Journal articles: 'Specific protein'

1

Sear, Richard P. "Specific protein–protein binding in many-component mixtures of proteins." Physical Biology 1, no. 2 (April 29, 2004): 53–60. http://dx.doi.org/10.1088/1478-3967/1/2/001.

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2

Hunte, C. "Specific protein–lipid interactions in membrane proteins." Biochemical Society Transactions 33, no. 5 (October 1, 2005): 938. http://dx.doi.org/10.1042/bst20050938.

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3

Hunte, C. "Specific protein–lipid interactions in membrane proteins." Biochemical Society Transactions 33, no. 5 (October 26, 2005): 938–42. http://dx.doi.org/10.1042/bst0330938.

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Many membrane proteins selectively bind defined lipid species. This specificity has an impact on correct insertion, folding, structural integrity and full functionality of the protein. How are these different tasks achieved? Recent advances in structural research of membrane proteins provide new information about specific protein–lipid interactions. Tightly bound lipids in membrane protein structures are described and general principles of the binding interactions are deduced. Lipid binding is stabilized by multiple non-covalent interactions from protein residues to lipid head groups and hydrophobic tails. Distinct lipid-binding motifs have been identified for lipids with defined head groups in membrane protein structures. The stabilizing interactions differ between the electropositive and electronegative membrane sides. The importance of lipid binding for vertical positioning and tight integration of proteins in the membrane, for assembly and stabilization of oligomeric and multisubunit complexes, for supercomplexes, as well as for functional roles are pointed out.

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4

Baldrich, Marcus, and Werner Goebel. "Rapid and efficient site-specific mutagenesis." "Protein Engineering, Design and Selection" 3, no. 6 (1990): 563. http://dx.doi.org/10.1093/protein/3.6.563.

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5

Parsons, Helen L., John C. Earnshaw, Jane Wilton, Kevin S. Johnson, Paula A. Schueler, Walt Mahoney, and John McCafferty. "Directing phage selections towards specific epitopes." "Protein Engineering, Design and Selection" 9, no. 11 (1996): 1043–49. http://dx.doi.org/10.1093/protein/9.11.1043.

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6

Jongen-Rêlo, Ana L., and Joram Feldon. "Specific neuronal protein." Physiology & Behavior 76, no. 4-5 (August 2002): 449–56. http://dx.doi.org/10.1016/s0031-9384(02)00732-1.

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7

Prasad Bahadur, Ranjit, Pinak Chakrabarti, Francis Rodier, and Joël Janin. "A Dissection of Specific and Non-specific Protein–Protein Interfaces." Journal of Molecular Biology 336, no. 4 (February 2004): 943–55. http://dx.doi.org/10.1016/j.jmb.2003.12.073.

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8

Kusakabe, Takahiro, Kiyohisa Motoki, Yasushi Sugimoto, Yozo Takasaki, and Katsuji Hori. "Human aldolase B: liver-specific properties of the isozyme depend on type B isozyme group-specific sequences." "Protein Engineering, Design and Selection" 7, no. 11 (1994): 1387–93. http://dx.doi.org/10.1093/protein/7.11.1387.

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9

Tindbaek, Nikolaj, Allan Svendsen, Peter Rahbek Oestergaard, and Henriette Draborg. "Engineering a substrate‐specific cold‐adapted subtilisin." Protein Engineering, Design and Selection 17, no. 2 (February 2004): 149–56. http://dx.doi.org/10.1093/protein/gzh019.

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10

Kumar, Challa V., Apinya Buranaprapuk, and Jyotsna Thota. "Protein scissors: Photocleavage of proteins at specific locations." Journal of Chemical Sciences 114, no. 6 (December 2002): 579–92. http://dx.doi.org/10.1007/bf02708852.

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11

Paoni, Nicholas F., Alice M. Chow, Luis C. Peña, Bruce A. Keyt, Mark J. Zoller, and William F. Bennett. "Making tissue-type plasminogen activator more fibrin specific." "Protein Engineering, Design and Selection" 6, no. 5 (1993): 529–34. http://dx.doi.org/10.1093/protein/6.5.529.

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12

Wingfield, Paul T., Robert J. Mattaliano, H. Robson MacDonald, Stewart Craig, G. Marius Clore, Angela M. Gronenborn, and Ursula Schmeissner. "Recombinant-derived interleukin-1α stabilized against specific deamidation." "Protein Engineering, Design and Selection" 1, no. 5 (1987): 413–17. http://dx.doi.org/10.1093/protein/1.5.413.

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13

Richter, Susanne A., Kay Stubenrauch, Hauke Lilie, and Rainer Rudolph. "Polyionic fusion peptides function as specific dimerization motifs." Protein Engineering, Design and Selection 14, no. 10 (October 2001): 775–83. http://dx.doi.org/10.1093/protein/14.10.775.

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14

Nyikos, Lajos, Ágnes Simon, Péter Barabás, and Julianna Kardos. "Ligand-specific conformations of an ionotropic glutamate receptor." Protein Engineering, Design and Selection 15, no. 9 (September 2002): 717–20. http://dx.doi.org/10.1093/protein/15.9.717.

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15

Jäger, Marcus, Xavier Michalet, and Shimon Weiss. "Protein-protein interactions as a tool for site-specific labeling of proteins." Protein Science 14, no. 8 (August 2005): 2059–68. http://dx.doi.org/10.1110/ps.051384705.

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16

Jonczyk, P., and A. Nowicka. "Specific in vivo protein-protein interactions between Escherichia coli SOS mutagenesis proteins." Journal of bacteriology 178, no. 9 (1996): 2580–85. http://dx.doi.org/10.1128/jb.178.9.2580-2585.1996.

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17

Lawrence, David S., and Jinkui Niu. "Protein Kinase InhibitorsThe Tyrosine-Specific Protein Kinases." Pharmacology & Therapeutics 77, no. 2 (February 1998): 81–114. http://dx.doi.org/10.1016/s0163-7258(97)00052-1.

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18

Schmid, Stefan W., Waldemar Uhl, Anne Steinle, Bettina Rau, Christian Seiler, and Markus W. Büchler. "Human pancreas-specific protein." International Journal of Pancreatology 19, no. 3 (June 1996): 165–70. http://dx.doi.org/10.1007/bf02787364.

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19

Stein, Richard A. "Protein-Specific Discovery Strategies." Genetic Engineering & Biotechnology News 34, no. 6 (March 15, 2014): 1, 12, 13, 15. http://dx.doi.org/10.1089/gen.34.06.01.

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20

Parekh, R. B. "Site-specific protein glycosylation." Advanced Drug Delivery Reviews 13, no. 3 (March 1994): 251–66. http://dx.doi.org/10.1016/0169-409x(94)90014-0.

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21

Ebke, Lindsey A., Satyabrata Sinha, Gayle J. T. Pauer, and Stephanie A. Hagstrom. "Photoreceptor Compartment-Specific TULP1 Interactomes." International Journal of Molecular Sciences 22, no. 15 (July 28, 2021): 8066. http://dx.doi.org/10.3390/ijms22158066.

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Photoreceptors are highly compartmentalized cells with large amounts of proteins synthesized in the inner segment (IS) and transported to the outer segment (OS) and synaptic terminal. Tulp1 is a photoreceptor-specific protein localized to the IS and synapse. In the absence of Tulp1, several OS-specific proteins are mislocalized and synaptic vesicle recycling is impaired. To better understand the involvement of Tulp1 in protein trafficking, our approach in the current study was to physically isolate Tulp1-containing photoreceptor compartments by serial tangential sectioning of retinas and to identify compartment-specific Tulp1 binding partners by immunoprecipitation followed by liquid chromatography tandem mass spectrometry. Our results indicate that Tulp1 has two distinct interactomes. We report the identification of: (1) an IS-specific interaction between Tulp1 and the motor protein Kinesin family member 3a (Kif3a), (2) a synaptic-specific interaction between Tulp1 and the scaffold protein Ribeye, and (3) an interaction between Tulp1 and the cytoskeletal protein microtubule-associated protein 1B (MAP1B) in both compartments. Immunolocalization studies in the wild-type retina indicate that Tulp1 and its binding partners co-localize to their respective compartments. Our observations are compatible with Tulp1 functioning in protein trafficking in multiple photoreceptor compartments, likely as an adapter molecule linking vesicles to molecular motors and the cytoskeletal scaffold.

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22

De Rosa, Lucia, Aitziber L. Cortajarena, Alessandra Romanelli, Lynne Regan, and Luca Domenico D'Andrea. "Site-specific protein double labeling by expressed protein ligation: applications to repeat proteins." Org. Biomol. Chem. 10, no. 2 (2012): 273–80. http://dx.doi.org/10.1039/c1ob06397a.

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23

Baldwin, Jack E., Stephen L. Martin, and John D. Sutherland. "Site-specific forced misincorporation mutagenesis using modified T7 DNA polymerase." "Protein Engineering, Design and Selection" 4, no. 5 (1991): 579–84. http://dx.doi.org/10.1093/protein/4.5.579.

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24

Casey, J. L., A. M. Sanalla, D. Tamvakis, C. Thalmann, E. L. Carroll, K. Parisi, A. M. Coley, et al. "Peptides specific for Mycobacterium avium subspecies paratuberculosis infection: diagnostic potential." Protein Engineering Design and Selection 24, no. 8 (June 13, 2011): 589–96. http://dx.doi.org/10.1093/protein/gzr026.

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25

Daffu, Gurdip K., Patricia Lopez, Francine Katz, Michael Vinogradov, Chang-Guo Zhan, Donald W. Landry, and Joanne Macdonald. "Sulfhydryl-specific PEGylation of phosphotriesterase cysteine mutants for organophosphate detoxification." Protein Engineering Design and Selection 28, no. 11 (August 4, 2015): 501–6. http://dx.doi.org/10.1093/protein/gzv036.

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26

Nicholson, Thomas B., and Clifford P. Stanners. "Specific inhibition of GPI-anchored protein function by homing and self-association of specific GPI anchors." Journal of Cell Biology 175, no. 4 (November 13, 2006): 647–59. http://dx.doi.org/10.1083/jcb.200605001.

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The functional specificity conferred by glycophosphatidylinositol (GPI) anchors on certain membrane proteins may arise from their occupancy of specific membrane microdomains. We show that membrane proteins with noninteractive external domains attached to the same carcinoembryonic antigen (CEA) GPI anchor, but not to unrelated neural cell adhesion molecule GPI anchors, colocalize on the cell surface, confirming that the GPI anchor mediates association with specific membrane domains and providing a mechanism for specific signaling. This directed targeting was exploited by coexpressing an external domain-defective protein with a functional protein, both with the CEA GPI anchor. The result was a complete loss of signaling capabilities (through integrin–ECM interaction) and cellular effect (differentiation blockage) of the active protein, which involved an alteration of the size of the microdomains occupied by the active protein. This work clarifies how the GPI anchor can determine protein function, while offering a novel method for its modulation.

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27

Stolarski, Ryszard. "Thermodynamics of specific protein-RNA interactions." Acta Biochimica Polonica 50, no. 2 (June 30, 2003): 297–318. http://dx.doi.org/10.18388/abp.2003_3688.

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Description of the recognition specificity between proteins and nucleic acids at the level of molecular interactions is one of the most challenging tasks in biophysics. It is key to understanding the course and control of gene expression and to the application of the thus acquired knowledge in chemotherapy. This review presents experimental results of thermodynamic studies and a discussion of the role of thermodynamics in formation and stability of functional protein-RNA complexes, with a special attention to the interactions involving mRNA 5' cap and cap-binding proteins in the initiation of protein biosynthesis in the eukaryotic cell. A theoretical framework for analysis of the thermodynamic parameters of protein-nucleic acid association is also briefly surveyed. Overshadowed by more spectacular achievements in structural studies, the thermodynamic investigations are of equal importance for full comprehension of biopolymers' activity in a quantitative way. In this regard, thermodynamics gives a direct insight into the energetic and entropic characteristics of complex macromolecular systems in their natural environment, aqueous solution, and thus complements the structural view derived from X-ray crystallography and multidimensional NMR. Further development of the thermodynamic approach toward interpretation of recognition and binding specificity in terms of molecular biophysics requires more profound contribution from statistical mechanics.

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28

Nalawansha, Dhanusha A., Ke Li, John Hines, and Craig M. Crews. "Hijacking Methyl Reader Proteins for Nuclear-Specific Protein Degradation." Journal of the American Chemical Society 144, no. 12 (March 21, 2022): 5594–605. http://dx.doi.org/10.1021/jacs.2c00874.

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29

Rose, Megan L. H., and Maxwell T. Hincke. "Protein constituents of the eggshell: eggshell-specific matrix proteins." Cellular and Molecular Life Sciences 66, no. 16 (May 19, 2009): 2707–19. http://dx.doi.org/10.1007/s00018-009-0046-y.

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30

Glover, Claiborne V. C. "Sequence-specific protein-DNA recognition by transcriptional regulatory proteins." Plant Molecular Biology Reporter 7, no. 3 (August 1989): 183–208. http://dx.doi.org/10.1007/bf02668686.

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31

Löwenadler, B., B. Nilsson, L. Abrahmsén, T. Moks, L. Ljungqvist, E. Holmgren, S. Paleus, S. Josephson, L. Philipson, and M. Uhlén. "Production of specific antibodies against protein A fusion proteins." EMBO Journal 5, no. 9 (September 1986): 2393–98. http://dx.doi.org/10.1002/j.1460-2075.1986.tb04509.x.

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32

Hemler, Martin E. "Specific tetraspanin functions." Journal of Cell Biology 155, no. 7 (December 24, 2001): 1103–8. http://dx.doi.org/10.1083/jcb.200108061.

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Relatively little attention has been given to the large family of abundantly expressed transmembrane proteins known as tetraspanins. Now, the importance of tetraspanins is strongly supported by emerging genetic evidence, coupled with new insights into the biochemistry and functions of tetraspanin protein complexes.

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33

Dan, Feng, and Zeng Zong-Hao. "Specific and Non-Specific Contacts in Protein Crystals." Protein & Peptide Letters 11, no. 4 (August 1, 2004): 361–66. http://dx.doi.org/10.2174/0929866043406959.

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34

Janin, Joël. "Specific versus non-specific contacts in protein crystals." Nature Structural Biology 4, no. 12 (December 1997): 973–74. http://dx.doi.org/10.1038/nsb1297-973.

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35

Gentzsch, Martina, and Widmar Tanner. "Protein-O-glycosylation in yeast: protein-specific mannosyltransferases." Glycobiology 7, no. 4 (1997): 481–86. http://dx.doi.org/10.1093/glycob/7.4.481.

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36

Lyons, Alan, David J. King, Raymond J. Owens, Geoffrey T. Yarranton, Andrew Millican, Nigel R. Whittle, and John R. Adair. "Site-specific attachment to recombinant antibodies via introduced surface cysteine residues." "Protein Engineering, Design and Selection" 3, no. 8 (1990): 703–8. http://dx.doi.org/10.1093/protein/3.8.703.

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37

Hong, S. H., Q. Hao, and W. Maret. "Domain-specific fluorescence resonance energy transfer (FRET) sensors of metallothionein/thionein." Protein Engineering, Design and Selection 18, no. 6 (May 23, 2005): 255–63. http://dx.doi.org/10.1093/protein/gzi031.

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38

Milovnik, P., D. Ferrari, C. A. Sarkar, and A. Pluckthun. "Selection and characterization of DARPins specific for the neurotensin receptor 1." Protein Engineering Design and Selection 22, no. 6 (April 22, 2009): 357–66. http://dx.doi.org/10.1093/protein/gzp011.

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39

Koide, A., J. Wojcik, R. N. Gilbreth, A. Reichel, J. Piehler, and S. Koide. "Accelerating phage-display library selection by reversible and site-specific biotinylation." Protein Engineering Design and Selection 22, no. 11 (September 8, 2009): 685–90. http://dx.doi.org/10.1093/protein/gzp053.

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40

Arai, Tomonori, Masayoshi Uehata, Hiroyuki Akatsuka, and Tsutomu Kamiyama. "A quantitative analysis to unveil specific binding proteins for bioactive compounds." Protein Engineering, Design and Selection 26, no. 4 (December 23, 2012): 249–54. http://dx.doi.org/10.1093/protein/gzs103.

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41

Hanioka, Nobumitsu, Kenneth Korzekwa, and Frank J. Gonzalez. "Sequence requirements for cytochromes P450IIA1 and P450IIA2 catalytic activity: evidence for both specific and non-specific substrate binding interactions through use of chimeric cDNAs and cDNA expression." "Protein Engineering, Design and Selection" 3, no. 7 (1990): 571–75. http://dx.doi.org/10.1093/protein/3.7.571.

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42

Wouters-Tyrou, D., A. Martin-Ponthieu, N. Ledoux-Andula, M. Kouach, M. Jaquinod, J. A. Subirana, and P. Sautière. "Squid spermiogenesis: molecular characterization of testis-specific pro-protamines." Biochemical Journal 309, no. 2 (July 15, 1995): 529–34. http://dx.doi.org/10.1042/bj3090529.

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Cuttlefish spermiogenesis is characterized by a two-step nuclear protein transition: histones-->spermatid-specific protein (protein T)-->sperm protamine (protein Sp). A similar situation can be observed in another Cephalopod species, the squid Loligo pealeii. The protein T from Loligo consists of two structural variants, T1 and T2 (molecular masses: 10788 and 10791 Da respectively), phosphorylated to different degrees (2-6 phosphate groups). The primary structures of these two variants and of the protamine variant Sp2 were established from sequence analysis and mass spectrometric data of the proteins and their fragments. T1 and T2 are closely related proteins of 79 residues. The complete structural identity of the C-terminal domain (residues 22-79) of protein T2 with the sperm protamine Sp2 (molecular mass 8562 Da, 58 residues) strongly suggests that the testis-specific protein T2 is indeed the precursor of the protamine. The transition between the precursor protein T and protein Sp results from a hydrolytic cleavage similar to that found in many proteins that are synthesized as precursors. The processing mechanism involves the specific cleavage of a Gly-Arg bond in the sequence Met/Leu18-Lys-Gly-Gly-Arg-Arg23. Furthermore, the study provides molecular evidence on the taxonomic relationship between Loligo and Sepia.

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43

Best, Robert B., Wenwei Zheng, and Jeetain Mittal. "Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association." Journal of Chemical Theory and Computation 10, no. 11 (October 16, 2014): 5113–24. http://dx.doi.org/10.1021/ct500569b.

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44

Jonczyk, Piotr, Adrianna Nowicka, and Iwona J. Fijalkowska. "P III B.4 Specific protein-protein interactions between E. coll DNA replication proteins." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 379, no. 1 (September 1997): S22. http://dx.doi.org/10.1016/s0027-5107(97)82666-8.

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45

Strandmann, E. P. v., C. Zoidl, H. Nakhei, B. Holewa, R. P. v. Strandmann, P. Lorenz, L. Klein-Hitpass, and G. U. Ryffel. "A highly specific and sensitive monoclonal antibody detecting histidine-tagged recombinant proteins." Protein Engineering Design and Selection 8, no. 7 (July 1, 1995): 733–35. http://dx.doi.org/10.1093/protein/8.7.733.

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46

Shukla, G. S., and D. N. Krag. "Cancer cell-specific internalizing ligands from phage displayed -lactamase-peptide fusion libraries." Protein Engineering Design and Selection 23, no. 6 (March 10, 2010): 431–40. http://dx.doi.org/10.1093/protein/gzq013.

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47

Nisbet, R. M., J. Nigro, K. Breheney, J. Caine, M. K. Hattarki, and S. D. Nuttall. "Central amyloid- -specific single chain variable fragment ameliorates A aggregation and neurotoxicity." Protein Engineering Design and Selection 26, no. 10 (June 13, 2013): 571–80. http://dx.doi.org/10.1093/protein/gzt025.

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48

Barinka, Cyril, Jakub Ptacek, Antonia Richter, Zora Novakova, Volker Morath, and Arne Skerra. "Selection and characterization of Anticalins targeting human prostate-specific membrane antigen (PSMA)." Protein Engineering Design and Selection 29, no. 3 (January 21, 2016): 105–15. http://dx.doi.org/10.1093/protein/gzv065.

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49

Gunneriusson, E., K. Nord, M. Uhlén, and P. Å. Nygren. "Affinity maturation of a Taq DNA polymerase specific affibody by helix shuffling." Protein Engineering, Design and Selection 12, no. 10 (October 1999): 873–78. http://dx.doi.org/10.1093/protein/12.10.873.

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50

Gould, Christine, and Chung F. Wong. "Designing specific protein kinase inhibitors:." Pharmacology & Therapeutics 93, no. 2-3 (February 2002): 169–78. http://dx.doi.org/10.1016/s0163-7258(02)00186-9.

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Journal articles on the topic 'Specific protein'

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