scholarly journals Marginal protein stability drives subcellular proteome isoelectric point

2018 ◽  
Vol 115 (46) ◽  
pp. 11778-11783 ◽  
Author(s):  
Kaiser Loell ◽  
Vikas Nanda
Keyword(s):  
Isoelectric Point ◽  
Neutral Evolution ◽  
Direct Result ◽  
Marginal Stability ◽  
Enzyme Active Site ◽  
Protein Model ◽  
Acidic Residues ◽  
Alkaline Conditions ◽  
Specific Proteins ◽  
Acidic Compartment

There exists a positive correlation between the pH of subcellular compartments and the median isoelectric point (pI) for the associated proteomes. Proteins in the human lysosome—a highly acidic compartment in the cell—have a median pI of ∼6.5, whereas proteins in the more basic mitochondria have a median pI of ∼8.0. Proposed mechanisms reflect potential adaptations to pH. For example, enzyme active site general acid/base residue pKs are likely evolved to match environmental pH. However, such effects would be limited to a few residues on specific proteins, and might not affect the proteome at large. A protein model that considers residue burial upon folding recapitulates the correlation between proteome pI and environmental pH. This correlation can be fully described by a neutral evolution process; no functional selection is included in the model. Proteins in acidic environments incur a lower energetic penalty for burying acidic residues than basic residues, resulting in a net accumulation of acidic residues in the protein core. The inverse is true under alkaline conditions. The pI distributions of subcellular proteomes are likely not a direct result of functional adaptations to pH, but a molecular spandrel stemming from marginal stability.

Role of Guanidinium-Carboxylate Interaction in Enzyme Inhibition with Implication for Drug Design

2019 ◽  
Author(s):  
Aswathy Muttathukattil ◽  
Sriraksha Srinivasan ◽  
Antarip Halder ◽  
Govardhan Reddy
Keyword(s):  
Amino Acids ◽  
Active Sites ◽  
Density Functional ◽  
Specific Interaction ◽  
Density Functional Theory Calculations ◽  
Enzyme Active Site ◽  
Acidic Amino Acids ◽  
Low Concentrations ◽  
Activity Measurements ◽  
Acidic Residues

Guanidinium cation (Gdm<sup>+</sup>) interacts strongly with amino acids of different polarities modulating protein structure and function. Using density functional theory calculations and molecular dynamics simulations we studied the interaction of Gdm<sup>+</sup> with carboxylate ions mimicking its interaction with acidic amino acids and explored its effect in enzymatic folding and activity. We show that in low concentrations, Gdm<sup>+</sup> stabilizes carboxylate ion dimers by acting as a bridge between them thereby reducing the electrostatic repulsion. We further show that this carboxylate-Gdm<sup>+</sup>-carboxylate interaction can have an effect on the structure-activity relationship in enzymes with active sites containing two acidic residues. Using five enzymes (hen egg white lysozyme, T4 lysozyme, HIV-1 protease, pepsin and creatine kinase), which have two acidic amino acids in their active sites, we show that in low concentrations (< 0.5 M), Gdm<sup>+</sup> strongly binds to the enzyme active site, thereby potentially inhibiting its activity without unfolding it. This can lead to misleading conclusions in experiments, which infer the extent of enzyme unfolding from activity measurements. However, the carboxylate-Gdm<sup>+</sup>-carboxylate specific interaction can be exploited in drug discovery as drugs based on guanidinium derivatives are already being used to treat various maladies related to muscle weakness, cancer, diabetes etc. Guanidinium derivatives can be designed as potential drug molecules to inhibit activity or functioning of enzymes, which have binding pockets with two acidic residues in close vicinity.<br>

Role of Guanidinium-Carboxylate Interaction in Enzyme Inhibition with Implication for Drug Design

2019 ◽  
Author(s):  
Aswathy Muttathukattil ◽  
Sriraksha Srinivasan ◽  
Antarip Halder ◽  
Govardhan Reddy
Keyword(s):  
Amino Acids ◽  
Active Sites ◽  
Density Functional ◽  
Specific Interaction ◽  
Density Functional Theory Calculations ◽  
Enzyme Active Site ◽  
Acidic Amino Acids ◽  
Low Concentrations ◽  
Activity Measurements ◽  
Acidic Residues

Guanidinium cation (Gdm<sup>+</sup>) interacts strongly with amino acids of different polarities modulating protein structure and function. Using density functional theory calculations and molecular dynamics simulations we studied the interaction of Gdm<sup>+</sup> with carboxylate ions mimicking its interaction with acidic amino acids and explored its effect in enzymatic folding and activity. We show that in low concentrations, Gdm<sup>+</sup> stabilizes carboxylate ion dimers by acting as a bridge between them thereby reducing the electrostatic repulsion. We further show that this carboxylate-Gdm<sup>+</sup>-carboxylate interaction can have an effect on the structure-activity relationship in enzymes with active sites containing two acidic residues. Using five enzymes (hen egg white lysozyme, T4 lysozyme, HIV-1 protease, pepsin and creatine kinase), which have two acidic amino acids in their active sites, we show that in low concentrations (< 0.5 M), Gdm<sup>+</sup> strongly binds to the enzyme active site, thereby potentially inhibiting its activity without unfolding it. This can lead to misleading conclusions in experiments, which infer the extent of enzyme unfolding from activity measurements. However, the carboxylate-Gdm<sup>+</sup>-carboxylate specific interaction can be exploited in drug discovery as drugs based on guanidinium derivatives are already being used to treat various maladies related to muscle weakness, cancer, diabetes etc. Guanidinium derivatives can be designed as potential drug molecules to inhibit activity or functioning of enzymes, which have binding pockets with two acidic residues in close vicinity.<br>

Temperature Dependence of the Critical Electron Dose for Fatty Acid Monolayers

1982 ◽  
Vol 40 ◽  
pp. 78-79
Author(s):  
Kenneth H. Downing ◽  
Robert M. Glaeser
Keyword(s):  
Electron Beam ◽  
Fatty Acid ◽  
Inelastic Scattering ◽  
Temperature Dependence ◽  
Structural Damage ◽  
Direct Result ◽  
Second Step ◽  
Strong Temperature Dependence ◽  
Electron Dose ◽  
Covalent Bonds

The structural damage of molecules irradiated by electrons is generally considered to occur in two steps. The direct result of inelastic scattering events is the disruption of covalent bonds. Following changes in bond structure, movement of the constituent atoms produces permanent distortions of the molecules. Since at least the second step should show a strong temperature dependence, it was to be expected that cooling a specimen should extend its lifetime in the electron beam. This result has been found in a large number of experiments, but the degree to which cooling the specimen enhances its resistance to radiation damage has been found to vary widely with specimen types.

Changes Occur in Plasma Membrane Turnover when K562 Leukemia Cells are Induced to Differentiate

1982 ◽  
Vol 40 ◽  
pp. 286-287
Author(s):  
L. M. Marshall
Keyword(s):  
Plasma Membrane ◽  
Membrane Proteins ◽  
Intracellular Transport ◽  
Parent Cell ◽  
Membrane Turnover ◽  
Coated Pits ◽  
Surface Distribution ◽  
Specific Proteins ◽  
Erythroleukemic Cell ◽  
Specific Membrane

A human erythroleukemic cell line, metabolically blocked in a late stage of erythropoiesis, becomes capable of differentiation along the normal pathway when grown in the presence of hemin. This process is characterized by hemoglobin synthesis followed by rearrangement of the plasma membrane proteins and culminates in asymmetrical cytokinesis in the absence of nuclear division. A reticulocyte-like cell buds from the nucleus-containing parent cell after erythrocyte specific membrane proteins have been sequestered into its membrane. In this process the parent cell faces two obstacles. First, to organize its erythrocyte specific proteins at one pole of the cell for inclusion in the reticulocyte; second, to reduce or abolish membrane protein turnover since hemoglobin is virtually the only protein being synthesized at this stage. A means of achieving redistribution and cessation of turnover could involve movement of membrane proteins by a directional lipid flow. Generation of a lipid flow towards one pole and accumulation of erythrocyte-specific membrane proteins could be achieved by clathrin coated pits which are implicated in membrane endocytosis, intracellular transport and turnover. In non-differentiating cells, membrane proteins are turned over and are random in surface distribution. If, however, the erythrocyte specific proteins in differentiating cells were excluded from endocytosing coated pits, not only would their turnover cease, but they would also tend to drift towards and collect at the site of endocytosis. This hypothesis requires that different protein species are endocytosed by the coated vesicles in non-differentiating than by differentiating cells.

Analysis of 3-d molecular distribution with the digital imaging microscope

1988 ◽  
Vol 46 ◽  
pp. 40-41
Author(s):  
W.A. Carrington ◽  
F.S. Fay ◽  
K.E. Fogarty ◽  
L. Lifshitz
Keyword(s):  
Image Restoration ◽  
Digital Imaging ◽  
Fluorescent Dyes ◽  
Optical Axis ◽  
Computer Hardware ◽  
Computer Algorithms ◽  
Low Contrast ◽  
Specific Proteins ◽  
Effective Use ◽  
Single Living Cells

Advances in digital imaging microscopy and in the synthesis of fluorescent dyes allow the determination of 3D distribution of specific proteins, ions, GNA or DNA in single living cells. Effective use of this technology requires a combination of optical and computer hardware and software for image restoration, feature extraction and computer graphics.The digital imaging microscope consists of a conventional epifluorescence microscope with computer controlled focus, excitation and emission wavelength and duration of excitation. Images are recorded with a cooled (-80°C) CCD. 3D images are obtained as a series of optical sections at .25 - .5 μm intervals.A conventional microscope has substantial blurring along its optical axis. Out of focus contributions to a single optical section cause low contrast and flare; details are poorly resolved along the optical axis. We have developed new computer algorithms for reversing these distortions. These image restoration techniques and scanning confocal microscopes yield significantly better images; the results from the two are comparable.

A crystalline–amorphous Ni–Ni(OH)2 core–shell catalyst for the alkaline hydrogen evolution reaction

2020 ◽  
Vol 8 (44) ◽  
pp. 23323-23329
Author(s):  
Jing Hu ◽  
Siwei Li ◽  
Yuzhi Li ◽  
Jing Wang ◽  
Yunchen Du ◽  
...  
Keyword(s):  
Hydrogen Evolution ◽  
Hydrogen Evolution Reaction ◽  
Electrocatalytic Activity ◽  
Core Shell ◽  
Alkaline Conditions

Crystalline–amorphous Ni–Ni(OH)2 core–shell assembled nanosheets exhibit outstanding electrocatalytic activity and stability for hydrogen evolution under alkaline conditions.

Cross-Linked αsγt-Chain Hybrids in Plasma Clots Studied by 1D- and 2D Electrophoresis and Western Blotting

1993 ◽  
Vol 70 (03) ◽  
pp. 438-442 ◽  
Author(s):  
B Grøn ◽  
C Filion-Myklebust ◽  
S Bjørnsen ◽  
P Haidaris ◽  
F Brosstad
Keyword(s):  
Molecular Weight ◽  
Monoclonal Antibodies ◽  
Human Plasma ◽  
Western Blotting ◽  
Isoelectric Point ◽  
Factor Xiii ◽  
Cross Linking ◽  
2D Electrophoresis ◽  
Complex Phenomenon ◽  
Fibrinopeptide A

SummaryFibrinogen and fibrin related chains in reduced human plasma as well as the bonds interlinking partially cross-linked fibrin from plasma clots have been studied by means of 1D- and 2D electrophoresis and Western blotting. Immunovisualization of reduced plasma or partially cross-linked fibrin with monoclonal antibodies specific for the α-chains or the γ-chains have shown that several bands represent material belonging to both chains. In order to decide whether these bands constitute αγ-chain hybrids or superimposed α- and γ-chain dimers, the cross-linked material was separated according to both isoelectric point (pI) and molecular weight (MW) using Pharmacia’s Multiphor II system. Western blotting of the second dimension gels revealed that partially cross-linked fibrin contains αsγt-chain hybrids and γ- polymers, in addition to the well-known γ-dimers and α-polymers. The main αsγt-chain hybrid has a pI between that of the α- and the γ-chains, a MW of about 200 kDa and contains Aα-chains with intact fibrinopeptide A (FPA). It was also observed that soluble fibrinogen/fibrin complexes as well as partially cross-linked fibrin contain degraded α-dimers with MWs close to the γ-dimers. These findings demonstrate that factor XIII-catalyzed cross-linking of fibrin is a more complex phenomenon than earlier recognized.

A Comparison of Plasminogen Activators Derived from Rat Plasma, Primary Rat Hepatocytes and Isolated Perfused Rat Liver

1982 ◽  
Vol 47 (02) ◽  
pp. 166-172 ◽  
Author(s):  
Yoav Sharoni ◽  
Maria C Topal ◽  
Patricia R Tuttle ◽  
Henry Berger
Keyword(s):  
Rat Liver ◽  
Isoelectric Point ◽  
Rat Hepatocytes ◽  
Cell Types ◽  
Plasminogen Activators ◽  
Rat Plasma ◽  
Isolated Perfused Rat Liver ◽  
Perfused Rat Liver ◽  
Molecular Weights ◽  
Physiological Relevance

SummaryOf the two cell types it was possible to culture from the dissociated rat liver, hepatocytes and Kupffer cells, only the former were fibrinolytically active. Rat hepatocytes during the first 24 hr in culture secreted two plasminogen activators with molecular weights identical to those found in rat plasma, an 80,000-dalton form (PA-80) and a 45,000-dalton form (PA-45). Partially purified preparations of plasminogen activators from both sources were subjected to isoelectric focusing (IEF) to compare characteristics further. There were three distinct peaks of PA-45 in each preparation with isoelectric points of 7.1, 7.2 and 7.4; all electrophoretic forms had the same low affinity to fibrin. PA-80 from both sources displayed similar IEF profiles with forms ranging from pH values of 7 to 8, all with the same high affinity to fibrin. The major form of PA-80 in the plasma preparation had an isoelectric point of 7.9 whereas that in the hepatocyte preparation had an isoelectric point of 7.6. The isolated perfused rat liver was also shown to produce both PA-80 and PA-45 emphasizing the physiological relevance of the findings with hepatocytes. It is concluded that in the rat hepatocytes contribute to the plasma profile with regard to the plasminogen activator content.

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