scholarly journals Rampant Exchange of the Structure and Function of Extramembrane Domains between Membrane and Water Soluble Proteins

2013 ◽  
Vol 9 (3) ◽  
pp. e1002997 ◽  
Author(s):  
Hyun-Jun Nam ◽  
Seong Kyu Han ◽  
James U. Bowie ◽  
Sanguk Kim
Keyword(s):  
Soluble Proteins ◽  
Structure And Function ◽  
Water Soluble ◽  
And Function

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.

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.

Surfactant-free purification of membrane proteins with intact native membrane environment

2011 ◽  
Vol 39 (3) ◽  
pp. 813-818 ◽  
Author(s):  
Mohammed Jamshad ◽  
Yu-Pin Lin ◽  
Timothy J. Knowles ◽  
Rosemary A. Parslow ◽  
Craig Harris ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Maleic Acid ◽  
Biochemical Study ◽  
Soluble Proteins ◽  
Structure And Function ◽  
Three Dimensions ◽  
Present Review ◽  
Protein Particles ◽  
And Function

In order to study the structure and function of a protein, it is generally required that the protein in question is purified away from all others. For soluble proteins, this process is greatly aided by the lack of any restriction on the free and independent diffusion of individual protein particles in three dimensions. This is not the case for membrane proteins, as the membrane itself forms a continuum that joins the proteins within the membrane with one another. It is therefore essential that the membrane is disrupted in order to allow separation and hence purification of membrane proteins. In the present review, we examine recent advances in the methods employed to separate membrane proteins before purification. These approaches move away from solubilization methods based on the use of small surfactants, which have been shown to suffer from significant practical problems. Instead, the present review focuses on methods that stem from the field of nanotechnology and use a range of reagents that fragment the membrane into nanometre-scale particles containing the protein complete with the local membrane environment. In particular, we examine a method employing the amphipathic polymer poly(styrene-co-maleic acid), which is able to reversibly encapsulate the membrane protein in a 10 nm disc-like structure ideally suited to purification and further biochemical study.

Structure and function of nonorthodox chromatins: I. aggregation sensitivity of DNA is correlated to the Protein content of chromosomal material

1990 ◽  
Vol 48 (3) ◽  
pp. 120-121
Author(s):  
J. Pelzer ◽  
B. Bohrmann ◽  
R. Johansen ◽  
M. Maeder ◽  
R. Gyalog ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Protein Content ◽  
Organic Solvents ◽  
Soluble Proteins ◽  
Structure And Function ◽  
Living World ◽  
Eukaryotic Chromatin ◽  
And Function

Aggregation insensitive eukaryotic chromatin in which DNA is associated with histones can be crosslinked by all fixatives commonly used in electron microscopy. By crosslinking it becomes protected from aggregation during dehydration with organic solvents. This is not the case with most nonorthodox chromatins, where the ratio of protein to DNA is estimated to be 5 to 10 times lower and where the basic, acid-soluble proteins are rather different from the histones. The aggregation sensitivity of different chromatins is summarized in table 1.Nonorthodox aggregation sensitive chromatins were found in Eubacteria, bacteriophage- pools (fig. 1a,b), Cyanobacteria, mitochondria, and Dinoflagellates (fig. 2a,b). The latter organisms are of particular interest because of morphologic similarities to other flagellates like Euglena with its aggregation insensitive histone-containing chromosomes (fig. 3a,b). With respect to the distribution over the living world, nonorthodox chromatins might be more frequent than the histone-containing ones.

Temporary Solubilizing Tags Method for the Chemical Synthesis of Hydrophobic Proteins

2019 ◽  
Vol 23 (1) ◽  
pp. 2-13 ◽  
Author(s):  
Dong-Dong Zhao ◽  
Xiao-Wen Fan ◽  
He Hao ◽  
Hong-Li Zhang ◽  
Ye Guo
Keyword(s):  
Water Solubility ◽  
Cellular Protein ◽  
Structure And Function ◽  
Water Soluble ◽  
Functional Studies ◽  
Hydrophobic Peptides ◽  
The Poor ◽  
Practical Strategy ◽  
Poor Water Solubility ◽  
And Function

Hydrophobic proteins, as one of the cellular protein classifications, play an essential function in maintaining the normal life cycle of living cells. Researches on the structure and function of hydrophobic proteins promote the exploration of the causes of major diseases, and development of new therapeutic agents for disease treatment. However, the poor water solubility of hydrophobic proteins creates problems for their preparation, separation, characterization and functional studies. The temporary solubilizing tags are considered a practical strategy to effectively solve the poor water solubility problem of hydrophobic proteins. This strategy can significantly improve the water solubility of hydrophobic peptides/proteins, making them like water-soluble peptides/proteins easy to be purified, characterized. More importantly, the temporary solubilizing tags can be removed after protein synthesis, so thus the structure and function of the hydrophobic proteins are not affected. At present, temporary solubilizing tags have been successfully used to prepare many important hydrophobic proteins such as membrane proteins, lipoproteins and chaperones. In this review, we summarize the recent researches and applications of temporary solubilizing tags.

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.

scholarly journals End-to-end multitask learning, from protein language to protein features without alignments

2019 ◽  
Author(s):  
Ahmed Elnaggar ◽  
Michael Heinzinger ◽  
Christian Dallago ◽  
Burkhard Rost
Keyword(s):  
Protein Structure ◽  
Secondary Structure ◽  
Structure And Function ◽  
Water Soluble ◽  
Language Models ◽  
Quality Data ◽  
Evolutionary Information ◽  
End To End ◽  
Sequence Databases ◽  
And Function

AbstractCorrectly predicting features of protein structure and function from amino acid sequence alone remains a supreme challenge for computational biology. For almost three decades, state-of-the-art approaches combined machine learning and evolutionary information from multiple sequence alignments. Exponentially growing sequence databases make it infeasible to gather evolutionary information for entire microbiomes or meta-proteomics. On top, for many important proteins (e.g. dark proteome and intrinsically disordered proteins) evolutionary information remains limited. Here, we introduced a novel approach combining recent advances of Language Models (LMs) with multi-task learning to successfully predict aspects of protein structure (secondary structure) and function (cellular component or subcellular localization) without using any evolutionary information from alignments. Our approach fused self-supervised pre-training LMs on an unlabeled big dataset (UniRef50, corresponding to 9.6 billion words) with supervised training on labelled high-quality data in one single end-to-end network. We provided a proof-of-principle for the novel concept through the semi-successful per-residue prediction of protein secondary structure and through per-protein predictions of localization (Q10=69%) and the distinction between integral membrane and water-soluble proteins (Q2=89%). Although these results did not reach the levels obtained by the best available methods using evolutionary information from alignments, these less accurate multi-task predictions have the advantage of speed: they are 300-3000 times faster (where HHblits needs 30-300 seconds on average, our method needed 0.045 seconds). These new results push the boundaries of predictability towards grayer and darker areas of the protein space, allowing to make reliable predictions for proteins which were not accessible by previous methods. On top, our method remains scalable as it removes the necessity to search sequence databases for evolutionary related proteins.

scholarly journals Synergistic Action of Membrane-Bound and Water-Soluble Antioxidants in Neuroprotection

Molecules ◽  
2021 ◽  
Vol 26 (17) ◽  
pp. 5385
Author(s):  
Stephanie K. Polutchko ◽  
Gabrielle N. E. Glime ◽  
Barbara Demmig-Adams
Keyword(s):  
Chronic Inflammation ◽  
Stress Reduction ◽  
Membrane Structure ◽  
Structure And Function ◽  
Synergistic Action ◽  
Water Soluble ◽  
Membrane Function ◽  
Membrane Structure And Function ◽  
And Function ◽  
Soluble Components

Prevention of neurodegeneration during aging, and support of optimal brain function throughout the lifespan, requires protection of membrane structure and function. We review the synergistic action of different classes of dietary micronutrients, as well as further synergistic contributions from exercise and stress reduction, in supporting membrane structure and function. We address membrane-associated inflammation involving reactive oxygen species (ROS) that produce immune regulators from polyunsaturated fatty acids (PUFAs) of membrane phospholipids. The potential of dietary micronutrients to maintain membrane fluidity and prevent chronic inflammation is examined with a focus on synergistically acting membrane-soluble components (zeaxanthin, lutein, vitamin E, and omega-3 PUFAs) and water-soluble components (vitamin C and various phenolics). These different classes of micronutrients apparently operate in a series of intertwined oxidation-reduction cycles to protect membrane function and prevent chronic inflammation. At this time, it appears that combinations of a balanced diet with regular moderate exercise and stress-reduction practices are particularly beneficial. Effective whole-food-based diets include the Mediterranean and the MIND diet (Mediterranean-DASH Intervention for Neurodegenerative Delay diet, where DASH stands for Dietary Approaches to Stop Hypertension).

scholarly journals Study of Molecular interaction in Binary Mixtures containing N, N-Dimethylformamide and n-Butanol

2021 ◽  
Vol 17 (01) ◽  
pp. 1-8
Author(s):  
BISWAJIT SAMANTARAY ◽  
◽  
MANOJ KUMAR PRAHARAJ ◽  
SMRUTI PRAVA DAS ◽  
◽  
...  
Keyword(s):  
Experimental Data ◽  
Free Energy ◽  
Acoustic Impedance ◽  
Molecular Interaction ◽  
Polar Solvent ◽  
Adiabatic Compressibility ◽  
Structure And Function ◽  
Water Soluble ◽  
Thermodynamical Parameters ◽  
And Function

The acoustic studies of the interactions between alcohol molecules and water soluble polar solvent DMF are significant for understanding the relationships between structure and function of polar molecule like DMF, and for explaining the mechanisms of interaction of alcoholic OH group with an electronegative moiety. In this piece of work Ultrasonic velocity, density and viscosity have been measured at 298 K, 308 K, 318 K and 328 K for mixture of N,N-dimethylformamide (DMF) and n-butanol, the frequency being maintained at a constant value. The experimental data have been used to calculate the acoustical and thermodynamical parameters like adiabatic compressibility, free length, free volume, internal pressure, acoustic impedance, Gibbs free energy

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