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Journal articles on the topic 'Protein functional analysis'

Author: Grafiati

Published: 5 June 2025

Last updated: 2 August 2025

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1

Levy-Cohen, Gal, and Michael Blank. "Functional analysis of protein ubiquitination." Analytical Biochemistry 484 (September 2015): 37–39. http://dx.doi.org/10.1016/j.ab.2015.04.040.

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2

Johri, Parul, Mala Trivedi, and Sujeet Pratap Singh. "Atom based Profiling and Functional Enrichment analysis of Aquaporins." Research Journal of Biotechnology 16, no. 10 (2021): 75–77. http://dx.doi.org/10.25303/1610rjbt7577.

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Sequence analysis is a computational biology method to study protein sequences by comparing amino acids of one protein sequence with the other (residual level comparison). This study reveals a new concept of comparing protein sequences at their basic atomic level. Aquaporins from various origin were compared at their atomic level and the study revealed that all the aquaporin proteins have a closed range of 31.0% to 34.2% of carbon atoms irrespective of their origin and amino acid sequence. Further the protein interaction and functional enrichment analysis of AQP7 showed significant interaction

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3

Yuan, Fei, Xiaoyong Pan, Lei Chen, Yu-Hang Zhang, Tao Huang, and Yu-Dong Cai. "Analysis of Protein–Protein Functional Associations by Using Gene Ontology and KEGG Pathway." BioMed Research International 2019 (July 18, 2019): 1–10. http://dx.doi.org/10.1155/2019/4963289.

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Protein–protein interaction (PPI) plays an extremely remarkable role in the growth, reproduction, and metabolism of all lives. A thorough investigation of PPI can uncover the mechanism of how proteins express their functions. In this study, we used gene ontology (GO) terms and biological pathways to study an extended version of PPI (protein–protein functional associations) and subsequently identify some essential GO terms and pathways that can indicate the difference between two proteins with and without functional associations. The protein–protein functional associations validated by experime

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4

Konig, Simone. "Functional Protein Analysis Using Mass Spectrometry." Current Organic Chemistry 9, no. 9 (2005): 875–87. http://dx.doi.org/10.2174/1385272054038291.

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5

Ranganathan, Vasudevan, and Kainaat Munir Khoja. "Characterization and functional analysis of the hypothetical protein in Yersinia pestis." Journal of Microbiology & Experimentation 10, no. 5 (2022): 170–79. http://dx.doi.org/10.15406/jmen.2022.10.00370.

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A hypothetical protein is a protein which exists but the function is not known. These are the proteins for which there is no experimental evidence that it is expressed in vivo. The usual scenario involving a hypothetical protein is gene identification during genome analysis. The function of a hypothetical protein can also be predicted by domain homology searches with various confidence levels. The Human Genome project and the genome projects of many other organisms has been a source for the information on the sequences and their functional aspects. However, this resulted in identification of m

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Christensen, Stefan Jarl, Silke Flindt Badino, Ana Mafalda Cavaleiro, Kim Borch, and Peter Westh. "Functional analysis of chimeric TrCel6A enzymes with different carbohydrate binding modules." Protein Engineering, Design and Selection 32, no. 9 (2019): 401–9. http://dx.doi.org/10.1093/protein/gzaa003.

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Abstract The glycoside hydrolase (GH) family 6 is an important group of enzymes that constitute an essential part of industrial enzyme cocktails used to convert lignocellulose into fermentable sugars. In nature, enzymes from this family often have a carbohydrate binding module (CBM) from the CBM family 1. These modules are known to promote adsorption to the cellulose surface and influence enzymatic activity. Here, we have investigated the functional diversity of CBMs found within the GH6 family. This was done by constructing five chimeric enzymes based on the model enzyme, TrCel6A, from the so

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A. Rahaman, Siti Nurulnabila, Jastina Mat Yusop, Zeti-Azura Mohamed-Hussein, et al. "Crystal structure and functional analysis of human C1ORF123." PeerJ 6 (September 28, 2018): e5377. http://dx.doi.org/10.7717/peerj.5377.

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Proteins of the DUF866 superfamily are exclusively found in eukaryotic cells. A member of the DUF866 superfamily, C1ORF123, is a human protein found in the open reading frame 123 of chromosome 1. The physiological role of C1ORF123 is yet to be determined. The only available protein structure of the DUF866 family shares just 26% sequence similarity and does not contain a zinc binding motif. Here, we present the crystal structure of the recombinant human C1ORF123 protein (rC1ORF123). The structure has a 2-fold internal symmetry dividing the monomeric protein into two mirrored halves that compris

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Buck, B. Logan, Eric Altermann, Tina Svingerud, and Todd R. Klaenhammer. "Functional Analysis of Putative Adhesion Factors in Lactobacillus acidophilus NCFM." Applied and Environmental Microbiology 71, no. 12 (2005): 8344–51. http://dx.doi.org/10.1128/aem.71.12.8344-8351.2005.

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ABSTRACT Lactobacilli are major inhabitants of the normal microflora of the gastrointestinal tract, and some select species have been used extensively as probiotic cultures. One potentially important property of these organisms is their ability to interact with epithelial cells in the intestinal tract, which may promote retention and host-bacterial communication. However, the mechanisms by which they attach to intestinal epithelial cells are unknown. The objective of this study was to investigate cell surface proteins in Lactobacillus acidophilus that may promote attachment to intestinal tissu

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van Staalduinen, Laura, Stefanie Novakowski, and Zongchao Jia. "Structure and Functional Analysis of a Ribosomal Oxygenase." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1408. http://dx.doi.org/10.1107/s205327331408591x.

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The 2-oxoglutarate/Fe(II)-dependent oxygenases (2OG oxygenases) are a large family of proteins that share a similar overall three-dimensional structure and catalyze a diverse array of oxidation reactions. The Jumonji C (JmjC)-domain containing proteins represent an important subclass of the 2OG oxygenase family that typically catalyze protein hydroxylation; however, recently other reactions have been identified, such as tRNA modification. The E. coli gene, ycfD, was predicted to be a JmjC-domain containing protein of unknown function based on primary sequence. Recently YcfD was determined to a

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10

Zybailov, Boris L., Alicia K. Byrd, Galina V. Glazko, Yasir Rahmatallah, and Kevin D. Raney. "Protein-protein interaction analysis for functional characterization of helicases." Methods 108 (October 2016): 56–64. http://dx.doi.org/10.1016/j.ymeth.2016.04.014.

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11

Martin-Nieto, J., and D. J. Roufa. "Functional analysis of human RPS14 null alleles." Journal of Cell Science 110, no. 8 (1997): 955–63. http://dx.doi.org/10.1242/jcs.110.8.955.

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Previously we described a large collection of cloned human DNAs that encode chemically defined missense mutations within the ribosomal protein S14 sequence. We determined that biologically inactive (i.e. null) alleles resulted primarily from point mutations targeted to two internal segments of the S14-coding sequence and designated these functionally critical regions as domains B and D. Further, we inferred that structural determinants within domains B and D are required for proper incorporation of the S14 protein into nascent 40 S ribosomal particles and/or for the normal function of mature c

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12

Saridakis, Vivian. "Structural-Functional Analysis of USP7." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C309. http://dx.doi.org/10.1107/s2053273314096909.

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Ubiquitin Specific Protease 7 (USP7) catalyzes the deubiquitination of several substrate proteins including p53, Mdm2 and UbE2E1. Deubiquitination results in their rescue from 26S proteasome mediated degradation thus USP7 is critical in maintaining the cellular steady state levels of its substrates. USP7 is also known to interact with several viral proteins including herpes simplex virus Infected Cell Protein 0 (ICP0), Epstein Barr Nuclear Antigen 1 (EBNA1) and Kaposi's sarcoma-associated viral interferon regulatory factor 4 (vIRF4). USP7 possesses several domains including an N-terminal TRAF,

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Chen, Frances E., Stephan Kempiak, De-Bin Huang, Christopher Phelps та Gourisankar Ghosh. "Construction, expression, purification and functional analysis of recombinant NFκB p50/p65 heterodimer". Protein Engineering, Design and Selection 12, № 5 (1999): 423–28. http://dx.doi.org/10.1093/protein/12.5.423.

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14

Ahmed, MS, M. Kamruzzaman, MM Rana, Z. Akond, and MNH Mollah. "In silico analyses of human collagen protein function prediction." Journal of Bio-Science 24 (July 18, 2018): 55–65. http://dx.doi.org/10.3329/jbs.v24i0.37487.

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Collagen is the extracellular matrix protein in the several connective tissues in the human body. It is an important component for mediating cell-cell interactions and pathological conditions in human body. In this study we perform the analysis of physiochemical properties and investigate the functional characteristics of human collagen proteins. Also investigate the functional protein groups by the statistical analysis. The collagen protein family consisting 28 members in human which are involving in the complex structure of protein. The protein function, protein sequence properties, domain c

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15

Mei, Juan, Ji Zhao, and Yi Fu. "Analysis of Functional Modules in Protein Networks Using Graph Clustering Method." Advanced Materials Research 482-484 (February 2012): 612–15. http://dx.doi.org/10.4028/www.scientific.net/amr.482-484.612.

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Interaction detection methods have led to the discovery of thousands of interactions between proteins, and discerning relevance within large-scale data sets is important to present-day biology. As an important means for knowledge discovery, graph clustering attracts much attention in analysis of protein-protein interaction networks. Here, a modularity-based method was used to find communities of protein-protein interaction networks. Using this method, 177 communities were detected from a network involving 11,855 interactions among 2617 proteins in yeast and annotated according to MIPS hierarch

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16

Muhammad, Muhammad, Fronthea Swastawati, and Putut Har Riyadi. "Protein Functional Groups Analysis of Smoked Vaname Shrimp (Litopenaeus Vannamei) with Various Cooking Methods." International Journal of Research Publication and Reviews 5, no. 5 (2024): 2717–24. http://dx.doi.org/10.55248/gengpi.5.0524.1242.

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17

Adé, Jules, Yosr Haffani, and François J. Belzile. "Functional analysis of the Arabidopsis thaliana mismatch repair gene MSH2." Genome 44, no. 4 (2001): 651–57. http://dx.doi.org/10.1139/g01-027.

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The Arabidopsis thaliana MSH2 (AtMSH2) gene encodes a protein that belongs to a family of highly conserved proteins (MutS homologues (MSH)) involved in DNA mismatch repair. Sequence analysis strongly suggests that this single copy gene is indeed a homologue of MSH2, a gene known to play a central role in eukaryotic mismatch repair. In this report, we show that the AtMSH2 protein has functional attributes characteristic of previously described mismatch repair proteins. First, over-expression of this protein in Escherichia coli leads to a mutator phenotype similar to that reported previously for

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18

Jurata, L. W., and G. N. Gill. "Functional analysis of the nuclear LIM domain interactor NLI." Molecular and Cellular Biology 17, no. 10 (1997): 5688–98. http://dx.doi.org/10.1128/mcb.17.10.5688.

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LIM homeodomain and LIM-only (LMO) transcription factors contain two tandemly arranged Zn2+-binding LIM domains capable of mediating protein-protein interactions. These factors have restricted patterns of expression, are found in invertebrates as well as vertebrates, and are required for cell type specification in a variety of developing tissues. A recently identified, widely expressed protein, NLI, binds with high affinity to the LIM domains of LIM homeodomain and LMO proteins in vitro and in vivo. In this study, a 38-amino-acid fragment of NLI was found to be sufficient for the association o

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19

Awano, Naoki, Masaru Wada, Hirotada Mori, Shigeru Nakamori, and Hiroshi Takagi. "Identification and Functional Analysis of Escherichia coli Cysteine Desulfhydrases." Applied and Environmental Microbiology 71, no. 7 (2005): 4149–52. http://dx.doi.org/10.1128/aem.71.7.4149-4152.2005.

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ABSTRACT In Escherichia coli, three additional proteins having l-cysteine desulfhydrase activity were identified as O-acetylserine sulfhydrylase-A, O-acetylserine sulfhydrylase-B, and MalY protein, in addition to tryptophanase and cystathionine β-lyase, which have been reported previously. The gene disruption for each protein was significantly effective for overproduction of l-cysteine and l-cystine. Growth phenotype and transcriptional analyses suggest that tryptophanase contributes primarily to l-cysteine degradation.

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20

Mee-Hie Cho, Catherine, Ashok Mulchandani, and Wilfred Chen. "Functional analysis of organophosphorus hydrolase variants with high degradation activity towards organophosphate pesticides." Protein Engineering, Design and Selection 19, no. 3 (2006): 99–105. http://dx.doi.org/10.1093/protein/gzj007.

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21

Harris, S. E., C. L. Winchester, and K. J. Johnson. "Functional analysis of the homeodomain protein SIX5." Nucleic Acids Research 28, no. 9 (2000): 1871–78. http://dx.doi.org/10.1093/nar/28.9.1871.

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22

OZEKI, Kenji. "Functional Analysis of Resistant Protein in Amazake." JOURNAL OF THE BREWING SOCIETY OF JAPAN 117, no. 9 (2022): 627–34. http://dx.doi.org/10.6013/jbrewsocjapan.117.627.

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23

Milchram, Lisa, Anita Fischer, Jasmin Huber, et al. "Functional Analysis of Autoantibody Signatures in Rheumatoid Arthritis." Molecules 27, no. 4 (2022): 1452. http://dx.doi.org/10.3390/molecules27041452.

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For the identification of antigenic protein biomarkers for rheumatoid arthritis (RA), we conducted IgG profiling on high density protein microarrays. Plasma IgG of 96 human samples (healthy controls, osteoarthritis, seropositive and seronegative RA, n = 24 each) and time-series plasma of a pristane-induced arthritis (PIA) rat model (n = 24 total) were probed on AIT’s 16k protein microarray. To investigate the analogy of underlying disease pathways, differential reactivity analysis was conducted. A total of n = 602 differentially reactive antigens (DIRAGs) at a significance cutoff of p < 0.0

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24

Saha, Sovan, Abhimanyu Prasad, Piyali Chatterjee, Subhadip Basu, and Mita Nasipuri. "Protein function prediction from protein–protein interaction network using gene ontology based neighborhood analysis and physico-chemical features." Journal of Bioinformatics and Computational Biology 16, no. 06 (2018): 1850025. http://dx.doi.org/10.1142/s0219720018500257.

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Protein Function Prediction from Protein–Protein Interaction Network (PPIN) and physico-chemical features using the Gene Ontology (GO) classification are indeed very useful for assigning biological or biochemical functions to a protein. They also lead to the identification of those significant proteins which are responsible for the generation of various diseases whose drugs are still yet to be discovered. So, the prediction of GO functional terms from PPIN and sequence is an important field of study. In this work, we have proposed a methodology, Multi Label Protein Function Prediction (ML_PFP)

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25

AKUTSU, HIDEO. "From structure to function.A new viewpoint of the protein functional analysis." Kagaku To Seibutsu 32, no. 12 (1994): 820–24. http://dx.doi.org/10.1271/kagakutoseibutsu1962.32.820.

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26

Mattos-Graner, Renata O., Kristen A. Porter, Daniel J. Smith, Yumiko Hosogi, and Margaret J. Duncan. "Functional Analysis of Glucan Binding Protein B from Streptococcus mutans." Journal of Bacteriology 188, no. 11 (2006): 3813–25. http://dx.doi.org/10.1128/jb.01845-05.

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ABSTRACT Mutans streptococci are major etiological agents of dental caries, and several of their secreted products contribute to bacterial accumulation on teeth. Of these, Streptococcus mutans glucan binding protein B (GbpB) is a novel, immunologically dominant protein. Its biological function is unclear, although GbpB shares homology with a putative peptidoglycan hydrolase from S. agalactiae and S. pneumoniae, indicative of a role in murein biosynthesis. To determine the cellular function of GbpB, we used several approaches to inactivate the gene, analyze its expression, and identify interact

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27

Muramatsu, T., and M. Suwa. "Statistical analysis and prediction of functional residues effective for GPCR-G-protein coupling selectivity." Protein Engineering Design and Selection 19, no. 6 (2006): 277–83. http://dx.doi.org/10.1093/protein/gzl010.

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28

Masters, Susan B., Robert M. Stroud та Henry R. Bourne. "Family of G protein α chains: amphipathic analysis and predicted structure of functional domains". "Protein Engineering, Design and Selection" 1, № 1 (1986): 47–54. http://dx.doi.org/10.1093/protein/1.1.47.

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29

Thomas, S. L., J. Hauber, and G. Casari. "Probing the structure of the HIV-1 Rev trans-activator protein by functional analysis." Protein Engineering Design and Selection 10, no. 2 (1997): 103–7. http://dx.doi.org/10.1093/protein/10.2.103.

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30

Jia, Yan, Jinshan Cao, and Zhanyong Wei. "Bioinformatics Analysis of Spike Proteins of Porcine Enteric Coronaviruses." BioMed Research International 2021 (July 1, 2021): 1–11. http://dx.doi.org/10.1155/2021/6689471.

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This article is aimed at analyzing the structure and function of the spike (S) proteins of porcine enteric coronaviruses, including transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), and swine acute diarrhea syndrome coronavirus (SADS-CoV) by applying bioinformatics methods. The physical and chemical properties, hydrophilicity and hydrophobicity, transmembrane region, signal peptide, phosphorylation and glycosylation sites, epitope, functional domains, and motifs of S proteins of porcine enteric coronaviruses were predicted and

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31

Wang, Chen, Jinhui Wang, Dai Zhang, Jianing Cheng, Jiehua Zhu, and Zhihui Yang. "Identification and functional analysis of protein secreted by Alternaria solani." PLOS ONE 18, no. 3 (2023): e0281530. http://dx.doi.org/10.1371/journal.pone.0281530.

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Early blight, caused by the necrotrophic fungus Alternaria solani, is an important foliar disease that causes major yield losses of potato. Effector proteins secreted by pathogens to host cells can inhibit host immune response to pathogens. Currently, the function of effector proteins secreted by A. solani during infection is poorly understood. In this study, we identified and characterized a novel candidate effector protein, AsCEP50. AsCEP50 is a secreted protein that is highly expressed throughout the infection stages of A. solani. Agrobacterium tumefaciens-mediated transient expression in N

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Coutinho, M., K. S. Aulak, and A. E. Davis. "Functional analysis of the serpin domain of C1 inhibitor." Journal of Immunology 153, no. 8 (1994): 3648–54. http://dx.doi.org/10.4049/jimmunol.153.8.3648.

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Abstract To analyze the role of the heavily glycosylated amino-terminal domain of C1 inhibitor in protease inhibitory activity, two truncated C1 inhibitor molecules were constructed. The abilities of the recombinant truncated inhibitors to complex with target proteases were compared with that of the wild-type recombinant protein. One recombinant truncated molecule consisted of amino acid residues 76 to 478 (C-serp(76)) and the other of residues 98 to 478 (C-serp(98)). The recombinant proteins were each expressed in similar quantities. The thermal denaturation profiles of the two truncated prot

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Anbo, Hiroto, Masaya Sato, Atsushi Okoshi, and Satoshi Fukuchi. "Functional Segments on Intrinsically Disordered Regions in Disease-Related Proteins." Biomolecules 9, no. 3 (2019): 88. http://dx.doi.org/10.3390/biom9030088.

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One of the unique characteristics of intrinsically disordered proteins (IPDs) is the existence of functional segments in intrinsically disordered regions (IDRs). A typical function of these segments is binding to partner molecules, such as proteins and DNAs. These segments play important roles in signaling pathways and transcriptional regulation. We conducted bioinformatics analysis to search these functional segments based on IDR predictions and database annotations. We found more than a thousand potential functional IDR segments in disease-related proteins. Large fractions of proteins relate

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Lian, Zheng, Yuval Kluger, Dov S. Greenbaum, et al. "Genomic and proteomic analysis of the myeloid differentiation program: global analysis of gene expression during induced differentiation in the MPRO cell line." Blood 100, no. 9 (2002): 3209–20. http://dx.doi.org/10.1182/blood-2002-03-0850.

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Abstract We have used an approach using 2-dimensional gel electrophoresis with mass spectrometry analysis combined with oligonucleotide chip hybridization for a comprehensive and quantitative study of the temporal patterns of protein and mRNA expression during myeloid development in the MPRO murine cell line. This global analysis detected 123 known proteins and 29 “new” proteins out of 220 protein spots identified by tandem mass spectroscopy, including proteins in 12 functional categories such as transcription factors and cytokines. Bioinformatic analysis of these proteins revealed clusters wi

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Johnson, D. Thor, Robert A. Harris, Paul V. Blair, and Robert S. Balaban. "Functional consequences of mitochondrial proteome heterogeneity." American Journal of Physiology-Cell Physiology 292, no. 2 (2007): C698—C707. http://dx.doi.org/10.1152/ajpcell.00109.2006.

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Potential functional consequences of the differences in protein distribution between the mitochondria of the rat liver, heart, brain, and kidney, as determined in the companion paper in this issue (Johnson DT, French S, Blair PV, You JS, Bemis KG, Wang M, Harris RA, and Balaban RS. The tissue heterogeneity of the mammalian mitochondrial proteome. Am J Physiol Cell Physiol292: C689–C697, 2006), were analyzed using a canonical metabolic pathway approach as well as a functional domain homology analysis. These data were inserted into the Kyoto Encyclopedia of Genes and Genomes pathway framework to

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36

Wanitchakorn, Raktham, Gregory J. Hafner, Robert M. Harding, and James L. Dale. "Functional analysis of proteins encoded by banana bunchy top virus DNA-4 to -6." Microbiology 81, no. 1 (2000): 299–306. http://dx.doi.org/10.1099/0022-1317-81-1-299.

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Green fluorescent protein (GFP)-tagging was used to determine the intracellular localization pattern of the proteins encoded by banana bunchy top virus (BBTV) DNA-3, -4 and -6. The protein encoded by BBTV DNA-4, which possesses a hydrophobic N terminus, was found to localize exclusively to the cell periphery while the proteins encoded by BBTV DNA-3 and -6 were found in both the nucleus and the cytoplasm. Co-expression of the DNA-4 protein and the proteins encoded by BBTV DNA-3 and -6 revealed that the DNA-4 protein was able to re-locate the DNA-6 protein, but not the DNA-3 protein, to the cell

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Kader, Md Abdul, Akash Ahammed, Md Sharif Khan, Sheikh Abdullah Al Ashik, Md Shariful Islam, and Mohammad Uzzal Hossain. "Hypothetical protein predicted to be tumor suppressor: a protein functional analysis." Genomics & Informatics 20, no. 1 (2022): e6. http://dx.doi.org/10.5808/gi.21073.

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Litorilituus sediminis is a Gram-negative, aerobic, novel bacterium under the family of Colwelliaceae, has a stunning hypothetical protein containing domain called von Hippel-Lindau that has significant tumor suppressor activity. Therefore, this study was designed to elucidate the structure and function of the biologically important hypothetical protein EMK97_00595 (QBG34344.1) using several bioinformatics tools. The functional annotation exposed that the hypothetical protein is an extracellular secretory soluble signal peptide and contains the von Hippel-Lindau (VHL; VHL beta) domain that has

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Kramer, W., F. Girbig, U. Gutjahr, and S. Kowalewski. "Radiation-inactivation analysis of the Na+/bile acid co-transport system from rabbit ileum." Biochemical Journal 306, no. 1 (1995): 241–46. http://dx.doi.org/10.1042/bj3060241.

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The functional-unit molecular size of the Na+/bile acid cotransport system and the apparent target size of the bile-acid-binding proteins in brush-border membrane vesicles from rabbit ileum were determined by radiation inactivation with high-energy electrons. The size of the functional transporting unit for Na(+)-dependent taurocholate uptake was determined to 451 +/- 35 kDa, whereas an apparent molecular mass of 434 +/- 39 kDa was measured for the Na(+)-dependent D-glucose transport system. Proteins of 93 kDa and 14 kDa were identified as putative protein components of the ileal Na+/bile acid

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Parvizpour, Sepideh, Ashraf Fadhil Jomah, and Jafar Razmara. "Structural and Functional Analysis of Mutated Human Pyrin B30.2 Domain." Current Proteomics 17, no. 1 (2020): 78–85. http://dx.doi.org/10.2174/1570164616666190628165835.

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Background: Familial Mediterranean Fever (FMF) is a prototypical hereditary autoinflammatory disease affecting principally Mediterranean populations and characterized by recurrent frequent fever and inflammation. The disease is essentially caused by inherited mutations in the MEFV gene which encodes pyrin protein. The reported mutations are mostly located on the B30.2 domain in the C-terminal end of the protein. Objective: The present study reports a structural comparison of the five most common mutated structures including M694V, V726A, M694I, R761H, and M680I. The aim of this study was to de

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Jervis, Adrian J., Alison G. Wood, Joel A. Cain, et al. "Functional analysis of the Helicobacter pullorum N-linked protein glycosylation system." Glycobiology 28, no. 4 (2018): 233–44. http://dx.doi.org/10.1093/glycob/cwx110.

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Abstract N-linked protein glycosylation systems operate in species from all three domains of life. The model bacterial N-linked glycosylation system from Campylobacter jejuni is encoded by pgl genes present at a single chromosomal locus. This gene cluster includes the pglB oligosaccharyltransferase responsible for transfer of glycan from lipid carrier to protein. Although all genomes from species of the Campylobacter genus contain a pgl locus, among the related Helicobacter genus only three evolutionarily related species (H. pullorum, H. canadensis and H. winghamensis) potentially encode N-lin

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Cui, Guangyu, Yu Chen, De-Shuang Huang, and Kyungsook Han. "An Algorithm for Finding Functional Modules and Protein Complexes in Protein-Protein Interaction Networks." Journal of Biomedicine and Biotechnology 2008 (2008): 1–10. http://dx.doi.org/10.1155/2008/860270.

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Biological processes are often performed by a group of proteins rather than by individual proteins, and proteins in a same biological group form a densely connected subgraph in a protein-protein interaction network. Therefore, finding a densely connected subgraph provides useful information to predict the function or protein complex of uncharacterized proteins in the highly connected subgraph. We have developed an efficient algorithm and program for finding cliques and near-cliques in a protein-protein interaction network. Analysis of the interaction network of yeast proteins using the algorit

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de Jong, Arjan S., Fabrizio de Mattia, Michiel M. Van Dommelen, et al. "Functional Analysis of Picornavirus 2B Proteins: Effects on Calcium Homeostasis and Intracellular Protein Trafficking." Journal of Virology 82, no. 7 (2008): 3782–90. http://dx.doi.org/10.1128/jvi.02076-07.

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ABSTRACT The family Picornaviridae consists of a large group of plus-strand RNA viruses that share a similar genome organization. The nomenclature of the picornavirus proteins is based on their position in the viral RNA genome but does not necessarily imply a conserved function of proteins of different genera. The enterovirus 2B protein is a small hydrophobic protein that, upon individual expression, is localized to the endoplasmic reticulum (ER) and the Golgi complex, reduces ER and Golgi complex Ca2+ levels, most likely by forming transmembrane pores, and inhibits protein trafficking through

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Borkiewicz, Lidia, Mateusz Mołoń, Eliza Molestak, et al. "Functional Analysis of the Ribosomal uL6 Protein of Saccharomyces cerevisiae." Cells 8, no. 7 (2019): 718. http://dx.doi.org/10.3390/cells8070718.

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The genome-wide duplication event observed in eukaryotes represents an interesting biological phenomenon, extending the biological capacity of the genome at the expense of the same genetic material. For example, most ribosomal proteins in Saccharomyces cerevisiae are encoded by a pair of paralogous genes. It is thought that gene duplication may contribute to heterogeneity of the translational machinery; however, the exact biological function of this event has not been clarified. In this study, we have investigated the functional impact of one of the duplicated ribosomal proteins, uL6, on the t

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Funke, Sebastian, Carsten Schmelter, Sascha D. Markowitsch, et al. "Comparative Quantitative Analysis of Porcine Optic Nerve Head and Retina Subproteomes." International Journal of Molecular Sciences 20, no. 17 (2019): 4229. http://dx.doi.org/10.3390/ijms20174229.

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Optic nerve head (ONH) and retina (RET) are the main sites of damage in neurodegenerative optic neuropathies including glaucoma. Up to date, little is known about the molecular interplay between these two adjoining ocular components in terms of proteomics. To close this gap, we investigated ONH and RET protein extracts derived from porcine eyes (n = 12) (Sus scrofa domestica Linnaeus 1758) using semi-quantitative mass spectrometry (MS)-based proteomics comprising bottom-up LC–ESI MS/MS and targeted SPE-MALDI-TOF MS analysis. In summary, more than 1600 proteins could be identified from the ONH/

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Petit, A., C. Ragu, G. Soler, et al. "Functional analysis of the NUP98-CCDC28A fusion protein." Haematologica 97, no. 3 (2011): 379–87. http://dx.doi.org/10.3324/haematol.2011.047969.

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Ruoppolo, Margherita, Stefania Orrù, Alfonsina D'Amato, et al. "Analysis of transglutaminase protein substrates by functional proteomics." Protein Science 12, no. 6 (2003): 1290–97. http://dx.doi.org/10.1110/ps.0239103.

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Murayama, Shuhei, Koji Karasawa, and Masaru Kato. "Photodegradable Nanoparticles for Functional Analysis of Intracellular Protein." Journal of Photopolymer Science and Technology 31, no. 1 (2018): 71–74. http://dx.doi.org/10.2494/photopolymer.31.71.

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Najarian, K., K. Gopalakrishnan, and R. H. Zadeh. "Signal processing for functional analysis of protein mutants." International Journal of Bioinformatics Research and Applications 1, no. 1 (2005): 102. http://dx.doi.org/10.1504/ijbra.2005.006905.

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Zidkova, J., K. Kontrova, V. Skop, et al. "FUNCTIONAL ANALYSIS OF PROTEIN VISFATIN USING RNA INTERFERENCE." Atherosclerosis Supplements 9, no. 1 (2008): 18. http://dx.doi.org/10.1016/s1567-5688(08)70064-3.

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Weiland, Katherine L., Nancee L. Oien, Fred Homa, and Michael W. Wathen. "Functional analysis of human cytomegalovirus polymerase accessory protein." Virus Research 34, no. 3 (1994): 191–206. http://dx.doi.org/10.1016/0168-1702(94)90124-4.

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