Unraveling cardiolipin-induced conformational change of cytochrome c through H/D exchange mass spectrometry and quartz crystal microbalance.

Cardiolipin (CL), a crucial component in inner mitochondrial membranes, interacts with cytochrome c (cyt c) to form a peroxidase complex for the catalysis of CL oxidation. Such interaction is pivotal to the mitochondrial regulation of apoptosis and is affected by the redox state of cyt c. In the present study, the redox-dependent interaction of cyt c with CL was investigated through amide hydrogen/deuterium exchange coupled with mass spectrometry (HDXMS) and quartz crystal microbalance with dissipation monitoring (QCM-D). Ferrous cyt c exhibited a more compact conformation compared with its ferric form, which was supported by the lower number of deuterons accumulated and the greater amplitude reduction on dissipation. Upon association with CL, ferrous cyt c resulted in a moderate increase in deuteration, whereas the ferric form caused a drastic increase of deuteration, which indicated that CL-bound ferric cyt c formed an extended conformation. These results were consistent with those of the frequency (f) - dissipation (D) experiments, which revealed that ferric cyt c yielded greater values of |ΔD/Δf| within the first minute. Further fragmentation analysis based on HDXMS indicated that the effect of CL binding was considerably different on ferric and ferrous cyt c in the C-helix and the Loop 9-24. In ferric cyt c, CL binding affected Met80 and destabilized His18 interaction with heme, which was not observed with ferrous cyt c. An interaction model was proposed to explain the aforementioned results.

Design Reliable Bus Structure Distributed Fiber Bragg Grating Sensor Network Using Gated Recurrent Unit Network.

The focus of this paper was designing and demonstrating bus structure FBG sensor networks using intensity wavelength division multiplexing (IWDM) techniques and a gated recurrent unit (GRU) algorithm to increase the capability of multiplexing and the ability to detect Bragg wavelengths with greater accuracy. Several Fiber Bragg grating (FBG) sensors are coupled with power ratios of 90:10 and 80:10, respectively in the suggested experimental setup. We used the latest IWDM multiplexing technique for the proposed scheme, as the IWDM system increases the number of sensors and allows us to alleviate the limited operational region drawback of conventional wavelength division multiplexing (WDM). However, IWDM has a crosstalk problem that causes high-sensor signal measurement errors. Thus, we proposed the GRU model to overcome this crosstalk or overlapping problem by converting the spectral detection problem into a regression problem and considered the sequence of spectral features as input. By feeding this sequential spectrum dataset into the GRU model, we trained the GRU system until we achieved optimal efficiency. Consequently, the well-trained GRU model quickly and accurately identifies the Bragg wavelength of each FBG from the overlapping spectra. The Bragg wavelength detection performance of our proposed GRU model is tested or validated using different numbers of FBG sensors, such as 3-FBG, 5-FBG, 7-FBG, and 10-FBG, separately. As a result, the experiment result proves that the well-trained GRU model accurately identifies each FBG Bragg wavelength, and even the number of FBG sensors increase, as well as the spectra of FBGs, which are partially or fully overlapped. Therefore, to boost the detection efficiency, reliability, and to increase the multiplexing capabilities of FBG sensor networks, the proposed sensor system is better than the other previously proposed methods.

Elucidation of tRNA-cytochrome c interactions through hydrogen/deuterium exchange mass spectrometry.

Cytochrome c (cyt c) is a mitochondrial protein responsible for transferring electrons between electron transport chain complexes III and IV. The release of cyt c from the mitochondria has been considered as a commitment step in intrinsic apoptosis. Transfer RNA (tRNA) has recently been found to interact with the released cyt c to prevent the formation of the apoptosome complex, thus preventing cell apoptosis. To understand the molecular basis of tRNA-cyt c interactions, we applied hydrogen/deuterium exchange mass spectrometry (HDXMS) to analyze the interactions between tRNA and cyt c. tRNAPhe binding to cyt c reduced the deuteration level of cyt c in all analyzed regions, indicating that tRNA binding blocks the solvent-accessible regions and results in the formation of a more compact conformation. Substitution of the tRNAPhe with the total tRNA from brewer's yeast in the HDXMS experiment significantly reduced deuteration in the N-terminus and the region 18-32 residue of cyt c, where all tRNAs are bound. To clarify the cause of binding, we used synthesized single-stranded oligonucleotides of 12-mer dA and dT to form complexes with cyt c. The exchange of the nucleotide bases between adenine and thymine did not affect the deuteration level of cyt c. However, the regions 1-10 and 65-82 showed minor decreases after unstructured dA or dT DNA binding. Collectively, these results reveal that cyt c maintains its globular structure to interact with tRNA. The region 18-32 selectively interacts with tRNA, and N-terminal 1-10 interacts with oligonucleotides electrostatically.

Guanine nucleotide induced conformational change of Cdc42 revealed by hydrogen/deuterium exchange mass spectrometry.

Cdc42 regulates pathways related to cell division. Dysregulation of Cdc42 can lead to cancer, cardiovascular diseases and neurodegenerative diseases. GTP induced activation mechanism plays an important role in the activity and biological functions of Cdc42. P-loop, Switch I and Switch II are critical regions modulating the enzymatic activity of Cdc42. We applied amide hydrogen/deuterium exchange coupled with liquid chromatography mass spectrometry (HDXMS) to investigate the dynamic changes of apo-Cdc42 after GDP, GTP and GMP-PCP binding. The natural substrate GTP induced significant decreases of deuteration in P-loop and Switch II, moderate changes of deuteration in Switch I and significant changes of deuteration in the α7 helix, a region far away from the active site. GTP binding induced similar effects on H/D exchange to its non-hydrolysable analog, GMP-PCP. HDXMS results indicate that GTP binding blocked the solvent accessibility in the active site leading to the decrease of H/D exchange rate surrounding the active site, and further triggered a conformational change resulting in the drastic decrease of H/D exchange rate at the remote α7 helix. Comparing the deuteration levels in three activation states of apo-Cdc42, Cdc42-GDP and Cdc42-GMP-PCP, the apo-Cdc42 has the most flexible structure, which can be stabilized by guanine nucleotide binding. The rates of H/D exchange of Cdc42-GDP are between the GMP-PCP-bound and the apo form, but more closely to the GMP-PCP-bound form. Our results show that the activation of Cdc42 is a process of conformational changes involved with P-loop, Switch II and α7 helix for structural stabilization.

Neural correlates of successful response inhibition in unmedicated patients with late-life depression.

OBJECTIVE: Accumulating evidence implicates a strong association between abnormal frontostriatal-limbic brain circuits, executive dysfunction, and late-life depression (LLD). The stop signal task (SST) was designed by Rubia et al. for use with functional magnetic resonance imaging (fMRI) to identify the neural correlates of motor response inhibition, a well-characterized executive function. In this study, we compared brain activation between a group of unmedicated participants with LLD and an unmedicated healthy cohort during SST performance. METHODS: Participants 55-85 years of age were screened, clinically evaluated, and entered into either the LLD (n = 15) or healthy comparison group (n = 13). Both groups underwent neuroimaging while performing the SST under similar conditions. The brain circuitry of successful motor inhibition was evaluated by contrasting the condition of correctly inhibiting responses with the condition of correctly responding to Go signals. Differential areas of brain activation between the LLD and comparison groups were determined with FMRIB Software Library. RESULTS: Despite comparable SST performance measures, LLD participants demonstrated greater blood oxygen level dependent activation relative to the comparison group in predominantly left-lateralized frontostriatal-limbic circuitry that included the bilateral superior frontal cortices and left-hemispheric orbitofrontal gyri, insular cortex, cingulate cortex, caudate, and putamen. Conversely, the healthy comparison group did not exhibit any areas of greater activation than the LLD group. CONCLUSION: Unmedicated participants with LLD activate additional areas within frontostriatal-limbic brain circuitry when performing the SST at a level comparable to a healthy cohort.

Distribution of allergens in children with different atopic disorders in central Taiwan.

Allergic disorders, including asthma, allergic rhinitis, and eczema, are the most common chronic childhood diseases. Exposure to house dust mites (HDMs) can exacerbate allergic disorders in sensitized individuals. The data for sensitization to HDMs and other frequent allergens amongst atopic children in Taiwan is limited. We studied 498 children (aged 2-16 years) with atopy in central Taiwan with CAP testing (Cationic Antimicrobial Protein system). Our results revealed a high prevalence of sensitization to Dermatophagoides pteronyssinus (Der p) (90.2%), Dermatophagoides farinae (Der f) (88.2%), Dermatophagoides microceras (Der m) (79.5%), and Blomia tropicalis (Blo t) (76.7%) amongst the children. In contrast to HDM, the sensitization rates for other aeroallergens including cockroaches, dog dander, cat dander, Aspergillus fumigatus, Candida albicans, Cladosporium herbarum, Penicillium notatum were not common among the study children. With respect to age, inhaled allergen sensitization predominated in older children, whereas the inverse occurred with food allergens. In addition, a relatively higher proportion of co-sensitization between Der m and the other three antigens, including Der p, Der f, Blo t was found. Our results suggest that HDMs, including Der p, Der f, Der m, and Blo t allergens, act as important inducers of symptoms in Taiwanese allergic children.