Deciphering the Binding Interactions between Acinetobacter baumannii ACP and β-ketoacyl ACP Synthase III to Improve Antibiotic Targeting Using NMR Spectroscopy

Fatty acid synthesis is essential for bacterial viability. Thus, fatty acid synthases (FASs) represent effective targets for antibiotics. Nevertheless, multidrug-resistant bacteria, including the human opportunistic bacteria, Acinetobacter baumannii, are emerging threats. Meanwhile, the FAS pathway of A. baumannii is relatively unexplored. Considering that acyl carrier protein (ACP) has an important role in the delivery of fatty acyl intermediates to other FAS enzymes, we elucidated the solution structure of A. baumannii ACP (AbACP) and, using NMR spectroscopy, investigated its interactions with β-ketoacyl ACP synthase III (AbKAS III), which initiates fatty acid elongation. The results show that AbACP comprises four helices, while Ca²⁺ reduces the electrostatic repulsion between acid residues, and the unconserved F47 plays a key role in thermal stability. Moreover, AbACP exhibits flexibility near the hydrophobic cavity entrance from D59 to T65, as well as in the α₁α₂ loop region. Further, F29 and A69 participate in slow exchanges, which may be related to shuttling of the growing acyl chain. Additionally, electrostatic interactions occur between the α₂ and α₃-helix of ACP and AbKAS III, while the hydrophobic interactions through the ACP α₂-helix are seemingly important. Our study provides insights for development of potent antibiotics capable of inhibiting A. baumannii FAS protein–protein interactions.     

Structural Studies of the Lipopolysaccharide of Aeromonas veronii bv. sobria Strain K133 Which Represents New Provisional Serogroup PGO1 Prevailing among Mesophilic Aeromonads on Polish Fish Farms

In the present work, we performed immunochemical studies of LPS, especially the O-specific polysaccharide (O-PS) of Aeromonas veronii bv. sobria strain K133, which was isolated from the kidney of carp (Cyprinus carpio L.) during an outbreak of motile aeromonad infection/motile aeromonad septicemia (MAI/MAS) on a Polish fish farm. The structural characterization of the O-PS, which was obtained by mild acid degradation of the LPS, was performed with chemical methods, MALDI-TOF mass spectrometry, and ¹H and ¹³C NMR spectroscopy. It was revealed that the O-PS has a unique composition of a linear tetrasaccharide repeating unit and contains a rarely occurring sugar 2,4-diamino-2,4,6-trideoxy-D-glucose (bacillosamine), which may determine the specificity of the serogroup. Western blotting and ELISA confirmed that A. veronii bv. sobria strain K133 belongs to the new serogroup PGO1, which is one of the most commonly represented immunotypes among carp and trout isolates of Aeromonas sp. in Polish aquacultures. Considering the increase in the MAI/MAS incidences and their impact on freshwater species, also with economic importance, and in the absence of an effective immunoprophylaxis, studies of the Aeromonas O-antigens are relevant in the light of epidemiological data and monitoring emergent pathogens representing unknown antigenic variants and serotypes.     

Precision Oncology via NMR-Based Metabolomics: A Review on Breast Cancer

Precision oncology is an emerging approach in cancer care. It aims at selecting the optimal therapy for the right patient by considering each patient’s unique disease and individual health status. In the last years, it has become evident that breast cancer is an extremely heterogeneous disease, and therefore, patients need to be appropriately stratified to maximize survival and quality of life. Gene-expression tools have already positively assisted clinical decision making by estimating the risk of recurrence and the potential benefit from adjuvant chemotherapy. However, these approaches need refinement to further reduce the proportion of patients potentially exposed to unnecessary chemotherapy. Nuclear magnetic resonance (NMR) metabolomics has demonstrated to be an optimal approach for cancer research and has provided significant results in BC, in particular for prognostic and stratification purposes. In this review, we give an update on the status of NMR-based metabolomic studies for the biochemical characterization and stratification of breast cancer patients using different biospecimens (breast tissue, blood serum/plasma, and urine).     

The Co-Culture of Staphylococcal Biofilm and Fibroblast Cell Line: The Correlation of Biological Phenomena with Metabolic NMR1 Footprint

Staphylococcus aureus is one of the most prevalent pathogens associated with several types of biofilm-based infections, including infections of chronic wounds. Mature staphylococcal biofilm is extremely hard to eradicate from a wound and displays a high tendency to induce recurring infections. Therefore, in the present study, we aimed to investigate in vitro the interaction between S. aureus biofilm and fibroblast cells searching for metabolites that could be considered as potential biomarkers of critical colonization and infection. Utilizing advanced microscopy and microbiological methods to examine biofilm formation and the staphylococcal infection process, we were able to distinguish 4 phases of biofilm development. The analysis of staphylococcal biofilm influence on the viability of fibroblasts allowed us to pinpoint the moment of critical colonization—12 h post contamination. Based on the obtained model we performed a metabolomics analysis by ¹H NMR spectroscopy to provide new insights into the pathophysiology of infection. We identified a set of metabolites related to the switch to anaerobic metabolism that was characteristic for staphylococcal biofilm co-cultured with fibroblast cells. The data presented in this study may be thus considered a noteworthy but preliminary step in the direction of developing a new, NMR-based tool for rapid diagnosing of infection in a chronic wound.     

A Methionine Chemical Shift Based Order Parameter Characterizing Global Protein Dynamics

Coupling of side chain dynamics over long distances is an important component of allostery. Methionine side chains show the largest intrinsic flexibility among methyl-containing residues but the actual degree of conformational averaging depends on the proximity and mobility of neighboring residues. The ¹³C NMR chemical shifts of the methyl groups of methionine residues located at long distances in the same protein show a similar scaling with respect to the values predicted from the static X-ray structure by quantum methods. This results in a good linear correlation between calculated and observed chemical shifts. The slope is protein dependent and ranges from zero for the highly flexible calmodulin to 0.7 for the much more rigid calcineurin catalytic domain. The linear correlation is indicative of a similar level of side-chain conformational averaging over long distances, and the slope of the correlation line can be interpreted as an order parameter of the global side-chain flexibility.     

Probing the Conformation States of Neurotensin Receptor 1 Variants by NMR Site-Directed Methyl Labeling

G protein-coupled receptors (GPCRs) are key players in mediating signal transduction across the cell membrane. However, due to their intrinsic instability, many GPCRs are not suitable for structural investigations. Various approaches have been developed in recent years to remedy this situation, ranging from the use of more native membrane mimetics to protein-stabilization methods. The latter approach typically results in GPCRs that contain various numbers of mutations. However, probing the functionality of such variants by in vitro and in vivo assays is often time consuming. In addition, to validate the suitability of such GPCRs for structural investigations, an assessment of their conformation state is required. NMR spectroscopy has been proven to be suitable to probe the conformation state of GPCRs in solution. Here, by using chemical labeling with an isotope-labeled methyl probe, we show that the activity and the conformation state of stabilized neurotensin receptor 1 variants obtained from directed evolution can be efficiently assayed in 2D NMR experiments. This strategy enables the quantification of the active and inactive conformation states and the derivation of an estimation of the basal as well as agonist-induced activity of the receptor. Furthermore, this assay can be used as a readout when re-introducing agonist-dependent signaling into a highly stabilized, and thus rigidified, receptor by mutagenesis. This approach will be useful in cases where low production yields do not permit the addition of labeled compounds to the growth medium and where 1D NMR spectra of selectively ¹⁹F-labeled receptors are not sufficient to resolve signal overlap for a more detailed analysis.     

Modification of phenol–formaldehyde resol resins by lignin,starch, and urea

Lignin‐based chemicals, starch, and urea were used as modifiers for phenol–formaldehyde resol resins. The effects of the addition stage of the modifiers used in the synthesis of the resins and the type of modification reagent on the structures of the resins and their molar masses and reactivities were investigated. The modifications with corn starch and lignin promoted condensation; this was verified by increased molar masses and high ratios of methylene bridges to the sum of free ortho and para aromatic groups with respect to the corresponding reference resin without a modification reagent. The later the modifier was added to the resin condensation mixture, the more methylene bridges were formed with respect to the amounts of free ortho and para aromatic groups. In addition, when urea or wheat starch was added in the later condensation stage, the final condensation also reached high stages. The modifications with lignosulfonate and starch, as well as the early addition of urea, enhanced p–p′ bridge structures. The lowest condensation stage and, therefore, the highest reactivity were found when wheat starch was added with the starting reagents. The curing heat of the wheat‐starch‐modified resins decreased according to the deferred addition point of starch. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 88: 582–588, 2003     

The mechanical property and phase structures of wheat proteins/polyvinyl alcohol blends studied by high-resolution solid-state NMR

The phase structures of thermally processed wheat proteins (WP) and polyvinyl alcohol (PVOH) blends were studied by solid-state high-resolution NMR spectroscopy. The intermolecular interactions among the multi-component systems and the behavior of each component in the blends on scales of nanometers were examined. The mechanical properties of the blends were also measured and related to the phase structure studies. The results indicated that the polymer chains of WP could be homogeneously mobilized when thermally processed with glycerol and water as plasticisers, but the glycerol predominately associated with WP rather than PVOH in the blends. The intermolecular hydrogen bonding interactions between WP and PVOH caused some extent of miscibility in the system on scales of nanometers especially when the PVOH content was low. The tensile strength and modulus of the blends were improved as compared to WP. However, the intermolecular interactions were relatively weak and could not be further enhanced by increasing PVOH component in the blends. The particle miscible WP/PVOH blends contained plasticised WP and PVOH phases in conjunction with the miscible WP/PVOH phase. Increasing the PVOH content in the blends did not result in an increase of the percentage of the miscible phase and the blends tented to be immiscible while the elongation of the blends was reduced when increasing the PVOH content in the blends.     

Solid-state NMR study of N labelled polyaniline upon reaction with DPPH

The quantitative investigation of the radical scavenging properties of polyaniline (PANI) upon reaction with excess of the stable DPPH radical (a 4:1 ratio of DPPH to aniline units in the polymer) was carried out using ¹⁵N and ¹³C solid state NMR spectroscopy. During the process the polyaniline was oxidised so that the imine content increased from 45 to 65%. The extent of oxidation measured by NMR was confirmed by N1s XPS analysis. However, within a 30 min reaction time, about 85% of the DPPH radicals were scavenged as monitored by the decay in its EPR signal. This is about 20 times greater than the fraction of DPPH required to oxidize PANI from an imine content of 45-65%. An identification of further redox processes is required to explain the high degree of radical scavenging. At the same time, there was no evidence of significant chemical binding or trapping of DPPH in the PANI structure.