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Journal articles on the topic 'Protein 2'

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Published: 4 June 2021

Last updated: 20 February 2023

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1

Hayashi, Masahiro, Masahiro Tomita, and Katsutoshi Yoshizato. "Interleukin-2-collagen chimeric protein which liberates interleukin-2 upon collagenolysis." Protein Engineering, Design and Selection 15, no. 5 (May 2002): 429–36. http://dx.doi.org/10.1093/protein/15.5.429.

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2

Olafsen, T., G. J. Tan, C. w. Cheung, P. J. Yazaki, J. M. Park, J. E. Shively, L. E. Williams, A. A. Raubitschek, M. F. Press, and A. M. Wu. "Characterization of engineered anti-p185HER-2 (scFv-CH3)2 antibody fragments (minibodies) for tumor targeting." Protein Engineering Design and Selection 17, no. 4 (May 4, 2004): 315–23. http://dx.doi.org/10.1093/protein/gzh040.

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3

Roesler, Keith R., and A. Gururaj Rao. "Conformation and stability of barley chymotrypsin inhibitor-2 (CI-2) mutants containing multiple lysine substitutions." Protein Engineering, Design and Selection 12, no. 11 (November 1999): 967–73. http://dx.doi.org/10.1093/protein/12.11.967.

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4

McCartney, John E., Mei-Sheng Tai, Robert M. Hudziak, Gregory P. Adams, Louis M. Weiner, Donald Jin, Walter F. Stafford, et al. "Engineering disulfide-linked single-chain Fv dimers [(sFv')2] with improved solution and targeting properties: anti-digoxin 26–10 (sFv')2 and anti-c-erbB-2 741F8 (sFv')2 made by protein folding and bonded through C-terminal cysteinyl peptides." "Protein Engineering, Design and Selection" 8, no. 3 (1995): 301–14. http://dx.doi.org/10.1093/protein/8.3.301.

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5

Minggu, Renaldo B., Janette M. Rumbajan, and Grace L. A. Turalaki. "Struktur Genom Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2)." JURNAL BIOMEDIK (JBM) 13, no. 2 (March 29, 2021): 233. http://dx.doi.org/10.35790/jbm.13.2.2021.31996.

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Abstract: The genome sequencing as well as the protein structure and function of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is known and helps in structurally characterizing viral proteins, determining evolutionary trajectories, identifying interactions with host proteins and providing biological insights. Knowledge of the structure of the SARS-CoV-2 genome is useful as a means of understanding the disease coronavirus disease 19 (COVID-19). This study aims to determine the genome structure of SARS-CoV-2. This study is a literature review, which was conducted on 23 literatures. This study showed that 23 literatures obtained, as many as in journals suggesting the structure of the genome, there are ORF (open reading frame) / NSP (non-structural protein) and structural protein, namely: S (spike, glycoprotein), E (Envelope), M (Membrane) and N (nucleocapsid) while the remaining 5 literatures do not discuss this structure. The result of this study showed that the genome structure of SARS-CoV-2 consisted of structural proteins, namely; glycoprotein (S), envelope protein (E), membrane protein (M), and nucleocapsid protein (N) and non-structural protein (NSP) encoded by ORF1a and ORF1b via two polyproteins pp1a and pp1b.Keywords: Genome, SARS-CoV-2 Abstrak: Urutan genom serta struktur dan fungsi protein dari severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) telah diketahui dan membantu dalam mengkarakterisasi protein virus secara struktural, menentukan lintasan evolusi, mengidentifikasi interaksi dengan protein inang dan memberikan wawasan biologi. Pengetahuan tentang struktur genom SARS-CoV-2 ini bermanfaat sebagai pengetahuan memahami penyakit coronavirus disease 19 (COVID-19). Penelitian ini bertujuan untuk mengetahui struktur genom SARS-CoV-2. Penelitian ini merupakan penelitian yang bersifat literature review, yang dilakukan terhadap 23 literatur yang memenuhi kriteria inklusi dan eksklusi dari penelitian ini. Penelitian ini menunjukkan bahwa 23 literatur yang didapat, sebanyak pada 18 jurnal mengemukakan tentang struktur genom terdapat ORF (open reading frame)/NSP (Non-Struktural Protein) dan protein struktural yaitu : S (lonjakan, glikoprotein), E (Envelope), M (Membran) dan N (Nukleocapsid) sedangkan sisanya terdapat 5 jurnal tidak membahas struktur tersebut. Hasil penelitian ini menunjukan bahwa struktur genom SARS-CoV-2 terdiri atas protein struktural yaitu; glikoprotein (S), protein amplop (E), protein membran (M), dan protein nuckleokapsid dan protein non-struktural (NSP) yang di kodekan oleh ORF1a dan ORF1b melalui dua poliprotein pp1a dan pp1b.Kata Kunci: Genome, SARS-CoV-2

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6

Marechal, V., B. Elenbaas, J. Piette, J. C. Nicolas, and A. J. Levine. "The ribosomal L5 protein is associated with mdm-2 and mdm-2-p53 complexes." Molecular and Cellular Biology 14, no. 11 (November 1994): 7414–20. http://dx.doi.org/10.1128/mcb.14.11.7414-7420.1994.

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Throughout the purification of the mdm-2 or mdm-2-p53 protein complexes, a protein with a molecular weight of 34,000 was observed to copurify with these proteins. Several monoclonal antibodies directed against distinct epitopes in the mdm-2 or p53 protein coimmunoprecipitated this 34,000-molecular-weight protein, which did not react to p53 or mdm-2 polyclonal antisera in a Western immunoblot. The N-terminal amino acid sequence of this 34,000-molecular-weight protein demonstrated that the first 40 amino acids were identical to the ribosomal L5 protein, found in the large rRNA subunit and bound to 5S RNA. Partial peptide maps of the authentic L5 protein and the 34,000-molecular-weight protein were identical. mdm-2-L5 and mdm-2-L5-p53 complexes were shown to bind 5S RNA specifically, presumably through the known specificity of L5 protein for 5S RNA. In 5S RNA-L5-mdm-2-p53 ribonucleoprotein complexes, it was also possible to detect the 5.8S RNA which has been suggested to be covalently linked to a percentage of the p53 protein in a cell. These experiments have identified a unique ribonucleoprotein complex composed of 5S RNA, L5 protein, mdm-2 proteins, p53 protein, and possibly the 5.8S RNA. While the function of such a ribonucleoprotein complex is not yet clear, the identity of its component parts suggests a role for these proteins and RNA species in ribosomal biogenesis, ribosomal transport from the nucleus to the cytoplasm, or translational regulation in the cell.

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7

Marechal, V., B. Elenbaas, J. Piette, J. C. Nicolas, and A. J. Levine. "The ribosomal L5 protein is associated with mdm-2 and mdm-2-p53 complexes." Molecular and Cellular Biology 14, no. 11 (November 1994): 7414–20. http://dx.doi.org/10.1128/mcb.14.11.7414.

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Throughout the purification of the mdm-2 or mdm-2-p53 protein complexes, a protein with a molecular weight of 34,000 was observed to copurify with these proteins. Several monoclonal antibodies directed against distinct epitopes in the mdm-2 or p53 protein coimmunoprecipitated this 34,000-molecular-weight protein, which did not react to p53 or mdm-2 polyclonal antisera in a Western immunoblot. The N-terminal amino acid sequence of this 34,000-molecular-weight protein demonstrated that the first 40 amino acids were identical to the ribosomal L5 protein, found in the large rRNA subunit and bound to 5S RNA. Partial peptide maps of the authentic L5 protein and the 34,000-molecular-weight protein were identical. mdm-2-L5 and mdm-2-L5-p53 complexes were shown to bind 5S RNA specifically, presumably through the known specificity of L5 protein for 5S RNA. In 5S RNA-L5-mdm-2-p53 ribonucleoprotein complexes, it was also possible to detect the 5.8S RNA which has been suggested to be covalently linked to a percentage of the p53 protein in a cell. These experiments have identified a unique ribonucleoprotein complex composed of 5S RNA, L5 protein, mdm-2 proteins, p53 protein, and possibly the 5.8S RNA. While the function of such a ribonucleoprotein complex is not yet clear, the identity of its component parts suggests a role for these proteins and RNA species in ribosomal biogenesis, ribosomal transport from the nucleus to the cytoplasm, or translational regulation in the cell.

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8

Rao, B. M., A. T. Girvin, T. Ciardelli, D. A. Lauffenburger, and K. D. Wittrup. "Interleukin-2 mutants with enhanced -receptor subunit binding affinity." Protein Engineering Design and Selection 16, no. 12 (December 1, 2003): 1081–87. http://dx.doi.org/10.1093/protein/gzg111.

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9

Williams, D. P., K. Parker, P. Bacha, W. Bishai, M. Borowski, F. Genbauffe, T. B. Strom, and J. R. Murphy. "Diphtheria toxin receptor binding domain substitution with interleukin-2: genetic construction and properties of a diphtheria toxin-related interleukin-2 fusion protein." "Protein Engineering, Design and Selection" 1, no. 6 (1987): 493–98. http://dx.doi.org/10.1093/protein/1.6.493.

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10

Kiyokawa, Tetsuyuki, Diane P. Williams, Catherine E. Snider, Terry B. Strom, and John R. Murphy. "Protein engineering of diphtheria-toxin-related interleukin-2 fusion toxins to increase cytotoxic potency for high-affinity IL-2-receptor-bearing target cells." "Protein Engineering, Design and Selection" 4, no. 4 (1991): 463–68. http://dx.doi.org/10.1093/protein/4.4.463.

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11

Szilágyi, András, Vera Grimm, Adrián K. Arakaki, and Jeffrey Skolnick. "Prediction of physical protein–protein interactions." Physical Biology 2, no. 2 (April 19, 2005): S1—S16. http://dx.doi.org/10.1088/1478-3975/2/2/s01.

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12

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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13

Martina, José A., Cecilia J. Bonangelino, Rubén C. Aguilar, and Juan S. Bonifacino. "Stonin 2." Journal of Cell Biology 153, no. 5 (May 28, 2001): 1111–20. http://dx.doi.org/10.1083/jcb.153.5.1111.

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Endocytosis of cell surface proteins is mediated by a complex molecular machinery that assembles on the inner surface of the plasma membrane. Here, we report the identification of two ubiquitously expressed human proteins, stonin 1 and stonin 2, related to components of the endocytic machinery. The human stonins are homologous to the Drosophila melanogaster stoned B protein and exhibit a modular structure consisting of an NH2-terminal proline-rich domain, a central region of homology specific to the stonins, and a COOH-terminal region homologous to the μ subunits of adaptor protein (AP) complexes. Stonin 2, but not stonin 1, interacts with the endocytic machinery proteins Eps15, Eps15R, and intersectin 1. These interactions occur via two NPF motifs in the proline-rich domain of stonin 2 and Eps15 homology domains of Eps15, Eps15R, and intersectin 1. Stonin 2 also interacts indirectly with the adaptor protein complex, AP-2. In addition, stonin 2 binds to the C2B domains of synaptotagmins I and II. Overexpression of GFP–stonin 2 interferes with recruitment of AP-2 to the plasma membrane and impairs internalization of the transferrin, epidermal growth factor, and low density lipoprotein receptors. These observations suggest that stonin 2 is a novel component of the general endocytic machinery.

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14

Cain, Dean, Susan Hutson, David Sane, Richard Loeser, and Reidar Wallin. "Modulation of the Binding of Matrix Gla Protein (MGP) to Bone Morphogenetic Protein-2 (BMP-2)." Thrombosis and Haemostasis 84, no. 12 (2000): 1039–44. http://dx.doi.org/10.1055/s-0037-1614168.

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SummaryMatrix Gla protein (MGP) is an inhibitor of calcification of the arterial wall but the mechanism of inhibition has not been resolved. Since chondrogenesis has been identified in calcified arteries from MPG null mice, we hypothesized that locally produced MGP might inhibit calcification by neutralizing the known effect of bone morphogenetic proteins (BMPs) as promotors of chondrogenesis and bone formation. As the first step to test this hypothesis, we demonstrate that MGP is a binding protein for 125I-BMP-2. Optimal binding is dependent on metals which suggests that the metal binding Gla region in MGP is involved. MGP is shown to undergo a Ca++ induced conformational change despite the presence of the γ-carboxylase binding site being part of the mature protein sequence. The data propose that MGP matures earlier in the secretory pathway than other vitamin K-dependent proteins. Antibodies were used in an attempt to identify MGP in bovine serum. Conformational specific MGP antibodies were shown to also recognize the Gla region in prothrombin and factor X but did not identify MGP in serum. This finding is supported by electrophoresis data which demonstrate the absence of MGP among Ba-citrate absorbed vitamin K-dependent serum proteins. We conclude that MGP does not exist in normal bovine serum.

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15

Raman, Karthik. "Construction and analysis of protein–protein interaction networks." Automated Experimentation 2, no. 1 (2010): 2. http://dx.doi.org/10.1186/1759-4499-2-2.

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16

Tamaoka, Akira. "2) Amyloid ^|^beta; Protein." Nihon Naika Gakkai Zasshi 100, no. 9 (2011): 2469–75. http://dx.doi.org/10.2169/naika.100.2469.

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17

Tamaoka, Akira. "2) Amyloid ^|^beta; Protein." Nihon Naika Gakkai Zasshi 100, Suppl (2011): 72b—73a. http://dx.doi.org/10.2169/naika.100.72b.

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18

Riley, Edward H., Joseph M. Lane, Marshall R. Urist, Karen M. Lyons, and Jay R. Lieberman. "Bone Morphogenetic Protein-2." Clinical Orthopaedics and Related Research 324 (March 1996): 39–46. http://dx.doi.org/10.1097/00003086-199603000-00006.

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19

Seedorf, Udo, Peter Ellinghaus, and Jerzy Roch Nofer. "Sterol carrier protein-2." Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids 1486, no. 1 (June 2000): 45–54. http://dx.doi.org/10.1016/s1388-1981(00)00047-0.

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20

Nakatani, Tomoyuki, Yu-Chun Lone, Junko Yamakawa, Masaharu Kanaoka, Hideyuki Gomi, John Wydenes, and Hiroshi Noguchi. "Humanization of mouse anti-human IL-2 receptor antibody B-B10." "Protein Engineering, Design and Selection" 7, no. 3 (1994): 435–43. http://dx.doi.org/10.1093/protein/7.3.435.

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21

Chu, Nai-Ming, Yang Chao, and Ru-Chang Bi. "The 2 Å crystal structure of subtilisin E with PMSF inhibitor." "Protein Engineering, Design and Selection" 8, no. 3 (1995): 211–15. http://dx.doi.org/10.1093/protein/8.3.211.

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22

Laub, M., M. Chatzinikolaidou, H. Rumpf, and H. P. Jennissen. "Modelling of Protein-Protein Interactions of Bone Morphogenetic Protein-2 (BMP-2) by 3D-Rapid Prototyping." Materialwissenschaft und Werkstofftechnik 33, no. 12 (December 2002): 729–37. http://dx.doi.org/10.1002/mawe.200290003.

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23

Alexanian, Anna, and Andrey Sorokin. "Cyclooxygenase 2: protein-protein interactions and posttranslational modifications." Physiological Genomics 49, no. 11 (November 1, 2017): 667–81. http://dx.doi.org/10.1152/physiolgenomics.00086.2017.

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Numerous studies implicate the cyclooxygenase 2 (COX2) enzyme and COX2-derived prostanoids in various human diseases, and thus, much effort has been made to uncover the regulatory mechanisms of this enzyme. COX2 has been shown to be regulated at both the transcriptional and posttranscriptional levels, leading to the development of nonsteroidal anti-inflammatory drugs (NSAIDs) and selective COX2 inhibitors (COXIBs), which inhibit the COX2 enzyme through direct targeting. Recently, evidence of posttranslational regulation of COX2 enzymatic activity by s-nitrosylation, glycosylation, and phosphorylation has also been presented. Additionally, posttranslational regulators that actively downregulate COX2 expression by facilitating increased proteasome degradation of this enzyme have also been reported. Moreover, recent data identified proteins, located in close proximity to COX2 enzyme, that serve as posttranslational modulators of COX2 function, upregulating its enzymatic activity. While the precise mechanisms of the protein-protein interaction between COX2 and these regulatory proteins still need to be addressed, it is likely these interactions could regulate COX2 activity either as a result of conformational changes of the enzyme or by impacting subcellular localization of COX2 and thus affecting its interactions with regulatory proteins, which further modulate its activity. It is possible that posttranslational regulation of COX2 enzyme by such proteins could contribute to manifestation of different diseases. The uncovering of posttranslational regulation of COX2 enzyme will promote the development of more efficient therapeutic strategies of indirectly targeting the COX2 enzyme, as well as provide the basis for the generation of novel diagnostic tools as biomarkers of disease.

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24

Reš, Ivica, and Olivier Lichtarge. "Character and evolution of protein–protein interfaces." Physical Biology 2, no. 2 (May 27, 2005): S36—S43. http://dx.doi.org/10.1088/1478-3975/2/2/s04.

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25

Andreeva, Alexandra V., Mikhail A. Kutuzov, and Tatyana A. Voyno- Yasenetskaya. "Scaffolding proteins in G-protein signaling." Journal of Molecular Signaling 2 (October 30, 2007): 13. http://dx.doi.org/10.1186/1750-2187-2-13.

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26

Plasterer, Thomas N. "PROTEAN: Protein Sequence Analysis and Prediction." Molecular Biotechnology 16, no. 2 (2000): 117–26. http://dx.doi.org/10.1385/mb:16:2:117.

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27

Uegaki, Koichi, Masahiro Shirakawa, Takashi Fujita, Tadatsugu Taniguchi, and Yoshimasa Kyogoku. "Characterization of the DNA binding domain of the mouse IRF-2 protein." "Protein Engineering, Design and Selection" 6, no. 2 (1993): 195–200. http://dx.doi.org/10.1093/protein/6.2.195.

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28

Frankel, Arthur E., Chris Burbage, Tao Fu, Edward Tagge, John Chandler, and Mark Willingham. "Characterization of a ricin fusion toxin targeted to the interleukin-2 receptor." "Protein Engineering, Design and Selection" 9, no. 10 (1996): 913–19. http://dx.doi.org/10.1093/protein/9.10.913.

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29

Ma, B., and R. Nussinov. "Molecular dynamics simulations of the unfolding of 2-microglobulin and its variants." Protein Engineering Design and Selection 16, no. 8 (August 1, 2003): 561–75. http://dx.doi.org/10.1093/protein/gzg079.

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30

Bajaj, C. L., R. Chowdhury, and V. Siddahanavalli. "$F^2$Dock: Fast Fourier Protein-Protein Docking." IEEE/ACM Transactions on Computational Biology and Bioinformatics 8, no. 1 (January 2011): 45–58. http://dx.doi.org/10.1109/tcbb.2009.57.

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31

Liedhegner, Elizabeth Sabens, Caleb D. Vogt, Daniel S. Sem, Christopher W. Cunningham, and Cecilia J. Hillard. "Sterol Carrier Protein-2: Binding Protein for Endocannabinoids." Molecular Neurobiology 50, no. 1 (February 9, 2014): 149–58. http://dx.doi.org/10.1007/s12035-014-8651-7.

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32

Khorsand, Babak, Abdorreza Savadi, and Mahmoud Naghibzadeh. "SARS-CoV-2-human protein-protein interaction network." Informatics in Medicine Unlocked 20 (2020): 100413. http://dx.doi.org/10.1016/j.imu.2020.100413.

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33

Ovek, Damla, Ameer Taweel, Zeynep Abali, Ece Tezsezen, Yunus Emre Koroglu, Chung-Jung Tsai, Ruth Nussinov, Ozlem Keskin, and Attila Gursoy. "SARS-CoV-2 Interactome 3D: A Web interface for 3D visualization and analysis of SARS-CoV-2–human mimicry and interactions." Bioinformatics 38, no. 5 (December 2, 2021): 1455–57. http://dx.doi.org/10.1093/bioinformatics/btab799.

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Abstract Summary We present a web-based server for navigating and visualizing possible interactions between SARS-CoV-2 and human host proteins. The interactions are obtained from HMI_Pred which relies on the rationale that virus proteins mimic host proteins. The structural alignment of the viral protein with one side of the human protein–protein interface determines the mimicry. The mimicked human proteins and predicted interactions, and the binding sites are presented. The user can choose one of the 18 SARS-CoV-2 protein structures and visualize the potential 3D complexes it forms with human proteins. The mimicked interface is also provided. The user can superimpose two interacting human proteins in order to see whether they bind to the same site or different sites on the viral protein. The server also tabulates all available mimicked interactions together with their match scores and number of aligned residues. This is the first server listing and cataloging all interactions between SARS-CoV-2 and human protein structures, enabled by our innovative interface mimicry strategy. Availability and implementation The server is available at https://interactome.ku.edu.tr/sars/.

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34

Zebboudj, Amina F., Minori Imura, and Kristina Boström. "Matrix GLA Protein, a Regulatory Protein for Bone Morphogenetic Protein-2." Journal of Biological Chemistry 277, no. 6 (December 6, 2001): 4388–94. http://dx.doi.org/10.1074/jbc.m109683200.

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35

Anderson, David R., Marvin J. Meyers, William F. Vernier, Matthew W. Mahoney, Ravi G. Kurumbail, Nicole Caspers, Gennadiy I. Poda, John F. Schindler, David B. Reitz, and Robert J. Mourey. "Pyrrolopyridine Inhibitors of Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MK-2)." Journal of Medicinal Chemistry 50, no. 11 (May 2007): 2647–54. http://dx.doi.org/10.1021/jm0611004.

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36

Anderson, David R., Shridhar Hegde, Emily Reinhard, Leslie Gomez, William F. Vernier, Len Lee, Shuang Liu, Aruna Sambandam, Patricia A. Snider, and Liaqat Masih. "Aminocyanopyridine inhibitors of mitogen activated protein kinase-activated protein kinase 2 (MK-2)." Bioorganic & Medicinal Chemistry Letters 15, no. 6 (March 2005): 1587–90. http://dx.doi.org/10.1016/j.bmcl.2005.01.067.

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37

Abd-Jamil, J., C. Y. Cheah, and S. AbuBakar. "Dengue virus type 2 envelope protein displayed as recombinant phage attachment protein reveals potential cell binding sites." Protein Engineering Design and Selection 21, no. 10 (July 1, 2008): 605–11. http://dx.doi.org/10.1093/protein/gzn041.

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38

Manning, Viola A., Linda K. Hardison, and Lynda M. Ciuffetti. "Ptr ToxA Interacts with a Chloroplast-Localized Protein." Molecular Plant-Microbe Interactions® 20, no. 2 (February 2007): 168–77. http://dx.doi.org/10.1094/mpmi-20-2-0168.

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Pyrenophora tritici-repentis, causal agent of tan spot of wheat, produces host-selective toxins that are determinants of pathogenicity or virulence. Ptr ToxA (ToxA), a proteina-ceous toxin produced by P. tritici-repentis, is a necrotizing toxin produced by the most common races isolated from infected wheat. Recent studies have shown that ToxA is internalized into the mesophyll cells and localizes to chloroplasts of sensitive wheat cultivars only. We employed a yeast two-hybrid screen in an effort to determine plant proteins that interact with ToxA and found that ToxA interacts with a chloroplast protein, designated ToxA binding protein 1 (ToxABP1). ToxABP1 contains a lysine-rich region within a coiled-coil domain that is similar to phosphotidyl-inositol binding sites present in animal proteins involved in endocytosis. In both ToxA-sensitive and -insensitive cultivars, ToxABP1 is expressed at similar levels and encodes an identical protein. ToxABP1 protein is present in both chloroplast membranes and chloroplast stroma. ToxA appears to interact primarily with a multimeric complex of ToxABP1 protein associated with the chloroplast membrane.

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Rosenstein, Jeffrey M., and Janette M. Krum. "Cytoskeletal Protein Immunoexpression in Fetal Neural Grafts: Distribution of Phosphorylated and Nonphosphorylated Neurofilament Protein and Microtubule-Associated Protein 2 (Map-2)." Cell Transplantation 5, no. 2 (March 1996): 233–41. http://dx.doi.org/10.1177/096368979600500212.

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The present study examined the immunocytochemical expression of important cytoskeletal proteins within the neurons of an extended series of neocortical grafts and smaller group of ventral mesencephalic (nigral) grafts. Using antibodies that were directed at all three neurofilament (NF) epitopes, NF-L, NF-M, and NF-H, we attempted to determine whether these neurons would have an altered cytoskeletal profile following the stress of transplantation, because previous studies have shown such changes following ischemia or direct brain injury. We studied phosphorylated NF protein, which is found predominantly in axons, nonphosphorylated NF protein, which is found predominantly in the somata-dendritic compartment, and MAP-2, a specific microtubule marker that is localized exclusively in the somato-dendritic compartment. The results show that in all neocortical grafts examined, both phosphorylated and nonphosphorylated NF immunoexpression was significantly downregulated and appeared only in relatively few axons and somatic profiles, respectively, even though there were numerous Nissl-stained neuronal profiles in the grafts. There was no particular pattern to the immunopositive profiles. At later times occasional neuronal profiles were positive for phosphorylated NF protein, suggesting a reaction to cellular injury. In contrast to neocortical grafts, the cytoskeletal profiles of MAP-2 and phosphorylated NF protein in nigral grafts appeared very similar to age-matched control although the nonphosphorylated NF protein expression did appear somewhat lessened at 1-2 mo postoperative. Because cytoskeletal proteins play important roles in neuronal size, shape, and structural stability, they may subserve key cellular issues in neural grafting. These results show a significant loss of cytoskeletal protein expression in neocortical grafts that does not occur in nigral grafts. These results suggest that fetal neurons from different brain regions (i.e., graft source) may respond differently to the grafting procedure insofar as their cytoskeletal makeup is concerned. In addition, a potential lack of appropriate growth substrates or synaptic contacts may also produce cytoskeletal alterations. As such, the cytoskeletal protein profiles in central nervous system (CNS) grafts may be useful markers for functional performance, perhaps reflecting a degree of cellular injury.

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40

Matthews, Alicia M., Thomas G. Biel, Uriel Ortega-Rodriguez, Vincent M. Falkowski, Xin Bush, Talia Faison, Hang Xie, Cyrus Agarabi, V. Ashutosh Rao, and Tongzhong Ju. "SARS-CoV-2 spike protein variant binding affinity to an angiotensin-converting enzyme 2 fusion glycoproteins." PLOS ONE 17, no. 12 (December 6, 2022): e0278294. http://dx.doi.org/10.1371/journal.pone.0278294.

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Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the Coronavirus disease 2019 (Covid-19) pandemic, continues to evolve and circulate globally. Current prophylactic and therapeutic countermeasures against Covid-19 infection include vaccines, small molecule drugs, and neutralizing monoclonal antibodies. SARS-CoV-2 infection is mainly mediated by the viral spike glycoprotein binding to angiotensin converting enzyme 2 (ACE2) on host cells for viral entry. As emerging mutations in the spike protein evade efficacy of spike-targeted countermeasures, a potential strategy to counter SARS-CoV-2 infection is to competitively block the spike protein from binding to the host ACE2 using a soluble recombinant fusion protein that contains a human ACE2 and an IgG1-Fc domain (ACE2-Fc). Here, we have established Chinese Hamster Ovary (CHO) cell lines that stably express ACE2-Fc proteins in which the ACE2 domain either has or has no catalytic activity. The fusion proteins were produced and purified to partially characterize physicochemical properties and spike protein binding. Our results demonstrate the ACE2-Fc fusion proteins are heavily N-glycosylated, sensitive to thermal stress, and actively bind to five spike protein variants (parental, alpha, beta, delta, and omicron) with different affinity. Our data demonstrates a proof-of-concept production strategy for ACE2-Fc fusion glycoproteins that can bind to different spike protein variants to support the manufacture of potential alternative countermeasures for emerging SARS-CoV-2 variants.

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41

Wood, EJ. "Introduction to proteins and protein engineering." Biochemical Education 16, no. 1 (January 1988): 52. http://dx.doi.org/10.1016/0307-4412(88)90036-2.

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Rock, Fernando, Margaret Everett, and Michel Klein. "Overexpression and structure-function analysis of a bioengineered IL-2/IL-6 chimeric lymphokine." "Protein Engineering, Design and Selection" 5, no. 6 (1992): 583–91. http://dx.doi.org/10.1093/protein/5.6.583.

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43

Clore, G. Marius, Angela M. Gronenborn, Michael N. G. James, Mogens Kjaer, Catherine A. McPhalen, and Fleming M. Poulsen. "Comparison of the solution and X-ray structures of barley serine proteinase inhibitor 2." "Protein Engineering, Design and Selection" 1, no. 4 (1987): 313–18. http://dx.doi.org/10.1093/protein/1.4.313.

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44

Gaulton, G. N., and D. D. Eardley. "Interleukin 2-dependent phosphorylation of interleukin 2 receptors and other T cell membrane proteins." Journal of Immunology 136, no. 7 (April 1, 1986): 2470–77. http://dx.doi.org/10.4049/jimmunol.136.7.2470.

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Abstract The addition of IL 2 to Con A-activated splenic T cells induced the rapid and time-dependent phosphorylation of membrane proteins with m.w. of 115,000 to 105,000, 90,000, and 66,000, and to a lesser extent 55,000 to 58,000, 40,000, and 34,000. Immunoprecipitations conducted with an anti-IL 2 receptor antibody indicated that the murine IL 2 receptor (55,000 to 58,000) was included in the set of IL 2-dependent phosphoproteins. Phosphorylation of these same proteins was also seen after IL 2 treatment of PHA-activated T cells and of the IL 2-dependent line CTLL-2. Membrane phosphorylation was dependent on physiologically relevant IL 2 concentrations (0.2 to 1 ng/ml), and was detected as early as 1 min after IL 2 addition, with maximal levels of phosphorylation achieved by 15 min. In contrast to these observations, the pattern of cytoplasmic protein phosphorylation remained unchanged after IL 2 addition, although IL 2 did augment the level of preexisting cytoplasmic phosphorylation induced by lectin. The pattern of membrane protein phosphorylation induced by IL 2 also overlapped in part with that induced after stimulation of Con A-activated T cells with the phorbol ester PMA. IL 2-stimulated phosphorylation was inhibited by the addition of agents that both stimulate cyclic AMP-dependent protein kinases and block lymphocyte mitogenesis. No effect was seen upon addition of agents that enhance cyclic GMP-dependent protein kinases. These observations support a role for specific membrane as opposed to cytoplasmic protein phosphorylation in the regulation of lymphocyte growth by IL 2, and also suggest that protein kinase A, and perhaps protein kinase C, participate as regulators of the IL 2 signaling mechanism.

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Mattola, Salla, Kari Salokas, Vesa Aho, Elina Mäntylä, Sami Salminen, Satu Hakanen, Einari A. Niskanen, et al. "Parvovirus nonstructural protein 2 interacts with chromatin-regulating cellular proteins." PLOS Pathogens 18, no. 4 (April 8, 2022): e1010353. http://dx.doi.org/10.1371/journal.ppat.1010353.

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Autonomous parvoviruses encode at least two nonstructural proteins, NS1 and NS2. While NS1 is linked to important nuclear processes required for viral replication, much less is known about the role of NS2. Specifically, the function of canine parvovirus (CPV) NS2 has remained undefined. Here we have used proximity-dependent biotin identification (BioID) to screen for nuclear proteins that associate with CPV NS2. Many of these associations were seen both in noninfected and infected cells, however, the major type of interacting proteins shifted from nuclear envelope proteins to chromatin-associated proteins in infected cells. BioID interactions revealed a potential role for NS2 in DNA remodeling and damage response. Studies of mutant viral genomes with truncated forms of the NS2 protein suggested a change in host chromatin accessibility. Moreover, further studies with NS2 mutants indicated that NS2 performs functions that affect the quantity and distribution of proteins linked to DNA damage response. Notably, mutation in the splice donor site of the NS2 led to a preferred formation of small viral replication center foci instead of the large coalescent centers seen in wild-type infection. Collectively, our results provide insights into potential roles of CPV NS2 in controlling chromatin remodeling and DNA damage response during parvoviral replication.

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Hikasa, Hiroki, and Sergei Y. Sokol. "Phosphorylation of TCF Proteins by Homeodomain-interacting Protein Kinase 2." Journal of Biological Chemistry 286, no. 14 (February 1, 2011): 12093–100. http://dx.doi.org/10.1074/jbc.m110.185280.

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47

Beckett, Dorothy. "Multilevel regulation of protein–protein interactions in biological circuitry." Physical Biology 2, no. 2 (July 5, 2005): S67—S73. http://dx.doi.org/10.1088/1478-3975/2/2/s07.

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Redpath, N. T., and C. G. Proud. "Activity of protein phosphatases against initiation factor-2 and elongation factor-2." Biochemical Journal 272, no. 1 (November 15, 1990): 175–80. http://dx.doi.org/10.1042/bj2720175.

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The protein phosphatases active against phosphorylase a, elongation factor-2 (EF-2) and the alpha-subunit of initiation factor-2 (eIF-2) [eIF-2(alpha P)] were studied in extracts of rabbit reticulocytes. Swiss-mouse 3T3 fibroblasts and rat hepatocytes, by use of the specific phosphatase inhibitors okadaic acid and inhibitor proteins-1 and -2. In all three extracts tested, both phosphatase-1 and phosphatase-2A contributed to overall phosphatase activity against phosphorylase and eIF-2(alpha P), but phosphatase-2B and -2C did not. In contrast, only protein phosphatase-2A was active against EF-2. Furthermore, in hepatocytes there was substantial type-2C phosphatase activity against EF-2, but not against phosphorylase or eIF-2 alpha. These findings in cell extracts were borne out by data obtained by studying the activities of purified protein phosphatase-1 and -2A against eIF-2(alpha P) and eIF-2(alpha P) was a moderately good substrate for both enzymes (relative to phosphorylase a). In contrast, EF-2 was a very poor substrate for protein phosphatase-1, but was dephosphorylated faster than phosphorylase a by protein phosphatase-2A. The implications of these findings for the control of translation and their relationships to previous work are discussed.

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Chakraborty, Chiranjib, Manojit Bhattacharya, Srijan Chatterjee, Ashish Ranjan Sharma, Rudra P. Saha, Kuldeep Dhama, and Govindasamy Agoramoorthy. "Integrative Bioinformatics Approaches Indicate a Particular Pattern of Some SARS-CoV-2 and Non-SARS-CoV-2 Proteins." Vaccines 11, no. 1 (December 23, 2022): 38. http://dx.doi.org/10.3390/vaccines11010038.

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Pattern recognition plays a critical role in integrative bioinformatics to determine the structural patterns of proteins of viruses such as SARS-CoV-2. This study identifies the pattern of SARS-CoV-2 proteins to depict the structure–function relationships of the protein alphabets of SARS-CoV-2 and COVID-19. The assembly enumeration algorithm, Anisotropic Network Model, Gaussian Network Model, Markovian Stochastic Model, and image comparison protein-like alphabets were used. The distance score was the lowest with 22 for “I” and highest with 40 for “9”. For post-processing and decision, two protein alphabets “C” (PDB ID: 6XC3) and “S” (PDB ID: 7OYG) were evaluated to understand the structural, functional, and evolutionary relationships, and we found uniqueness in the functionality of proteins. Here, models were constructed using “SARS-CoV-2 proteins” (12 numbers) and “non-SARS-CoV-2 proteins” (14 numbers) to create two words, “SARS-CoV-2” and “COVID-19”. Similarly, we developed two slogans: “Vaccinate the world against COVID-19” and “Say no to SARS-CoV-2”, which were made with the proteins structure. It might generate vaccine-related interest to broad reader categories. Finally, the evolutionary process appears to enhance the protein structure smoothly to provide suitable functionality shaped by natural selection.

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Lin, Hening, and Virginia W. Cornish. "In Vivo Protein-Protein Interaction Assays: Beyond Proteins." Angewandte Chemie International Edition 40, no. 5 (March 2, 2001): 871–75. http://dx.doi.org/10.1002/1521-3773(20010302)40:5<871::aid-anie871>3.0.co;2-s.

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