• Genomics & Informatics
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• v.7 no.2
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• pp.111-121
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• 2009

Cell membrane proteins play crucial roles in the cell's molecular interaction with its environment and within itself. They consist of membrane-bound proteins and many types of transmembrane (TM) proteins such as receptors, transporters, channel proteins, and enzymes. Membrane proteomes of cellular organisms reveal some characteristics in their global topological distribution according to their evolutionary positions, and show their own information transfer complexity. Predicted transmembrane segments (TMSs) in membrane proteomes with HMMTOP showed near power-law distribution and frequency characteristics in 6-TMS and 7-TMS proteins in prokaryotes and eukaryotes, respectively. This reaffirms the important roles of membrane receptors in cellular communication and biological evolutionary history.

• Bulletin of the Korean Chemical Society
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• v.27 no.3
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• pp.386-388
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• 2006

Membrane proteins in highly oriented lipid bilayer samples are useful for membrane protein structure determination. We used in the past planar lipid bilayers which were aligned and supported on the glass slide. These samples were mechanically aligned in a magnetic field. However, these stacks of glass slides with planar lipid bilayers are not well suited for use with a commercial solid-state NMR probe with a round coil. Therefore, a homebuilt solid-state NMR probe was built and used with a stack of thin glass plates wherein the RF coil was wrapped directly around the flat square sample. Recently, we began to use magnetically aligned bicelles that are suitable for the structure determination of membrane proteins by solid-state NMR spectroscopy without any effort to build a flat square coil probe. These bicelle samples are well suited for use with a commercial solidstate NMR probe with a round coil, are very easy to prepare and are very stable, so that they can be kept for more than a year. In this paper, we present the solid-state NMR spectra of optimized and magnetically oriented bicelle samples of membrane proteins.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.12
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• pp.1678-1682
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• 2001

The total proteins were estimated in both deoxycholate (DOC)-extract of sperm membrane and seminal plasma of chilled as well as frozen semen obtained from five Murrah buffalo bulls. Proteins were further characterized by polyacrylamide gel electrophoresis (PAGE) in three bulls. The protein content of sperm membrane extract (SME) and that of seminal plasma (SP) decreased gradually with increase in freezing period from 6 to 24 mo when compared with the values observed in freshly chilled semen in all bulls. The total decrease in protein content of SME and SP varied from 30-40% and 28-59% respectively during 6-24 mo of freezing. The number of glycoproteins/proteins (GP/P) in SME varied from 4-8 in freshly-chilled semen of all bulls and reduced to 2-4 after 24 mo of freezing. In SP, the number of proteins varied from 6-10 in freshly chilled semen of all bulls and reduced to 3-8 after 24 mo of freezing. Some of the proteins in SME and SP disappeared, others got altered and appeared with change in molecular weight after different freezing times. These studies reveal that alterations in the sperm membrane proteins may be responsible for damage to their membrane during freezing and thus lowering their fertilizability.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.30 no.3
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• pp.186-192
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• 2004

Purpose: Human tooth proteins are highly heterogeneous, comprising diverse proteins derived from a number of genes. The attempts to identify protein for activity of tooth matrix proteins have been defied by several factors. First, the amount of proteins within teeth is very small relative to many extracellular matrix proteins of other tissues. Second, the bioassay system is tedious and needed for long time. Therefore we tried to find easy techniques, which increase the product rate, and an assay of small proteins, with which amino acid sequence is possible without additional procedures. Materials and Methods: Total protein were extracted from 300 g enamel removed teeth and 600 g teeth with 4 mol/L guanidine HCl and purified by gel chromatography. Aliquot of proteins was implanted into muscle pouches in Sprague-Dawley rats for bioassay. By SDS-PAGE and membrane blotting, molecular weight of each protein was estimated and a partial amino acid sequence was obtained. Each fraction blotted on the membrane was cut out and inserted in rat ectopic model. Results: In dissociative method, total tooth proteins were obtained 1mg/ml from enamel removed teeth and 3.5 mg/ml from teeth. In SDS-PAGE, four clear bands at the sites corresponding to 66, 40, 20 and 18 kD. Especially The 66 kD band was clearly exhibited. Amino acid sequencing from tooth could be possible using PVDF membrane blotting technique. In amino acid sequencing, 66 kD protein was identified as albumin. Conclusion: Compared with conventional method for extraction of teeth protein and bioassay of proteins, the methods in this study were easy, time-saving and more productive technique. The matured tooth proteins omitting additional procedure of mechanical removal of enamel were simply analyzed using blotted PVDF membrane. This method seems to make a contribution as a technique for bioassay and amino acid sequencing of protein.

• Journal of the Korean Society of Food Science and Nutrition
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• v.13 no.4
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• pp.459-468
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• 1984

The currently accepted model of membrane structure proposes a dynamic, asymmetric lipid matrix of phospholipids and cholesterol with globular proteins embedded across the membrane to various degrees. Most phospholipids are in the bilayer arrangement and also closely associated with integral membrane proteins or loosely associated with peripheral proteins. Biological functions of membrane, such as membrane-bound enzyme functions and transport systems, are influenced by the membrane physical properties, which are determined by fatty acid composition of phospholipids, polar head group composition and membrane cholesterol content. Polar and non-polar region of the phospholipid molecule can interact, with changes in the conformation of a membrane-associated protein altering either its catalytic activity or the protein's interaction with other membrane proteins. Mammalian dietary studies attempted to change the lipid composition of a few cell membranes have shown comparisons, using essential fatty acid-deficient diets. In recent years, Clandinin and a few other workers have pioneered the study proving the influence of dietary fat fed in a nutritionally complete diet on composition of phospholipid classes of cell membrane. Modulation caused by diet fat was rapid and reversible in phospholipid fatty acyl composition of membranes of cardiac mitochondria, liver cell, brain synaptosome and lymphocytes. These changes were at the same time, accompanied by variety of membrane associated functions controlled by membrane-bound enzymes, tranporter and receptor proteins. The findings suggest the basic concept of the necessity of dietary fatty acid balance if consistency of optimal membrane structural lipid composition is to be maintained, as well as the overall inadequacy of describing the nutritional-biochemical quality of a dietary fat solely by its content of linoleic acid. Furthermore, they give light on the possible application to clinical and preventive medicine.

• Mass Spectrometry Letters
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• v.10 no.3
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• pp.84-87
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• 2019

Liquid chromatography mass spectrometry is widely employed in proteomics studies. One of such instruments is the Liquid Chromatography (LC)-Matrix-assisted laser desorption ionisation (MALDI)-Time of flight (TOF) or LC-MALDI-TOF/TOF. In this study, this instrument was used to identify the membrane proteins of a protozoan parasite namely Entamoeba histolytica. It causes amoebiasis in human. The E. histolytica trophozoites were cultured prior to the membrane protein extraction using the conventional method, $ProteoPrep^{(R)}$ and $ProteoExtract^{(R)}$ kits. Then, the membrane protein extracts were trypticdigested and analysed by LC-MALDI-TOF/TOF. Approximately, 194 proteins were identified and 27.8% (54) were predicted as membrane proteins having 1 to 15 transmembrane regions and signal peptides by combining all three extraction methods. Also, this study has discovered 3 unique proteins as compared to our previous study which merit further investigation.

• Korean Journal of Clinical Laboratory Science
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• v.51 no.1
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• pp.78-85
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• 2019

Membrane proteins are involved in many common diseases, including heart disease and cancer. In various disease states, such as cancer, abnormal signaling pathways that are related to the membrane proteins cause the cells to divide out of control and the expression of membrane proteins can be altered. Membrane proteins have the hydrophobic environment of a lipid bilayer, which makes an analysis of the membrane proteins notoriously difficult. Therefore, this study evaluated the efficacy of two different methods for optimal membrane protein extraction. High-speed centrifuge and reagent-based method with a -/+ filter aided sample preparation (FASP) were compared. As a result, the high-speed centrifuge method is quite effective in analyzing the mitochondrial inner membranes, while the reagent-based method is useful for endoplasmic reticulum membrane analysis. In addition, the function of the membrane proteins extracted from the two methods were analyzed using GeneGo software. GO processes showed that the endoplasmic reticulum-related responses had higher significance in the reagent-based method. An analysis of the process networks showed that one cluster in the high-speed centrifuge method and four clusters in the reagent-based method were visualized. In conclusion, the two methods are useful for the analysis of different subcellular membrane proteins, and are expected to assist in selecting the membrane protein extraction method by considering the target subcellular membrane proteins for study.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.3
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• pp.137-142
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• 2015

NMR-based structural studies on membrane proteins are appreciated quite challenging due to various reasons, generally including the narrow dispersion of NMR spectra, the severe peak broadening, and the lack of long range NOEs. In spite of the poor biophysical properties, structural studies on membrane proteins have got to go on, considering their functional importance in biological systems. In this review, we provide a simple overview of the techniques generally used in structural studies of membrane proteins by solution NMR, with experimental examples of a helical membrane protein, caveolin 3. Detergent screening is usually employed as the first step and the selection of appropriate detergent is the most important for successful approach to membrane proteins. Various tools can then be applied as specialized NMR techniques in solution that include sample deteuration, amino-acid selective isotope labeling, residual dipolar coupling, and paramagnetic relaxation enhancement.

• Animal cells and systems
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• v.4 no.2
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• pp.165-171
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• 2000

Ubiquitinated proteins in lysosomes were characterized by using two monoclonal antibodies (mAbs): LYS8-1, a mAb to lysosomal proteins, and NYA124, a mAb to ubiquitin. LYS8-1 stained lysosome-like vesicles in immunofluorescence microscopy of Amoeba proteus and Acanthamoeba castellanii. In immunoblotting, LYS8-1's antigens (LYS proteins) were detected as 68-kDa and 77-kDa proteins in A. proteus, and as 30-kDa and 39-kDa proteins in A. castellanii. In immunoprecipitation of A. castellanii, at least four distinct LYS proteins, LVS35p, LyS39p, LyS42p, and LYS46p, were detected and accumulated upon inhibition of lysosome functions but not upon that of 26S proteasome functions. They were all found to be ubiquitinated, and were recovered in the lysosome fractions in subcellular fractionation experiments. In chemical fractionation analyses, LYS35p and LYS39p were demonstrated to be peripherally associated with lysosome membrane, while LYS42p and LYS46p tightly bound to the membrane. These results suggest that the LYS proteins become associated to lysosomal membrane upon ubiquitination.

• BMB Reports
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• v.42 no.11
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• pp.697-704
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• 2009

Membrane proteins play important roles in the biology of the cell, including intercellular communication and molecular transport. Their well-established importance notwithstanding, the high-resolution structures of membrane proteins remain elusive due to difficulties in protein expression, purification and crystallization. Thus, accurate prediction of membrane protein topology can increase the understanding of membrane protein function. Here, we provide a brief review of the diverse computational methods for predicting membrane protein structure and function, including recent progress and essential bioinformatics tools. Our hope is that this review will be instructive to users studying membrane protein biology in their choice of appropriate bioinformatics methods.