Browsing by Subject "ACTIVE-SITE"

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  • Pantsar, Tatu; Rissanen, Sami; Dauch, Daniel; Laitinen, Tuomo; Vattulainen, Ilpo; Poso, Antti (2018)
    A mutated KRAS protein is frequently observed in human cancers. Traditionally, the oncogenic properties of KRAS missense mutants at position 12 (G12X) have been considered as equal. Here, by assessing the probabilities of occurrence of all KRAS G12X mutations and KRAS dynamics we show that this assumption does not hold true. Instead, our findings revealed an outstanding mutational bias. We conducted a thorough mutational analysis of KRAS G12X mutations and assessed to what extent the observed mutation frequencies follow a random distribution. Unique tissue-specific frequencies are displayed with specific mutations, especially with G12R, which cannot be explained by random probabilities. To clarify the underlying causes for the nonrandom probabilities, we conducted extensive atomistic molecular dynamics simulations (170 its) to study the differences of G12X mutations on a molecular level. The simulations revealed an allosteric hydrophobic signaling network in KRAS, and that protein dynamics is altered among the G12X mutants and as such differs from the wild-type and is mutation-specific. The shift in long-timescale conformational dynamics was confirmed with Markov state modeling. A G12X mutation was found to modify KRAS dynamics in an allosteric way, which is especially manifested in the switch regions that are responsible for the effector protein binding. The findings provide a basis to understand better the oncogenic properties of KRAS G12X mutants and the consequences of the observed nonrandom frequencies of specific G12X mutations.
  • Al-Hunaiti, Afnan; Abu-Radaha, Batool; Wraith, Darren; Repo, Timo (2022)
    Here, we disclose a new copper(i)-Schiff base complex series for selective oxidation of primary alcohols to aldehydes under benign conditions. The catalytic protocol involves 2,2,6,6-tetramethylpiperidine-N-oxyl (TEMPO), N-methylimidazole (NMI), ambient air, acetonitrile, and room temperature. This system provides a straightforward and rapid pathway to a series of Schiff bases, particularly, the copper(i) complexes bearing the substituted (furan-2-yl)imine bases N-(4-fluorophenyl)-1-(furan-2-yl)methanimine (L2) and N-(2-fluoro-4-nitrophenyl)-1-(furan-2-yl)methanimine (L4) have shown excellent yields. Both benzylic and aliphatic alcohols were converted to aldehydes selectively with 99% yield (in 1-2 h) and 96% yield (in 16 h). The mechanistic studies via kinetic analysis of all components demonstrate that the ligand type plays a key role in reaction rate. The basicity of the ligand increases the electron density of the metal center, which leads to higher oxidation reactivity. The Hammett plot shows that the key step does not involve H-abstraction. Additionally, a generalized additive model (GAM, including random effect) showed that it was possible to correlate reaction composition with catalytic activity, ligand structure, and substrate behavior. This can be developed in the form of a predictive model bearing in mind numerous reactions to be performed or in order to produce a massive data-set of this type of oxidation reaction. The predictive model will act as a useful tool towards understanding the key steps in catalytic oxidation through dimensional optimization while reducing the screening of statistically poor active catalysis.
  • Das, Biswanath; Al-Hunaiti, Afnan; Sanchez-Eguia, Brenda N.; Zeglio, Erica; Demeshko, Serhiy; Dechert, Sebastian; Braunger, Steffen; Haukka, Matti; Repo, Timo; Castillo, Ivan; Nordlander, Ebbe (2019)
    The new di- and tetranuclear Fe(III) mu-oxido complexes [Fe-4(mu-O)(4) (PTEBIA)(4)]CF3SO3)(4)(CH3CN)(2)] (1a) , [Fe-2(mu-O)Cl-2(PTEBIA)(2)(CF3SO3)(2) (1b), and [Fe-2(mu-O)(HCOO)(2)(PTEBIA)(2)](ClO4)(2) (MeOH) (2) were prepared from the sulfur-containing ligand (2-((2,4-dimethylphenyl)thiO)-N,N-bis ((1-methyl-benzimidazol-2-yl)methyl)ethanamine (PTEBIA). The tetrairon complex 1a features four mu-oxido bridges, while in dinuclear 1b, the sulfur moiety of the ligand occupies one of the six coordination sites of each Fe(III) ion with a long Fe-S distance of 2.814(6) angstrom . In 2, two Fe(III) centers are bridged by one oxido and two formate units, the latter likely formed by methanol oxidation. Complexes 1a and 1 b show broad sulfur-toiron charge transfer bands around 400-430 nm at room temperature, consistent with mononuclear structures featuring Fe-S interactions. In contrast, acetonitrile solutions of 2 display a sulfur-to-iron charge transfer band only at low temperature (228 K) upon addition of H2O2/CH3COOH, with an absorption maximum at 410 nm. Homogeneous oxidative catalytic activity was observed for 1a and 1b using H2O2 as oxidant, but with low product selectivity. High valent iron-oxo intermediates could not be detected by UV-vis spectroscopy or ESI mass spectrometry. Rather, evidence suggest preferential ligand oxidation, in line with the relatively low selectivity and catalytic activity observed in the reactions.
  • Raulinaitis, Vytas; Tossavainen, Helena; Aitio, Olli; Juuti, Jarmo T.; Hiramatsu, Keiichi; Kontinen, Vesa; Permi, Perttu (2017)
    We introduce LytU, a short member of the lysostaphin family of zinc-dependent pentaglycine endopeptidases. It is a potential antimicrobial agent for S. aureus infections and its gene transcription is highly upregulated upon antibiotic treatments along with other genes involved in cell wall synthesis. We found this enzyme to be responsible for the opening of the cell wall peptidoglycan layer during cell divisions in S. aureus. LytU is anchored in the plasma membrane with the active part residing in the periplasmic space. It has a unique Ile/Lys insertion at position 151 that resides in the catalytic site-neighbouring loop and is vital for the enzymatic activity but not affecting the overall structure common to the lysostaphin family. Purified LytU lyses S. aureus cells and cleaves pentaglycine, a reaction conveniently monitored by NMR spectroscopy. Substituting the cofactor zinc ion with a copper or cobalt ion remarkably increases the rate of pentaglycine cleavage. NMR and isothermal titration calorimetry further reveal that, uniquely for its family, LytU is able to bind a second zinc ion which is coordinated by catalytic histidines and is therefore inhibitory. The pH-dependence and high affinity of binding carry further physiological implications.
  • Collier, Aaron M.; Lyytinen, Outi L.; Guo, Yusong R.; Toh, Yukimatsu; Poranen, Minna M.; Tao, Yizhi J. (2016)
    During the replication cycle of double-stranded (ds) RNA viruses, the viral RNA-dependent RNA polymerase (RdRP) replicates and transcribes the viral genome from within the viral capsid. How the RdRP molecules are packaged within the virion and how they function within the confines of an intact capsid are intriguing questions with answers that most likely vary across the different dsRNA virus families. In this study, we have determined a 2.4 angstrom resolution structure of an RdRP from the human picobirnavirus (hPBV). In addition to the conserved polymerase fold, the hPBV RdRP possesses a highly flexible 24 amino acid loop structure located near the C-terminus of the protein that is inserted into its active site. In vitro RNA polymerization assays and site-directed mutagenesis showed that: (1) the hPBV RdRP is fully active using both ssRNA and dsRNA templates; (2) the insertion loop likely functions as an assembly platform for the priming nucleotide to allow de novo initiation; (3) RNA transcription by the hPBV RdRP proceeds in a semi-conservative manner; and (4) the preference of virus-specific RNA during transcription is dictated by the lower melting temperature associated with the terminal sequences. Co-expression of the hPBV RdRP and the capsid protein (CP) indicated that, under the conditions used, the RdRP could not be incorporated into the recombinant capsids in the absence of the viral genome. Additionally, the hPBV RdRP exhibited higher affinity towards the conserved 5'-terminal sequence of the viral RNA, suggesting that the RdRP molecules may be encapsidated through their specific binding to the viral RNAs during assembly.
  • Svarcbahs, Reinis; Julku, Ulrika; Kilpelainen, Tommi; Kyyrö, Mirva; Jäntti, Maria; Myohänen, Timo T. (2019)
    Changes in prolyl oligopeptidase (PREP) expression levels, protein distribution, and activity correlate with aging and are reported in many neurodegenerative conditions. Together with decreased neuropeptide levels observed in aging and neurodegeneration, and PREP's ability to cleave only small peptides, PREP was identified as a druggable target. Known PREP non-enzymatic functions were disregarded or attributed to PREP enzymatic activity, and several potent small molecule PREP inhibitors were developed during early stages of PREP research. These showed a lot of potential but with variable results in experimental memory models, however, the initial excitement was short-lived and all of the clinical trials were discontinued in either Phase I or II clinical trials for unknown reasons. Recently, PREP's ability to form protein-protein interactions, alter cell proliferation and autophagy has gained more attention than earlier recognized catalytical activity. Of new findings, particularly the aggregation of alpha-synuclein (aSyn) that is seen in the presence of PREP is especially interesting because PREP inhibitors are capable of altering aSyn-PREP interaction in a manner that reduces the aSyn dimerization process. Therefore, it is possible that PREP inhibitors that are altering interactions could have different characteristics than those aimed for strong inhibition of catalytic activity. Moreover, PREP co-localization with aSyn, tau, and amyloid-beta hints to PREP's possible role not only in the synucleinopathies but in other neurodegenerative diseases as well. This commentary will focus on less well-acknowledged non-enzymatic functions of PREP that may provide a better approach for the development of PREP inhibitors for the treatment of neurodegenerative disorders.
  • Gorbikova, Elena; Samsonov, Sergey; Kalendar, Ruslan (2020)
    Crystal structure analyses at atomic resolution and FTIR spectroscopic studies of cytochrome c oxidase have yet not revealed protonation or deprotonation of key sites of proton transfer in a time-resolved mode. Here, a sensitive technique to detect protolytic transitions is employed. In this work, probing a proton-loading site of cytochrome c oxidase from Paracoccus denitrificans with time-resolved Fourier transform infrared spectroscopy is presented for the first time. For this purpose, variants with single-site mutations of N131V, D124N, and E278Q, the key residues in the D-channel, were studied. The reaction of mutated CcO enzymes with oxygen was monitored and analyzed. Seven infrared bands in the “fast” kinetic spectra were found based on the following three requirements: (1) they are present in the “fast” phases of N131V and D124N mutants, (2) they have reciprocal counterparts in the “slow” kinetic spectra in these mutants, and (3) they are absent in “fast” kinetic spectra of the E278Q mutant. Moreover, the double-difference spectra between the first two mutants and E278Q revealed more IR bands that may belong to the proton-loading site protolytic transitions. From these results, it is assumed that several polar residues and/or water molecule cluster(s) share a proton as a proton-loading site. This site can be propionate itself (holding only a fraction of H+), His403, and/or water cluster(s).
  • Lagerspets, Emi; Lagerblom, Kalle; Heliövaara, Eeva; Hiltunen, Otto-Matti; Moslova, Karina; Nieger, Martin; Repo, Timo (2019)
    We report here new copper(I)-Schiff base complexes for the selective oxidation of primary alcohols to aldehydes under ambient conditions (with 2,2,6,6-tetramethylpiperdine-N-oxyl (TEMPO), N-methylimidazole (NMI), ambient air, acetonitril and RT). Particularly, the copper(I) complex bearing N-(4-fluorophenyl)-1-(furan-2-yl)methanimine (L2) showed high activity in the series and gave near- quantitative yields in the oxidations of benzyl alcohol (99% yield in 1 h) and 1-octanol (96% yield in 24 h). Based on the X-ray structure determination, the complex has a square pyramidal coordination accomplished by two L2 ligands and bromide as a counter anion. The oxidation reactions were monitored with UV vis and in situ ATR-IR spectroscopy to study the changes in the catalytic structure and to elucidate the catalytic properties and the mechanistic details. Accordingly, detachment of one of the L2 ligands from the complexes is related to the oxidation activity.
  • Kilpeläinen, Tommi P.; Hellinen, Laura; Vrijdag, Johannes; Yan, Xu; Svarcbahs, Reinis; Vellonen, Kati-Sisko; Lambeir, Anne-Marie; Huttunen, Henri; Urtti, Arto; Wallen, Erik A. A.; Myohanen, Timo T. (2020)
    Previous studies have shown that prolyl oligopeptidase (PREP) negatively regulates autophagy and increases the aggregation of alpha-synuclein (alpha Syn), linking it to the pathophysiology of Parkinson's disease. Our earlier results have revealed that the potent small molecular PREP inhibitor KYP-2047 is able to increase autophagy and decrease dimerization of alpha Syn but other PREP inhibitors have not been systematically studied for these two protein-protein interaction mediated biological functions of PREP. In this study, we characterized these effects for 12 known PREP inhibitors with IC50-values ranging from 0.2 nM to 1010 nM. We used protein-fragment complementation assay (PCA) to assess alpha Syn dimerization and Western Blot of microtubule-associated protein light chain 3B II (LC3B-II) and a GFP-LC3-RFP expressing cell line to study autophagy. In addition, we tested selected compounds in a cell-free alpha Syn aggregation assay, native gel electrophoresis, and determined the compound concentration inside the cell by LC-MS. We found that inhibition of the proteolytic activity of PREP did not predict decreased alpha Syn dimerization or increased autophagy, and we also confirmed that this result did not simply reflect concentration differences of the compounds inside the cell. Thus, PREP ligands regulate the effect of PREP on autophagy and alpha Syn aggregation through a conformational stabilization of the enzyme that is not equivalent to inhibiting its proteolytic activity.