scholarly journals The multilayered organization of water-soluble proteins

2021 ◽  
Author(s):  
Lincong Wang
Keyword(s):  
Active Site ◽  
Negative Charge ◽  
Three Dimensional ◽  
Water Soluble ◽  
Partial Charge ◽  
Solvent Interaction ◽  
Upper Limit ◽  
Water Soluble Protein ◽  
Monomeric Proteins

The structural analysis of proteins has focused primarily on secondary structure, three-dimensional fold and active site while whole surface has been analyzed to a lesser extent and interior has not received much attention. Here we present an analysis of both the surfaces and the interiors of a set of water-soluble monomeric proteins in terms of solvent-excluded surface (SES) and atomic partial charge. The analysis shows that the surface of a soluble monomer has a net negative charge and is much smoother than the interior. Most interestingly with regard to both atomic partial charge and SES-defined geometric property there exists a multilayered organization from the exterior to the interior of a soluble monomer. The multilayered organization is closely related to protein-solvent interaction and should be a general feature of a water-soluble protein. Particularly the multilayered organization may set an upper limit for the size of a water-soluble monomer and plays an important role in the determination of its overall shape in solution.

scholarly journals The solvent-excluded surfaces of water-soluble proteins

2018 ◽  
Author(s):  
Lincong Wang
Keyword(s):  
Protein Solubility ◽  
Soluble Proteins ◽  
Water Soluble ◽  
Solvent Interaction ◽  
Geometrical Properties ◽  
Protein Size ◽  
Protein Interfaces ◽  
Water Soluble Protein ◽  
Solvent Molecules ◽  
And Function

AbstractThe solvent-excluded surface (SES) of a protein is determined by and in turn affects protein-solvent interaction and consequently plays important roles in its solvation, folding and function. However, accurate quantitative relationships between them remain largely unknown at present. To evaluate SES’s contribution to protein-solvent interaction we have applied our accurate and robust SES computation algorithm to various sets of proteins and ligand-protein interfaces. Our results show that each of the analyzed water-soluble proteins has a negative net charge on its SES. In addition we have identified a list of SES-defined physical and geometrical properties that likely pertain to protein solvation and folding based on their characteristic changes with protein size, their differences between folded and extended conformations, and their correlations with known hydrophobicity scales and with experimentally-determined protein solubility. The relevance of the list of SES-defined properties to protein structure and function is supported by their differences between water-soluble proteins and transmembrane proteins and between solvent-accessible regions and ligand-binding interfaces. Taken together our analyses reveal the importance of SES for protein solvation, folding and function. In particular the universal enrichment of negative charge and the larger than average SES area for a polar atom on the surface of a water-soluble protein suggest that from a protein-solvent interaction perspective to fold into a native state is to optimize the electrostatic and hydrogen-bonding interactions between solvent molecules and the surface polar atoms of a protein rather than to only minimize its apolar surface area.

Self-Assembled Combination of Graphene with Au Nanoparticle-Doped Copper-Hexacyanoferrate Multilayer for Sensitive Detection of Hydrazine

2012 ◽  
Vol 586 ◽  
pp. 18-23 ◽  
Author(s):  
Dong Jiao Zhao ◽  
Fei Yan ◽  
Yao Fang Xuan ◽  
Xiao Ping Dong ◽  
Feng Na Xi
Keyword(s):  
Self Assembly ◽  
Three Dimensional ◽  
Water Soluble ◽  
Sensitive Detection ◽  
Au Nanoparticle ◽  
Copper Hexacyanoferrate ◽  
Self Assembled ◽  
Modified Graphene ◽  
Net Positive Charge

Based on self-assembled combination of graphene with Au nanoparticle-doped copper hexacyanoferrate (CuHCF) multilayers, a electrochemical biosensor for sensitive detection of hydrazine has been reported. Graphene was functionalized by wrapping with poly(diallyldimethylammonium chloride) (PDDA). Such polyelectrolyte modified graphene (PDDA-G) was water-soluble and possessed net positive charge. Based on electrostatic self-assembly, graphene multilayers modified electrode (ITO/G-M) was fabricated. After binding with mercaptopropionic acid stabled Au nanoparticles (MPA-AuNPs), three dimensional graphene-AuNPs electrode was obtained. CuHCF multilayers were then formed on AuNPs center by successive self-assembly and solution epitaxy. Due to the synergistic effect of graphene and AuNPs, the developed biosensor (ITO/G-M/CuHCF-M) exhibited fast and sensitive amperometric response for the determination of hydrazine in near physiological pH. The linear response for the determination of hydrazine ranged from 4.0 × 10-7 to 1.3 × 10-4 M with a detection limit of 7.2 × 10-8 M. The biosensor exhibited high reproducibility and stability resulted from simple and reproducible self-assembly methodology.

Time Evolution of Exposed Hydrophobicity of Water-Soluble Proteins During their Depolymerisation by Endo-Proteases

2004 ◽  
Vol 10 (6) ◽  
pp. 399-408
Author(s):  
J. M. Sendra ◽  
E. Sentandreu ◽  
J. V. Carbonell
Keyword(s):  
Bovine Serum Albumin ◽  
Time Evolution ◽  
Online Monitoring ◽  
Soluble Proteins ◽  
Water Soluble ◽  
Mathematical Function ◽  
Water Soluble Protein ◽  
Adjustable Rate ◽  
Β Lactoglobulin

During the depolymerisation of a water-soluble protein by an endo-protease, the exposed hydrophobicity of the substrate, that is the hydrophobicity that is accessible to hydrophobic probes, changes with the progress of the reaction. This work describes the depolymerisation of bovine serum albumin, α-casein and β-lactoglobulin using the proteases Alcalase, Flavourzyme, α-chymotrypsin, mercuripapain and trypsin. Time evolution of substrate hydrophobicity was monitored by a flow-injection analysis (FIA) system with fluorescence detection and an aqueous eluant containing p-toluidinylnaphthalene-6-sulfonate (2,6-TNS) as the fluorescent probe. In all cases, the time evolution of the substrate hydrophobicity was fitted using a derived mathematical function containing two adjustable rate constants and two constant parameters. This methodology allowed the determination of protease activities, as well as online monitoring of the depolymerisation process, when using water-soluble proteins as substrate.

scholarly journals Active Site Architecture and Reaction Mechanism Determination of Cold Adapted β-d-galactosidase from Arthrobacter sp. 32cB

2019 ◽  
Vol 20 (17) ◽  
pp. 4301 ◽  
Author(s):  
Maria Rutkiewicz ◽  
Anna Bujacz ◽  
Marta Wanarska ◽  
Anna Wierzbicka-Wos ◽  
Hubert Cieslinski
Keyword(s):  
Reaction Mechanism ◽  
Active Site ◽  
Three Dimensional ◽  
Binding Mode ◽  
Wild Form ◽  
Cold Adapted ◽  
Transglycosylation Activity ◽  
Inactive Form ◽  
Key Factor

ArthβDG is a dimeric, cold-adapted β-d-galactosidase that exhibits high hydrolytic and transglycosylation activity. A series of crystal structures of its wild form, as well as its ArthβDG_E441Q mutein complexes with ligands were obtained in order to describe the mode of its action. The ArthβDG_E441Q mutein is an inactive form of the enzyme designed to enable observation of enzyme interaction with its substrate. The resulting three-dimensional structures of complexes: ArthβDG_E441Q/LACs and ArthβDG/IPTG (ligand bound in shallow mode) and structures of complexes ArthβDG_E441Q/LACd, ArthβDG/ONPG (ligands bound in deep mode), and galactose ArthβDG/GAL and their analysis enabled structural characterization of the hydrolysis reaction mechanism. Furthermore, comparative analysis with mesophilic analogs revealed the most striking differences in catalysis mechanisms. The key role in substrate transfer from shallow to deep binding mode involves rotation of the F581 side chain. It is worth noting that the 10-aa loop restricting access to the active site in mesophilic GH2 βDGs, in ArthβDG is moved outward. This facilitates access of substrate to active site. Such a permanent exposure of the entrance to the active site may be a key factor for improved turnover rate of the cold adapted enzyme and thus a structural feature related to its cold adaptation.

Two and Three Dimensional Nuclear Quadrupole Resonance in the Investigation of Structure and Bonding

2000 ◽  
Vol 55 (1-2) ◽  
pp. 29-36 ◽  
Author(s):  
Ming-Yuan Liao ◽  
Raju Subramanian ◽  
Rachel L. Yung ◽  
Gerard S. Harbison
Keyword(s):  
Active Site ◽  
Three Dimensional ◽  
Coupling Constants ◽  
Bovine Erythrocyte ◽  
Coupling Tensor ◽  
Field Gradients ◽  
Quadrupole Coupling ◽  
Quadrupole Resonance ◽  
Nuclear Quadrupole

A variety of two dimensional two-and three-dimensional NQR experiments are reviewed, showing their application to the determination of field gradients for important sites in peptides and proteins, for assigning connected transitions of nuclei with spin ≥ 5/2, and for determining hexadecapolar coupling constants. The quadrupole coupling tensor for 63Cu in the active site of a protein, bovine erythrocyte (Cu, Zn) superoxide dismutase, has been measured and is compared with the results of ab initio calculations.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Quantitative Radioisotope Measurement of Duodenogastric Reflux in Patients with Ulcer or Gastrectomized for Ulcer

1985 ◽  
Vol 24 (03) ◽  
pp. 107-110
Author(s):  
M. Pääkkönen ◽  
S. Aukee ◽  
K. Korhonen ◽  
A. Pääkkönen ◽  
E. Länsimies ◽  
...  
Keyword(s):  
Gamma Camera ◽  
Background Activity ◽  
Bile Reflux ◽  
Duodenogastric Reflux ◽  
Upper Limit ◽  
Visual Evidence ◽  
Biochemical Measurement

SummaryIn this work the duodenogastric reflux was quantified as the amount of radioactivity entering the stomach after an i.v. administration of 99mmTc-HIDA in ulcer patients and in patients who had undergone BI gastrectomy. The results were compared with visual evidence of gastric activity in the gamma camera images and biochemical determination of gastric bile reflux. The method is useful in quantifying the reflux if the activity is above the background activity. It allows the determination of an upper limit for the reflux when the reflux is evident visually. Only two or three images are needed for the quantitation. No correlation was found between biochemical measurement of fasting bile reflux in the stomach and radioisotopic quantification.

Simultaneous Spectrophotometric Determination of Salbutamol by Coupling with Diazotized 4-Aminobenzoic acid

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Hind Hadi ◽  
Gufran Salim
Keyword(s):  
Pharmaceutical Preparations ◽  
Coupling Reaction ◽  
Dosage Forms ◽  
Water Soluble ◽  
Trace Determination ◽  
Aminobenzoic Acid ◽  
Optimum Conditions ◽  
Colored Product ◽  
Versus Concentration

A simple, rapid and sensitive spectrophotmetric method for trace determination of salbutamol (SAL) in aqueous solution and in pharmaceutical preparations is described. The method is based on the diazotization coupling reaction of the intended compound with 4-amino benzoic acid (ABA) in alkaline medium to form an intense orange, water soluble dye that is stable and shows maximum absorption at 410 nm. A graph of absorbance versus concentration indicates that Beer’s law is obeyed over the concentration range of 0.5-30 ppm, with a molar absorbtivity 3.76×104 L.mol-1 .cm-1 depending on the concentration of SAL. The optimum conditions and stability of the colored product have been investigated and the method was applied successfully to the determination of SAL in dosage forms.

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