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Wyświetlanie 1-10 z 2022
Tytuł:
Identification of specific interaction of juvenile hormone binding protein with isocitrate dehydrogenase
Autorzy:
Zalewska, Marta
Ożyhar, Andrzej
Kochman, Marian
Tematy:
protein-protein interaction
JHBP
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Wydawca:
Polskie Towarzystwo Biochemiczne
Powiązania:
https://bibliotekanauki.pl/articles/1039963.pdf  Link otwiera się w nowym oknie
Opis:
Juvenile hormone (JH) is essential for multiple physiological processes: it controls larval development, metamorphosis and adult reproduction. In insect hemolymph more than 99 % of JH is bound to juvenile hormone binding protein (JHBP), which protects JH from degradation by nonspecific hydrolases and serves as a carrier to supply the hormone to the target tissues. In Galleria mellonella hemolymph, JHBP is found in a complex with lipid-binding high molecular weight proteins (HMWP) and this interaction is enhanced in the presence of JH. In this report, we present studies on the interaction of JHBP with low molecular weight proteins (LMWP) in the hemolymph. Using ligand blotting we found that JHBP interacts with a protein of about 44 kDa. To identify the protein that preferentially binds JHBP, a LMWP fraction was applied to a Sepharose-bound JHBP and, after washing, the column was eluted with free JHBP acting as a specific competitor or with carbonic anhydrase as a negative control. The eluted proteins were separated by SDS/PAGE and analyzed by mass spectrometry. Isocitrate dehydrogenase was identified as a component of the supramolecular complex of JHBP with hemolymph proteins.
Dostawca treści:
Biblioteka Nauki
Artykuł
Autorzy:
Osyczka, Artur
Sarewicz, Marcin
Czapla, Monika
Opis:
Fusing proteins is an attractive genetic tool used in several biochemical and biophysical investigations. Within a group of redox proteins, certain fusion constructs appear to provide valuable templates for spectroscopy with which specific bioenergetic questions can be addressed. Here we briefly summarize three different cases of fusions reported for bacterial cytochrome bc1 (prokaryotic equivalent of mitochondrial respiratory complex III), a common component of electron transport chains. These fusions were used to study supramolecular organization of enzymatic complexes in bioenergetic membrane, influence of the accessory subunits on the activity and stability of the complex, and molecular mechanism of operation of the enzyme in the context of its dimeric structure. Besides direct connotation to molecular bioenergetics, these fusions also appeared interesting from the protein design, biogenesis, and assembly points of view. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
Dostawca treści:
Repozytorium Uniwersytetu Jagiellońskiego
Artykuł
Tytuł:
Methionyl-tRNA synthetase.
Autorzy:
Deniziak, Marzanna
Barciszewski, Jan
Tematy:
protein-protein interactions
tRNA binding
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Wydawca:
Polskie Towarzystwo Biochemiczne
Powiązania:
https://bibliotekanauki.pl/articles/1044120.pdf  Link otwiera się w nowym oknie
Opis:
Methionyl-tRNA synthetase (MetRS) belongs to the family of 20 enzymes essential for protein biosynthesis. It links covalently methionine with its cognate tRNA. Crystal structures solved for bacterial MetRSs have given a number of interesting insights into enzyme architecture and methionylation catalysis. A comparison of sequences of MetRSs belonging to all kingdoms of life, as well as numerous biochemical and genetic studies have revealed the presence of various additional domains appended to the catalytic core of synthetase. They are responsible for interactions with tRNA and proteins. Tertiary structure of C-terminal tRNA-binding appendices can be deduced from those determined for their homologues: tRNA binding protein 111 and endothelial monocyte-activating polypeptide II. Contacts between MetRS and other proteins could be mediated not only by noncatalytic peptides but also by structural elements present in the catalytic core, e.g. Arg-Gly-Asp (RGD) motifs. Additional activities involve MetRS in the maintenance of translational fidelity and in coordination of ribosome biogenesis with protein synthesis.
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Structure-function relationship of serine protease-protein inhibitor interaction.
Autorzy:
Otlewski, Jacek
Jaskólski, Mariusz
Buczek, Olga
Cierpicki, Tomasz
Czapińska, Honorata
Krowarsch, Daniel
Smalas, Arne
Stachowiak, Damian
Szpineta, Agnieszka
Dadlez, Michał
Tematy:
calorimetry
serine proteases
structural thermodynamics
protein inhibitor
protein-protein recognition
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Wydawca:
Polskie Towarzystwo Biochemiczne
Powiązania:
https://bibliotekanauki.pl/articles/1044133.pdf  Link otwiera się w nowym oknie
Opis:
We report our progress in understanding the structure-function relationship of the interaction between protein inhibitors and several serine proteases. Recently, we have determined high resolution solution structures of two inhibitors Apis mellifera chymotrypsin inhibitor-1 (AMCI-I) and Linum usitatissimum trypsin inhibitor (LUTI) in the free state and an ultra high resolution X-ray structure of BPTI. All three inhibitors, despite totally different scaffolds, contain a solvent exposed loop of similar conformation which is highly complementary to the enzyme active site. Isothermal calorimetry data show that the interaction between wild type BPTI and chymotrypsin is entropy driven and that the enthalpy component opposes complex formation. Our research is focused on extensive mutagenesis of the four positions from the protease binding loop of BPTI: P1, P1', P3, and P4. We mutated these residues to different amino acids and the variants were characterized by determination of the association constants, stability parameters and crystal structures of protease-inhibitor complexes. Accommodation of the P1 residue in the S1 pocket of four proteases: chymotrypsin, trypsin, neutrophil elastase and cathepsin G was probed with 18 P1 variants. High resolution X-ray structures of ten complexes between bovine trypsin and P1 variants of BPTI have been determined and compared with the cognate P1 Lys side chain. Mutations of the wild type Ala16 (P1') to larger side chains always caused a drop of the association constant. According to the crystal structure of the Leu16 BPTI-trypsin complex, introduction of the larger residue at the P1' position leads to steric conflicts in the vicinity of the mutation. Finally, mutations at the P4 site allowed an improvement of the association with several serine proteases involved in blood clotting. Conversely, introduction of Ser, Val, and Phe in place of Gly12 (P4) had invariably a destabilizing effect on the complex with these proteases.
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Structure of small G proteins and their regulators.
Autorzy:
Paduch, Marcin
Jeleń, Filip
Otlewski, Jacek
Tematy:
small G protein
GAP
protein-protein interaction
GTPase
GDI
Rho
Ras
protein tertiary structure
GEF
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Wydawca:
Polskie Towarzystwo Biochemiczne
Powiązania:
https://bibliotekanauki.pl/articles/1043851.pdf  Link otwiera się w nowym oknie
Opis:
In recent years small G proteins have become an intensively studied group of regulatory GTP hydrolases involved in cell signaling. More than 100 small G proteins have been identified in eucaryotes from protozoan to human. The small G protein superfamily includes Ras, Rho Rab, Rac, Sar1/Arf and Ran homologs, which take part in numerous and diverse cellular processes, such as gene expression, cytoskeleton reorganization, microtubule organization, and vesicular and nuclear transport. These proteins share a common structural core, described as the G domain, and significant sequence similarity. In this paper we review the available data on G domain structure, together with a detailed analysis of the mechanism of action. We also present small G protein regulators: GTPase activating proteins that bind to a catalytic G domain and increase its low intrinsic hydrolase activity, GTPase dissociation inhibitors that stabilize the GDP-bound, inactive state of G proteins, and guanine nucleotide exchange factors that accelerate nucleotide exchange in response to cellular signals. Additionally, in this paper we describe some aspects of small G protein interactions with downstream effectors.
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Monte Carlo simulations of protein-like heteropolymers.
Autorzy:
Sikorski, Andrzej
Romiszowski, Piotr
Tematy:
lattice models
protein structure
Monte Carlo method
protein dynamics
protein folding
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Wydawca:
Polskie Towarzystwo Biochemiczne
Powiązania:
https://bibliotekanauki.pl/articles/1044166.pdf  Link otwiera się w nowym oknie
Opis:
Properties of a simple model of polypeptide chains were studied by the means of the Monte Carlo method. The chains were built on the (310) hybrid lattice. The residues interacted with long-range potential. There were two kinds of residues: hydrophobic and hydrophilic forming a typical helical pattern -HHPPHPP-. Short range potential was used to prefer helical conformations of the chain. It was found that at low temperatures the model chain formes dense and partially ordered structures (non-unique). The presence of the local potential led to an increase of helicity. The effect of the interplay between the two potentials was studied. After the collapse of the chain further annealing caused rearrangement of helical structures. Dynamic properties of the chain at low temperature depended strongly on the local chain ordering.
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Evaluation of the effect of various nitrogen forms on the Lupinus albus seed protein composition
Autorzy:
Ciesiolka, D
Aniszewski, T.
Wysocki, W.
Pilarski, R.
Gulewicz, K.
Tematy:
Lupinus albus
protein
seed
protein composition
botany
fractional composition
protein yield
protein content
lupin
nitrogen form
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Wydawca:
Polskie Towarzystwo Botaniczne
Powiązania:
https://bibliotekanauki.pl/articles/57059.pdf  Link otwiera się w nowym oknie
Opis:
The influence of different nitrogen forms: (N2), [N2+(NH4++NO3-)], (NH4+), (NO3-), (NH4++NO3-) and (-NH2) on changes of albumin, globulin, prolamin-glutelin, non-fractioned nitrogen and non-protein nitrogen fractions of the protein seed of alkaloid-low content Lupinus albus L. cv. Butan has been studied. The experiments were performed in a greenhouse on perlite using in all cases the constant P, K, Mg and micronutrients (B, Zn, Mn, Cu, Mo, Fe) fertilization. The control was the treatment without any nitrogen support (Nd). It was clearly shown that nitrogen form has significant effect not only on the seed yield and seed protein content, but also on the composition of protein fractions and on the biological value of lupin protein. The main protein fraction of the seeds from all treatments were albumins (16.73-26.10 mgN/g). Among all the treatments, the highest level of globulin was observed for the seeds of plant growing with the symbiotic nitrogen form (15.26 mgN/g), while the lowest one for the control (Nd) (6.86 mgN/g). Symbiotic nitrogen (N2) treatment clearly increased the glutelin-prolamin fraction while the addition of mineral nitrogen (NH4++NO3-) decreased this fraction from 8.40 to 4.48 mgN/g. The lowest level of the glutelin-prolamin fraction was in the absence of any nitrogen (Nd). Non-protein fraction (Nnp) was highest in the case of plants treated with (-NH2) (9.92 mgN/g), and the lowest in the absence of nitrogen (Nd) (4.90 mgN/g). The level of non-fractioned nitrogen (Nr), with exception of [N2+(NH4++NO3-)] and -NH2 treatments, was closest to the start material. The protein fractions (albumins, globulins and glutelins and prolamins) were also electrophoretically characterized. These analysis confirmed the changes in protein composition of particular fractions under the effect of various nitrogen forms used as a fertilizer.
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Coarse-grained modeling of protein structure, dynamics and protein-protein interactions
Autorzy:
Koliński, A.
Kmiecik, S.
Jamróz, M.
Błaszczyk, M.
Kouza, M.
Kurciński, M.
Tematy:
coarse-grained modeling
protein folding
protein dynamics
molecular docking
protein docking
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Wydawca:
Politechnika Gdańska
Powiązania:
https://bibliotekanauki.pl/articles/1954428.pdf  Link otwiera się w nowym oknie
Opis:
Theoretical prediction of protein structures and dynamics is essential for understanding the molecular basis of drug action, metabolic and signaling pathways in living cells, designing new technologies in the life science and material sciences . We developed and validated a novel multiscale methodology for the study of protein folding processes including flexible docking of proteins and peptides. The new modeling technique starts from coarse-grained large-scale simulations, followed by selection of the most plausible final structures and intermediates and, finally, by an all-atom rectification of the obtained structures. Except for the most basic bioinformatics tools, the entire computational methodology is based on the models and algorithms developed in our lab. The coarse-grained simulations are based on a high-resolution lattice representation of protein structures, a knowledge based statistical force field and efficient Monte Carlo dynamics schemes, including Replica Exchange algorithms. This paper focuses on the description of the coarse-grained CABS model and its selected applications.
Dostawca treści:
Biblioteka Nauki
Artykuł
Wyświetlanie 1-10 z 2022

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