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1.
J Colloid Interface Sci ; 677(Pt A): 781-789, 2025 Jan.
Article in English | MEDLINE | ID: mdl-39121662

ABSTRACT

HYPOTHESIS: Multi-walled tubular aggregates formed by hierarchical self-assembly of beta-cyclodextrin (ß-CD) and sodium dodecylsulfate (SDS) hold a great potential as microcarriers. However, the underlying mechanism for this self-assembly is not well understood. To advance the application of these structures, it is essential to fine-tune the cavity size and comprehensively elucidate the energetic balance driving their formation: the bending modulus versus the microscopic line tension. EXPERIMENTS: We investigated temperature-induced changes in the hierarchical tubular aggregates using synchrotron small-angle X-ray scattering across a broad concentration range. Detailed analysis of the scattering patterns enabled us to determine the structural parameters of the microtubes and to construct a phase diagram of the system. FINDINGS: The microtubes grow from the outside in and melt from the inside out. We relate derived structural parameters to enthalpic changes driving the self-assembly process on the molecular level in terms of their bending modulus and microscopic line tension. We find that the conformation of the crystalline bilayer affects the saturation concentration, providing an example of a phenomenon we call conformational freezing point depression. Inspired by the colligative phenomenon of freezing point depression, well known from undergraduate physics, we model this system by including the membrane conformation, which can describe the energetics of this hierarchical system and give access to microscopic properties without free parameters.

2.
Protein Sci ; 33(10): e5152, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39275999

ABSTRACT

γ-Hydroxybutyric acid (GHB) analogs are small molecules that bind competitively to a specific cavity in the oligomeric CaMKIIα hub domain. Binding affects conformation and stability of the hub domain, which may explain the neuroprotective action of some of these compounds. Here, we describe molecular details of interaction of the larger-type GHB analog 2-(6-(4-chlorophenyl)imidazo[1,2-b]pyridazine-2-yl)acetic acid (PIPA). Like smaller-type analogs, PIPA binding to the CaMKIIα hub domain promoted thermal stability. PIPA additionally modulated CaMKIIα activity under sub-maximal CaM concentrations and ultimately led to reduced substrate phosphorylation. A high-resolution X-ray crystal structure of a stabilized CaMKIIα (6x mutant) hub construct revealed details of the binding mode of PIPA, which involved outward placement of tryptophan 403 (Trp403), a central residue in a flexible loop close to the upper hub cavity. Small-angle X-ray scattering (SAXS) solution structures and mass photometry of the CaMKIIα wild-type hub domain in the presence of PIPA revealed a high degree of ordered self-association (stacks of CaMKIIα hub domains). This stacking neither occurred with the smaller compound 3-hydroxycyclopent-1-enecarboxylic acid (HOCPCA), nor when Trp403 was replaced with leucine (W403L). Additionally, CaMKIIα W403L hub was stabilized to a larger extent by PIPA compared to CaMKIIα hub wild type, indicating that loop flexibility is important for holoenzyme stability. Thus, we propose that ligand-induced outward placement of Trp403 by PIPA, which promotes an unforeseen mechanism of hub domain stacking, may be involved in the observed reduction in CaMKIIα kinase activity. Altogether, this sheds new light on allosteric regulation of CaMKIIα activity via the hub domain.


Subject(s)
Calcium-Calmodulin-Dependent Protein Kinase Type 2 , Protein Domains , Calcium-Calmodulin-Dependent Protein Kinase Type 2/chemistry , Calcium-Calmodulin-Dependent Protein Kinase Type 2/metabolism , Calcium-Calmodulin-Dependent Protein Kinase Type 2/genetics , Crystallography, X-Ray , Humans , Ligands , Models, Molecular , Scattering, Small Angle , Tryptophan/chemistry , Tryptophan/metabolism , Pyridazines/chemistry , Pyridazines/metabolism , Phosphorylation
3.
J Biol Chem ; 300(10): 107770, 2024 Sep 11.
Article in English | MEDLINE | ID: mdl-39270823

ABSTRACT

Dynamic ADP-ribosylation signaling is a crucial pathway that controls fundamental cellular processes, in particular, the response to cellular stresses such as DNA damage, reactive oxygen species, and infection. In some pathogenic microbes, the response to oxidative stress is controlled by a SirTM/zinc-containing macrodomain (Zn-Macro) pair responsible for establishment and removal of the modification, respectively. Targeting this defence mechanism against the host's innate immune response may lead to novel approaches to support the fight against emerging antimicrobial resistance. Earlier studies suggested that Zn-Macros play a key role in the activation of this defence. Therefore, we used phylogenetic, biochemical, and structural approaches to elucidate the functional properties of these enzymes. Using the substrate mimetic asparagine-ADP-ribose as well as the ADP-ribose product, we characterize the catalytic role of the zinc ion in the removal of the ADP-ribosyl modification. Furthermore, we determined structural properties that contribute to substrate selectivity within the different Zn-Macro branches. Together, our data not only give new insights into the Zn-Macro family but also highlight their distinct features that may be exploited for the development of future therapies.

4.
Article in English | MEDLINE | ID: mdl-39311060

ABSTRACT

Small-angle X-ray scattering (SAXS) is a widely used method for nanoparticle characterization. A common approach to analysing nanoparticles in solution by SAXS involves fitting the curve using a parametric model that relates real-space parameters, such as nanoparticle size and electron density, to intensity values in reciprocal space. Selecting the optimal model is a crucial step in terms of analysis quality and can be time-consuming and complex. Several studies have proposed effective methods, based on machine learning, to automate the model selection step. Deploying these methods in software intended for both researchers and industry raises several issues. The diversity of SAXS instrumentation requires assessment of the robustness of these methods on data from various machine configurations, involving significant variations in the q-space ranges and highly variable signal-to-noise ratios (SNR) from one data set to another. In the case of laboratory instrumentation, data acquisition can be time-consuming and there is no universal criterion for defining an optimal acquisition time. This paper presents an approach that revisits the nanoparticle model selection method proposed by Monge et al. [Acta Cryst. (2024), A80, 202-212], evaluating and enhancing its robustness on data from device configurations not seen during training, by expanding the data set used for training. The influence of SNR on predictor robustness is then assessed, improved, and used to propose a stopping criterion for optimizing the trade-off between exposure time and data quality.

5.
bioRxiv ; 2024 Aug 24.
Article in English | MEDLINE | ID: mdl-39229138

ABSTRACT

Arginyltransferase 1 (ATE1) catalyzes arginylation, an important post-translational modification (PTM) in eukaryotes that plays a critical role in cellular homeostasis. The disruption of ATE1 function is implicated in mammalian neurodegenerative disorders and cardiovascular maldevelopment, while post-translational arginylation has also been linked to the activities of several important human viruses such as SARS-CoV-2 and HIV. Despite the known significance of ATE1 in mammalian cellular function, past biophysical studies of this enzyme have mainly focused on yeast ATE1, leaving the mechanism of arginylation in mammalian cells unclear. In this study, we sought to structurally and biophysically characterize mouse (Mus musculus) ATE1. Using size-exclusion chromatography (SEC), small angle X-ray scattering (SAXS), and hydrogen deuterium exchange mass spectrometry (HDX-MS), assisted by AlphaFold modeling, we found that mouse ATE1 is structurally more complex than yeast ATE1. Importantly, our data indicate the existence of an intrinsically disordered region (IDR) in all mouse ATE1 splice variants. However, comparative HDX-MS analyses show that yeast ATE1 does not have such an IDR, consistent with prior X-ray, cryo-EM, and SAXS analyses. Furthermore, bioinformatics approaches reveal that mammalian ATE1 sequences, as well as in a large majority of other eukaryotes, contain an IDR-like sequence positioned in proximity to the ATE1 GNAT active-site fold. Computational analysis suggests that the IDR likely facilitates the formation of the complex between ATE1 and tRNAArg, adding a new complexity to ATE1 structure and providing new insights for future studies of ATE1 functions.

6.
bioRxiv ; 2024 Sep 09.
Article in English | MEDLINE | ID: mdl-39314299

ABSTRACT

The structures of RNA:RNA complexes regulate many biological processes. Despite their importance, protein-free RNA:RNA complexes represent a tiny fraction of experimentally-determined structures. Here, we describe a joint small-angle X-ray and neutron scattering (SAXS/SANS) approach to structurally interrogate conformational changes in a model RNA:RNA complex. Using SAXS, we measured the solution structures of the individual RNAs in their free state and of the overall RNA:RNA complex. With SANS, we demonstrate, as a proof-of-principle, that isotope labeling and contrast matching (CM) can be combined to probe the bound state structure of an RNA within a selectively deuterated RNA:RNA complex. Furthermore, we show that experimental scattering data can validate and improve predicted AlphaFold 3 RNA:RNA complex structures to reflect its solution structure. Our work demonstrates that in silico modeling, SAXS, and CM-SANS can be used in concert to directly analyze conformational changes within RNAs when in complex, enhancing our understanding of RNA structure in functional assemblies.

7.
Mol Pharm ; 21(9): 4553-4564, 2024 Sep 02.
Article in English | MEDLINE | ID: mdl-39163212

ABSTRACT

The solution viscosity and protein-protein interactions (PPIs) as a function of temperature (4-40 °C) were measured at a series of protein concentrations for a monoclonal antibody (mAb) with different formulation conditions, which include NaCl and sucrose. The flow activation energy (Eη) was extracted from the temperature dependence of solution viscosity using the Arrhenius equation. PPIs were quantified via the protein diffusion interaction parameter (kD) measured by dynamic light scattering, together with the osmotic second virial coefficient and the structure factor obtained through small-angle X-ray scattering. Both viscosity and PPIs were found to vary with the formulation conditions. Adding NaCl introduces an attractive interaction but leads to a significant reduction in the viscosity. However, adding sucrose enhances an overall repulsive effect and leads to a slight decrease in viscosity. Thus, the averaged (attractive or repulsive) PPI information is not a good indicator of viscosity at high protein concentrations for the mAb studied here. Instead, a correlation based on the temperature dependence of viscosity (i.e., Eη) and the temperature sensitivity in PPIs was observed for this specific mAb. When kD is more sensitive to the temperature variation, it corresponds to a larger value of Eη and thus a higher viscosity in concentrated protein solutions. When kD is less sensitive to temperature change, it corresponds to a smaller value of Eη and thus a lower viscosity at high protein concentrations. Rather than the absolute value of PPIs at a given temperature, our results show that the temperature sensitivity of PPIs may be a more useful metric for predicting issues with high viscosity of concentrated solutions. In addition, we also demonstrate that caution is required in choosing a proper protein concentration range to extract kD. In some excipient conditions studied here, the appropriate protein concentration range needs to be less than 4 mg/mL, remarkably lower than the typical concentration range used in the literature.


Subject(s)
Antibodies, Monoclonal , Sodium Chloride , Sucrose , Temperature , Antibodies, Monoclonal/chemistry , Viscosity , Sucrose/chemistry , Sodium Chloride/chemistry , Solutions , Scattering, Small Angle
8.
IUCrJ ; 11(Pt 5): 675-694, 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-39088001

ABSTRACT

Owing to their exceptional properties, hard materials such as advanced ceramics, metals and composites have enormous economic and societal value, with applications across numerous industries. Understanding their microstructural characteristics is crucial for enhancing their performance, materials development and unleashing their potential for future innovative applications. However, their microstructures are unambiguously hierarchical and typically span several length scales, from sub-ångstrom to micrometres, posing demanding challenges for their characterization, especially for in situ characterization which is critical to understanding the kinetic processes controlling microstructure formation. This review provides a comprehensive description of the rapidly developing technique of ultra-small angle X-ray scattering (USAXS), a nondestructive method for probing the nano-to-micrometre scale features of hard materials. USAXS and its complementary techniques, when developed for and applied to hard materials, offer valuable insights into their porosity, grain size, phase composition and inhomogeneities. We discuss the fundamental principles, instrumentation, advantages, challenges and global status of USAXS for hard materials. Using selected examples, we demonstrate the potential of this technique for unveiling the microstructural characteristics of hard materials and its relevance to advanced materials development and manufacturing process optimization. We also provide our perspective on the opportunities and challenges for the continued development of USAXS, including multimodal characterization, coherent scattering, time-resolved studies, machine learning and autonomous experiments. Our goal is to stimulate further implementation and exploration of USAXS techniques and inspire their broader adoption across various domains of hard materials science, thereby driving the field toward discoveries and further developments.

9.
Luminescence ; 39(8): e4856, 2024 Aug.
Article in English | MEDLINE | ID: mdl-39129424

ABSTRACT

Most nonconventional luminogens enjoy good water solubility and biocompatibility, showing unique application prospects in fields like biological imaging. Although clustering-triggered emission (CTE) mechanisms have been proposed to explain such emissions, the have not been thoroughly elucidated, which limits their development and application. Here, the photoluminescence properties of carboxymethyl ß-cyclodextrin (CM-ß-CD) aqueous solution are utilized to further investigate the effects of changes in concentration, in order to elucidate the emission mechanism through cryo-transmission electron microscopy (cryo-TEM), small-angle X-ray scattering (SAXS), molecular interaction analysis, and theoretical calculation. The results showed that the size distribution, morphology, and distance between water aggregates were successfully correlated with the cluster emission centers. The emission mechanism of nonconventional luminogen solutions was more clearly and intuitively elucidated, which has a promoting effect on the emission and application of this field. It is interesting that temperature-dependent emission spectra show the blue-shift phenomenon of PL with increasing excitation wavelengths. Moreover, due to its strong static quenching effect for Fe3+, CM-ß-CD can efficiently detect Fe3+ in mixed-ion aqueous solutions. It provides a strategy to clarify the CTE mechanism of nonconventional luminogen solutions more clearly and its application of mixed-ion detection.


Subject(s)
Water , beta-Cyclodextrins , beta-Cyclodextrins/chemistry , Water/chemistry , Luminescence , Ions/chemistry , Solutions , X-Ray Diffraction , Scattering, Small Angle , Molecular Structure , Ferric Compounds/chemistry
10.
Food Res Int ; 192: 114680, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39147535

ABSTRACT

Driven by the acknowledged health and functional properties of milk fat globules (MFGs), there is a growing interest to develop gentle methodologies for separation of fat from milk. In this study, separation of fat from raw milk and fractionation in streams containing MFGs of different size was achieved using a series of two silicon carbide ceramic membranes. A first step consisting of a 1.4 µm membrane aimed to concentrate the bulk of the fat, i.e. the larger MFGs (D[4,3] âˆ¼ 4 µm) followed by a 0.5 µm fractionation aimed to concentrate the residual milk fat in the permeate, i.e. fraction with the smaller MFGs (D[4,3] âˆ¼ 1.8-2.4 µm. The fat separation performance showed a yield of 92 % for the 1.4 µm membrane and 97 % for the 0.5 µm membrane. Both fat enriched retentates showed, by the confocal laser scanning microscopy, intact MFGs with limited damage in the MFG membrane. The fatty acid profile analysis and SAXS showed minor differences in fat acid composition and the crystallization behavior was related to differences in the fat content. The 0.5 µm permeate containing the smallest MFGs however showed larger aggregates and a trinomial particle size distribution, due to probably pore pressure induced coalescences. The series of silicon carbide membranes showed potential to concentrate some of MFGM proteins such as Periodic Schiff base 3/4 and cluster of differentiation 36 especially in the 0.5 µm retentates. A shift in casein to whey protein ratio from 80:20 (milk) to 50:50 was obtained in the final 0.5 µm permeate, which opens new opportunities for product development.


Subject(s)
Carbon Compounds, Inorganic , Glycolipids , Glycoproteins , Lipid Droplets , Milk , Silicon Compounds , Lipid Droplets/chemistry , Silicon Compounds/chemistry , Glycolipids/chemistry , Carbon Compounds, Inorganic/chemistry , Glycoproteins/chemistry , Glycoproteins/analysis , Animals , Milk/chemistry , Membranes, Artificial , Particle Size , Fatty Acids/analysis , Fatty Acids/chemistry , X-Ray Diffraction , Sialoglycoproteins , Scattering, Small Angle , Chemical Fractionation/methods
11.
J Appl Crystallogr ; 57(Pt 4): 1127-1136, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-39108810

ABSTRACT

Small-angle X-ray and neutron scattering (SAXS and SANS) patterns from certain semicrystalline polymers and liquid crystals contain discrete reflections from ordered assemblies and central diffuse scattering (CDS) from uncorrelated structures. Systems with imperfectly ordered lamellar structures aligned by stretching or by a magnetic field produce four distinct SAXS patterns: two-point 'banana', four-point pattern, four-point 'eyebrow' and four-point 'butterfly'. The peak intensities of the reflections lie not on a layer line, or the arc of a circle, but on an elliptical trajectory. Modeling shows that randomly placed lamellar stacks modified by chain slip and stack rotation or interlamellar shear can create these forms. On deformation, the isotropic CDS becomes an equatorial streak with an oval, diamond or two-bladed propeller shape, which can be analyzed by separation into isotropic and oriented components. The streak has elliptical intensity contours, a natural consequence of the imperfect alignment of the elongated scattering objects. Both equatorial streaks and two- and four-point reflections can be fitted in elliptical coordinates with relatively few parameters. Equatorial streaks can be analyzed to obtain the size and orientation of voids, fibrils or surfaces. Analyses of the lamellar reflection yield lamellar spacing, stack orientation (interlamellar shear) angle α and chain slip angle ϕ, as well as the size distribution of the lamellar stacks. Currently available computational tools allow these microstructural parameters to be rapidly refined.

12.
J Appl Crystallogr ; 57(Pt 4): 955-965, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-39108817

ABSTRACT

Small-angle scattering (SAS) is a key experimental technique for analyzing nanoscale structures in various materials. In SAS data analysis, selecting an appropriate mathematical model for the scattering intensity is critical, as it generates a hypothesis of the structure of the experimental sample. Traditional model selection methods either rely on qualitative approaches or are prone to overfitting. This paper introduces an analytical method that applies Bayesian model selection to SAS measurement data, enabling a quantitative evaluation of the validity of mathematical models. The performance of the method is assessed through numerical experiments using artificial data for multicomponent spherical materials, demonstrating that this proposed analysis approach yields highly accurate and interpretable results. The ability of the method to analyze a range of mixing ratios and particle size ratios for mixed components is also discussed, along with its precision in model evaluation by the degree of fitting. The proposed method effectively facilitates quantitative analysis of nanoscale sample structures in SAS, which has traditionally been challenging, and is expected to contribute significantly to advancements in a wide range of fields.

13.
J Appl Crystallogr ; 57(Pt 4): 986-1000, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-39108827

ABSTRACT

Small-angle X-ray tensor tomography and the related wide-angle X-ray tensor tomography are X-ray imaging techniques that tomographically reconstruct the anisotropic scattering density of extended samples. In previous studies, these methods have been used to image samples where the scattering density depends slowly on the direction of scattering, typically modeling the directionality, i.e. the texture, with a spherical harmonics expansion up until order ℓ = 8 or lower. This study investigates the performance of several established algorithms from small-angle X-ray tensor tomography on samples with a faster variation as a function of scattering direction and compares their expected and achieved performance. The various algorithms are tested using wide-angle scattering data from an as-drawn steel wire with known texture to establish the viability of the tensor tomography approach for such samples and to compare the performance of existing algorithms.

14.
Carbohydr Polym ; 343: 122473, 2024 Nov 01.
Article in English | MEDLINE | ID: mdl-39174098

ABSTRACT

A thermoresponsive highly branched polysaccharide derivative was revealed from commercially available highly branched cyclic dextrin (HBCD), originally synthesized from amylopectin. Eight samples of partially substituted ethyl carbamate derivatives of HBCD (HEC) were prepared with a degree of substitution DS ranging from 0.27 to 1.46. Three samples with DS = 0.88, 1.05, and 1.22 showed LCST type phase separation in water. The intrinsic viscosity and form factor in water were typical of the hyperbranched structure. The intermolecular interactions between HEC and iodine or 1-anilinonaphthalene-8-sulfonic acid (ANS) were appreciably different from those of the linear analog (AEC), suggesting that the locally bent helical conformation of highly branched HEC chains has a different interaction with small molecules. The phase diagram of HEC-water systems was accidentally similar to that of the linear chain with the same molar mass and DS, although the one phase region of the branched polymer chain-poor solvent system is usually wider than that of the corresponding linear chain. This is likely due to the lower hydration nature of the polymer segment of HEC chains than that of the corresponding linear chain.

15.
FEBS J ; 2024 Aug 23.
Article in English | MEDLINE | ID: mdl-39180270

ABSTRACT

The Nipah and Hendra viruses are severe human pathogens. In addition to the P protein, their P gene also encodes the V and W proteins that share with P their N-terminal intrinsically disordered domain (NTD) and possess distinct C-terminal domains (CTDs). The W protein is a key player in the evasion of the host innate immune response. We previously showed that the W proteins are intrinsically disordered and can form amyloid-like fibrils. However, structural information on W CTD (CTDW) and its potential contribution to the fibrillation process is lacking. In this study, we demonstrate that CTDWS are disordered and able to form dimers mediated by disulfide bridges. We also show that the NTD and the CTDW interact with each other and that this interaction triggers both a gain of secondary structure and a chain compaction within the NTD. Finally, despite the lack of intrinsic fibrillogenic properties, we show that the CTDW favors the formation of fibrils by the NTD both in cis and in trans. Altogether, the results herein presented shed light on the molecular mechanisms underlying Henipavirus pathogenesis and may thus contribute to the development of targeted therapies.

16.
Curr Res Struct Biol ; 8: 100156, 2024.
Article in English | MEDLINE | ID: mdl-39131116

ABSTRACT

Bacteria have evolved elaborate mechanisms to thrive in stressful environments. F-like plasmids in gram-negative bacteria encode for a multi-protein Type IV Secretion System (T4SSF) that is functional for bacterial proliferation and adaptation through the process of conjugation. The periplasmic protein TrbB is believed to have a stabilizing chaperone role in the T4SSF assembly, with TrbB exhibiting disulfide isomerase (DI) activity. In the current report, we demonstrate that the deletion of the disordered N-terminus of TrbBWT, resulting in a truncation construct TrbB37-161, does not affect its catalytic in vitro activity compared to the wild-type protein (p = 0.76). Residues W37-K161, which include the active thioredoxin motif, are sufficient for DI activity. The N-terminus of TrbBWT is disordered as indicated by a structural model of GST-TrbBWT based on ColabFold-AlphaFold2 and Small Angle X-Ray Scattering data and 1H-15N Heteronuclear Single Quantum Correlation (HSQC) spectroscopy of the untagged protein. This disordered region likely contributes to the protein's dynamicity; removal of this region results in a more stable protein based on 1H-15N HSQC and Circular Dichroism Spectroscopies. Lastly, size exclusion chromatography analysis of TrbBWT in the presence of TraW, a T4SSF assembly protein predicted to interact with TrbBWT, does not support the inference of a stable complex forming in vitro. This work advances our understanding of TrbB's structure and function, explores the role of structural disorder in protein dynamics in the context of a T4SSF accessory protein, and highlights the importance of redox-assisted protein folding in the T4SSF.

17.
Proc Natl Acad Sci U S A ; 121(34): e2315510121, 2024 Aug 20.
Article in English | MEDLINE | ID: mdl-39133851

ABSTRACT

Mechanical energy, specifically in the form of ultrasound, can induce pressure variations and temperature fluctuations when applied to an aqueous media. These conditions can both positively and negatively affect protein complexes, consequently altering their stability, folding patterns, and self-assembling behavior. Despite much scientific progress, our current understanding of the effects of ultrasound on the self-assembly of amyloidogenic proteins remains limited. In the present study, we demonstrate that when the amplitude of the delivered ultrasonic energy is sufficiently low, it can induce refolding of specific motifs in protein monomers, which is sufficient for primary nucleation; this has been revealed by MD. These ultrasound-induced structural changes are initiated by pressure perturbations and are accelerated by a temperature factor. Furthermore, the prolonged action of low-amplitude ultrasound enables the elongation of amyloid protein nanofibrils directly from natively folded monomeric lysozyme protein, in a controlled manner, until it reaches a critical length. Using solution X-ray scattering, we determined that nanofibrillar assemblies, formed either under the action of sound or from natively fibrillated lysozyme, share identical structural characteristics. Thus, these results provide insights into the effects of ultrasound on fibrillar protein self-assembly and lay the foundation for the potential use of sound energy in protein chemistry.


Subject(s)
Amyloid , Muramidase , Amyloid/chemistry , Amyloid/metabolism , Muramidase/chemistry , Muramidase/metabolism , Protein Folding , Temperature , Ultrasonic Waves , Molecular Dynamics Simulation
18.
Appl Spectrosc ; : 37028241272257, 2024 Sep 05.
Article in English | MEDLINE | ID: mdl-39094006

ABSTRACT

In this study, a new system was developed to carry out simultaneous near-infrared (NIR) and small-angle X-ray scattering (SAXS) measurements. Aged polypropylene (PP) was examined with the NIR-SAXS system to demonstrate how it can be utilized to derive pertinent information about the polymer structure. Pairs of SAXS profiles and NIR spectra of PP in its initial state and after aging were measured to derive an in-depth understanding of the aging phenomenon. The SAXS profiles of the PP samples showed a clear shift of the SAXS peak to the lower q direction induced by the thermal aging, indicating an increase in the length of the long-period structure. Two-trace two-dimensional (2T2D) asynchronous correlation spectra derived from NIR spectra clearly revealed that the aging treatment leads to a substantial increase in the spectral intensity of the regularity bands representing the longer helix present in a folded lamellar structure. In other words, it suggests that the long helix structure is more abundantly present than the short helix structure in the aged PP than in the initial PP. By combining the information derived from the SAXS profiles and NIR spectra, the details of the aging-induced variation were clearly determined. Namely, aging causes additional crystallization of the PP by developing more helical structures, which involves an increase in the lamellar thickness as well as a decrease in the amorphous region. The growth of the rigid crystalline phase restricts the elastic deformation in the amorphous structure, which eventually induces the deterioration of PP by making the polymer hard but brittle. Such observation, in turn, implies that retarding or accelerating the crystallized structure of PP substantially works to control the progress of aging.

19.
J Struct Biol ; 216(3): 108115, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39117045

ABSTRACT

Human RAD52 protein binds DNA and is involved in genomic stability maintenance and several forms of DNA repair, including homologous recombination and single-strand annealing. Despite its importance, there are very few structural details about the variability of the RAD52 ring size and the RAD52 C-terminal protein-protein interaction domains. Even recent attempts to employ cryogenic electron microscopy (cryoEM) methods on full-length yeast and human RAD52 do not reveal interpretable structures for the C-terminal half that contains the replication protein A (RPA) and RAD51 binding domains. In this study, we employed the monodisperse purification of two RAD52 deletion constructs and small angle X-ray scattering (SAXS) to construct a structural model that includes RAD52's RPA binding domain. This model is of interest to DNA repair specialists as well as for drug development against HR-deficient cancers.


Subject(s)
Protein Binding , Rad52 DNA Repair and Recombination Protein , Replication Protein A , Scattering, Small Angle , Humans , Rad52 DNA Repair and Recombination Protein/metabolism , Rad52 DNA Repair and Recombination Protein/genetics , Rad52 DNA Repair and Recombination Protein/chemistry , Replication Protein A/metabolism , Replication Protein A/chemistry , Replication Protein A/genetics , Rad51 Recombinase/metabolism , Rad51 Recombinase/chemistry , Rad51 Recombinase/genetics , X-Ray Diffraction/methods , DNA Repair , Models, Molecular , Protein Domains
20.
Int J Biol Macromol ; 278(Pt 1): 134556, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39128762

ABSTRACT

Structural insight eludes on how full-length gelsolin depolymerizes and caps filamentous (F-)actin, while the same entity can nucleate polymerization of G-actins. Analyzing small angle X-ray scattering (SAXS) data, we deciphered assemblies which enable these contrasting processes. Mixing Ca2+-gelsolin with F-actin in high salt F-buffer resulted in depolymerization of ordered F-actin rods to smaller sized species which became monodispersed upon dialysis with low salt G-buffer. These entities were the ternary (GA2) and binary (GA) complexes of gelsolin and actin with radius of gyration and maximum linear dimension of 4.55 and 4.68 nm, and 15 and 16 nm, respectively. Using size exclusion chromatography in-line with SAXS, we confirmed that initially GA and GA2 species are formed as seen upon depolymerization of F-actin followed by dialysis. Interestingly, while GA2 could seed formation of native-like F-actin in both G- and F-buffer, GA failed in G-buffer. Thus, GA2 and GA are the central species formed via depolymerization or towards nucleation. SAXS profile referenced modeling revealed that: 1) in GA, actin is bound to the C-terminal half of gelsolin, and 2) in GA2, second actin binds to the open N-terminal half accompanied by dramatic rearrangements across g1-g2 and g3-g4 linkers.


Subject(s)
Actins , Calcium , Gelsolin , Scattering, Small Angle , X-Ray Diffraction , Gelsolin/chemistry , Actins/chemistry , Calcium/chemistry , Models, Molecular , Protein Binding , Animals , Protein Conformation
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