scholarly journals Evidence for a major structural change in Escherichia coli chorismate synthase induced by flavin and substrate binding

1998 ◽  
Vol 335 (2) ◽  
pp. 319-327 ◽  
Author(s):  
Peter MACHEROUX ◽  
Ernst SCHÖNBRUNN ◽  
Dmitri I. SVERGUN ◽  
Vladimir V. VOLKOV ◽  
Michel H. J. KOCH ◽  
...  
Keyword(s):  
Ternary Complex ◽  
Structural Changes ◽  
Tertiary Structure ◽  
Tryptophan Fluorescence ◽  
Cd Spectroscopy ◽  
Scattering Data ◽  
Discrete State ◽  
Chorismate Synthase ◽  
X Ray Scattering ◽  
Ft Ir

Chorismate synthase (EC 4.6.1.4) catalyses the conversion of 5-enolpyruvylshikimate 3-phosphate (EPSP) into chorismate, and requires reduced FMN as a cofactor. The enzyme can bind first oxidized FMN and then EPSP to form a stable ternary complex which does not undergo turnover. This complex can be considered to be a model of the ternary complex between enzyme, EPSP and reduced FMN immediately before catalysis commences. It is shown that the binding of oxidized FMN and EPSP to chorismate synthase affects the properties and structure of the protein. Changes in small-angle X-ray scattering data, decreased susceptibility to tryptic digestion and altered Fourier-transform (FT)-IR spectra provide the first strong evidence for major structural changes in the protein. The tetrameric enzyme undergoes correlated screw movements leading to a more overall compact shape, with no change in oligomerization state. The changes in the FT-IR spectrum appear to reflect changes in the environment of the secondary-structural elements rather than alterations in their distribution, because the far-UV CD spectrum changes very little. Changes in the mobility of the protein during non-denaturing PAGE indicate that the ternary complex may exhibit less conformational flexibility than the apoprotein. Increased enzyme solubility and decreased tryptophan fluorescence are discussed in the light of the observed structural changes. The secondary structure of the enzyme was investigated using far-UV CD spectroscopy, and the tertiary structure was predicted to be an α–β-barrel using discrete state-space modelling.

scholarly journals Effect of cosolvents (polyols) on structural and foaming properties of soy protein isolate  

2017 ◽  
Vol 35 (No. 1) ◽  
pp. 57-66 ◽  
Author(s):  
Pan Mingzhe ◽  
Meng Xianjun ◽  
Jiang Lianzhou ◽  
Yu Dianyu ◽  
Liu Tianyi
Keyword(s):  
Soy Protein ◽  
Structural Changes ◽  
Foam Stability ◽  
Soy Protein Isolate ◽  
Tryptophan Fluorescence ◽  
Surface Hydrophobicity ◽  
Cd Spectroscopy ◽  
Protein Isolate ◽  
Foaming Properties ◽  
Intrinsic Tryptophan Fluorescence

Effect of polyols (mannitol, sorbitol, and xylitol) at three concentrations (5, 10, and 15% w/w) on the structure of soy protein isolates (SPI) was investigated. Changes in foaming properties of SPI were then examined with the addition of polyols at different concentrations. The interactions between SPI and polyols resulted in a substantial decrease in protein surface hydrophobicity and intrinsic tryptophan fluorescence intensity, along with the covering of tyrosine. Furthermore, circular dichroism (CD) spectroscopy of SPI suggested that a more ordered and compact conformation was induced by polyols. Consequently, these structural changes led to lower foamability of SPI. An increase in the viscosity of SPI suspension seemed to be advantageous for improving the foam stability of SPI.

scholarly journals SAXSDom: Modeling multi-domain protein structures using small-angle X-ray scattering data

2019 ◽  
Author(s):  
Jie Hou ◽  
Badri Adhikari ◽  
John J. Tanner ◽  
Jianlin Cheng
Keyword(s):  
Homology Modeling ◽  
Small Angle ◽  
Tertiary Structure ◽  
Protein Structures ◽  
Scattering Data ◽  
Multidomain Proteins ◽  
X Ray ◽  
X Ray Scattering ◽  
Domain Protein ◽  
Ray Scattering

AbstractMany proteins are composed of several domains that pack together into a complex tertiary structure. Some multidomain proteins can be challenging for protein structure modeling, particularly those for which templates can be found for the domains but not for the entire sequence. In such cases, homology modeling can generate high quality models of the domains but not for the assembled protein. Small-angle X-ray scattering (SAXS) reports on the solution structural properties of proteins and has the potential for guiding homology modeling of multidomain proteins. In this work, we describe a novel multi-domain protein assembly modeling method, SAXSDom, that integrates experimental knowledge from SAXS profiles with probabilistic Input-Output Hidden Markov model (IOHMM). Four scoring functions to account for the energetic contribution of SAXS restraints for domain assembly were developed and tested. The method was evaluated on multi-domain proteins from two public datasets. Based on the results, the accuracy of domain assembly was improved for 40 out of 46 CASP multi-domain proteins in terms of RMSD and TM-score when SAXS information was used. Our method also achieved higher accuracy for at least 45 out of 73 multi-domain proteins according to RMSD and TM-score metrics in the AIDA dataset. The results demonstrate that SAXS data can provide useful information to improve the accuracy of domain-domain assembly. The source code and tool packages are available at http://github.com/multicom-toolbox/SAXSDom.

scholarly journals Direct Evidence of Effect of Glycerol on Hydration and Helix-to-Sheet Transition of Myoglobin

2018 ◽  
Author(s):  
M. Hirai ◽  
S. Ajito ◽  
M. Sugiyama ◽  
H. Iwase ◽  
S.-I. Takata ◽  
...  
Keyword(s):  
Neutron Scattering ◽  
Tertiary Structure ◽  
Hydration Shell ◽  
Scattering Data ◽  
Variation Method ◽  
Protein Surface ◽  
X Ray ◽  
X Ray Scattering ◽  
Structural Levels ◽  
Ray Scattering

AbstractBy using wide-angle X-ray scattering (WAXS), small-angle neutron scattering, and theoretical scattering function simulation, we have clarified the effect of glycerol on both the thermal structure transition and the hydration-shell of myoglobin. At the glycerol concentration, ≤ ∼40 % v/v, the decreasing tendency in the maximum dimension and the radius of gyration was observed by X-ray scattering. The neutron scattering result using the inverse contrast variation method directly shows the preservation of the hydration-shell density at the concentration ≤ ∼40 % v/v. This phenomenon is reasonably explained by the preferential exclusion of glycerol from the protein surface to preserve the hydration shell, as suggested by the previous studies. While, at the concentration, ≥ 50 % v/v, the opposite tendency was observed. It suggests the preferential solvation (partial preferential penetration or replacement of glycerol into or with hydration-shell water surrounding the protein surface) occurs at the higher concentration. The observed WAXS scattering data covers the distinct hierarchical structural levels of myoglobin structure ranging from the tertiary structure to the secondary one. Therefore, we have clarified the effect of glycerol on the thermal structural stability myoglobin at different hierarchical structural levels separately. Against the temperature rise, the structural transition temperatures for all hierarchical structural levels were elevated. Especially, the tertiary structure of myoglobin was more stabilized compared with the internal-structure and the helix-to-cross transition. It suggests that the protective action of glycerol on protein structures essentially results from the preservation of the preferential hydration-shell of proteins.

Peroxynitrite-Mediated Structural Changes in Histone H2A: Biochemical and Biophysical Analysis

2020 ◽  
Vol 27 (10) ◽  
pp. 989-998
Author(s):  
Md. Asad Khan ◽  
Md. Faiz Akram ◽  
Khursheed Alam ◽  
Haseeb Ahsan ◽  
Moshahid A. Rizvi
Keyword(s):  
Oxidative Stress ◽  
Structural Changes ◽  
Tertiary Structure ◽  
Histone H2a ◽  
Folded Structure ◽  
Highly Sensitive ◽  
Biophysical Analysis ◽  
Core Histones ◽  
Ft Ir ◽  
Biophysical Techniques

Background: Peroxynitrite, a nitrating and oxidizing agent, is formed by the interaction between nitric oxide and superoxide radicals. H2A histone is a basic nucleoprotein and is one of the major core histones responsible for packaging DNA. It has been shown that they are highly sensitive to oxidizing and nitrating agents. Objective: Nitration of tyrosine residues in proteins by peroxynitrite is regarded as a marker of nitrosative damage. The dityrosine bond, an oxidative covalent cross-link between two tyrosines in protein, is increasingly identified as a marker of oxidative stress, aging and neurodegerative diseases. Methods: Peroxinitrite-mediated nitration and dinitration in H2A histone was assessed by various biophysical techniques. Results: The data presented in this study showed that the dityrosine content was found to be elevated in H2A histone modified with peroxynitrite. The formation of dityrosine showed a decrease in fluorescence intensity, generation of a new peak in FT-IR, increase in hydrodynamic size, and loss of secondary and tertiary structure of H2A resulting in a partially folded structure. Conclusion: We report that H2A may undergo conformational and structural changes under nitrosative and oxidative stress from the deleterious effects of peroxynitrite.

scholarly journals Tumor protein D54 binds intracellular nanovesicles via an amphipathic lipid packing sensor (ALPS) motif

2021 ◽  
Author(s):  
Antoine Reynaud ◽  
Maud Magdeleine ◽  
Amanda Patel ◽  
Anne Sophie Gay ◽  
Delphine Debayle ◽  
...  
Keyword(s):  
Lipid Membranes ◽  
Structural Changes ◽  
Covalent Binding ◽  
Limited Proteolysis ◽  
Coiled Coil ◽  
Tryptophan Fluorescence ◽  
Cd Spectroscopy ◽  
Dependent Manner ◽  
Lipid Packing ◽  
Physicochemical Features

AbstractTumor Protein D54 (TPD54) is an abundant cytosolic protein that belongs to the TPD52 family, a family of four proteins (TPD52, 53, 54 and 55) that are overexpressed in several cancer cells. Even though the functions of these proteins remain elusive, recent investigations indicate that TPD54 binds to very small cytosolic vesicles with a diameter of ca. 30 nm, half the size of classical transport vesicles (e.g. COPI and COPII). Here, we investigated the mechanism of intracellular nanovesicle capture by TPD54. Bioinformatical analysis suggests that TPD54 contains a small coiled-coil followed by several amphipathic helices, which could fold upon binding to lipid membranes. One of these helices has the physicochemical features of an Amphipathic Lipid Packing Sensor (ALPS) motif, which, in other proteins, enables membrane binding in a curvature-dependent manner. Limited proteolysis, CD spectroscopy, tryptophan fluorescence and cysteine mutagenesis coupled to covalent binding of a membrane sensitive probe show that binding of TPD54 to small liposomes is accompanied by large structural changes in the amphipathic helix region. TPD54 binding to artificial liposomes is very sensitive to liposome size and to lipid unsaturation but is poorly dependent on lipid charge. Cellular investigations confirmed the key role of the ALPS motif in vesicle targeting. Surprisingly, the vesicles selected by TPD54 poorly overlap with those captured by the golgin GMAP-210, a long vesicle tether at the Golgi apparatus, which displays a dimeric coiled-coil architecture and an N-terminal ALPS motif. We propose that TPD54 recognizes nanovesicles through a combination of ALPS-dependent and -independent mechanisms.

Structure and catalytic mechanism of the evolutionarily unique bacterial chalcone isomerase

2015 ◽  
Vol 71 (4) ◽  
pp. 907-917 ◽  
Author(s):  
Maren Thomsen ◽  
Anne Tuukkanen ◽  
Jonathan Dickerhoff ◽  
Gottfried J. Palm ◽  
Hanna Kratzat ◽  
...  
Keyword(s):  
Active Site ◽  
Catalytic Mechanism ◽  
Tertiary Structure ◽  
Degradation Pathway ◽  
Chalcone Isomerase ◽  
Scattering Data ◽  
Chlorite Dismutase ◽  
H Nmr ◽  
X Ray Scattering ◽  
Flower Pigmentation

Flavonoids represent a large class of secondary metabolites produced by plants. These polyphenolic compounds are well known for their antioxidative abilities, are antimicrobial phytoalexins responsible for flower pigmentation to attract pollinators and, in addition to other properties, are also specific bacterial regulators governing the expression ofRhizobiumgenes involved in root nodulation (Firminet al., 1986). The bacterial chalcone isomerase (CHI) fromEubacterium ramuluscatalyses the first step in a flavanone-degradation pathway by ring opening of (2S)-naringenin to form naringenin chalcone. The structural biology and enzymology of plant CHIs have been well documented, whereas the existence of bacterial CHIs has only recently been elucidated. This first determination of the structure of a bacterial CHI provides detailed structural insights into the key step of the flavonoid-degradation pathway. The active site could be confirmed by co-crystallization with the substrate (2S)-naringenin. The stereochemistry of the proposed mechanism of the isomerase reaction was verified by specific1H/2H isotope exchange observed by1H NMR experiments and was further supported by mutagenesis studies. The active site is shielded by a flexible lid, the varying structure of which could be modelled in different states of the catalytic cycle using small-angle X-ray scattering data together with the crystallographic structures. Comparison of bacterial CHI with the plant enzyme fromMedicago sativareveals that they have unrelated folds, suggesting that the enzyme activity evolved convergently from different ancestor proteins. Despite the lack of any functional relationship, the tertiary structure of the bacterial CHI shows similarities to the ferredoxin-like fold of a chlorite dismutase and the stress-related protein SP1.

scholarly journals Structure of the amorphous titania precursor phase of N-doped photocatalysts

RSC Advances ◽  
2021 ◽  
Vol 11 (15) ◽  
pp. 8619-8627
Author(s):  
I. E. Grey ◽  
P. Bordet ◽  
N. C. Wilson
Keyword(s):  
Thermal Analyses ◽  
Real Space ◽  
Ammonia Solution ◽  
Scattering Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Amorphous Titania ◽  
Precursor Phase ◽  
Titania Precursor ◽  
Titanyl Sulphate

Amorphous titania samples prepared by ammonia solution neutralization of titanyl sulphate have been characterized by chemical and thermal analyses, and with reciprocal-space and real-space fitting of wide-angle synchrotron X-ray scattering data.

scholarly journals Effects on Lignin Redistribution in Eucalyptus globulus Fibres Pre-Treated by Steam Explosion: A Microscale Study to Cellulose Accessibility

Biomolecules ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 507
Author(s):  
Eduardo Troncoso-Ortega ◽  
Rosario del P. Castillo ◽  
Pablo Reyes-Contreras ◽  
Patricia Castaño-Rivera ◽  
Regis Teixeira Mendonça ◽  
...  
Keyword(s):  
Enzymatic Hydrolysis ◽  
Eucalyptus Globulus ◽  
Steam Explosion ◽  
Laser Scanning ◽  
Structural Changes ◽  
Micro Particles ◽  
Cellulose Accessibility ◽  
Ft Ir ◽  
Enzymatic Accessibility ◽  
Physical And Chemical

The objective of this study was to investigate structural changes and lignin redistribution in Eucalyptus globulus pre-treated by steam explosion under different degrees of severity (S0), in order to evaluate their effect on cellulose accessibility by enzymatic hydrolysis. Approximately 87.7% to 98.5% of original glucans were retained in the pre-treated material. Glucose yields after the enzymatic hydrolysis of pre-treated material improved from 19.4% to 85.1% when S0 was increased from 8.53 to 10.42. One of the main reasons for the increase in glucose yield was the redistribution of lignin as micro-particles were deposited on the surface and interior of the fibre cell wall. This information was confirmed by laser scanning confocal fluorescence and FT-IR imaging; these microscopic techniques show changes in the physical and chemical characteristics of pre-treated fibres. In addition, the results allowed the construction of an explanatory model for microscale understanding of the enzymatic accessibility mechanism in the pre-treated lignocellulose.

scholarly journals Structure and Function of Trypsin-Loaded Fibrinolytic Liposomes

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Anna Tanka-Salamon ◽  
Attila Bóta ◽  
András Wacha ◽  
Judith Mihály ◽  
Miklós Lovas ◽  
...  
Keyword(s):  
Freeze Fracture ◽  
Product Concentration ◽  
Plasma Clot ◽  
Dynamic Conditions ◽  
X Ray Scattering ◽  
Transmission Electron ◽  
Ft Ir ◽  
And Function ◽  
Targeted Release ◽  
Fibrinolytic Action

Protease encapsulation and its targeted release in thrombi may contribute to the reduction of haemorrhagic complications of thrombolysis. We aimed to prepare sterically stabilized trypsin-loaded liposomes (SSLT) and characterize their structure and fibrinolytic efficiency. Hydrogenated soybean phosphatidylcholine-basedSSLTwere prepared and their structure was studied by transmission electron microscopy combined with freeze fracture (FF-TEM), Fourier transform infrared spectroscopy (FT-IR), and small-angle X-ray scattering (SAXS). Fibrinolytic activity was examined at 45, 37, or 24°C on fibrin or plasma clots with turbidimetric and permeation-driven lysis assays. Trypsin was shown to be attached to the inner surface of vesicles (SAXS and FF-TEM) close to the lipid hydrophilic/hydrophobic interface (FT-IR). The thermosensitivity ofSSLTwas evidenced by enhanced fibrinolysis at 45°C: time to reduce the maximal turbidity to 20% decreased by 8.6% compared to 37°C and fibrin degradation product concentration in the permeation lysis assay was 2-fold to 5-fold higher than that at 24°C.SSLTexerted its fibrinolytic action on fibrin clots under both static and dynamic conditions, whereas plasma clot dissolution was observed only in the permeation-driven assay. The improved fibrinolytic efficiency ofSSLTunder dynamic conditions suggests that they may serve as a novel therapeutic candidate for dissolution of intravascular thrombi, which are typically exposed to permeation forces.

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