scholarly journals Dimerization of Human Angiogenin and of Variants Involved in Neurodegenerative Diseases

2021 ◽  
Vol 22 (18) ◽  
pp. 10068
Author(s):  
Sabrina Fasoli ◽  
Ilaria Bettin ◽  
Riccardo Montioli ◽  
Andrea Fagagnini ◽  
Daniele Peterle ◽  
...  
Keyword(s):  
Neurodegenerative Diseases ◽  
Three Dimensional ◽  
Size Exclusion ◽  
Active Site Residues ◽  
Ribonucleolytic Activity ◽  
Pathogenic Variants ◽  
Neuronal Progenitors ◽  
Tumor Tissues ◽  
Exclusion Chromatography ◽  
The Central Nervous System

Human Angiogenin (hANG, or ANG, 14.1 kDa) promotes vessel formation and is also called RNase 5 because it is included in the pancreatic-type ribonuclease (pt-RNase) super-family. Although low, its ribonucleolytic activity is crucial for angiogenesis in tumor tissues but also in the physiological development of the Central Nervous System (CNS) neuronal progenitors. Nevertheless, some ANG variants are involved in both neurodegenerative Parkinson disease (PD) and Amyotrophic Lateral Sclerosis (ALS). Notably, some pt-RNases acquire new biological functions upon oligomerization. Considering neurodegenerative diseases correlation with massive protein aggregation, we analyzed the aggregation propensity of ANG and of three of its pathogenic variants, namely H13A, S28N, and R121C. We found no massive aggregation, but wt-ANG, as well as S28N and R121C variants, can form an enzymatically active dimer, which is called ANG-D. By contrast, the enzymatically inactive H13A-ANG does not dimerize. Corroborated by a specific cross-linking analysis and by the behavior of H13A-ANG that in turn lacks one of the two His active site residues necessary for pt-RNases to self-associate through the three-dimensional domain swapping (3D-DS), we demonstrate that ANG actually dimerizes through 3D-DS. Then, we deduce by size exclusion chromatography (SEC) and modeling that ANG-D forms through the swapping of ANG N-termini. In light of these novelties, we can expect future investigations to unveil other ANG determinants possibly related with the onset and/or development of neurodegenerative pathologies.

Molecular cloning and biochemical characterization of a NAD-dependent sorbitol dehydrogenase from cold-adapted Pseudomonas mandelii

2021 ◽  
Author(s):  
Quynh DangThu ◽  
Thu-Thuy Nguyen ◽  
Sei-Heon Jang ◽  
ChangWoo Lee
Keyword(s):  
Biochemical Characterization ◽  
Size Exclusion ◽  
Sorbitol Dehydrogenase ◽  
High Catalytic Activity ◽  
Active Site Residues ◽  
Tertiary Structures ◽  
Cold Adapted ◽  
Pseudomonas Mandelii ◽  
Catalytic Active Site ◽  
Exclusion Chromatography

Abstract Sugar alcohols (polyols) have important roles as nutrients, anti-freezing agents, and scavengers of free radicals in cold-adapted bacteria, but the characteristics of polyol dehydrogenases in cold-adapted bacteria remain largely unknown. In this study, based on the observation that a cold-adapted bacterium Pseudomonas mandelii JR-1 predominantly utilized D-sorbitol as its carbon source, among the four polyols examined (D-galactitol, D-mannitol, D-sorbitol, or D-xylitol), we cloned and characterized a sorbitol dehydrogenase (SDH, EC 1.1.1.14) belonging to the short-chain dehydrogenase/reductase family from this bacterium (the SDH hereafter referred to as PmSDH). PmSDH contained Asn111, Ser140, Tyr153, and Lys157 as catalytic active site residues and existed as a ∼67 kDa dimer in size-exclusion chromatography. PmSDH converted D-sorbitol to D-fructose using NAD+ as a coenzyme and, vice versa, D-fructose to D-sorbitol using NADH as a coenzyme. PmSDH maintained its conformational flexibility, secondary and tertiary structures, and thermal stability at 4–25°C. At 40°C, PmSDH was rapidly denatured. These results indicate that PmSDH, which has a flexible structure and a high catalytic activity at colder temperatures, is well-suited to sorbitol utilization in the cold-adapted bacterium P. mandelii JR-1.

scholarly journals Functional Comparison of the Two Bacillus anthracis Glutamate Racemases

2007 ◽  
Vol 189 (14) ◽  
pp. 5265-5275 ◽  
Author(s):  
Dylan Dodd ◽  
Joseph G. Reese ◽  
Craig R. Louer ◽  
Jimmy D. Ballard ◽  
M. Ashley Spies ◽  
...  
Keyword(s):  
Bacillus Anthracis ◽  
Active Site ◽  
Genomic Sequence ◽  
Ph Dependence ◽  
Size Exclusion ◽  
Kinetic Properties ◽  
Active Site Residues ◽  
Glutamate Racemase ◽  
Genes Encoding ◽  
Exclusion Chromatography

ABSTRACT Glutamate racemase activity in Bacillus anthracis is of significant interest with respect to chemotherapeutic drug design, because l-glutamate stereoisomerization to d-glutamate is predicted to be closely associated with peptidoglycan and capsule biosynthesis, which are important for growth and virulence, respectively. In contrast to most bacteria, which harbor a single glutamate racemase gene, the genomic sequence of B. anthracis predicts two genes encoding glutamate racemases, racE1 and racE2. To evaluate whether racE1 and racE2 encode functional glutamate racemases, we cloned and expressed racE1 and racE2 in Escherichia coli. Size exclusion chromatography of the two purified recombinant proteins suggested differences in their quaternary structures, as RacE1 eluted primarily as a monomer, while RacE2 demonstrated characteristics of a higher-order species. Analysis of purified recombinant RacE1 and RacE2 revealed that the two proteins catalyze the reversible stereoisomerization of l-glutamate and d-glutamate with similar, but not identical, steady-state kinetic properties. Analysis of the pH dependence of l-glutamate stereoisomerization suggested that RacE1 and RacE2 both possess two titratable active site residues important for catalysis. Moreover, directed mutagenesis of predicted active site residues resulted in complete attenuation of the enzymatic activities of both RacE1 and RacE2. Homology modeling of RacE1 and RacE2 revealed potential differences within the active site pocket that might affect the design of inhibitory pharmacophores. These results suggest that racE1 and racE2 encode functional glutamate racemases with similar, but not identical, active site features.

scholarly journals A sensitive core region in the structure of glutathione S-transferases

2003 ◽  
Vol 373 (3) ◽  
pp. 759-765 ◽  
Author(s):  
Jantana WONGSANTICHON ◽  
Thasaneeya HARNNOI ◽  
Albert J. KETTERMAN
Keyword(s):  
Active Site ◽  
Site Directed Mutagenesis ◽  
Size Exclusion ◽  
Single Amino Acid ◽  
Variant Form ◽  
Active Site Residues ◽  
Glutathione S Transferase ◽  
Anopheles Dirus ◽  
Single Amino Acid Change ◽  
Exclusion Chromatography

A variant form of an Anopheles dirus glutathione S-transferase (GST), designated AdGSTD4-4, possesses a single amino acid change of leucine to arginine (Leu-103-Arg). Although residue 103 is outside of the active site, it has major effects on enzymic properties. To investigate these structural effects, site-directed mutagenesis was used to generate mutants by changing the non-polar leucine to alanine, glutamate, isoleucine, methionine, asparagine, or tyrosine. All of the recombinant GSTs showed approximately the same expression level at 25° C. Several of the mutants lacked glutathione (GSH)-binding affinity but were purified by S-hexyl-GSH-based affinity chromatography. However the protein yields (70-fold lower), as well as the GST activity (100-fold lower), of Leu-103-Tyr and Leu-103-Arg purifications were surprisingly low and precluded the performance of kinetic experiments. Size-exclusion chromatography showed that both GSTs Leu-103-Tyr and Leu-103-Arg formed dimers. Using 1-chloro-2,4-dinitrobenzene (CDNB) and GSH substrates to determine kinetic constants it was demonstrated that the other Leu-103 mutants possessed a greater Km towards GSH and a differing Km towards CDNB. The Vmax ranged from 44.7 to 87.0 μmol/min per mg (wild-type, 44.7 μmol/min per mg). Substrate-specificity studies showed different selectivity properties for each mutant. The structural residue Leu-103 affects the active site through H-bond and van-der-Waal contacts with six active-site residues in the GSH binding site. Changes in this interior core residue appear to disrupt internal packing, which affects active-site residues as well as residues at the subunit–subunit interface. Finally, the data suggest that Leu-103 is noteworthy as a sensitive residue in the GST structure that modulates enzyme activity as well as stability.

scholarly journals Myriapod haemocyanin: the first three-dimensional reconstruction of Scolopendra subspinipes and preliminary structural analysis of S. viridicornis

Open Biology ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 190258
Author(s):  
K. C. T. Riciluca ◽  
A. C. Borges ◽  
J. F. R. Mello ◽  
U. C. de Oliveira ◽  
D. C. Serdan ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Signal Peptide ◽  
Oxygen Transport ◽  
Three Dimensional ◽  
Size Exclusion ◽  
Tem Analysis ◽  
Arthropod Species ◽  
Dimensional Reconstruction ◽  
Exclusion Chromatography ◽  
Respiratory Proteins

Haemocyanins (Hcs) are copper-containing, respiratory proteins that occur in the haemolymph of many arthropod species. Here, we report the presence of Hcs in the chilopode Myriapoda, demonstrating that these proteins are more widespread among the Arthropoda than previously thought. The analysis of transcriptome of S. subspinipes subpinipes reveals the presence of two distinct subunits of Hc, where the signal peptide is present, and six of prophenoloxidase (PPO), where the signal peptide is absent, in the 75 kDa range. Size exclusion chromatography profiles indicate different quaternary organization for Hc of both species, which was corroborated by TEM analysis: S. viridicornis Hc is a 6 × 6-mer and S. subspinipes Hc is a 3 × 6-mer, which resembles the half-structure of the 6 × 6-mer but also includes the presence of phenoloxidases, since the 1 × 6-mer quaternary organization is commonly associated with hexamers of PPO. Studies with Chelicerata showed that PPO activity are exclusively associated with the Hcs. This study indicates that Scolopendra may have different proteins playing oxygen transport (Hc) and PO function, both following the hexameric oligomerization observed in Hcs.

scholarly journals Organophosphorus acid anhydrolase fromAlteromonas macleodii: structural study and functional relationship to prolidases

2013 ◽  
Vol 69 (4) ◽  
pp. 346-354 ◽  
Author(s):  
Andrea Štěpánková ◽  
Jarmila Dušková ◽  
Tereza Skálová ◽  
Jindřich Hašek ◽  
Tomáš Koval' ◽  
...  
Keyword(s):  
Active Site ◽  
Three Dimensional ◽  
Size Exclusion ◽  
Dimensional Structure ◽  
Cell Parameters ◽  
Bacterial Enzyme ◽  
Organophosphorus Acid Anhydrolase ◽  
Full Structure ◽  
Exclusion Chromatography ◽  
Pita Bread

The bacterial enzyme organophosphorus acid anhydrolase (OPAA) is able to catalyze the hydrolysis of both proline dipeptides (Xaa-Pro) and several types of organophosphate (OP) compounds. The full three-dimensional structure of the manganese-dependent OPAA enzyme is presented for the first time. This enzyme, which was originally isolated from the marine bacteriumAlteromonas macleodii, was prepared recombinantly inEscherichia coli. The crystal structure was determined at 1.8 Å resolution in space groupC2, with unit-cell parametersa= 133.8,b= 49.2,c= 97.3 Å, β = 125.0°. The enzyme forms dimers and their existence in solution was confirmed by dynamic light scattering and size-exclusion chromatography. The enzyme shares the pita-bread fold of its C-terminal domain with related prolidases. The binuclear manganese centre is located in the active site within the pita-bread domain. Moreover, an Ni2+ion from purification was localized according to anomalous signal. This study presents the full structure of this enzyme with complete surroundings of the active site and provides a critical analysis of its relationship to prolidases.

scholarly journals Structure of Human Cyclophilin A in Complex with the Novel Immunosuppressant Sanglifehrin A at 1.6 Å Resolution

2005 ◽  
Vol 280 (23) ◽  
pp. 21965-21971 ◽  
Author(s):  
Joerg Kallen ◽  
Richard Sedrani ◽  
Gerhard Zenke ◽  
Juergen Wagner
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Cyclophilin A ◽  
The Other ◽  
Size Exclusion ◽  
Dimensional Structure ◽  
The Novel ◽  
Immunosuppressive Activity ◽  
Exclusion Chromatography ◽  
Sanglifehrin A

Sanglifehrin A (SFA) is a novel immunosuppressant isolated from Streptomyces sp. that binds strongly to the human immunophilin cyclophilin A (CypA). SFA exerts its immunosuppressive activity through a mode of action different from that of all other known immunophilin-binding substances, namely cyclosporine A (CsA), FK506, and rapamycin. We have determined the crystal structure of human CypA in complex with SFA at 1.6 Å resolution. The high resolution of the structure revealed the absolute configuration at all 17 chiral centers of SFA as well as the details of the CypA/SFA interactions. In particular, it was shown that the 22-membered macrocycle of SFA is deeply embedded in the same binding site as CsA and forms six direct hydrogen bonds with CypA. The effector domain of SFA, on the other hand, has a chemical and three-dimensional structure very different from CsA, already strongly suggesting different immunosuppressive mechanisms. Furthermore, two CypA·SFA complexes form a dimer in the crystal as well as in solution as shown by light scattering and size exclusion chromatography experiments. This observation raises the possibility that the dimer of CypA·SFA complexes is the molecular species mediating the immunosuppressive effect.

Impact of extracted algogenic organic matter on coagulation performance

2015 ◽  
Vol 15 (3) ◽  
pp. 617-624 ◽  
Author(s):  
Linan Xing ◽  
Christopher W. K. Chow ◽  
Jiane Zuo ◽  
Dongsheng Wang ◽  
Rolando Fabris ◽  
...  
Keyword(s):  
Organic Matter ◽  
Algal Blooms ◽  
High Performance ◽  
Three Dimensional ◽  
Product Formation ◽  
Size Exclusion ◽  
Uv Absorbance ◽  
Fluorescence Excitation ◽  
Before And After ◽  
Exclusion Chromatography

Understanding coagulation behaviour and treatability of waters impacted by algogenic organic matter (AOM) is important for waters with frequent algal blooms. Physico­­–chemical characteristics of AOM spiked into a water sample, before and after coagulation, were investigated using high-performance size exclusion chromatography (HPSEC) with UV and fluorescence detection, three dimensional-fluorescence excitation emission matrix (3D-FEEM) measurement and resin fractionation in which three fractions were determined including very hydrophobic acid (VHA), slightly hydrophobic acid (SHA) and hydrophilic fractions. Release of AOM from algal cells with consequential increases in dissolved organic carbon and UV absorbance led to changes in 3D-FEEM spectra indicative of increased aromatic protein presence. Changes in disinfection by-product formation potential after the AOM spiking indicated possible interactions between natural organic matter and AOM. A study of the treatability of the AOM spiked water using two coagulants, alum and a polyaluminum composite coagulant, was conducted with the relative percentages of UV absorbance values of both the SHA and hydrophilic fractions higher in the post coagulated AOM spiked water than in the coagulated water, with corresponding reductions in the VHA proportion. It was found that the increased SHA and hydrophilic components in the AOM spiked natural water were recalcitrant to removal by both coagulants.

Fine-fibrous cellulose II aerogels of high specific surface from pulp solutions in TBAF·H2O/DMSO

Holzforschung ◽  
2018 ◽  
Vol 73 (1) ◽  
pp. 65-81 ◽  
Author(s):  
Christian B. Schimper ◽  
Paul Pachschwoell ◽  
Martin Wendland ◽  
Ena Smid ◽  
Marie-Alexandra Neouze ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Solvent Mixture ◽  
Size Exclusion ◽  
Cellulose Ii ◽  
Cellulose Solvent ◽  
Low Viscosity ◽  
A Value ◽  
Micron Size ◽  
Exclusion Chromatography ◽  
Chemical Integrity

Abstract Lightweight cellulose II aerogels featuring densities of about 40–70 mg cm−3 were prepared from 1 to 3% solutions of different pulps in hot (60°C) tetra-n-butylammonium fluoride (TBAF)·H2O/dimethyl sulfoxide (DMSO) by (i) the coagulation of cellulose with EtOH to afford self-standing, transparent and homogeneous gels, (ii) gel ripening and washing, (iii) solvent exchange and (iv) supercritical carbon dioxide (scCO2) drying. Size exclusion chromatography (SEC) analyses confirmed that the chemical integrity of cellulose is largely preserved at short dissolution times. Dissolution of more than 2% of cellulose at a sufficiently low viscosity for solution, casting was achieved after the water content of TBAF was reduced to a value equaling that of the monohydrate. Intriguingly, the obtained aerogels featured higher specific surfaces (≤470 m2 g−1) than comparable materials prepared from other cellulose solvents. This is due to the particular morphology of TBAF aerogels, which is supposedly formed by spinodal decomposition of the cellulose/solvent mixture upon exposure to the cellulose antisolvent. As a result, largely homogeneous three-dimensional (3D) networks of agglomerated cellulose spheres were formed, which simultaneously acted as supporting scaffolds for interconnected micron-size voids. As cellulose spheres are composed of very small interwoven nanofibers, TBAF-derived aerogels contain a high portion of micropores and small amounts of mesopores, too.

Three-dimensional structure of dendritic spines, neuronal specializations that impart both stability and flexibility to synaptic function

1993 ◽  
Vol 51 ◽  
pp. 92-93
Author(s):  
Kristen M. Harris
Keyword(s):  
Dendritic Spines ◽  
Three Dimensional ◽  
Synaptic Function ◽  
Dimensional Structure ◽  
Excitatory Synapses ◽  
Concept Of Function ◽  
Section Electron ◽  
High Quality Information ◽  
The Central Nervous System ◽  
Mathematical Analyses

Dendritic spines are the tiny protrusions that stud the surface of many neurons and they are the location of over 90% of all excitatory synapses that occur in the central nervous system. Their small size and variable shapes has in large part made detailed study of their structure refractory to conventional light microscopy and single section electron microscopy (EM). Yet their widespread occurrence and likely involvement in learning and memory has motivated extensive efforts to obtain quantitative descriptions of spines in both steady state and dynamic conditions. Since the seminal mathematical analyses of D’Arcy Thompson, the power of establishing quantitatively key parameters of structure has become recognized as a foundation of successful biological inquiry. For dendritic spines highly precise determinations of structure and its variation are proving themselves as the kingpin for establishing a valid concept of function. The recent conjunction of high quality information about the structure, function, and theoretical implications of dendritic spines has produced a flurry of new considerations of their role in synaptic transmission.

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