BACKGROUND: Cellobiose dehydrogenase (CDH) is a fungal extracellular oxidoreductase which fuels lytic polysaccharide monooxygenase with electrons during cellulose degradation. Interdomain electron transfer between the flavin and cytochrome domain in CDH, preceding the electron flow to lytic polysaccharide monooxygenase, is known to be pH dependent, but the exact mechanism of this regulation has not been experimentally proven so far. METHODS: To investigate the structural aspects underlying the domain interaction in CDH, hydrogen/deuterium exchange (HDX-MS) with improved proteolytic setup (combination of nepenthesin-1 with rhizopuspepsin), native mass spectrometry with ion mobility and electrostatics calculations were used. RESULTS: HDX-MS revealed pH-dependent changes in solvent accessibility and hydrogen bonding at the interdomain interface. Electrostatics calculations identified these differences to result from charge neutralization by protonation and together with ion mobility pointed at higher electrostatic repulsion between CDH domains at neutral pH. In addition, we uncovered extensive O-glycosylation in the linker region and identified the long-unknown exact cleavage point in papain-mediated domain separation. CONCLUSIONS: Transition of CDH between its inactive (open) and interdomain electron transfer-capable (closed) state is shown to be governed by changes in the protein surface electrostatics at the domain interface. Our study confirms that the interdomain electrostatic repulsion is the key factor modulating the functioning of CDH. GENERAL SIGNIFICANCE: The results presented in this paper provide experimental evidence for the role of charge repulsion in the interdomain electron transfer in cellobiose dehydrogenases, which is relevant for exploiting their biotechnological potential in biosensors and biofuel cells.

• MeSH
• celobiosa metabolismus   MeSH
• cytochromy metabolismus   MeSH
• deuterium metabolismus   MeSH
• elektrony MeSH
• flaviny metabolismus   MeSH
• fungální proteiny metabolismus   MeSH
• glykosylace MeSH
• houby metabolismus   MeSH
• karbohydrátdehydrogenasy metabolismus   MeSH
• koncentrace vodíkových iontů MeSH
• oxygenasy se smíšenou funkcí metabolismus   MeSH
• polysacharidy metabolismus   MeSH
• proteinové domény MeSH
• proteolýza MeSH
• sekvence aminokyselin MeSH
• statická elektřina MeSH
• transport elektronů fyziologie   MeSH
• vodík metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Hyaluronic acid (HA) is a natural polysaccharide present in the connective tissues of vertebrates, often used in the cosmetics and pharmaceutical industries. HA is a strongly hydrophilic macromolecule forming highly swollen random coils in aqueous solutions. Although some authors reported the secondary and tertiary structures of HA chain, others brought convincing evidence contradicting this hypothesis. This study aims at investigation of the stability and dynamics of the temporary duplex HA structures at different NaCl concentrations by molecular-dynamics (MD) simulations. The tendency to duplex formation grows with NaCl concentration reaching its maximum at 0.6 M. This profile is a result of two counteracting NaCl-concentration dependent phenomena, the growing electrostatic-repulsion screening on one side and the disturbance of hydrogen-bonds formation on the other side. Although the weak intermolecular attraction cannot lead to long-lived secondary and tertiary structures, it may influence the properties of large HA macromolecules and concentrated HA solutions.

• MeSH
• chlorid sodný * MeSH
• kyselina hyaluronová * chemie   MeSH
• simulace molekulární dynamiky MeSH
• statická elektřina MeSH
• voda MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Abstract Aromatic stacking of nucleic acid bases is one of the key players in determining the structure and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive overlap of their aromatic rings gave rise to numerous often contradictory suggestions about the physical origins of stacking and the possible role of delocalized electrons in stacked aromatic π systems, leading to some confusion about the issue. The recent advance of computer hardware and software finally allowed the application of state of the art quantum-mechanical approaches with inclusion of electron correlation effects to study aromatic base stacking, now providing an ultimitate qualitative description of the phenomenon. Base stacking is determined by an interplay of the three most commonly encountered molecular interactions: dispersion attraction, electrostatic interaction, and short-range repulsion. Unusual (aromatic- stacking specific) energy contributions were in fact not evidenced and are not necessary to describe stacking. The currently used simple empirical potential form, relying on atom-centered constant point charges and Lennard-Jones van der Waals terms, is entirely able to reproduce the essential features of base stacking. Thus, we can conclude that base stacking is in principle one of the best described interactions in current molecular modeling and it allows to study base stacking in DNA using large-scale classical molecular dynamics simulations. Neglect of cooperativity of stacking appears to be the most serious approximation of the currently used force field form. This review summarizes recent developments in the field. It is written for an audience that is not necessarily expert in computational quantum chemistry and follows up on our previous contribution (Sponer et. al., J. Biomol. Struct. Dyn. 14, 117, (1997)). First, the applied methodology, its accuracy, and the physical nature of base stacking is briefly overviewed, including a comment on the accuracy of other molecular orbital methods and force fields. Then, base stacking is contrasted with hydrogen bonding, the other dominant force in nucleic acid structure. The sequence dependence and cooperativity of base stacking is commented on, and finally a brief introduction into recent progress in large-scale molecular dynamics simulations of nucleic acids is provided. Using four stranded DNA assemblies as an example, we demonstrate the efficacy of current molecular dynamics techniques that utilize refined and verified force fields in the study of stacking in nucleic acid molecules.

• MeSH
• DNA * chemie   MeSH
• konformace nukleové kyseliny MeSH
• molekulární modely MeSH
• nukleové kyseliny chemie   MeSH
• simulace molekulární dynamiky * MeSH
• statická elektřina MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

Small-angle X-ray scattering (SAXS) measurements reveal a striking difference in intermolecular interactions between two short highly charged peptides-deca-arginine (R10) and deca-lysine (K10). Comparison of SAXS curves at high and low salt concentration shows that R10 self-associates, while interactions between K10 chains are purely repulsive. The self-association of R10 is stronger at lower ionic strengths, indicating that the attraction between R10 molecules has an important electrostatic component. SAXS data are complemented by NMR measurements and potentials of mean force between the peptides, calculated by means of umbrella-sampling molecular dynamics (MD) simulations. All-atom MD simulations elucidate the origin of the R10-R10 attraction by providing structural information on the dimeric state. The last two C-terminal residues of R10 constitute an adhesive patch formed by stacking of the side chains of two arginine residues and by salt bridges formed between the like-charge ion pair and the C-terminal carboxyl groups. A statistical analysis of the Protein Data Bank reveals that this mode of interaction is a common feature in proteins.

• MeSH
• arginin chemie   MeSH
• chemické modely MeSH
• difrakce rentgenového záření MeSH
• magnetická rezonanční spektroskopie MeSH
• maloúhlový rozptyl MeSH
• osmolární koncentrace MeSH
• peptidy chemie   MeSH
• počítačová simulace MeSH
• sekvence aminokyselin MeSH
• statická elektřina MeSH
• vazba proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The partially disordered δ subunit of RNA polymerase was studied by various NMR techniques. The structure of the well-folded N-terminal domain was determined based on inter-proton distances in NOESY spectra. The obtained structural model was compared to the previously determined structure of a truncated construct (lacking the C-terminal domain). Only marginal differences were identified, thus indicating that the first structural model was not significantly compromised by the absence of the C-terminal domain. Various (15) N relaxation experiments were employed to describe the flexibility of both domains. The relaxation data revealed that the C-terminal domain is more flexible, but its flexibility is not uniform. By using paramagnetic labels, transient contacts of the C-terminal tail with the N-terminal domain and with itself were identified. A propensity of the C-terminal domain to form β-type structures was obtained by chemical shift analysis. Comparison with the paramagnetic relaxation enhancement indicated a well-balanced interplay of repulsive and attractive electrostatic interactions governing the conformational behavior of the C-terminal domain. The results showed that the δ subunit consists of a well-ordered N-terminal domain and a flexible C-terminal domain that exhibits a complex hierarchy of partial ordering.

• MeSH
• Bacillus subtilis enzymologie   MeSH
• bakteriální proteiny chemie   genetika   metabolismus   MeSH
• DNA řízené RNA-polymerasy chemie   genetika   metabolismus   MeSH
• molekulární sekvence - údaje MeSH
• nukleární magnetická rezonance biomolekulární MeSH
• podjednotky proteinů chemie   genetika   metabolismus   MeSH
• rekombinantní proteiny biosyntéza   chemie   metabolismus   MeSH
• sekundární struktura proteinů MeSH
• sekvence aminokyselin MeSH
• statická elektřina MeSH
• terciární struktura proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Retroviral gene transfer is the preferred method for stable, long-term integration of genetic material into cellular genomes, commonly used to generate chimeric antigen receptor (CAR)-T cells designed to target tumor antigens. However, the efficiency of retroviral gene transfer is often limited by low transduction rates due to low vector titers and electrostatic repulsion between viral particles and cellular membranes. To overcome these limitations, peptide nanofibrils (PNFs) can be applied as transduction enhancers. Among these, PNFs derived from the 12-mer peptide EF-C are well-investigated and commercially available. EF-C PNFs enhance transduction by forming EF-C PNFs/virus complexes that overcome electrostatic repulsion through their polycationic surface and interaction with cellular protrusions. However, the safe application of PNFs as transduction enhancers in gene therapeutic applications requires a fundamental understanding of their transduction-enhancing mechanisms, uptake, and degradation. In this study, we demonstrate that EF-C PNFs induce plasma membrane invaginations, increasing the membrane surface for viral attachment and reducing the distance to the nuclear membrane, thereby facilitating viral entry and transport to the nucleus. Furthermore, we identified macropinocytosis as the main entry pathway for EF-C PNFs and their subsequent degradation by lysosomal peptidases. The lysosomal degradation of EF-C PNFs prevents their accumulation as amyloid deposits, mitigating potential side effects and supporting their safe use in clinical applications.

• MeSH
• endocytóza MeSH
• HEK293 buňky MeSH
• lidé MeSH
• myši MeSH
• nanovlákna * chemie   MeSH
• peptidy * chemie   metabolismus   MeSH
• pinocytóza * MeSH
• transdukce genetická metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

In this work, interactions of carboxylated core shell magnetic nanoparticles with polymyxin B sulfate were studied by connecting capillary electrophoresis with inductively coupled plasma mass spectrometry. The interaction was probed by affinity mode of capillary electrophoresis with 25 mM phosphate buffer at physiological pH. 54Fe, 56Fe, 57Fe, 34S, and 12C isotopes were used to monitor the migration of an electroosmotic flow marker and the interaction of the nanoparticles with polymyxin B. The analysis of interaction data showed two distinct interaction regions, one with low polymyxin B concentration, the second with high polymyxin B concentration. These regions differed in the strength of the interaction, 1.49 × 107 M-1 and 1.60 × 104 M-1, and in the stoichiometry of 0.7 and 3.5, respectively. These differences can be explained by the decrease of electrostatic repulsion between nanoparticles caused by polymyxin B. This is also in agreement with the nanoparticles peak shapes: sharp for low polymyxin B concentrations and broad for high polymyxin B concentrations.

• MeSH
• elektroforéza kapilární metody   MeSH
• hmotnostní spektrometrie metody   MeSH
• magnetické nanočástice chemie   MeSH
• polymyxin B analýza   MeSH
• tlak MeSH
• Publikační typ
• časopisecké články MeSH

Phosphorylation patterns of the C-terminal domain (CTD) of largest subunit of RNA polymerase II (called the CTD code) orchestrate the recruitment of RNA processing and transcription factors. Recent studies showed that not only serines and tyrosines but also threonines of the CTD can be phosphorylated with a number of functional consequences, including the interaction with yeast transcription termination factor, Rtt103p. Here, we report the solution structure of the Rtt103p CTD-interacting domain (CID) bound to Thr4 phosphorylated CTD, a poorly understood letter of the CTD code. The structure reveals a direct recognition of the phospho-Thr4 mark by Rtt103p CID and extensive interactions involving residues from three repeats of the CTD heptad. Intriguingly, Rtt103p's CID binds equally well Thr4 and Ser2 phosphorylated CTD A doubly phosphorylated CTD at Ser2 and Thr4 diminishes its binding affinity due to electrostatic repulsion. Our structural data suggest that the recruitment of a CID-containing CTD-binding factor may be coded by more than one letter of the CTD code.

• MeSH
• fosforylace MeSH
• genetická transkripce MeSH
• proteinkinasy metabolismus   MeSH
• proteolýza MeSH
• RNA-polymerasa II chemie   metabolismus   MeSH
• Saccharomyces cerevisiae - proteiny chemie   metabolismus   MeSH
• serin metabolismus   MeSH
• terciární struktura proteinů MeSH
• threonin chemie   metabolismus   MeSH
• transkripční faktory chemie   metabolismus   MeSH
• tyrosin metabolismus   MeSH
• vazba proteinů MeSH
• Publikační typ
• časopisecké články MeSH

• MeSH
• fyzikální chemie MeSH
• Publikační typ
• monografie MeSH

• Konspekt
• Fyzikální chemie
• NLK Obory
• chemie, klinická chemie

Protein glycosylation analysis is challenging due to the structural variety of complex conjugates. However, chromatographically separating glycans attached to tryptic peptides enables their site-specific characterization. For this purpose, we have shown the importance of selecting a suitable hydrophilic interaction liquid chromatography (HILIC) stationary phase in the separation of glycopeptides and their isomers. Three different HILIC stationary phases, i.e., HALO® penta-HILIC, Glycan ethylene bridged hybrid (BEH) Amide, and ZIC-HILIC, were compared in the separation of complex N-glycopeptides of hemopexin and Immunoglobulin G glycoproteins. The retention time increased with the polarity of the glycans attached to the same peptide backbone in all HILIC columns tested in this study, except for the ZIC-HILIC column when adding sialic acid to the glycan moiety, which caused electrostatic repulsion with the negatively charged sulfobetaine functional group, thereby decreasing retention. The HALO® penta-HILIC column provided the best separation results, and the ZIC-HILIC column the worst. Moreover, we showed the potential of these HILIC columns for the isomeric separation of fucosylated and sialylated glycoforms. Therefore, HILIC is a useful tool for the comprehensive characterization of glycoproteins and their isomers.

• MeSH
• amidy chemie   MeSH
• chromatografie kapalinová přístrojové vybavení   metody   MeSH
• glykopeptidy chemie   izolace a purifikace   metabolismus   MeSH
• glykosylace MeSH
• hemopexin chemie   izolace a purifikace   MeSH
• hydrofobní a hydrofilní interakce MeSH
• imunoglobulin G chemie   izolace a purifikace   MeSH
• isomerie MeSH
• lidé MeSH
• polysacharidy chemie   MeSH
• teplota MeSH
• trypsin chemie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• srovnávací studie MeSH