (ADAM17), a Zn2+-dependent metalloenzyme of the adamalysin family of the metzincin superfamily, is associated with various pathophysiological conditions including rheumatoid arthritis and cancer. However, no specific inhibitors have been marketed yet for ADAM17-related disorders. In this study, 94 quinolinyl methoxyphenyl sulphonyl-based hydroxamates as ADAM17 inhibitors were subjected to classification-based molecular modelling and binding pattern analysis to identify the significant structural attributes contributing to ADAM17 inhibition. The statistically validated classification-based models identified the importance of the P1' substituents such as the quinolinyl methoxyphenyl sulphonyl group of these compounds for occupying the S1' - S3' pocket of the enzyme. The quinolinyl function of these compounds was found to explore stable binding of the P1' substituents at the S1' - S3' pocket whereas the importance of the sulphonyl and the orientation of the P1' moiety also revealed stable binding. Based on the outcomes of the current study, four novel compounds of different classes were designed as promising ADAM17 inhibitors. These findings regarding the crucial structural aspects and binding patterns of ADAM17 inhibitors will aid the design and discovery of novel and effective ADAM17 inhibitors for therapeutic advancements of related diseases.


Asunto(s)
Ácidos Hidroxámicos , Relación Estructura-Actividad Cuantitativa , Proteína ADAM17 , Modelos Moleculares , Ácidos Hidroxámicos/química
5.
J Phys Chem B ; 128(6): 1515-1526, 2024 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-38315822

RESUMEN

Monoclonal antibodies (mAbs) are an important modality of protein therapeutics with broad applications for numerous diseases. However, colloidal instabilities occurring at high protein concentrations can limit the ability to develop stable, high-concentration liquid dosage forms that are required for patient-centric, device-mediated products. Therefore, it is advantageous to identify colloidally stable mAbs early in the discovery process to ensure that they are selected for development. Experimental screening for colloidal stability can be time- and resource-consuming and is most feasible at the later stages of drug development due to material requirements. Alternatively, computational approaches have emerging potential to provide efficient screening and focus developmental efforts on mAbs with the greatest developability potential, while providing mechanistic relationships for colloidal instability. In this work, coarse-grained, molecular-scale models were fine-tuned to screen for colloidal stability at amino-acid resolution. This model parameterization provides a framework to screen for mAb self-interactions and extrapolate to bulk solution behavior. This approach was applied to a wide array of mAbs under multiple buffer conditions, demonstrating the utility of the presented computational approach to augment early candidate screening and later formulation strategies for protein therapeutics.


Asunto(s)
Anticuerpos Monoclonales , Humanos , Modelos Moleculares
6.
Molecules ; 29(3)2024 Jan 24.
Artículo en Inglés | MEDLINE | ID: mdl-38338326

RESUMEN

Deoxycholic acid derivatives containing various heterocyclic functional groups at C-3 on the steroid scaffold were designed and synthesized as promising dual tyrosyl-DNA phosphodiesterase 1 and 2 (TDP1 and TDP2) inhibitors, which are potential targets to potentiate topoisomerase poison antitumor therapy. The methyl esters of DCA derivatives with benzothiazole or benzimidazole moieties at C-3 demonstrated promising inhibitory activity in vitro against TDP1 with IC50 values in the submicromolar range. Furthermore, methyl esters 4d-e, as well as their acid counterparts 3d-e, inhibited the phosphodiesterase activity of both TDP1 and TDP2. The combinations of compounds 3d-e and 4d-e with low-toxic concentrations of antitumor drugs topotecan and etoposide showed significantly greater cytotoxicity than the compounds alone. The docking of the derivatives into the binding sites of TDP1 and TDP2 predicted plausible binding modes of the DCA derivatives.


Asunto(s)
Inhibidores de Fosfodiesterasa , Hidrolasas Diéster Fosfóricas , Inhibidores de Fosfodiesterasa/química , Hidrolasas Diéster Fosfóricas/metabolismo , Modelos Moleculares , Ácido Desoxicólico/farmacología , Relación Estructura-Actividad
7.
Int J Mol Sci ; 25(3)2024 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-38339061

RESUMEN

From the point of view of the search for new pharmaceuticals, pyridazinone derivatives are a very promising group of compounds. In our previous works, we have proved that newly synthesized ligands from this group have desirable biological and pharmacokinetic properties. Therefore, we decided to continue the research evaluating the activity of pyrrolo[3,4-dpyridazinone derivatives. In this work, we focused on the interactions of five pyridazinone derivatives with the following biomolecules: DNA and two plasma proteins: orosomucoid and gamma globulin. Using several of spectroscopic methods, such as UV-Vis, CD, and fluorescence spectroscopy, we proved that the tested compounds form stable complexes with all biomacromolecules selected for analysis. These findings were also confirmed by the results obtained by molecular modeling. All tested pyridazinone derivatives bind to the ctDNA molecule via groove binding mechanisms. All these molecules can also be bound and transported by the tested plasma proteins; however, the stability of the complexes formed is lower than those formed with serum albumin.


Asunto(s)
Antiinflamatorios , Antioxidantes , ADN/química , Modelos Moleculares , Proteínas Sanguíneas , Simulación del Acoplamiento Molecular
8.
Sci Adv ; 10(6): eadl4000, 2024 Feb 09.
Artículo en Inglés | MEDLINE | ID: mdl-38324676

RESUMEN

Through evolution, nature has presented a set of remarkable protein materials, including elastins, silks, keratins and collagens with superior mechanical performances that play crucial roles in mechanobiology. However, going beyond natural designs to discover proteins that meet specified mechanical properties remains challenging. Here, we report a generative model that predicts protein designs to meet complex nonlinear mechanical property-design objectives. Our model leverages deep knowledge on protein sequences from a pretrained protein language model and maps mechanical unfolding responses to create proteins. Via full-atom molecular simulations for direct validation, we demonstrate that the designed proteins are de novo, and fulfill the targeted mechanical properties, including unfolding energy and mechanical strength, as well as the detailed unfolding force-separation curves. Our model offers rapid pathways to explore the enormous mechanobiological protein sequence space unconstrained by biological synthesis, using mechanical features as the target to enable the discovery of protein materials with superior mechanical properties.


Asunto(s)
Seda , Proteínas Virales , Modelos Moleculares
9.
Int J Mol Sci ; 25(4)2024 Feb 19.
Artículo en Inglés | MEDLINE | ID: mdl-38397115

RESUMEN

Zika virus (ZIKV) is a positive-sense single-stranded virus member of the Flaviviridae family. Among other arboviruses, ZIKV can cause neurological disorders such as Guillain Barré syndrome, and it can have congenital neurological manifestations and affect fertility. ZIKV nonstructural protein 5 (NS5) is essential for viral replication and limiting host immune detection. Herein, we performed virtual screening to identify novel small-molecule inhibitors of the ZIKV NS5 methyltransferase (MTase) domain. Compounds were tested against the MTases of both ZIKV and DENV, demonstrating good inhibitory activities against ZIKV MTase. Extensive molecular dynamic studies conducted on the series led us to identify other derivatives with improved activity against the MTase and limiting ZIKV infection with an increased selectivity index. Preliminary pharmacokinetic parameters have been determined, revealing excellent stability over time. Preliminary in vivo toxicity studies demonstrated that the hit compound 17 is well tolerated after acute administration. Our results provide the basis for further optimization studies on novel non-nucleoside MTase inhibitors.


Asunto(s)
Infección por el Virus Zika , Virus Zika , Humanos , Virus Zika/metabolismo , Infección por el Virus Zika/tratamiento farmacológico , Modelos Moleculares , Antivirales/química , Proteínas no Estructurales Virales/metabolismo
10.
Int J Mol Sci ; 25(3)2024 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-38339036

RESUMEN

Human Galectin-3 (hGal-3) is a protein that selectively binds to ß-galactosides and holds diverse roles in both normal and pathological circumstances. Therefore, targeting hGal-3 has become a vibrant area of research in the pharmaceutical chemistry. As a step towards the development of novel hGal-3 inhibitors, we synthesized and investigated derivatives of thiodigalactoside (TDG) modified with different aromatic substituents. Specifically, we describe a high-yielding synthetic route of thiodigalactoside (TDG); an optimized procedure for the synthesis of the novel 3,3'-di-O-(quinoline-2-yl)methyl)-TDG and three other known, symmetric 3,3'-di-O-TDG derivatives ((naphthalene-2yl)methyl, benzyl, (7-methoxy-2H-1-benzopyran-2-on-4-yl)methyl). In the present study, using competition Saturation Transfer Difference (STD) NMR spectroscopy, we determined the dissociation constant (Kd) of the former three TDG derivatives produced to characterize the strength of the interaction with the target protein (hGal-3). Based on the Kd values determined, the (naphthalen-2-yl)methyl, the (quinolin-2-yl)methyl and the benzyl derivatives bind to hGal-3 94, 30 and 24 times more strongly than TDG. Then, we studied the binding modes of the derivatives in silico by molecular docking calculations. Docking poses similar to the canonical binding modes of well-known hGal-3 inhibitors have been found. However, additional binding forces, cation-π interactions between the arginine residues in the binding pocket of the protein and the aromatic groups of the ligands, have been established as significant features. Our results offer a molecular-level understanding of the varying affinities observed among the synthesized thiodigalactoside derivatives, which can be a key aspect in the future development of more effective ligands of hGal-3.


Asunto(s)
Galectina 3 , Tiogalactósidos , Humanos , Galectina 3/antagonistas & inhibidores , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Simulación del Acoplamiento Molecular , Unión Proteica , Tiogalactósidos/química , Tiogalactósidos/farmacología
11.
J Phys Chem Lett ; 15(7): 1930-1935, 2024 Feb 22.
Artículo en Inglés | MEDLINE | ID: mdl-38346015

RESUMEN

Non-equilibrium kinetics techniques like pressure-jump nuclear magnetic resonance (NMR) are powerful in tracking changes in oligomeric populations and are not limited by relaxation rates for the time scales of exchange that can be probed. However, these techniques are less sensitive to minor, transient populations than are Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments. We integrated non-equilibrium pressure-jump and equilibrium CPMG relaxation dispersion data to fully map the kinetic landscape of melittin tetramerization. While monomeric peptides weakly form dimers (Kd,D/M ≈ 26 mM) whose population never exceeds 1.6% at 288 K, dimers associate tightly to form stable tetrameric species (Kd,T/D ≈ 740 nM). Exchange between the monomer and dimer, along with exchange between the dimer and tetramer, occurs on the millisecond time scale. The NMR approach developed herein can be readily applied to studying the folding and misfolding of a wide range of oligomeric assemblies.


Asunto(s)
Imagen por Resonancia Magnética , Meliteno , Resonancia Magnética Nuclear Biomolecular/métodos , Modelos Moleculares , Espectroscopía de Resonancia Magnética
12.
Biochemistry ; 63(2): 212-218, 2024 Jan 16.
Artículo en Inglés | MEDLINE | ID: mdl-38163326

RESUMEN

Amyloid-ß (Aß) forms heterogeneous oligomers, which are implicated in the pathogenesis of Alzheimer's disease (AD). Many Aß oligomers consist of ß-hairpin building blocks─Aß peptides in ß-hairpin conformations. ß-Hairpins of Aß can adopt a variety of alignments, but the role that ß-hairpin alignment plays in the formation and heterogeneity of Aß oligomers is poorly understood. To explore the effect of ß-hairpin alignment on the oligomerization of Aß peptides, we designed and studied two model peptides with two different ß-hairpin alignments. Peptides Aßm17-36 and Aßm17-35 mimic two different ß-hairpins that Aß can form, the Aß17-36 and Aß17-35 ß-hairpins, respectively. These hairpins are similar in composition but differ in hairpin alignment, altering the facial arrangements of the side chains of the residues that they contain. X-ray crystallography and SDS-PAGE demonstrate that the difference in facial arrangement between these peptides leads to distinct oligomer formation. In the crystal state, Aßm17-36 forms triangular trimers that further assemble to form hexamers, while Aßm17-35 forms tetrameric ß-barrels. In SDS-PAGE, Aßm17-36 assembles to form a ladder of oligomers, while Aßm17-35 either assembles to form a dimer or does not assemble at all. The differences in the behavior of Aßm17-36 and Aßm17-35 suggest ß-hairpin alignment as a source of the observed heterogeneity of Aß oligomers.


Asunto(s)
Enfermedad de Alzheimer , Péptidos beta-Amiloides , Humanos , Péptidos beta-Amiloides/química , Modelos Moleculares , Conformación Proteica , Cristalografía por Rayos X , Fragmentos de Péptidos/química
13.
Commun Biol ; 7(1): 59, 2024 01 12.
Artículo en Inglés | MEDLINE | ID: mdl-38216663

RESUMEN

Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature versus. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Altogether, our work indicates that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.


Asunto(s)
Proteínas , Temperatura , Modelos Moleculares , Proteínas/química , Conformación Molecular
14.
Adv Protein Chem Struct Biol ; 138: 179-210, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38220424

RESUMEN

Intrinsically disordered proteins (IDPs), which are functional proteins without stable tertiary structure, and hybrid proteins containing ordered domains and intrinsically disordered regions (IDRs) constitute prominent parts of all proteomes collectively known as unfoldomes. IDPs/IDRs exist as highly dynamic structural ensembles of rapidly interconverting conformations and are characterized by the exceptional structural heterogeneity, where their different parts are (dis)ordered to different degree, and their overall structure represents a complex mosaic of foldons, inducible foldons, inducible morphing foldons, non-foldons, semifoldons, and even unfoldons. Despite their lack of unique 3D structures, IDPs/IDRs play crucial roles in the control of various biological processes and the regulation of different cellular pathways and are commonly involved in recognition and signaling, indicating that the disorder-based functional repertoire is complementary to the functions of ordered proteins. Furthermore, IDPs/IDRs are frequently multifunctional, and this multifunctionality is defined by their structural flexibility and heterogeneity. Intrinsic disorder phenomenon is at the roots of the structure-function continuum model, where the structure continuum is defined by the presence of differently (dis)ordered regions, and the function continuum arises from the ability of all these differently (dis)ordered parts to have different functions. In their everyday life, IDPs/IDRs utilize a broad spectrum of interaction mechanisms thereby acting as interaction specialists. They are crucial for the biogenesis of numerous proteinaceous membrane-less organelles driven by the liquid-liquid phase separation. This review introduces functional unfoldomics by representing some aspects of the intrinsic disorder-based functionality.


Asunto(s)
Proteínas Intrínsecamente Desordenadas , Conformación Proteica , Modelos Moleculares , Proteínas Intrínsecamente Desordenadas/metabolismo , Transducción de Señal , Proteoma
15.
Chem Commun (Camb) ; 60(7): 870-873, 2024 Jan 18.
Artículo en Inglés | MEDLINE | ID: mdl-38164786

RESUMEN

Herein, we present the first application of target-directed dynamic combinatorial chemistry (tdDCC) to the whole complex of the highly dynamic transmembrane, energy-coupling factor (ECF) transporter ECF-PanT in Streptococcus pneumoniae. In addition, we successfully employed the tdDCC technique as a hit-identification and -optimization strategy that led to the identification of optimized ECF inhibitors with improved activity. We characterized the best compounds regarding cytotoxicity and performed computational modeling studies on the crystal structure of ECF-PanT to rationalize their binding mode. Notably, docking studies showed that the acylhydrazone linker is able to maintain the crucial interactions.


Asunto(s)
Proteínas Bacterianas , Streptococcus pneumoniae , Modelos Moleculares , Proteínas Bacterianas/química
16.
Eur J Med Chem ; 265: 116090, 2024 Feb 05.
Artículo en Inglés | MEDLINE | ID: mdl-38169272

RESUMEN

The role of AXL in various oncogenic processes has made it an attractive target for cancer therapy. Currently, kinase selectivity profiles, especially circumventing MET inhibition, remain a scientific issue of great interest in the discovery of selective type II AXL inhibitors. Starting from a dual MET/AXL-targeted lead structure from our previous work, we optimized a 1,6-naphthyridinone series using molecular modeling-assisted compound design to improve AXL potency and selectivity over MET, resulting in the potent and selective type II AXL-targeted compound 25c. This showed excellent AXL inhibitory activity (IC50 = 1.1 nM) and 343-fold selectivity over the highly homologous kinase MET in biochemical assays. Moreover, compound 25c significantly inhibited AXL-driven cell proliferation, dose-dependently suppressed 4T1 cell migration and invasion, and induced apoptosis. Compound 25c also showed noticeable antitumor efficacy in a BaF3/TEL-AXL xenograft model at well-tolerated doses. Overall, this study presented a potent and selective type II AXL-targeted lead compound for further drug discovery.


Asunto(s)
Antineoplásicos , Inhibidores de Proteínas Quinasas , Humanos , Línea Celular Tumoral , Inhibidores de Proteínas Quinasas/farmacología , Inhibidores de Proteínas Quinasas/química , Relación Estructura-Actividad , Proliferación Celular , Modelos Moleculares , Antineoplásicos/farmacología , Antineoplásicos/química , Estructura Molecular
17.
Sci Rep ; 14(1): 2565, 2024 01 31.
Artículo en Inglés | MEDLINE | ID: mdl-38297014

RESUMEN

The unique potential of fullerene C60 for various biological applications has ignited significant interest. However, its inherent non-polarity poses a critical challenge for its effective integration within biological systems. This study delves into the intricate physicochemical characteristics of the innovative [C60 + NO] complex using density functional theory and time-dependent density functional theory. The computational analyses encompass molecular charge, surface electrostatic potential, and dipole moment evaluations. Impressively, the dipole moment of the [C60 + NO] complex significantly increases to 12.92 D. Meticulous surface analysis reveals a subtle interplay between molecular structures, indicating weak interactions. The analysis of the absorption spectrum unveils a noteworthy red-shift of 200 nm subsequent to complex formation. To elucidate the electron transfer mechanisms, we explore photo-induced electron transfer through CAM-B3LYP. This exploration elucidates intricate pathways governing electron transfer, with complementary insights gleaned from Marcus theory's outputs, especially the Gibbs free energy of electron transfer. Changes in the physicochemical properties of approaching C60 and NO molecules reveal interesting results compared to separate molecules. These findings resonate profoundly in the context of potential biological and pharmaceutical utilization. With implications for the biomedical area, the outcomes linked to the [C60 + NO] complex kindle optimism for pioneering biomedical applications.


Asunto(s)
Fulerenos , Fulerenos/química , Óxido Nítrico , Modelos Moleculares , Transporte de Electrón , Estructura Molecular
18.
Acta Crystallogr C Struct Chem ; 80(Pt 2): 21-29, 2024 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-38252461

RESUMEN

α-D-2'-Deoxyribonucleosides are products of the γ-irradiation of DNA under oxygen-free conditions and are constituents of anomeric DNA. They are not found as natural building blocks of canonical DNA. Reports on their conformational properties are limited. Herein, the single-crystal X-ray structure of α-D-2'-deoxyadenosine (α-dA), C10H13N5O3, and its conformational parameters were determined. In the crystalline state, α-dA forms two conformers in the asymmetric unit which are connected by hydrogen bonds. The sugar moiety of each conformer is arranged in a `clamp'-like fashion with respect to the other conformer, forming hydrogen bonds to its nucleobase and sugar residue. For both conformers, a syn conformation of the nucleobase with respect to the sugar moiety was found. This is contrary to the anti conformation usually preferred by α-nucleosides. The sugar conformation of both conformers is C2'-endo, and the 5'-hydroxyl groups are in a +sc orientation, probably due to the hydrogen bonds formed by the conformers. The formation of the supramolecular assembly of α-dA is controlled by hydrogen bonding and stacking interactions, which was verified by a Hirshfeld and curvedness surface analysis. Chains of hydrogen-bonded nucleobases extend parallel to the b direction and are linked to equivalent chains by hydrogen bonds involving the sugar moieties to form a sheet. A comparison of the solid-state structures of the anomeric 2'-deoxyadenosines revealed significant differences of their conformational parameters.


Asunto(s)
Desoxiadenosinas , Ácidos Nucleicos , Ácidos Nucleicos/química , Modelos Moleculares , Enlace de Hidrógeno , Cristalografía por Rayos X , ADN/química , Azúcares
19.
Nat Commun ; 15(1): 25, 2024 Jan 02.
Artículo en Inglés | MEDLINE | ID: mdl-38167383

RESUMEN

Lipid nanodiscs have become a standard tool for studying membrane proteins, including using single particle cryo-electron microscopy (cryo-EM). We find that reconstituting the pentameric ligand-gated ion channel (pLGIC), Erwinia ligand-gated ion channel (ELIC), in different nanodiscs produces distinct structures by cryo-EM. The effect of the nanodisc on ELIC structure extends to the extracellular domain and agonist binding site. Additionally, molecular dynamic simulations indicate that nanodiscs of different size impact ELIC structure and that the nanodisc scaffold directly interacts with ELIC. These findings suggest that the nanodisc plays a crucial role in determining the structure of pLGICs, and that reconstitution of ion channels in larger nanodiscs may better approximate a lipid membrane environment.


Asunto(s)
Canales Iónicos Activados por Ligandos , Canales Iónicos Activados por Ligandos/química , Canales Iónicos Activados por Ligandos/metabolismo , Microscopía por Crioelectrón , Modelos Moleculares , Sitios de Unión , Lípidos
20.
Acta Crystallogr D Struct Biol ; 80(Pt 2): 113-122, 2024 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-38265877

RESUMEN

Phenuiviridae nucleoprotein is the main structural and functional component of the viral cycle, protecting the viral RNA and mediating the essential replication/transcription processes. The nucleoprotein (N) binds the RNA using its globular core and polymerizes through the N-terminus, which is presented as a highly flexible arm, as demonstrated in this article. The nucleoprotein exists in an `open' or a `closed' conformation. In the case of the closed conformation the flexible N-terminal arm folds over the RNA-binding cleft, preventing RNA adsorption. In the open conformation the arm is extended in such a way that both RNA adsorption and N polymerization are possible. In this article, single-crystal X-ray diffraction and small-angle X-ray scattering were used to study the N protein of Toscana virus complexed with a single-chain camelid antibody (VHH) and it is shown that in the presence of the antibody the nucleoprotein is unable to achieve a functional assembly to form a ribonucleoprotein complex.


Asunto(s)
Nucleoproteínas , Virus de Nápoles de la Fiebre de la Mosca de los Arenales , Nucleoproteínas/química , Virus de Nápoles de la Fiebre de la Mosca de los Arenales/genética , Virus de Nápoles de la Fiebre de la Mosca de los Arenales/metabolismo , Proteínas de la Nucleocápside/química , Modelos Moleculares , ARN Viral/química , ARN Viral/metabolismo
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