Decreased TET2/5-hmC reduces the integrity of the epidermal barrier via epigenetic dysregulation of filaggrin in psoriatic lesions.

BACKGROUND: TET2 participates in tumor progression and intrinsic immune homeostasis via epigenetic regulation. TET2 has been reported to be involved in maintaining epithelial barrier homeostasis and inflammation. Abnormal epidermal barrier function and TET2 expression have been detected in psoriatic lesions. However, the mechanisms underlying the role of TET2 in psoriasis have not yet been elucidated. OBJECTIVE: To define the role of TET2 in maintaining epithelial barrier homeostasis and the exact epigenetic mechanism in the dysfunction of the epidermal barrier in psoriasis. METHODS: We analyzed human psoriatic skin lesions and datasets from the GEO database, and detected the expression of TET2/5-hmC together with barrier molecules by immunohistochemistry. We constructed epidermal-specific TET2 knockout mice to observe the effect of TET2 deficiency on epidermal barrier function via toluidine blue penetration assay. Further, we analyzed changes in the expression of epidermal barrier molecules by immunofluorescence in TET2-specific knockout mice and psoriatic model mice. RESULTS: We found that decreased expression of TET2/5-hmC correlated with dysregulated barrier molecules in human psoriatic lesions. Epidermal-specific TET2 knockout mice showed elevated transdermal water loss associated with abnormal epidermal barrier molecules. Furthermore, we observed that TET2 knockdown in keratinocytes reduced filaggrin expression via filaggrin promoter methylation. CONCLUSION: Aberrant epidermal TET2 affects the integrity of the epidermal barrier through the epigenetic dysregulation of epidermal barrier molecules, particularly filaggrin. Reduced TET2 expression is a critical factor contributing to an abnormal epidermal barrier in psoriasis.

Fast and Low-Overhead Time Synchronization for Industrial Wireless Sensor Networks with Mesh-Star Architecture.

Low-overhead, robust, and fast-convergent time synchronization is important for resource-constrained large-scale industrial wireless sensor networks (IWSNs). The consensus-based time synchronization method with strong robustness has been paid more attention in wireless sensor networks. However, high communication overhead and slow convergence speed are inherent drawbacks for consensus time synchronization due to inefficient frequent iterations. In this paper, a novel time synchronization algorithm for IWSNs with a mesh-star architecture is proposed, namely, fast and low-overhead time synchronization (FLTS). The proposed FLTS divides the synchronization phase into two layers: mesh layer and star layer. A few resourceful routing nodes in the upper mesh layer undertake the low-efficiency average iteration, and the massive low-power sensing nodes in the star layer synchronize with the mesh layer in a passive monitoring manner. Therefore, a faster convergence and lower communication overhead time synchronization is achieved. The theoretical analysis and simulation results demonstrate the efficiency of the proposed algorithm in comparison with the state-of-the-art algorithms, i.e., ATS, GTSP, and CCTS.

Suprabasin-derived polypeptides: SBSN(50-63) induces inflammatory response via TLR4-mediated mast cell activation.

Psoriasis is a chronic, relapsing, immune-mediated, and papulosquamous skin disorder. Excessive mast cell activation, in psoriatic lesions, contributes to inflammation. Various endogenous peptides can participate in the pathogenesis of inflammatory diseases by activating mast cells. Suprabasin (SBSN) is expressed in multiple epithelial tissues and it regulates the normal epidermal barrier function. We have recently shown that suprabasin-derived polypeptides, SBSN(50-63), are significantly increased in psoriatic lesions, through differential peptide analysis. This study was conducted to clarify whether SBSN(50-63) plays a pivotal role in activating mast cells and mediating proinflammatory cytokines and chemokines production in psoriasis. The increased expression of SBSN in psoriatic lesions was confirmed by bioinformatics analysis, PCR and ELISA. Wild-type mice injected subcutaneously with SBSN(50-63) exhibited infiltration of inflammatory cells and the release of cytokines in vivo. SBSN(50-63) stimulated mouse primary mast cells (MPMC) and the laboratory of allergic disease 2 (LAD2) human mast cells to produce more inflammatory mediators than the control group, which were measured ex vivo and in vitro. Toll-like receptor 4 was identified as the receptor of SBSN on mast cells by molecular docking analysis, molecular dynamics simulation, and siRNA transfection. Collectively, SBSN(50-63) could activate mast cells through TLR4, which may increase the inflammatory response in psoriasis.

Neuroblast Differentiation-Associated Protein Derived Polypeptides: AHNAK(5758-5775) Induces Inflammation by Activating Mast Cells via ST2.

Psoriasis is a chronic inflammatory skin disease. Mast cells are significantly increased and activated in psoriatic lesions and are involved in psoriatic inflammation. Some endogenous substances can interact with the surface receptors of mast cells and initiate the release of downstream cytokines that participate in inflammatory reactions. Neuroblast differentiation-associated protein (AHNAK) is mainly expressed in the skin, esophagus, kidney, and other organs and participates in various biological processes in the human body. AHNAK and its derived peptides have been reported to be involved in the activation of mast cells and other immune processes. This study aimed to investigate whether AHNAK (5758-5775), a neuroblast differentiation-associated protein-derived polypeptide, could be considered a new endogenous substance in psoriasis patients, which activates mast cells and induces the skin inflammatory response contributing to psoriasis. Wild-type mice were treated with AHNAK(5758-5775) to observe the infiltration of inflammatory cells in the skin and cytokine release in vivo. The release of inflammatory mediators by mouse primary mast cells and the laboratory of allergic disease 2 (LAD2) human mast cells was measured in vitro. Molecular docking analysis, molecular dynamics simulation, and siRNA transfection were used to identify the receptor of AHNAK(5758-5775). AHNAK(5758-5775) could cause skin inflammation and cytokine release in wild-type mice and activated mast cells in vitro. Moreover, suppression of tumorigenicity 2 (ST2) might be a key receptor mediating AHNAK(5758-5775)'s effect on mast cells and cytokine release. We propose a novel polypeptide, AHNAK(5758-5775), which induces an inflammatory reaction and participates in the occurrence and development of psoriasis by activating mast cells.

A Current Noise Cancellation Method Based on Fractional Linear Prediction for Bearing Fault Detection.

The stator current in an induction motor contains a large amount of information, which is unrelated to bearing faults. This information is considered as the noise component for the detection of bearing faults. When there is noise information in the current signal, it can affect the detection of motor bearing faults and lead to the possibility of false alarms. Therefore, to accomplish an effective bearing fault detection, all or some of these noise components must be properly eliminated. This paper proposes the use of fractional linear prediction (FLP) as a noise elimination method in bearing fault diagnosis, which makes these noise components the predictable components and this bearing fault information the unpredictable components. The basis of the FLP is to eliminate noise components in the current signal by predicting predictable components through linear prediction theory and optimal prediction order. Meanwhile, this paper adopts the FLP model with limited memory samples. After determining the optimal number of memories, only the fractional derivative order parameter needs to be optimized, which greatly reduces the computational complexity and difficulty in parameter optimization. In addition, this paper uses spectral analysis of the current signals through experimental simulation to compare the FLP method with the linear prediction (LP) method and the time-shifting (TS) method that have been successfully applied to bearing fault diagnosis. Based on the analysis results, the FLP method can better extract fault features and achieve better bearing fault diagnosis results, verifying the effectiveness and superiority of the FLP method in the field of bearing fault diagnosis. Additionally, the predictive performance of thevFLP and LP was compared based on experimental data, verifying the advantages of the FLP method in predictive performance, indicating that this method has a better noise cancellation effect.

Characteristics of COVID-19 (Delta Variant)/HIV Co-infection: A Cross-sectional Study in Henan Province, China.

Background: Since the end of July 2021, SARS-CoV-2 (Delta variant) invaded Henan Province, China, causing a rapid COVID-19 spread in the province. Among them, the clinical features of COVID-19 (Delta Variant)/HIV co-infection have attracted our attention. Methods: We included 12 COVID-19 patients living with HIV (human immunodeficiency virus) from July 30, 2021 to September 17, 2021 in Henan Province, China. Demographic, clinical, laboratory, and computed tomography (CT) imaging data were dynamically collected from first nucleic acid positive to hospital discharge. Laboratory findings included SARS-CoV-2 viral load, HIV viral load, IgM, IgG, cytokines, lymphocyte subpopulation, ferritin, etc. Statistical analyses were performed using IBM SPSS version 26·0 and GraphPad Prism version 9·0. Results: It was founded that the low Ct value persisted for about 21 days, and the viral shedding time (turn negative time) of the patients was 32·36 ± 2·643 days. Furthermore, chest CT imaging revealed that lesions were obviously and rapidly absorbed. It was surprising that IgM levels were statistically higher in patients taking azvudine or convalescent plasma than in patients not taking these drugs (P < 0·001, P = 0·0002, respectively). IgG levels were significantly higher in patients treated with the combined medication of BRII/196 and BRII/198 than in those not treated with these drugs (P = 0·0029). IgM was significantly higher in those with low HIV viral load than those with high HIV viral load (P < 0·001). In addition, as treatment progressed and patients' condition improved, IL-17a showed a decreasing trend. Conclusions: Based on this study, we found that HIV infection might not exacerbate COVID-19 severity. Supplementary Information: The online version contains supplementary material available at 10.1007/s44231-022-00018-z.

Bioinformatic analysis of differentially expressed genes and pathways in idiopathic pulmonary fibrosis.

BACKGROUND: Using bioinformatic methods to explore the differentially expressed genes (DEGs) of human idiopathic pulmonary fibrosis (IPF) and to elucidate the pathogenesis of IPF from the genetic level. METHODS: The GSE110147 gene expression profile was downloaded from the GEO database. The data of lung adenocarcinoma (LUAD) samples, lung squamous cell carcinoma (LUSC) samples and normal samples were downloaded from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases. DEGs between IPF patients and healthy donors were analyzed using the GEO2R tool. Use the "clusterprofiler" package in R software to perform gene ontology (GO) and KEGG pathway enrichment analysis, and then perform function annotation and protein-protein interaction (PPI) network construction in the STRING online tool. The Genome Browser tool of the university of california santa cruz (UCSC) online website was used to predict transcription factors (TFs) of genes. In the final, the results were analyzed synthetically. RESULTS: A total of 9,183 DEGs were identified, of which 4,545 genes were down-regulated, and 4638 were up-regulated. MMP1, SPP1, and BPIFB1 were the top three DEGs with the highest significant up-regulation. These DEGs played an important role in the occurrence of IPF through the MAPK (mitogen-activated protein kinase) signaling pathway. Furthermore, 50 DEGs were enriched in the expression of PD-L1 and the PD-1 checkpoint pathway in cancer, of which 11 genes were re-enriched in the pathway of non-small cell lung cancer. The expression of the 11 genes were extensively regulated by CTCFL, SP2 and ZNF341. Most of them were differentially expressed between lung cancers and normal lung tissues. The overall survival (OS) curve of LUAD were significantly stratified by AKT2, KRAS, PIK3R1, meanwhile the OS curve of LUAC was significantly stratified by MAPK3. CONCLUSIONS: Bioinformatics analysis revealed that DEGs including MPP1 might be potential targets and biomarkers of IPF, and the MAPK signaling pathway is related to the occurrence and development of IPF. The development of IPF lung cancer complications may be related to the activation of genes enriched in PD-L1 expression and PD-1 checkpoint pathway, which provides clues to the pathogenesis of IPF combined with lung cancer.

Action of substance P and PAMP(9-20) on different excitation sites of MRGPRX2 induces differences in mast cell activation.

MRGPRX2 on mast cells (MCs) is the target that directly mediates MC activation through the activity of small molecular substances. Previous work has attempted to prove that substance P (SP) and PAMP(9-20) induce an MRGPRX2-mediated MC degranulation reaction. However, SP activates MRGPRX2-induced histamine release, which may lead to allergic airway inflammation, while PAMP(9-20)-induced MrgprB2 activation releases more tryptase and fewer monoamines. Due to the lack of direct available comparisons, the different types of sensitizing mediators released by the action of SP and PAMP(9-20) inducing pseudo-allergic reactions via MRGPRX2 are unclear. To investigate whether the action sites of excited MRGPRX2 are different for SP and PAMP(9-20), leading to different effects, the release of inflammatory mediators was measured using MC degranulation reactions and RNA-seq assay in vitro. Mice were treated to observe local inflammation and MC degranulation in vivo. Moreover, site-directed mutagenesis was used to verify the excited sites of SP and PAMP(9-20). SP and PAMP(9-20) both activated MRGPRX2 and led MCs to release inflammatory mediators. Significantly different levels of histamine, tryptase, TNF-α, MCP-1, and other cytokines were released in vivo and in vitro. G165E, D184N, W243R, and H259Y were necessary for SP to activate MRGPRX2, while only D184N and W243R were important for PAMP(9-20). The downstream signaling pathways activated by SP and PAMP(9-20) also differed in the phosphorylation level of PKC. There were differences in the sites via which SP and PAMP(9-20) activate MRGPRX2 and also in the activated downstream signaling pathways, which led to the differences the activation of the pathways and effects of SP- and PAMP(9-20)-induced MRGPRX2 activation.

Clinical Characteristics and Prognosis of Patients With Pulmonary Mucoepidermoid Carcinoma: A SEER-Based Analysis.

BACKGROUND: Primary pulmonary mucoepidermoid carcinoma (PMEC) is an extremely rare malignancy. Its clinical characteristics and prognosis are not fully understood. This study evaluated clinical characteristics and prognostic factors of PMEC and established a nomogram to predict its 1-, 3-, 5- and 10-year cancer-specific survival (CSS) rates. METHODS: In the Surveillance, Epidemiology, and End Results database from January 1, 2016 to December 31, 2016, patients pathologically diagnosed with PMEC were identified. Kaplan-Meier analysis and Cox regression were performed to evaluate the CSS stratified by different covariates. A predictive nomogram model was built and validated by the concordance index (C-index) and calibration curves. RESULTS: A total of 585 PMEC patients were identified. A total of 408 (70%) of patients were placed into the training cohort, and 177 (30%) patients were placed into the validation cohort. The 5- and 10-year CSS rates of stage I-II PMEC patients were 91.4 and 88.9, respectively. The 1-, 3- and 5-year CSS rates of stage III-IV PMEC were 56.5, 39.45, and 32.1%, respectively. Survival curves showed that older age, large tumor size, poor differentiation, and high TNM stage were associated with a significantly worse prognosis. CSS outcomes were significantly better in patients who received surgical treatments (surgical alone, surgery plus radiation and/or chemotherapy). Patients who received radiation and/or chemotherapy had the worst prognosis. Multivariate Cox results revealed that covariates, including age, tumor laterality, tumor sizes, pathological differentiation, lymph node metastasis, distant metastasis, TNM stage and therapy, were independent prognostic factors for PMEC. These factors were used to construct a nomogram. The C-index of the nomogram was 0.921. The calibration curve presented favorable consistency between the predicted CSS and actual observations. This nomogram was validated by the validation cohort. The C-index of the validation cohort was 0.968. CONCLUSION: Age, bilateral tumors, tumor size, pathological differentiation grade, lymph node metastasis, distant metastasis, TNM stage and therapy were independent prognostic factors of PMEC patients. The first nomogram for predicting the CSS of PMEC was built and validated, showing its potential value in practice.

The efficacy of probiotics in patients with severe COVID-19.

BACKGROUND: To examine the incidence of diarrhea in severe and critical coronavirus disease 2019 (COVID-19) patients, and to observe the efficacy and prognosis of probiotic use in such patients. METHODS: A retrospective study was conducted to investigate the symptoms and incidence of diarrhea in 156 cases of COVID-19 confirmed by the First Affiliated Hospital of Zhengzhou University and the Xinyang Fifth People's Hospital, China. A total of 58 cases of severe and critical COVID-19 were identified and divided into the treatment group or the control group. The control group was given standard treatment according to the Protocols for Diagnosis and Treatment of COVID-19: Prevention, Control, Diagnosis and Management. Patients in the treatment group were administered oral probiotics as well as the standard treatment. The 2 groups were compared in terms of nutritional status (serum albumin), improvement of diarrhea symptoms, changes in inflammatory condition [procalcitonin (PCT) and C-reactive protein (CRP)], the time taken to register a negative result for respiratory tract pathogens on the nucleic acid test, and changes to white blood cell and lymphocyte cell counts. RESULTS: In this study cohort, diarrhea was detected in 15.38% (24/156) of COVID-19 patients. The incidence of diarrhea in patients with mild and moderate COVID-19 was approximately 8.16% (8/98), and the incidence of diarrhea in severe and critically ill patients was approximately 27.59% (16/58). In patients with severe and critical COVID-19, probiotic treatment obviously shortened the duration of diarrhea. Furthermore, compared with the control group, patients treated with probiotics showed a significantly reduced time to achieving a negative nucleic acid test and the inflammation indexes including PCT and CRP were significantly reduced (P<0.05). CONCLUSIONS: The incidence of diarrhea in severe and critically ill COVID-19 patients was significantly higher than that in patients with mild and moderate COVID-19. Probiotics may have a good supporting role in the treatment of patients with COVID-19 and its early application is recommended.

MicroRNA-206 promotes lipopolysaccharide-induced inflammation injury via regulation of IRAK1 in MRC-5 cells.

BACKGROUND: MicroRNAs (miRNAs) have been reported to play crucial role in the airway inflammatory diseases. However, the involvement of miR-206 in airway inflammatory diseases is still uninvestigated. The study aimed to explore the effect of miR-206 on lipopolysaccharide (LPS)-induced inflammation injury in MRC-5 cells, and point out a potential relevance for chronic obstructive pulmonary disease (COPD). METHODS: LPS was utilized to expose MRC-5 cells, then cell viability, cell migration, apoptosis, apoptosis-associated factors, as well as the concentrations and protein levels of IL-6 and IL-8 were explored. After transfected with miR-206 mimic and inhibitor, above parameters were reassessed in LPS-injured cells. Expression level of IRAK1 was examined in miR-206 mimic/inhibitor transfected cells by using RT-qPCR. The effect of IRAK1 on LPS-induced inflammation injury was investigated in MRC-5 cells after transfection with pc-IRAK1 and sh-IRAK1. The effects of miR-206 and IRAK1 on MEK/ERK and JNK pathways were determined by western blot assay. RESULTS: LPS significantly triggered inflammation injury in MRC-5 cells by inhibiting cell viability, suppressing the healing of scratches, inducing cell apoptosis, down-regulating Bcl-2 expression and up-regulating Bax, cleaved-Caspase-3 and cleaved-Caspase-9 expression, and concurrently increasing the concentrations and the protein levels of IL-6 and IL-8. MiR-206 overexpression aggravated LPS-induced inflammation injury in MRC-5 cells. Up-regulation of IRAK1 was observed in miR-206 mimic-transfected cells. Moreover, IRAK1 overexpression promoted LPS-induced inflammation injury in MRC-5 cells. MiR-206 activated MEK/ERK and JNK pathways by regulating IRAK1. CONCLUSIONS: MiR-206 promotes LPS-induced inflammation injury through regulation of IRAK1 in MRC-5 cells.

Avian responses to an extreme ice storm are determined by a combination of functional traits, behavioural adaptations and habitat modifications.

The extent to which species' traits, behavior and habitat synergistically determine their response to extreme weather events (EWE) remains poorly understood. By quantifying bird and vegetation assemblages before and after the 2008 ice storm in China, combined with interspecific interactions and foraging behaviours, we disentangled whether storm influences avian reassembly directly via functional traits (i.e. behavioral adaptations), or indirectly via habitat variations. We found that overall species richness decreased, with 20 species detected exclusively before the storm, and eight species detected exclusively after. These shifts in bird relative abundance were linked to habitat preferences, dietary guild and flocking behaviours. For instance, forest specialists at higher trophic levels (e.g. understory-insectivores, woodpeckers and kingfishers) were especially vulnerable, whereas open-habitat generalists (e.g. bulbuls) were set to benefit from potential habitat homogenization. Alongside population fluctuations, we found that community reassembly can be rapidly adjusted via foraging plasticity (i.e. increased flocking propensity and reduced perching height). And changes in preferred habitat corresponded to a variation in bird assemblages and traits, as represented by intact canopy cover and high density of large trees. Accurate predictions of community responses to EWE are crucial to understanding ecosystem disturbances, thus linking species-oriented traits to a coherent analytical framework.

Effector-induced structural fluctuation regulates the ligand affinity of an allosteric protein: binding of inositol hexaphosphate has distinct dynamic consequences for the T and R states of hemoglobin.

The present study reports distinct dynamic consequences for the T- and R-states of human normal adult hemoglobin (Hb A) due to the binding of a heterotropic allosteric effector, inositol hexaphosphate (IHP). A nuclear magnetic resonance (NMR) technique based on modified transverse relaxation optimized spectroscopy (TROSY) has been used to investigate the effect of conformational exchange of Hb A in both deoxy and CO forms, in the absence and presence of IHP, at 14.1 and 21.1 T, and at 37 degrees C. Our results show that the majority of the polypeptide backbone amino acid residues of deoxy- and carbonmonoxy-forms of Hb A in the absence of IHP is not mobile on the micros-ms time scale, with the exception of several amino acid residues, that is, beta109Val and beta132Lys in deoxy-Hb A, and alpha40Lys in HbCO A. The mobility of alpha40Lys in HbCO A can be explained by the crystallographic data showing that the H-bond between alpha40Lys and beta146His in deoxy-Hb A is absent in HbCO A. However, the conformational exchange of beta109Val, which is located in the intradimer (alpha 1beta 1 or alpha 2beta 2) interface, is not consistent with the crystallographic observations that show rigid packing at this site. IHP binding appears to rigidify alpha40Lys in HbCO A, but does not significantly affect the flexibility of beta109Val in deoxy-Hb A. In the presence of IHP, several amino acid residues, especially those at the interdimer (alpha 1beta 2 or alpha 2beta 1) interface of HbCO A, exhibit significant conformational exchange. The affected residues include the proximal beta92His in the beta-heme pocket, as well as some other residues located in the flexible joint (betaC helix-alphaFG corner) and switch (alphaC helix-betaFG corner) regions that play an important role in the dimer-dimer rotation of Hb during the oxygenation process. These findings suggest that, upon IHP binding, HbCO A undergoes a conformational fluctuation near the R-state but biased toward the T-state, apparently along the trajectory of its allosteric transition, accompanied by structural fluctuations in the heme pocket of the beta-chain. In contrast, no significant perturbation of the dynamic features on the ms-micros time scale has been observed upon IHP binding to deoxy-Hb A. We propose that the allosteric effector-induced quaternary structural fluctuation may contribute to the reduced ligand affinity of ligated hemoglobin. Conformational exchange mapping of the beta-chain of HbCO A observed at 21.1 T shows significantly increased scatter in the chemical exchange contribution to the transverse relaxation rate ( R ex) values, relative to those at lower fields, due to the enhanced effect of the local chemical shift anisotropy (CSA) fluctuation. A spring-on-scissors model is proposed to interpret the dynamic phenomena induced by the heterotropic effector, IHP.

A comparative NMR study of the polypeptide backbone dynamics of hemoglobin in the deoxy and carbonmonoxy forms.

Model-free-based NMR dynamics studies have been undertaken for polypeptide backbone amide N-H bond vectors for both the deoxy and carbonmonoxy forms of chain-specific, isotopically (15N and 2H) labeled tetrameric hemoglobin (Hb) using 15N-relaxation parameters [longitudinal relaxation rate (R1), transverse relaxation rate (R2), and heteronuclear nuclear Overhauser effect (NOE)] measured at two temperatures (29 and 34 degrees C) and two magnetic field strengths (11.7 and 14.1 T). In both deoxy and carbonmonoxy forms of human normal adult hemoglobin (Hb A), the amide N-H bonds of most amino acid residues are rigid on the fast time scale (nanosecond to picosecond), except for the loop regions and certain helix-helix connections. Although rigid in deoxy-Hb A, beta146His has been found to be free from restriction of its backbone motions in the CO form, presumably due to the rupture of its hydrogen bond/salt bridge network. We now have direct dynamics evidence for this structural transition of Hb in solution. While remarkably flexible in the deoxy state, alpha31Arg and beta123Thr, neighbors in the intradimer (alpha1beta1) interface, exhibit stiffening upon CO binding. These findings imply a role for alpha31Arg and beta123Thr in the intradimer communication but contradict the results from X-ray crystallography. We have also found that there is considerable flexibility in the intradimer (alpha1beta1) interface (i.e., B, G, and H helices and the GH corner) and possible involvement of several amino acid residues (e.g., alpha31Arg, beta3Leu, beta41Phe, beta123Thr, and beta146His) in the allosteric pathway. Several amino acid residues at the intradimer interfaces, such as beta109Val, appear to be involved in possible conformational exchange processes. The dynamic picture derived from the present study provides new insights into the traditional description of the stereochemical mechanism for the cooperative oxygenation of Hb A based on X-ray crystallographic results.

Temperature dependence of fast dynamics in proteins.

The temperature dependence of the internal dynamics of recombinant human ubiquitin has been measured using solution NMR relaxation techniques. Nitrogen-15 relaxation has been employed to obtain a measure of the amplitude of subnanosecond motion at amide N-H sites in the protein. Deuterium relaxation has been used to obtain a measure of the amplitude of motion of methyl-groups in amino-acid side chains. Data was obtained between 5 and 55 degrees C. The majority of amide N-H and methyl groups show a roughly linear (R(2)>0.75) temperature dependence of the associated Lipari-Szabo model-free squared generalized-order parameter (O(2)) describing the amplitude of motion. Interestingly, for those sites showing a linear response, the temperature dependence of the backbone is distinct from that of the methyl-bearing side chains with the former being characterized by a significantly larger Lambda-value, where Lambda is defined as d ln(1 - O)/d lnT. These results are comparable to the sole previous such study of the temperature dependence of protein motion obtained for a calmodulin-peptide complex. This suggests that the distinction between the main chain and methyl-bearing side chains may be general. Insight into the temperature dependence is gathered from a simple two-state step potential model.

Nucleotide exchange from the high-affinity ATP-binding site in SecA is the rate-limiting step in the ATPase cycle of the soluble enzyme and occurs through a specialized conformational state.

We have characterized the kinetic and thermodynamic consequences of adenine nucleotide interaction with the low-affinity and high-affinity nucleotide-binding sites in free SecA. ATP binds to the hydrolytically active high-affinity site approximately 3-fold more slowly than ADP when SecA is in its conformational ground state, suggesting that ATP binding probably occurs when the enzyme is in another conformational state during the productive ATPase/transport cycle. The steady-state ATP hydrolysis rate is equivalent to the rate of ADP release from the high-affinity site under a number of conditions, indicating that this process is the rate-limiting step in the ATPase cycle of the free enzyme. Because efficient protein translocation requires at least a 100-fold acceleration in the ATPase rate, the rate-limiting process of ADP release from the high-affinity site is likely to play a controlling role in the conformational reaction cycle of SecA. This release process involves a large enthalpy of activation, suggesting that it involves a protein conformational change, and two observations indicate that this conformational change is different from the well-characterized endothermic conformational transition believed to gate the binding of SecA to SecYEG. First, nucleotide binding to the low-affinity site strongly inhibits the endothermic transition but does not reduce the rate of ADP release. Second, removal of Mg(2+) from an allosteric binding site on SecA does not perturb the endothermic transition but produces a 10-fold acceleration in the rate of ADP release. These divergent effects suggest that a specialized conformational transition mediates the rate-limiting ADP-release process in SecA. Finally, ADP, 2'-O-(N-methylanthraniloyl)-adenosine-5'-diphosphate (MANT-ADP), and adenosine 5'-O-(3-thiotriphosphate) (ATP-gamma-S) bind with similar affinities to the high-affinity site and also to the low-affinity site as inferred from their consistent effects in inhibiting the endothermic transition. In contrast, adenosine 5'-(beta,gamma-imino)triphosphate (AMPPNP) shows 100-fold weaker affinity than ADP for the high-affinity site and no detectable interaction with the low-affinity site at concentrations up to 1 mM, suggesting that this nonhydrolyzable analogue may not be a faithful mimic of ATP in its interactions with SecA.

Temperature dependence of the internal dynamics of a calmodulin-peptide complex.

The temperature dependence of the fast internal dynamics of calcium-saturated calmodulin in complex with a peptide corresponding to the calmodulin-binding domain of the smooth muscle myosin light chain kinase is examined using 15N and 2H NMR relaxation methods. NMR relaxation studies of the complex were carried out at 13 temperatures that span 288-346 K. The dynamics of the backbone and over four dozen methyl-bearing side chains, distributed throughout the calmodulin molecule, were probed. The side chains show a much more variable and often considerably larger response to temperature than the backbone. A significant variation in the temperature dependence of the amplitude of motion of individual side chains is seen. The amplitude of motion of some side chains is essentially temperature-independent while many show a simple roughly linear temperature dependence. In a few cases, angular order increases with temperature, which is interpreted as arising from interactions with neighboring residues. In addition, a number of side chains display a nonlinear temperature dependence. The significance of these and other results is illuminated by several simple interpretative models. Importantly, analysis of these models indicates that changes in generalized order parameters can be robustly related to corresponding changes in residual entropy. A simple cluster model that incorporates features of cooperative or conditional motion reproduces many of the unusual features of the experimentally observed temperature dependence and illustrates that side chain interactions result in a dynamically changing environment that significantly influences the motion of internal side chains. This model also suggests that the intrinsic entropy of interacting clusters of side chains is only modestly reduced from that of independent side chain motion. Finally, estimates of protein heat capacity support the view that the major contribution to the heat capacity of protein solutions largely arises from local bond vibrations and solvent interactions and not from torsional oscillations of side chains.