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.

scholarly journals Removal of Multi-Class Antibiotic Drugs from Wastewater Using Water-Soluble Protein of Moringa stenopetala Seeds

Water ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 595 ◽  
Author(s):  
Temesgen Kebede ◽  
Simiso Dube ◽  
Mathew Nindi
Keyword(s):  
Soluble Protein ◽  
Soluble Proteins ◽  
Water Soluble ◽  
Wastewater Sample ◽  
Analyte Concentration ◽  
Moringa Stenopetala ◽  
The Real ◽  
Antibiotic Drugs ◽  
Water Soluble Protein ◽  
Real Wastewater

The removal of ten selected antibiotic drugs belonging to different classes (sulphonamides, fluoroquinolones, macrolides, and tetracycline) was investigated using water-soluble proteins from the seeds of Moringa stenopetala. The surface functional groups of water-soluble protein powder before and after removal of antibiotics were characterized using Fourier transform infrared (FTIR). Processing parameters that could affect the removal efficiency, such as initial analyte concentration, protein dosage, and pH were studied. An optimized method was applied to a real wastewater sample collected from Daspoort Wastewater Treatment Plant (WWTP) located in Pretoria, South Africa. Under optimal conditions, the results indicated good agreement between the efficiency of water-soluble proteins to remove antibiotics from the real wastewater sample and from the synthetic wastewater sample prepared in the laboratory using standard solutions with known concentrations. The percentage of removal under optimum conditions (protein dosage of 40 mg, initial analyte concentration of 0.1 mg L−1, and pH 7) was between 85.2 ± 0.01% and 96.3 ± 0.03% for standard mixture solution and from 72.4 ± 0.32% to 92.5 ± 0.84% and 70.4 ± 0.82% to 91.5 ± 0.71% for the real wastewater (effluent and influent) sample.

Small membrane proteins – elucidating the function of the needle in the haystack

2014 ◽  
Vol 395 (12) ◽  
pp. 1365-1377 ◽  
Author(s):  
Grant Kemp ◽  
Florian Cymer
Keyword(s):  
Amino Acids ◽  
Membrane Proteins ◽  
Soluble Proteins ◽  
Structure And Function ◽  
Ribosome Profiling ◽  
Water Soluble ◽  
Eukaryotic Cells ◽  
Large Numbers ◽  
A Cell ◽  
And Function

Abstract Membrane proteins are important mediators between the cell and its environment or between different compartments within a cell. However, much less is known about the structure and function of membrane proteins compared to water-soluble proteins. Moreover, until recently a subset of membrane proteins, those shorter than 100 amino acids, have almost completely evaded detection as a result of technical difficulties. These small membrane proteins (SMPs) have been underrepresented in most genomic and proteomic screens of both pro- and eukaryotic cells and, hence, we know much less about their functions in both. Currently, through a combination of bioinformatics, ribosome profiling, and more sensitive proteomics, large numbers of SMPs are being identified and characterized. Herein we describe recent advances in identifying SMPs from genomic and proteomic datasets and describe examples where SMPs have been successfully characterized biochemically. Finally we give an overview of identified functions of SMPs and speculate on the possible roles SMPs play in the cell.

Modifying the Physicochemical and Functional Properties of Water-soluble Protein from Mussels by High-pressure Homogenization Treatment

2020 ◽  
Vol 16 (3) ◽  
Author(s):  
Henan Zou ◽  
Ning Zhao ◽  
Xiaojie Shi ◽  
Shuang Sun ◽  
Cuiping Yu
Keyword(s):  
High Pressure ◽  
Functional Properties ◽  
Soluble Protein ◽  
Protein Solubility ◽  
Water Soluble ◽  
Initial Structure ◽  
High Pressure Homogenization ◽  
Homogenization Treatment ◽  
Water Soluble Protein ◽  
Physicochemical And Functional Properties

AbstractThis study investigated the changes in physicochemical and functional properties of water-soluble protein from mussels (MWP) induced by high-pressure homogenization (HPH). The results indicated that HPH treatment unfolded or disrupted the initial structure of MWP, exposing free sulfhydryl groups and buried hydrophobic groups. As the homogenization pressure increased, the aggregation of MWP particles gradually decreased. Moreover, protein solubility and dispersion stability increased in aqueous solution. Foaming and emulsifying properties were also improved. HPH treatment has proven to be an effective technique for enhancing the functional properties of shellfish protein, and 120 MPa was the optimum homogenization pressure to modify MWP.

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.

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 A comprehensive review of the lipid cubic phase orin mesomethod for crystallizing membrane and soluble proteins and complexes

2015 ◽  
Vol 71 (1) ◽  
pp. 3-18 ◽  
Author(s):  
Martin Caffrey
Keyword(s):  
Molecular Mechanisms ◽  
Heavy Atom ◽  
Soluble Proteins ◽  
Water Soluble ◽  
Rational Approach ◽  
Cubic Phase ◽  
Screening Process ◽  
Experimental Phasing ◽  
Set Up ◽  
And Function

The lipid cubic phase orin mesomethod is a robust approach for crystallizing membrane proteins for structure determination. The uptake of the method is such that it is experiencing what can only be described as explosive growth. This timely, comprehensive and up-to-date review introduces the reader to the practice ofin mesocrystallogenesis, to the associated challenges and to their solutions. A model of how crystallization comes about mechanistically is presented for a more rational approach to crystallization. The possible involvement of the lamellar and inverted hexagonal phases in crystallogenesis and the application of the method to water-soluble, monotopic and lipid-anchored proteins are addressed. How to set up trials manually and automatically with a robot is introduced with reference to open-access online videos that provide a practical guide to all aspects of the method. These range from protein reconstitution to crystal harvesting from the hosting mesophase, which is noted for its viscosity and stickiness. The sponge phase, as an alternative medium in which to perform crystallization, is described. The compatibility of the method with additive lipids, detergents, precipitant-screen components and materials carried along with the protein such as denaturants and reducing agents is considered. The powerful host and additive lipid-screening strategies are described along with how samples that have low protein concentration and cell-free expressed protein can be used. Assaying the protein reconstituted in the bilayer of the cubic phase for function is an important element of quality control and is detailed. Host lipid design for crystallization at low temperatures and for large proteins and complexes is outlined. Experimental phasing by heavy-atom derivatization, soaking or co-crystallization is routine and the approaches that have been implemented to date are described. An overview and a breakdown by family and function of the close to 200 published structures that have been obtained usingin meso-grown crystals are given. Recommendations for conducting the screening process to give a more productive outcome are summarized. The fact that thein mesomethod also works with soluble proteins should not be overlooked. Recent applications of the method forin situserial crystallography at X-ray free-electron lasers and synchrotrons are described. The review ends with a view to the future and to the bright prospects for the method, which continues to contribute to our understanding of the molecular mechanisms of some of nature's most valued proteinaceous robots.

EFFECT OF PARTIAL PROTEIN REMOVAL FROM MUSCLE CUBES ON PROPERTIES OF POULTRY MEAT LOAVES1

1972 ◽  
Vol 35 (10) ◽  
pp. 571-573 ◽  
Author(s):  
J. C. Acton ◽  
L. H. McCaskill
Keyword(s):  
Soluble Protein ◽  
Pectoral Muscle ◽  
Soluble Proteins ◽  
Cooking Loss ◽  
Water Soluble ◽  
Poultry Meat ◽  
Binding Strength ◽  
Water Soluble Protein ◽  
And Control

Pectoral muscle cubes from 10-week old broilers were “water-washed” or “salt-washed” ( 0.6 M NaCl) to provide tissue with various quantities of water-soluble and salt-soluble proteins. Approximately 30% of the water-soluble protein was removed when cubes were water-washed. Salt-washed cubes had decreases of 42% and 54% in salt-soluble and water-soluble protein concentrations, respectively. Loaves prepared with meat from the two washing treatments and control cubes showed significant (P<0.01) differences in both cooking loss and binding strength of meat slices. The quantity of salt-soluble proteins available for solubilization to reduce cooking loss and increase binding strength among meat particles appeared more important to poultry loaf processing than the quantity of extractable water-soluble proteins.

THE SOLUBLE PROTEINS OF THE MUSCLE TISSUE OF THE HADDOCK

1931 ◽  
Vol 6 (1) ◽  
pp. 1-11 ◽  
Author(s):  
J. F. LOGAN
Keyword(s):  
Sodium Chloride ◽  
Aqueous Solutions ◽  
Muscle Tissue ◽  
Soluble Protein ◽  
Potassium Phosphate ◽  
Extraction Methods ◽  
Water Soluble ◽  
Tabular Form ◽  
Water Soluble Protein ◽  
Isoelectric Points

As a contribution to the chemistry of muscle tissue, the solubility of the protein of haddock muscle in aqueous solutions of sodium chloride and neutral potassium phosphate, respectively, was determined. The results are expressed in tabular form and graphically in the form of solubility curves. A water-soluble protein and also a salt-soluble protein were isolated from dialyzed haddock muscle by extraction methods. These proteins were obtained in a comparatively pure condition by precipitation from solution in the region of their isoelectric points.

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