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Classification of Cell Membrane Proteins

Seyed Koosha Golmohammadi, Lukasz Kurgan, Brendan Crowley, Marek Reformat
2007 2007 Frontiers in the Convergence of Bioscience and Information Technologies  
Knowledge of a given type of cell membrane protein is crucial for determining its function.  ...  Membrane proteins are an important class of proteins that serve as channels, receptors, and energy transducers in a cell membrane.  ...  Knowledge of a given type of cell membrane protein is crucial in determining its function.  ... 
doi:10.1109/fbit.2007.21 dblp:conf/fbit/GolmohammadiKCR07 fatcat:kbh2auq2vzhl7jdq76w3mouski

Classification of Trispanins: A Diverse Group of Proteins That Function in Membrane Synthesis and Transport Mechanisms

Misty M. Attwood, Helgi B. Schiöth
2020 Frontiers in Cell and Developmental Biology  
This first overall study of trispanins provides a unique analysis of a diverse group of membrane proteins.  ...  Our comprehensive identification and classification using bioinformatic methods describe 152 3TM proteins.  ...  The plasma membrane is the most studied of cell membranes, and is composed of a phospholipid bilayer that contains phospholipids, glycolipids, sterols, and proteins.  ... 
doi:10.3389/fcell.2019.00386 pmid:32039202 pmcid:PMC6987440 fatcat:qb2w2xndmrap7hka2e6cynvfpq

A Prediction Model for Membrane Proteins Using Moments Based Features

Ahmad Hassan Butt, Sher Afzal Khan, Hamza Jamil, Nouman Rasool, Yaser Daanial Khan
2016 BioMed Research International  
These membrane proteins exhibit their effect in cellular activities inside and outside of the cell.  ...  The most expedient unit of the human body is its cell. Encapsulated within the cell are many infinitesimal entities and molecules which are protected by a cell membrane.  ...  Conflict of Interests The authors declare that there is no conflict of interests regarding the publication of this paper.  ... 
doi:10.1155/2016/8370132 pmid:26966690 pmcid:PMC4761391 fatcat:4vljgug4z5dw3nhafapyuzw42a

Entamoeba histolytica: Proteomics Bioinformatics Reveal Predictive Functions and Protein–Protein Interactions of Differentially Abundant Membrane and Cytosolic Proteins

Norhidayah Azmi, Nurulhasanah Othman
2021 Membranes  
The results showed 24 (44.4%) out of the 54 proteins that increased in abundance were membrane proteins and 30 were cytosolic proteins.  ...  Therefore, this study aimed to quantify the differential abundance of membrane and cytosolic proteins in membrane versus cytosolic fractions and analyze their predicted functions and interaction.  ...  Conflicts of Interest: The authors declare no conflict of interest. Membranes 2021, 11, 376  ... 
doi:10.3390/membranes11060376 pmid:34063994 fatcat:m6ics6mlr5bsvgyb7c7ftlj6oa

Membrane protein structure determination using cryo-electron tomography and 3D image averaging

Alberto Bartesaghi, Sriram Subramaniam
2009 Current Opinion in Structural Biology  
of membrane protein assemblies in intact cells and non-symmetric viruses.  ...  The vast majority of membrane protein complexes of biological interest cannot be purified to homogeneity, or removed from a physiologically relevant context without loss of function.  ...  Structural analysis of receptors in cell membranes While there is beginning to be major progress in the use of X-ray crystallography to determine the structures of integral membrane proteins, the challenge  ... 
doi:10.1016/j.sbi.2009.06.005 pmid:19646859 pmcid:PMC2752674 fatcat:e4w33fdiajfpxiggtdcfjrrxla

Profiling the size-dependent heterogeneity of membrane proteins in a mixed population of small extracellular vesicle for potential cancer diagnosis [article]

Chunhui Zhai, Feng Xie, Qiang Zeng, Weiqiang Zheng, Jingan Wang, Haiyan Hu, Yuting Yang, Xianting Ding, Hui Yu
2022 bioRxiv   pre-print
Heterogeneous membrane protein expression is correlated with sizes of small EVs, but accessing this correlative information is limited by the precise isolation of size-dependent subpopulations.  ...  Using small EVs derived from different cancer cell lines, highly heterogeneous protein profiles are recorded in the three subpopulations.  ...  For example, by profiling the expression level of membrane proteins from sEV, early diagnosis of breast cancer 12 13 and classification of cancer types 14 have been demonstrated.  ... 
doi:10.1101/2022.04.13.488159 fatcat:x3ymjbiibvbu5hnqnirh4rm3pu

The Landscape of Pseudomonas aeruginosa Membrane-Associated Proteins

Sara Motta, Davide Vecchietti, Alessandra M. Martorana, Pietro Brunetti, Giovanni Bertoni, Alessandra Polissi, Pierluigi Mauri, Dario Di Silvestre
2020 Cells  
Following application of extraction methods enriching specific protein domains, about 15% of total identified peptides were classified in trans inner-membrane, inner-membrane exposed, trans outer-membrane  ...  They can contribute to the antibiotic resistance of the bacterial cells and be involved in the interaction with host cells.  ...  Classification of peptides from P. aeruginosa proteins localized in membranes. The number of inner-and outer-membrane classified peptides per protein is highlighted in yellow and blue, respectively.  ... 
doi:10.3390/cells9112421 pmid:33167383 fatcat:y3ihhdd2ergz3dt4uwadfc22fm

A hybrid machine-learning approach for segmentation of protein localization data

P. M. Kasson, J. B. Huppa, M. M. Davis, A. T. Brunger
2005 Bioinformatics  
Such data are acquired via observation and quantitative analysis of fluorescently labeled proteins in living cells.  ...  Results: We have employed this classifier to analyze signaling protein localization in T-cell activation.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bti615 pmid:16091410 fatcat:4fybop67kfeqzet5lz27rxydve

A Dynamic-time Distance Based on Wavelet Decomposition for Subcellular Localization Classification

Cuifang Gao, Wanqiang Shen, Yanglijun Zhang
2020 IEEE Access  
Consequently, the use of isoelectric point numericalized protein sequences cannot effectively distinguish between cytoplasmic and cell membrane protein sequences, and this eventually results in lower classification  ...  by KNN Cytoplasm Cell membrane Cytoplasm 461 (TP) 197 (FP) Cell membrane 227 (FN) 856 (TN)  ... 
doi:10.1109/access.2020.3040555 fatcat:af2hmpvn3vfdvkidvyh4eobr2a

Pseudo Amino Acid Feature-based Protein Function Prediction using Support Vector Machine and K-Nearest Neighbors

Anjna Jayant Deen, Manasi Gyanchandani
2020 International Journal of Advanced Computer Science and Applications  
Every protein cell sequence length and size are in different sequence order.  ...  Therefore machine learning computational tool synthesizes accurate identification of structure and function class of membrane protein.  ...  The membrane protein is the type of protein residing around a cell membrane, or their subcellular locations are also defined as various types of protein.  ... 
doi:10.14569/ijacsa.2020.0110922 fatcat:bfyexz46t5gndeq6zpuxmrmfpe

Bioinformatics Analysis and Functional Prediction of Transmembrane Proteins in Entamoeba histolytica

Tamanna Anwar, Gourinath Samudrala
2018 Genes  
A classification of the repertoire of TM transporters in the present study augments several hints on potential methods of targeting the parasite for therapeutic benefits.  ...  The percentage of TM proteins was found to be lower in comparison to the free-living eukaryotes, due to the extracellular nature and functional diversification of the TM proteins.  ...  TM proteins perform numerous integral functions in the cells such as adhesion, signaling, transport of membrane-impermeable molecules, cell recognition, cell-cell communication, etc.  ... 
doi:10.3390/genes9100499 fatcat:kmdsl2ok6jfgte4hkqyyofu7uy

Feature selection for human membrane protein type classification using filter methods

Glenda Anak Kaya, Nor Ashikin Mohamad Kamal
2019 IAES International Journal of Artificial Intelligence (IJ-AI)  
Two datasets of human membrane protein are used, S1 and S2.  ...  Finally, our proposed methods present competitive results when compared with the previous works on membrane protein classification</span><span>.</span>  ...  INTRODUCTION The three main classes of protein are globular, fibrous and membrane. Membranes are a universal feature of all cell types which separates the cells and the environment outside the cell.  ... 
doi:10.11591/ijai.v8.i4.pp375-381 fatcat:wy7yis3xwzawrp5ackx7tocpiy

Prediction of Membrane Protein Types Using Pseudo-Amino Acid Composition and Ensemble Classification

Maqsood Hayat, Asifullah Khan
2013 International Journal of Computer and Electrical Engineering  
The knowledge of membrane proteins types often provides crucial hints for determining the function of uncharacterized membrane proteins.  ...  It is thus highly desirable to develop an automated method that can serve as a high throughput tool in identifying the types of newly found membrane proteins by their primary sequence information only.  ...  INTRODUCTION Cell membrane is vital to living organisms. Biologically, membrane proteins are the most imperative proteins because they control the cell processes inside or outside the cell.  ... 
doi:10.7763/ijcee.2013.v5.752 fatcat:nuzios532zectew2st7bfknh3u

Multiplexed imaging of surface enhanced Raman scattering nanotags in living mice using noninvasive Raman spectroscopy

C. L. Zavaleta, B. R. Smith, I. Walton, W. Doering, G. Davis, B. Shojaei, M. J. Natan, S. S. Gambhir
2009 Proceedings of the National Academy of Sciences of the United States of America  
The capability of BCA to unveil fine biochemical changes in cell spectra and excellent accuracy in classification can impel the broad application of Raman spectroscopy in biological research.  ...  The differences in terms of classification accuracy and interpretability of resulting data between these two methods in Raman spectroscopy have not been systematically investigated to our knowledge.  ...  The rupture of cell plasma membrane causes the leakage of cell content into the surroundings as the ruptured membrane allows the random diffusion of cell content across the membrane.  ... 
doi:10.1073/pnas.0813327106 pmid:19666578 pmcid:PMC2726370 fatcat:3nmlsdyq75gu3cdefcve7aqmuy

Comparison of principal component analysis and biochemical component analysis in Raman spectroscopy for the discrimination of apoptosis and necrosis in K562 leukemia cells

Yi Hong Ong, Mayasari Lim, Quan Liu
2012 Optics Express  
The capability of BCA to unveil fine biochemical changes in cell spectra and excellent accuracy in classification can impel the broad application of Raman spectroscopy in biological research.  ...  The differences in terms of classification accuracy and interpretability of resulting data between these two methods in Raman spectroscopy have not been systematically investigated to our knowledge.  ...  The rupture of cell plasma membrane causes the leakage of cell content into the surroundings as the ruptured membrane allows the random diffusion of cell content across the membrane.  ... 
doi:10.1364/oe.20.022158 pmid:23037364 fatcat:2cvgwcevsndstgy3qdtw5pmfvi
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