PsbP (23 kDa) is an extrinsic eukaryotic protein of photosystem II found in the thylakoid membrane of higher plants and green algae. It has been proven to be indispensable for proper functioning of the oxygen evolving complex. By interaction with other extrinsic proteins (PsbQ, PsbO and PsbR), it modulates the concentration of two cofactors of the water splitting reaction, Ca(2+) and Cl(-). The crystallographic structure of PsbP from Spinacia oleracea lacks the N-terminal part as well as two inner regions which were modelled as loops. Those unresolved parts are believed to be functionally crucial for the binding of PsbP to the thylakoid membrane. In this NMR study we report (1)H, (15)N and (13)C resonance assignments of the backbone and side chain atoms of the PsbP protein. Based on these data, an estimate of the secondary structure has been made. The structural motifs found fit the resolved parts of the crystallographic structure very well. In addition, the complete assignment set provides preliminary insight into the dynamic regions.

• MeSH
• fotosystém II (proteinový komplex) chemie   MeSH
• krystalografie rentgenová MeSH
• molekulární sekvence - údaje MeSH
• protonová magnetická rezonanční spektroskopie * MeSH
• rostlinné proteiny chemie   MeSH
• sekundární struktura proteinů MeSH
• sekvence aminokyselin MeSH
• Spinacia oleracea chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

A pair of 4D NMR experiments for the backbone assignment of disordered proteins is presented. The experiments exploit (13)C direct detection and non-uniform sampling of the indirectly detected dimensions, and provide correlations of the aliphatic proton (H(α), and H(β)) and carbon (C(α), C(β)) resonance frequencies to the protein backbone. Thus, all the chemical shifts regularly used to map the transient secondary structure motifs in the intrinsically disordered proteins (H(α), C(α), C(β), C', and N) can be extracted from each spectrum. Compared to the commonly used assignment strategy based on matching the C(α) and C(β) chemical shifts, inclusion of the H(α) and H(β) provides up to three extra resonance frequencies that decrease the chance of ambiguous assignment. The experiments were successfully applied to the original assignment of a 12.8 kDa intrinsically disordered protein having a high content of proline residues (26 %) in the sequence.

• MeSH
• izotopy uhlíku chemie   MeSH
• molekulární sekvence - údaje MeSH
• nukleární magnetická rezonance biomolekulární metody   MeSH
• prolin chemie   MeSH
• proteiny chemie   MeSH
• sekundární struktura proteinů MeSH
• sekvence aminokyselin MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The self-processing module (SPM) is an internal segment of the FrpC protein (P415-F591) secreted by the pathogenic Gram-negative bacterium Neisseria meningitidis during meningococcal infection of human upper respiratory tract. SPM mediates 'protein trans-splicing', a unique natural mechanism for editing of proteins, which involves a calcium-dependent autocatalytic cleavage of the peptide bond between D414 and P415 and covalent linkage of the cleaved fragment through its carboxy-terminal group of D414 to [Formula: see text]-amino group of lysine residue within a neighboring polypeptide chain. We present an NMR resonance assignment of the calcium-free SPM, which displays characteristic features of intrinsically disordered proteins. Non-uniformly sampled 5D HN(CA)CONH, 4D HCBCACON, and HCBCANCO spectra were recorded to resolve poorly dispersed resonance frequencies of the disordered protein and 91 % of SPM residues were unambiguously assigned. Analysis of the chemical shifts revealed that two regions of the intrinsically disordered SPM (A95-S101 and R120-I127) have a tendency to form a helical structure, whereas the residues P1-D7 and G36-A40 have the propensity to adopt a [Formula: see text]-structure.

• MeSH
• bakteriální proteiny chemie   MeSH
• membránové proteiny chemie   MeSH
• Neisseria meningitidis metabolismus   MeSH
• nukleární magnetická rezonance biomolekulární * MeSH
• sekundární struktura proteinů MeSH
• vnitřně neuspořádané proteiny chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly repetitive sequence is presented. The protocol is based on three resolution-enhanced NMR experiments: 5D HN(CA)CONH provides sequential connectivity, 5D HabCabCONH is utilized to identify amino acid types, and 5D HC(CC-TOCSY)CONH is used to assign the side-chain resonances. The improved resolution was achieved by a combination of high dimensionality and long evolution times, allowed by non-uniform sampling in the indirect dimensions. Random distribution of the data points and Sparse Multidimensional Fourier Transform processing were used. Successful application of the assignment procedure to a particularly difficult protein, δ subunit of RNA polymerase from Bacillus subtilis, is shown to prove the efficiency of the strategy. The studied protein contains a disordered C-terminal region of 81 amino acids with a highly repetitive sequence. While the conventional assignment methods completely failed due to a very small differences in chemical shifts, the presented strategy provided a complete backbone and side-chain assignment.

• MeSH
• algoritmy MeSH
• deuterium MeSH
• Fourierova analýza MeSH
• izotopy dusíku MeSH
• izotopy uhlíku MeSH
• molekulární sekvence - údaje MeSH
• nukleární magnetická rezonance biomolekulární metody   MeSH
• proteiny chemie   MeSH
• repetitivní sekvence nukleových kyselin MeSH
• sekundární struktura proteinů MeSH
• sekvence aminokyselin MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Microtubule-associated proteins (MAPs) are abundantly present in axons and dendrites, and have been shown to play crucial role during the neuronal morphogenesis. The period of main dendritic outgrowth and synaptogenesis coincides with high expression levels of one of MAPs, the MAP2c, in rats. The MAP2c is a 49.2 kDa intrinsically disordered protein. To achieve an atomic resolution characterization of such a large protein, we have developed a protocol based on the acquisition of two five-dimensional (13)C-directly detected NMR experiments. Our previously published 5D CACONCACO experiment (Nováček et al. in J Biomol NMR 50(1):1-11, 2011) provides the sequential assignment of the backbone resonances, which is not interrupted by the presence of the proline residues in the amino acid sequence. A novel 5D HC(CC-TOCSY)CACON experiment facilitates the assignment of the aliphatic side chain resonances. To streamline the data analysis, we have developed a semi-automated procedure for signal assignments. The obtained data provides the first atomic resolution insight into the conformational state of MAP2c and constitutes a model for further functional studies of MAPs.

• MeSH
• algoritmy MeSH
• glycin MeSH
• krysa rodu rattus MeSH
• molekulární sekvence - údaje MeSH
• molekulová hmotnost MeSH
• nukleární magnetická rezonance biomolekulární MeSH
• proteiny asociované s mikrotubuly chemie   metabolismus   MeSH
• sekundární struktura proteinů MeSH
• sekvence aminokyselin MeSH
• vnitřně neuspořádané proteiny chemie   metabolismus   MeSH
• zvířata MeSH
• Check Tag
• krysa rodu rattus MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• MeSH
• molekulární biologie MeSH
• proteiny MeSH
• Publikační typ
• monografie MeSH

• Konspekt
• Biochemie. Molekulární biologie. Biofyzika
• NLK Obory
• biochemie
• molekulární biologie, molekulární medicína

Complex II (CII) activity controls phenomena that require crosstalk between metabolism and signaling, including neurodegeneration, cancer metabolism, immune activation, and ischemia-reperfusion injury. CII activity can be regulated at the level of assembly, a process that leverages metastable assembly intermediates. The nature of these intermediates and how CII subunits transfer between metastable complexes remains unclear. In this work, we identify metastable species containing the SDHA subunit and its assembly factors, and we assign a preferred temporal sequence of appearance of these species during CII assembly. Structures of two species show that the assembly factors undergo disordered-to-ordered transitions without the appearance of significant secondary structure. The findings identify that intrinsically disordered regions are critical in regulating CII assembly, an observation that has implications for the control of assembly in other biomolecular complexes.

• MeSH
• katalytická doména * MeSH
• sekundární struktura proteinů MeSH
• Publikační typ
• časopisecké články MeSH

Nuclear polyadenylated RNA-binding (Nab)3 protein is an RNA-binding protein that is involved in the poly(A) independent termination pathway. Here, we report the NMR spectral assignments of RNA-recognition motif (RRM) of Nab3. The assignment will allow performing NMR structural and RNA-binding studies of Nab3 with the aim to investigate its role in the poly(A) independent termination pathway.

• MeSH
• aminokyselinové motivy MeSH
• izotopy dusíku chemie   MeSH
• izotopy uhlíku chemie   MeSH
• jaderné proteiny chemie   MeSH
• nukleární magnetická rezonance biomolekulární MeSH
• proteiny vázající RNA chemie   MeSH
• Saccharomyces cerevisiae - proteiny chemie   MeSH
• Saccharomyces cerevisiae MeSH
• sekundární struktura proteinů MeSH
• vodík chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The extrinsic proteins of photosystem II of higher plants and green algae PsbO, PsbP, PsbQ, and PsbR are essential for stable oxygen production in the oxygen evolving center. In the available X-ray crystallographic structure of higher plant PsbQ residues S14-Y33 are missing. Building on the backbone NMR assignment of PsbQ, which includes this "missing link", we report the extended resonance assignment including side chain atoms. Based on nuclear Overhauser effect spectra a high resolution solution structure of PsbQ with a backbone RMSD of 0.81 Å was obtained from torsion angle dynamics. Within the N-terminal residues 1-45 the solution structure deviates significantly from the X-ray crystallographic one, while the four-helix bundle core found previously is confirmed. A short α-helix is observed in the solution structure at the location where a β-strand had been proposed in the earlier crystallographic study. NMR relaxation data and unrestrained molecular dynamics simulations corroborate that the N-terminal region behaves as a flexible tail with a persistent short local helical secondary structure, while no indications of forming a β-strand are found.

• MeSH
• fotosystém II (proteinový komplex) chemie   genetika   metabolismus   MeSH
• krystalografie rentgenová MeSH
• magnetická rezonanční spektroskopie metody   MeSH
• rekombinantní proteiny chemie   metabolismus   MeSH
• rostlinné proteiny chemie   genetika   metabolismus   MeSH
• roztoky MeSH
• sekundární struktura proteinů * MeSH
• sekvence aminokyselin MeSH
• simulace molekulární dynamiky * MeSH
• Spinacia oleracea genetika   metabolismus   MeSH
• terciární struktura proteinů MeSH
• termodynamika MeSH
• vazba proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

DCL-1 (CD302) is a single-pass type one transmembrane protein which is predominantly expressed on myeloid cell lines. It possess the ability of endocytosis and is assumed to play a role in cell adhesion and migration. It has been also connected to several illnesses but more on the level of mRNA than on the protein expression level. More interestingly it is alternatively expressed in the form of a fusion protein with another single-pass type one transmembrane protein DEC205 (CD205) which is normally involved in antigen-uptake and endocytosis. The fusion protein has been assigned to have altered function compared to the wild type proteins. We have performed NMR structural analysis of the 16.2 kDa extracellular domain of DCL-1 to get a better insight onto this molecule. We have been able to assign nearly 97 % of resonance frequencies for the (15)N and (13)C labeled recombinant protein. The assignments have been deposited into Biological Magnetic Resonance Data Bank under the accession number 25802.

• MeSH
• extracelulární prostor * MeSH
• lektiny typu C chemie   MeSH
• lidé MeSH
• nukleární magnetická rezonance biomolekulární * MeSH
• proteinové domény MeSH
• receptory buněčného povrchu chemie   MeSH
• sekundární struktura proteinů MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH