Browsing by Subject "PROTEIN INTERACTIONS"

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  • Manoilov, Kyrylo Yu; Verkhusha, Vladislav V.; Shcherbakova, Daria M. (2021)
    Genetically encoded tools for the regulation of endogenous molecules (RNA, DNA elements and protein) are needed to study and control biological processes with minimal interference caused by protein overexpression and overactivation of signaling pathways. Here we focus on light-controlled optogenetic tools (OTs) that allow spatiotemporally precise regulation of gene expression and protein function. To control endogenous molecules, OTs combine light-sensing modules from natural photoreceptors with specific protein or nucleic acid binders. We discuss OT designs and group OTs according to the principles of their regulation. We outline characteristics of OT performance, discuss considerations for their use in vivo and review available OTs and their applications in cells and in vivo. Finally, we provide a brief outlook on the development of OTs. This Review discusses optogenetic tools for manipulating endogenous targets such as genes and signaling pathways in a physiological range.
  • Simmons, Suzanne C.; Jaemsae, Hannaleena; Silva, Dilson; Cortez, Celia M.; McKenzie, Edward A.; Bitu, Carolina C.; Salo, Sirpa; Nurmenniemi, Sini; Nyberg, Pia; Risteli, Juha; deAlmeida, Carlos E. B.; Brenchley, Paul E. C.; Salo, Tuula; Missailidisi, Sotiris (2014)
  • Rumyantsev, Konstantin A.; Shcherbakova, Daria M.; Zakharova, Natalia I.; Emelyanov, Alexander V.; Turoverov, Konstantin K.; Verkhusha, Vladislav V. (2015)
    Fluorescent proteins (FP) are used to study various biological processes. Recently, a series of nearinfrared (NIR) FPs based on bacterial phytochromes was developed. Finding ways to improve NIR FPs is becoming progressively important. By applying rational design and molecular evolution we have engineered R. palustris bacterial phytochrome into a single-domain NIR FP of 19.6 kDa, termed GAF-FP, which is 2-fold and 1.4-fold smaller than bacterial phytochrome-based NIR FPs and GFP-like proteins, respectively. Engineering of GAF-FP involved a substitution of 15% of its amino acids and a deletion of the knot structure. GAF-FP covalently binds two tetrapyrrole chromophores, biliverdin (BV) and phycocyanobilin (PCB). With the BV chromophore GAF-FP absorbs at 635 nm and fluoresces at 670 nm. With the PCB chromophore GAF-FP becomes blue-shifted and absorbs at 625 nm and fluoresces at 657 nm. The GAF-FP structure has a high tolerance to small peptide insertions. The small size of GAF-FP and its additional absorbance band in the violet range has allowed for designing a chimeric protein with Renilla luciferase. The chimera exhibits efficient non-radiative energy transfer from luciferase to GAF-FP, resulting in NIR bioluminescence. This study opens the way for engineering of small NIR FPs and NIR luciferases from bacterial phytochromes.
  • Guryanov, Ivan; Tennikova, Tatiana; Urtti, Arto (2021)
    Vascular endothelial growth factors (VEGFs) are the family of extracellular signaling proteins involved in the processes of angiogenesis. VEGFA overexpression and altered regulation of VEGFA signaling pathways lead to pathological angiogenesis, which contributes to the progression of various diseases, such as age-related macular degeneration and cancer. Monoclonal antibodies and decoy receptors have been extensively used in the anti-angiogenic therapies for the neutralization of VEGFA. However, multiple side effects, solubility and aggregation issues, and the involvement of compensatory VEGFA-independent pro-angiogenic mechanisms limit the use of the existing VEGFA inhibitors. Short chemically synthesized VEGFA binding peptides are a promising alternative to these full-length proteins. In this review, we summarize anti-VEGFA peptides identified so far and discuss the molecular basis of their inhibitory activity to highlight their pharmacological potential as anti-angiogenic drugs.
  • Rahikainen, Moona; Trotta, Andrea; Alegre, Sara; Pascual, Jesus; Vuorinen, Katariina; Overmyer, Kirk; Moffatt, Barbara; Ravanel, Stephane; Glawischnig, Erich; Kangasjarvi, Saijaliisa (2017)
    Glucosinolates (GSL) of cruciferous plants comprise a major group of structurally diverse secondary compounds which act as deterrents against aphids and microbial pathogens and have large commercial and ecological impacts. While the transcriptional regulation governing the biosynthesis and modification of GSL is now relatively well understood, post-translational regulatory components that specifically determine the structural variation of indole glucosinolates have not been reported. We show that the cytoplasmic protein phosphatase 2A regulatory subunit B'gamma (PP2A-B'gamma) physically interacts with indole glucosinolate methyltransferases and controls the methoxylation of indole glucosinolates and the formation of 4-meth-oxy-indol-3-yl-methyl glucosinolate in Arabidopsis leaves. By taking advantage of proteomic approaches and metabolic analysis we further demonstrate that PP2A-B'gamma is required to control the abundance of oligomeric protein complexes functionally linked with the activated methyl cycle and the trans-methylation capacity of leaf cells. These findings highlight the key regulatory role of PP2A-B'gamma in methionine metabolism and provide a previously unrecognized perspective for metabolic engineering of glucosinolate metabolism in cruciferous plants.
  • Adamczyk, Bartosz; Simon, Judy; Kitunen, Veikko; Adamczyk, Sylwia; Smolander, Aino (2017)
    Tannins, an abundant group of plant secondary compounds, raise interest in different fields of science, owing to their unique chemical characteristics. In chemical ecology, tannins play a crucial role in plant defense against pathogens, herbivores, and changing environmental conditions. In the food industry and in medicine, tannins are important because of their proven positive effect on human health and disease treatment, Such wide interests fueled studies on tannin chemistry, especially on their flagship ability to precipitate proteins. In this Review, we expand the basic knowledge on tannin chemistry to the newest insights from the field. We focus especially on tannin reactions with different non-protein organic N compounds, as well as the complex interactions of tannins with enzymes, resulting in either an increase or decrease in enzyme activity.
  • Rouvinen, Juha; Jänis, Janne; Laukkanen, Marja-Leena; Jylhä, Sirpa; Niemi, Merja; Päivinen, Tero; Mäkinen-Kiljunen, Soili; Haahtela, Tari Markku Kallevi; Soderlund, Hans; Takkinen, Kristiina (2010)