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Journal articles on the topic 'Protein mechanism'

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Published: 14 March 2023

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1

Schreiber, G., D. Reichmann, M. Cohen, Y. Pillip, O. Rahat, O. Dym, V. Potapov, V. Sobolev, and M. Edelman. "Protein–protein interaction: from mechanism to protein design." Acta Crystallographica Section A Foundations of Crystallography 63, a1 (August 22, 2007): s18. http://dx.doi.org/10.1107/s0108767307099606.

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2

Gianni, Stefano, Nicoletta Calosci, Jan M. A. Aelen, Geerten W. Vuister, Maurizio Brunori, and Carlo Travaglini-Allocatelli. "Kinetic folding mechanism of PDZ2 from PTP-BL." Protein Engineering, Design and Selection 18, no. 8 (July 25, 2005): 389–95. http://dx.doi.org/10.1093/protein/gzi047.

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3

Barford, D. "The mechanism of protein kinase regulation by protein phosphatases." Biochemical Society Transactions 29, no. 4 (August 1, 2001): 385–91. http://dx.doi.org/10.1042/bst0290385.

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Protein kinases are an important class of substrate of the protein phosphatases. We have examined the mechanism of dephosphorylation of the activation segments of the insulin receptor kinase and cyclin-dependent kinase 2 by their respective phosphatases, namely the tyrosine specific phosphatase PTP1B and the dual specificity phosphatase KAP. These studies reveal that PTP1B and KAP utilize contrasting mechanisms in order to dephosphorylate their substrates specifically.

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4

HIROSE, Masaaki. "Folding Mechanism of Protein." Kagaku To Seibutsu 36, no. 5 (1998): 290–96. http://dx.doi.org/10.1271/kagakutoseibutsu1962.36.290.

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5

Wong, Chi-Ming, Lucia Marcocci, Dividutta Das, Xinhong Wang, Haibei Luo, Makhosazane Zungu-Edmondson, and Yuichiro J. Suzuki. "Mechanism of protein decarbonylation." Free Radical Biology and Medicine 65 (December 2013): 1126–33. http://dx.doi.org/10.1016/j.freeradbiomed.2013.09.005.

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6

Yoshimura, Takatoshi, Hidehiko Noguchi, Takayuki Inoue, and Nobuhiko Saitô. "Mechanism of protein folding." Biophysical Chemistry 40, no. 3 (July 1991): 277–91. http://dx.doi.org/10.1016/0301-4622(91)80026-n.

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7

Watanabe, Kazunori, Atsuhiko Nakamura, Yoshinori Fukuda, and Nobuhiko Saitô. "Mechanism of protein folding." Biophysical Chemistry 40, no. 3 (July 1991): 293–301. http://dx.doi.org/10.1016/0301-4622(91)80027-o.

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8

N�lting, Bengt, and Karl Andert. "Mechanism of protein folding." Proteins: Structure, Function, and Genetics 41, no. 3 (2000): 288–98. http://dx.doi.org/10.1002/1097-0134(20001115)41:3<288::aid-prot20>3.0.co;2-c.

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9

Zheng, Ya-Jun, Kenneth M. Merz, and Gregory K. Farber. "Theoretical examination of the mechanism of aldose–ketose isomerization." "Protein Engineering, Design and Selection" 6, no. 5 (1993): 479–84. http://dx.doi.org/10.1093/protein/6.5.479.

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10

Abaturov, A. E., and V. L. Babуch. "Mechanisms of action of cytoplasmic microRNAs. Part 3. TNRC6-associated mechanism of miRNA-mediated mRNA degradation." CHILD`S HEALTH 17, no. 4 (September 20, 2022): 209–16. http://dx.doi.org/10.22141/2224-0551.17.4.2022.1519.

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The scientific review presents the mechanisms of action of cytoplasmic miRNAs, namely posttranscriptional silencing: the TNRC6-associated mechanism of miRNA-mediated mRNA degradation. To write the article, information was searched using databases Scopus, Web of Science, MedLine, PubMed, Google Scholar, EMBASE, Global Health, The Cochrane Library, CyberLeninka. It is known that in the cytoplasm of cells in cases of short region, miRNA complementarities cause posttranscriptional silencing, using the first of the main molecular mechanisms: the TNRC6-associated mechanism of miRNA-mediated mRNA degradation. Mammalian AGO proteins have been shown to contain the conserved m7G-cap-binding protein motif (known as the MID domain), which is required to induce microRNA-mediated translation repression. After binding of this AGO motif to microRNAs, TNRC6 proteins (GW182) are recruited that, in turn, recruits various proteins (PABPC1, PAN3 and NOT1) involved in the induction of the target gene silencing. The authors state that tryptophan residues, which are placed in the hydrophobic pockets of TNRC6 protein partners, cause a high degree of affinity and specificity of interactions. Scientists believe that the TNRC6 protein when interacting with AGO proteins can simultaneously use three GW/WG repeats (motif 1, motif 2 and hook motif), which are located in the Argonaute-binding domain. Therefore, the TNRC6 protein can bind to three AGO molecules simultaneously. TNRC6 proteins are known to be PABP-interacting proteins whose interaction with PABP is mediated by conservative PABP-binding motif 2. TNRC6 proteins have been shown to interact with the cytoplasmic PABPC1 protein during mRNA translation and stabilization. It is shown that the CCR4-NOT protein complex is a highly conserved multifunctional multiprotein formation having 3’-5’-exoribonuclease activity, due to which it controls mRNA metabolism. Thus, the TNRC6-associated mechanism of miRNA-mediated mRNA degradation in the cytoplasm of the cell causes posttranscriptional silencing. In this mechanism, there is an interaction of TNRC6 with PABPC1 protein, recruitment of deadenylating complexes PAN2-PAN3 and CCR4-NOT by the TNRC6 proteins.

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11

Stone, Stuart R., and Jan Hofsteenge. "Recombinant hirudin: kinetic mechanism for the inhibition of human thrombin." "Protein Engineering, Design and Selection" 4, no. 3 (1991): 295–300. http://dx.doi.org/10.1093/protein/4.3.295.

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12

Englander, S. Walter, Leland Mayne, and Mallela M. G. Krishna. "Protein folding and misfolding: mechanism and principles." Quarterly Reviews of Biophysics 40, no. 4 (November 2007): 1–41. http://dx.doi.org/10.1017/s0033583508004654.

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AbstractTwo fundamentally different views of how proteins fold are now being debated. Do proteins fold through multiple unpredictable routes directed only by the energetically downhill nature of the folding landscape or do they fold through specific intermediates in a defined pathway that systematically puts predetermined pieces of the target native protein into place? It has now become possible to determine the structure of protein folding intermediates, evaluate their equilibrium and kinetic parameters, and establish their pathway relationships. Results obtained for many proteins have serendipitously revealed a new dimension of protein structure. Cooperative structural units of the native protein, called foldons, unfold and refold repeatedly even under native conditions. Much evidence obtained by hydrogen exchange and other methods now indicates that cooperative foldon units and not individual amino acids account for the unit steps in protein folding pathways. The formation of foldons and their ordered pathway assembly systematically puts native-like foldon building blocks into place, guided by a sequential stabilization mechanism in which prior native-like structure templates the formation of incoming foldons with complementary structure. Thus the same propensities and interactions that specify the final native state, encoded in the amino-acid sequence of every protein, determine the pathway for getting there. Experimental observations that have been interpreted differently, in terms of multiple independent pathways, appear to be due to chance misfolding errors that cause different population fractions to block at different pathway points, populate different pathway intermediates, and fold at different rates. This paper summarizes the experimental basis for these three determining principles and their consequences. Cooperative native-like foldon units and the sequential stabilization process together generate predetermined stepwise pathways. Optional misfolding errors are responsible for 3-state and heterogeneous kinetic folding.

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13

Jaremko, Matt J., Tony D. Davis, Joshua C. Corpuz, and Michael D. Burkart. "Type II non-ribosomal peptide synthetase proteins: structure, mechanism, and protein–protein interactions." Natural Product Reports 37, no. 3 (2020): 355–79. http://dx.doi.org/10.1039/c9np00047j.

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This review highlights type II non-ribosomal peptide synthetase (NRPS) proteins, which incorporate and functionalize small alkyl, aromatic, and amino acid precursors in medicinally-relevant compounds.

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14

Nosoh, Yoshiaki, and Takeshi Sekiguchi. "Protein Thermostability: Mechanism and Control Through Protein Engineering." Biocatalysis 1, no. 4 (January 1988): 257–73. http://dx.doi.org/10.3109/10242428808998167.

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15

Barford, D. "Mechanism of Protein Kinase Inactivation by Protein Phosphatases." Biochemical Society Transactions 29, no. 3 (June 1, 2001): A48. http://dx.doi.org/10.1042/bst029a048.

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16

Maksimov, Eugene G., Nikolai N. Sluchanko, Yury B. Slonimskiy, Kirill S. Mironov, Konstantin E. Klementiev, Marcus Moldenhauer, Thomas Friedrich, Dmitry A. Los, Vladimir Z. Paschenko, and Andrew B. Rubin. "The Unique Protein-to-Protein Carotenoid Transfer Mechanism." Biophysical Journal 113, no. 2 (July 2017): 402–14. http://dx.doi.org/10.1016/j.bpj.2017.06.002.

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17

Kuttner-Kondo, Lisa, M. Edward Medof, William Brodbeck, and Menachem Shoham. "Molecular modeling and mechanism of action of human decay-accelerating factor." "Protein Engineering, Design and Selection" 9, no. 12 (1996): 1143–49. http://dx.doi.org/10.1093/protein/9.12.1143.

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18

Noppen, B., L. Fonteyn, F. Aerts, A. De Vriese, M. De Maeyer, F. Le Floch, P. Barbeaux, R. Zwaal, and M. Vanhove. "Autolytic degradation of ocriplasmin: a complex mechanism unraveled by mutational analysis." Protein Engineering Design and Selection 27, no. 7 (May 1, 2014): 215–23. http://dx.doi.org/10.1093/protein/gzu015.

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19

Doughty, S. W., F. E. Blaney, B. S. Orlek, and W. G. Richards. "A molecular mechanism for toxin block in N-type calcium channels." Protein Engineering Design and Selection 11, no. 2 (February 1, 1998): 95–99. http://dx.doi.org/10.1093/protein/11.2.95.

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20

Shipingana, N. N., N. Raghu, S. Veerana Gowda, T. S. Gopenath, M. S. Ranjith, A. Gnanasekaran, M. Karthikeyan, et al. "Cell signaling in yeast: A mini review." Journal of Biomedical Sciences 5, no. 2 (April 17, 2019): 18–22. http://dx.doi.org/10.3126/jbs.v5i2.23634.

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Background: Understanding cellular mechanism of communication is the main goal of systems biology. Unicellular yeasts are effective model to understand the molecular interactions that generate cell polarity induced by external inputs. The mechanisms of many extracellular stimuli are induced by complexes of cell surface receptors, G proteins. The mechanisms of many extracellular stimuli are induced by complexes of cell surface receptors, G proteins and mitogen activated protein (MAP) kinase complexes. Many components, their interrelationships, and their regulators of these mechanisms were initially identified in yeast. A complex web of sensing mechanisms and cooperation among signaling networks such as a cyclic adenosine monophosphate dependent protein kinase, mitogen-activated protein kinase cascade and 5-adenosine monophosphate activated protein kinase induce various changes in physiology, cell polarity, cell cycle progression and gene expression to achieve differentiation. Ras-cAMP pathway explained in yeast model with signalling function of the oncogenic mammalian Ras protein. So studies on yeast cells may enlighten some underlying mechanism which will be beneficial to understand the mechanisms of disease.

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21

Rana, Mitra S., Chul-Jin Lee, and Anirban Banerjee. "The molecular mechanism of DHHC protein acyltransferases." Biochemical Society Transactions 47, no. 1 (December 17, 2018): 157–67. http://dx.doi.org/10.1042/bst20180429.

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Abstract Protein S-acylation is a reversible lipidic posttranslational modification where a fatty acid chain is covalently linked to cysteine residues by a thioester linkage. A family of integral membrane enzymes known as DHHC protein acyltransferases (DHHC-PATs) catalyze this reaction. With the rapid development of the techniques used for identifying lipidated proteins, the repertoire of S-acylated proteins continues to increase. This, in turn, highlights the important roles that S-acylation plays in human physiology and disease. Recently, the first molecular structures of DHHC-PATs were determined using X-ray crystallography. This review will comment on the insights gained on the molecular mechanism of S-acylation from these structures in combination with a wealth of biochemical data generated by researchers in the field.

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22

Fernández-Borges, Natalia, Hasier Eraña, Saioa R. Elezgarai, Chafik Harrathi, Mayela Gayosso, and Joaquín Castilla. "Infectivity versus Seeding in Neurodegenerative Diseases Sharing a Prion-Like Mechanism." International Journal of Cell Biology 2013 (2013): 1–9. http://dx.doi.org/10.1155/2013/583498.

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Prions are considered the best example to prove that the biological information can be transferred protein to protein through a conformational change. The term “prion-like” is used to describe molecular mechanisms that share similarities with the mammalian prion protein self-perpetuating aggregation and spreading characteristics. Since prions are presumably composed only of protein and are infectious, the more similar the mechanisms that occur in the different neurodegenerative diseases, the more these processes will resemble an infection.In vitroandin vivoexperiments carried out during the last decade in different neurodegenerative disorders such as Alzheimer's disease (AD), Parkinson's diseases (PD), and amyotrophic lateral sclerosis (ALS) have shown a convergence toward a unique mechanism of misfolded protein propagation. In spite of the term “infection” that could be used to explain the mechanism governing the diversity of the pathological processes, other concepts as “seeding” or “de novoinduction” are being used to describe thein vivopropagation and transmissibility of misfolded proteins. The current studies are demanding an extended definition of “disease-causing agents” to include those already accepted as well as other misfolded proteins. In this new scenario, “seeding” would be a type of mechanism by which an infectious agent can be transmitted but should not be used to define a whole “infection” process.

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23

Babst, Markus. "Quality control at the plasma membrane: One mechanism does not fit all." Journal of Cell Biology 205, no. 1 (April 14, 2014): 11–20. http://dx.doi.org/10.1083/jcb.201310113.

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The plasma membrane quality control system of eukaryotic cells is able to recognize and degrade damaged cell surface proteins. Recent studies have identified two mechanisms involved in the recognition of unfolded transmembrane proteins. One system uses chaperones to detect unfolded cytoplasmic domains of transmembrane proteins, whereas the second mechanism relies on an internal quality control system of the protein, which can trigger degradation when the protein deviates from the folded state. Both quality control mechanisms are key to prevent proteotoxic effects at the cell surface and to ensure cell integrity.

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24

ATAKA, Mitsuo. "Mechanism of Protein Crystal Growth." Nihon Kessho Gakkaishi 34, no. 4 (1992): 238–43. http://dx.doi.org/10.5940/jcrsj.34.238.

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25

Levy, Y., P. G. Wolynes, and J. N. Onuchic. "Protein topology determines binding mechanism." Proceedings of the National Academy of Sciences 101, no. 2 (December 23, 2003): 511–16. http://dx.doi.org/10.1073/pnas.2534828100.

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26

Garlid, K. D., M. Jaburek, and P. Jezek. "Mechanism of uncoupling protein action." Biochemical Society Transactions 29, no. 6 (November 1, 2001): 803–6. http://dx.doi.org/10.1042/bst0290803.

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Two competing models of uncoupling protein (UCP) transport mechanism agree that fatty acids (FAs) are obligatory for uncoupling, but they disagree about which ion is transported. In Klingenberg's model, UCPs conduct protons. In Garlid's model, UCPs conduct anions, like all members of this gene family. In the latter model, UCP transports the anionic FA head group from one side of the membrane to the other, and the cycle is completed by rapid flip-flop of protonated FAs across the bilayer. The head groups of the FA analogues, long-chain alkylsulphonates, are translocated by UCP, but they cannot induce uncoupling, because these strong acids cannot be protonated for the flip-flop part of the cycle. We have overcome this limitation by ion-pair transport of undecanesulphonate with propranolol, which causes the sulphonate to deliver protons across the membrane as if it were an FA. Full GDP-sensitive uncoupling is seen in the presence of propranolol and undecanesulphonate. This result confirms that the mechanism of UCP uncoupling requires transport of the anionic FA head group by UCP and that the proton transport occurs via the bilayer and not via UCP.

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27

Garlid, K. D., M. Jaburek, and P. Jezek. "Mechanism of uncoupling protein action." Biochemical Society Transactions 29, no. 5 (October 1, 2001): A100. http://dx.doi.org/10.1042/bst029a100b.

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28

Johnson, L. N. "PROTEIN KINASE STRUCTURE AND MECHANISM." Biochemical Society Transactions 27, no. 1 (February 1, 1999): A1. http://dx.doi.org/10.1042/bst027a001c.

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29

Li, Yue-Jin, David M. Rothwarf, and Harold A. Scheraga. "Mechanism of reductive protein unfolding." Nature Structural & Molecular Biology 2, no. 6 (June 1995): 489–94. http://dx.doi.org/10.1038/nsb0695-489.

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30

Robert Matthews, C. "The mechanism of protein folding." Current Opinion in Structural Biology 1, no. 1 (February 1991): 28–35. http://dx.doi.org/10.1016/0959-440x(91)90007-g.

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31

Schmid, Franz X. "The mechanism of protein folding." Current Opinion in Structural Biology 2, no. 1 (February 1992): 21–25. http://dx.doi.org/10.1016/0959-440x(92)90171-3.

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32

Yang, Won Ho, Peter V. Aziz, Douglas M. Heithoff, Michael J. Mahan, Jeffrey W. Smith, and Jamey D. Marth. "An intrinsic mechanism of secreted protein aging and turnover." Proceedings of the National Academy of Sciences 112, no. 44 (October 21, 2015): 13657–62. http://dx.doi.org/10.1073/pnas.1515464112.

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The composition and functions of the secreted proteome are controlled by the life spans of different proteins. However, unlike intracellular protein fate, intrinsic factors determining secreted protein aging and turnover have not been identified and characterized. Almost all secreted proteins are posttranslationally modified with the covalent attachment of N-glycans. We have discovered an intrinsic mechanism of secreted protein aging and turnover linked to the stepwise elimination of saccharides attached to the termini of N-glycans. Endogenous glycosidases, including neuraminidase 1 (Neu1), neuraminidase 3 (Neu3), beta-galactosidase 1 (Glb1), and hexosaminidase B (HexB), possess hydrolytic activities that temporally remodel N-glycan structures, progressively exposing different saccharides with increased protein age. Subsequently, endocytic lectins with distinct binding specificities, including the Ashwell–Morell receptor, integrin αM, and macrophage mannose receptor, are engaged in N-glycan ligand recognition and the turnover of secreted proteins. Glycosidase inhibition and lectin deficiencies increased protein life spans and abundance, and the basal rate of N-glycan remodeling varied among distinct proteins, accounting for differences in their life spans. This intrinsic multifactorial mechanism of secreted protein aging and turnover contributes to health and the outcomes of disease.

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33

Kawagoe, Soichiro, Koichiro Ishimori, and Tomohide Saio. "Structural and Kinetic Views of Molecular Chaperones in Multidomain Protein Folding." International Journal of Molecular Sciences 23, no. 5 (February 24, 2022): 2485. http://dx.doi.org/10.3390/ijms23052485.

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Despite recent developments in protein structure prediction, the process of the structure formation, folding, remains poorly understood. Notably, folding of multidomain proteins, which involves multiple steps of segmental folding, is one of the biggest questions in protein science. Multidomain protein folding often requires the assistance of molecular chaperones. Molecular chaperones promote or delay the folding of the client protein, but the detailed mechanisms are still unclear. This review summarizes the findings of biophysical and structural studies on the mechanism of multidomain protein folding mediated by molecular chaperones and explains how molecular chaperones recognize the client proteins and alter their folding properties. Furthermore, we introduce several recent studies that describe the concept of kinetics–activity relationships to explain the mechanism of functional diversity of molecular chaperones.

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34

Jodaitis, Léni, Thomas van Oene, and Chloé Martens. "Assessing the Role of Lipids in the Molecular Mechanism of Membrane Proteins." International Journal of Molecular Sciences 22, no. 14 (July 6, 2021): 7267. http://dx.doi.org/10.3390/ijms22147267.

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Membrane proteins have evolved to work optimally within the complex environment of the biological membrane. Consequently, interactions with surrounding lipids are part of their molecular mechanism. Yet, the identification of lipid–protein interactions and the assessment of their molecular role is an experimental challenge. Recently, biophysical approaches have emerged that are compatible with the study of membrane proteins in an environment closer to the biological membrane. These novel approaches revealed specific mechanisms of regulation of membrane protein function. Lipids have been shown to play a role in oligomerization, conformational transitions or allosteric coupling. In this review, we summarize the recent biophysical approaches, or combination thereof, that allow to decipher the role of lipid–protein interactions in the mechanism of membrane proteins.

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35

Lycklama a Nijeholt, Jelger A., and Arnold J. M. Driessen. "The bacterial Sec-translocase: structure and mechanism." Philosophical Transactions of the Royal Society B: Biological Sciences 367, no. 1592 (April 19, 2012): 1016–28. http://dx.doi.org/10.1098/rstb.2011.0201.

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Most bacterial secretory proteins pass across the cytoplasmic membrane via the translocase, which consists of a protein-conducting channel SecYEG and an ATP-dependent motor protein SecA. The ancillary SecDF membrane protein complex promotes the final stages of translocation. Recent years have seen a major advance in our understanding of the structural and biochemical basis of protein translocation, and this has led to a detailed model of the translocation mechanism.

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36

Erbse, A., M. P. Mayer, and B. Bukau. "Mechanism of substrate recognition by Hsp70 chaperones." Biochemical Society Transactions 32, no. 4 (August 1, 2004): 617–21. http://dx.doi.org/10.1042/bst0320617.

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The role of Hsp70 (heat-shock protein 70) chaperones in assisting protein-folding processes relies on their ability to associate with short peptide stretches of protein substrates in a transient and ATP-controlled manner. In the present study, we review the molecular details of the mechanism behind substrate recognition by Hsp70 proteins.

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37

Taira, Kazunari, Masami Uebayasi, Hidekatsu Maeda, and Kensuke Furukawa. "Energetics of RNA cleavage: implications for the mechanism of action of ribozymes." "Protein Engineering, Design and Selection" 3, no. 8 (1990): 691–701. http://dx.doi.org/10.1093/protein/3.8.691.

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38

Lecomte, Juliette T. J., and C. Robert Matthews. "Unraveling the mechanism of protein folding: new tricks for an old problem." "Protein Engineering, Design and Selection" 6, no. 1 (1993): 1–10. http://dx.doi.org/10.1093/protein/6.1.1.

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39

Sültemeyer, Dieter, Barbara Klughammer, Murray R. Badger, and G. Dean Price. "Protein phosphorylation and its possible involvement in the induction of the high-affinity CO2 concentrating mechanism in cyanobacteria." Canadian Journal of Botany 76, no. 6 (June 1, 1998): 954–61. http://dx.doi.org/10.1139/b98-083.

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Cyanobacteria as well as eukaryotic algae possess a CO2 concentrating mechanism that enables the cells to use low CO2 concentrations very efficiently for photosynthesis. The efficiency of the CO2 concentrating mechanism changes in response to environmental changes, especially the availability of inorganic carbon, but the underlying mechanisms that are involved in the regulation of the induction are unknown. This review deals with the occurrence of protein phosphorylation in cyanobacteria and highlights the possible involvement of post-translational modifications of existing proteins in the induction process, which leads to a high-affinity state of the CO2 concentrating mechanism.Key words: cyanobacteria, CO2 concentrating mechanism, protein kinase, protein phosphorylation, post-translational regulation.

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40

GALZITSKAYA, OXANA V., NATALYA S. BOGATYREVA, and DMITRY N. IVANKOV. "COMPACTNESS DETERMINES PROTEIN FOLDING TYPE." Journal of Bioinformatics and Computational Biology 06, no. 04 (August 2008): 667–80. http://dx.doi.org/10.1142/s0219720008003618.

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We have demonstrated here that protein compactness, which we define as the ratio of the accessible surface area of a protein to that of the ideal sphere of the same volume, is one of the factors determining the mechanism of protein folding. Proteins with multi-state kinetics, on average, are more compact (compactness is 1.49 ± 0.02 for proteins within the size range of 101–151 amino acid residues) than proteins with two-state kinetics (compactness is 1.59 ± 0.03 for proteins within the same size range of 101–151 amino acid residues). We have shown that compactness for homologous proteins can explain both the difference in folding rates and the difference in folding mechanisms.

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41

Kurachi, Sumiko, Taku Tanaka, Muneyoshi Kanai, Emi Suenaga, Elena Solovieva, and Kotoku Kurachi. "Age-Related Homeostasis: Molecular Mechanism, Disease and Predictions from Global Analyses of Mouse Liver Proteins." Blood 108, no. 11 (November 16, 2006): 1611. http://dx.doi.org/10.1182/blood.v108.11.1611.1611.

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Abstract We previously reported the first molecular mechanism underlying the age-related homeostasis, ASE/AIE-mediated genetic mechanism for age-related regulation of gene expression, which turned out to be a mechanism of puberty-onset gene switching, specifically controlling a group of genes for their expression from puberty into old age (Kurachi & Kurachi J Thromb Haemost 2005; Zahng et al J Biol Chem277:4532, 2002; Kurachi et al Science285:739, 1999). This led us to successful construction of a transgenic mouse model of hemophilia B Leyden, a unique subset of hemophilia B with its mechanism being remained mysterious, robustly mimicking its unusual pattern of puberty-onset spontaneous amelioration. With this background, we hypothesized that besides the ASE/AIE-mediated mechanism, there exist more unidentified fundamental regulatory mechanisms for age-related homeostasis, which individually or in various combinations generate age-related complex and dynamic regulatory patterns of liver proteins. We launched a series of global and quantitative analysis of age-related changes in expression of liver nuclear proteins of mice (C57BL/6xSJL, [male], 1 through-24 month of age) by taking a procedure composed of two-dimensional gel electrophoresis (2DE) for separation and quantification of liver nuclear protein spots and of MALDI-TOF/MS PMF analyses to identify proteins in the spots. Out of over 6000 spots recognized and quantified in 2DE, 4547 protein spots were subjected to MALDI-TOF/MS analysis for protein identification. Finally, 2765 protein spots including many isomers were found unique. Systematic analyses of their age-related expression identified several major phases in protein expression throughout the lifespan. These findings supported our hypothesis that there exist multiple novel molecular mechanisms responsible for maintaining age-related homeostasis. The comprehensive liver nuclear protein data set was then used to construct a comprehensive database, which allows rapid and reliable searches for expression of specific proteins, their age-related dynamic profiles, isomers, protein identification from 2DE image, and other related information. This will serve as a valuable platform resource for studying epigenetic challenges, evaluation of drugs as well as gaining further insights into the molecular mechanisms underlying age-related homeostasis.

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42

Fanelli, Franceses, M. Cristina Menziani, and Pier G. de Benedetti. "Computer simulations of signal transduction mechanism in α1B-adrenergic and m3-muscarinic receptors." "Protein Engineering, Design and Selection" 8, no. 6 (1995): 557–64. http://dx.doi.org/10.1093/protein/8.6.557.

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Suzuki, Toshiharu, Masako Yasugi, Fumio Arisaka, Tairo Oshima, and Akihiko Yamagishi. "Cold-adaptation mechanism of mutant enzymes of 3-isopropylmalate dehydrogenase from Thermus thermophilus." Protein Engineering, Design and Selection 15, no. 6 (June 2002): 471–76. http://dx.doi.org/10.1093/protein/15.6.471.

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Mullenbach, Guy T., Azita Tabrizi, Bruce D. Irvine, Graeme I. Bell, John A. Tainer, and Robert A. Hallewell. "Selenocysteine's mechanism of incorporation and evolution revealed in cDNAs of three glutathione peroxidases." "Protein Engineering, Design and Selection" 2, no. 3 (1988): 239–46. http://dx.doi.org/10.1093/protein/2.3.239.

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Tatham, Arthur S., Larry Hayes, Peter R. Shewry, and Dan W. Urry. "Wheat seed proteins exhibit a complex mechanism of protein elasticity." Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology 1548, no. 2 (August 2001): 187–93. http://dx.doi.org/10.1016/s0167-4838(01)00232-1.

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Berger, Raphaëlle, and Anthony W. Partridge. "Protein Polymerization as a Novel Targeted Protein Degradation Mechanism." Biochemistry 60, no. 15 (March 24, 2021): 1145–47. http://dx.doi.org/10.1021/acs.biochem.1c00163.

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Furukawa, T., F. Matsuda, K. Ishimori, and I. Morishima. "The recognition mechanism in the protein-protein electron transfer." Seibutsu Butsuri 41, supplement (2001): S99. http://dx.doi.org/10.2142/biophys.41.s99_4.

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Selzer, Tzvia, and Gideon Schreiber. "New insights into the mechanism of protein-protein association." Proteins: Structure, Function, and Genetics 45, no. 3 (2001): 190–98. http://dx.doi.org/10.1002/prot.1139.

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Schmalz, D., F. Hucho, and K. Buchner. "Nuclear import of protein kinase C occurs by a mechanism distinct from the mechanism used by proteins with a classical nuclear localization signal." Journal of Cell Science 111, no. 13 (July 1, 1998): 1823–30. http://dx.doi.org/10.1242/jcs.111.13.1823.

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Abstract:

Protein kinase C does not have any known nuclear localization signal but, nevertheless, is redistributed from the cytoplasm to the nucleus upon various stimuli. In NIH 3T3 fibroblasts stimulation with phorbol ester leads to a translocation of protein kinase C alpha to the plasma membrane and into the cell nucleus. We compared the mechanism of protein kinase C alpha's transport into the nucleus with the transport mechanism of a protein with a classical nuclear localization signal at several steps. To this end, we co-microinjected fluorescently labeled bovine serum albumin to which a nuclear localization signal peptide was coupled, together with substances interfering with conventional nuclear protein import. Thereafter, the distribution of both the nuclear localization signal-bearing reporter protein and protein kinase C alpha was analyzed in the same cells. We can show that, in contrast to the nuclear localization signal-dependent transport, the phorbol ester-induced transport of protein kinase C alpha is not affected by microinjection of antibodies against the nuclear import factor p97/importin/karyopherin beta or microinjection of non-hydrolyzable GTP-analogs. This suggests that nuclear import of protein kinase C alpha is independent of p97/importin/karyopherin beta and independent of GTP. At the nuclear pore there are differences between the mechanisms too, since nuclear transport of protein kinase C alpha cannot be inhibited by wheat germ agglutinin or an antibody against nuclear pore complex proteins. Together these findings demonstrate that the nuclear import of protein kinase C alpha occurs by a mechanism distinct from the one used by classical nuclear localization signal-bearing proteins at several stages.

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Linder, Maurine E., and Benjamin C. Jennings. "Mechanism and function of DHHC S-acyltransferases." Biochemical Society Transactions 41, no. 1 (January 29, 2013): 29–34. http://dx.doi.org/10.1042/bst20120328.

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Abstract:

Protein S-palmitoylation is a reversible post-translational modification of proteins with fatty acids. In the last 5 years, improved proteomic methods have increased the number of proteins identified as substrates for palmitoylation from tens to hundreds. Palmitoylation regulates protein membrane interactions, activity, trafficking and stability and can be constitutive or regulated by signalling inputs. A family of PATs (protein acyltransferases) is responsible for modifying proteins with palmitate or other long-chain fatty acids on the cytoplasmic face of cellular membranes. PATs share a signature DHHC (Asp-His-His-Cys) cysteine-rich domain that is the catalytic centre of the enzyme. The biomedical importance of members of this family is underscored by their association with intellectual disability, Huntington's disease and cancer in humans, and raises the possibility of DHHC PATs as targets for therapeutic intervention. In the present paper, we discuss recent progress in understanding enzyme mechanism, regulation and substrate specificity.

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