Structures Of Related Proteins Research Articles

CIUSuite 3: Next-Generation CCS Calibration and Automated Data Analysis Tools for Gas-Phase Protein Unfolding Data.

Ion mobility-mass spectrometry (IM-MS) has become a technology deployed across a wide range of structural biology applications despite the challenges in characterizing closely related protein structures. Collision-induced unfolding (CIU) has emerged as a valuable technique for distinguishing closely related, iso-cross-sectional protein and protein complex ions through their distinct unfolding pathways in the gas phase. With the speed and sensitivity of CIU analyses, there has been a rapid growth of CIU-based assays, especially regarding biomolecular targets that remain challenging to assess and characterize with other structural biology tools. With information-rich CIU data, many software tools have been developed to automate laborious data analysis. However, with the recent development of new IM-MS technologies, such as cyclic IM-MS, CIU continues to evolve, necessitating improved data analysis tools to keep pace with new technologies and facilitating the automation of various data processing tasks. Here, we present CIUSuite 3, a software package that contains updated algorithms that support various IM-MS platforms and supports the automation of various data analysis tasks such as peak detection, multidimensional classification, and collision cross section (CCS) calibration. CIUSuite 3 uses local maxima searches along with peak width and prominence filters to detect peaks to automate CIU data extraction. To support both the primary CIU (CIU1) and secondary CIU (CIU2) experiments enabled by cyclic IM-MS, two-dimensional data preprocessing is deployed, which allows multidimensional classification. Our data suggest that additional dimensions in classification improve the overall accuracy of class assignments. CIUSuite 3 also supports CCS calibration for both traveling wave and drift tube IM-MS, and we demonstrate the accuracy of a new single-field CCS calibration method designed for drift tube IM-MS leveraging calibrant CIU data. Overall, CIUSuite 3 is positioned to support current and next-generation IM-MS and CIU assay development deployed in an automated format.

A Multi-dimensional Review on Severe Acute Respiratory Syndrome Coronavirus-2.

The advent and spread of novel coronavirus (nCoV) has posed a new public health crisis since December 2019. Several cases of unexplained pneumonia occurred in Wuhan, Hubei Province, China, only a month before the Chinese Spring festival. After the diagnosis of bronchoalveolar fluid samples of people infected, the new coronavirus was identified using nextgeneration sequence technology. This work aims to provide information regarding COVID-19 that will help the researchers to identify the vital therapeutic targets for SARS-CoV-2 and also will provide insights into some significant findings of recent times highlighted by scientific communities around the globe. In this review, we have tried to explore multiple aspects related to COVID-19, including epidemiology, etiology, COVID-19 variants, vaccine candidates, potential therapeutic targets, the role of natural products, and computational studies in drug design and development, repurposing, and analysis of crystal structures available for COVID-19 related protein structures. Druggable targets include all viral enzymes and proteins involved in viral replication and regulation of host cellular machines. The medical community tracks several therapies to combat the infection by investigating various antiviral and immunomodulatory mechanisms. While some vaccines are approved in this worldwide health crisis, a more precise therapy or drug is formally recommended to be used against SARS-CoV-2 infection. Natural products other than synthetic drugs have been tested by in silico analysis against COVID-19. However, important issues still need to be addressed regarding in vivo bioavailability and better efficacy.

The actin cytoskeleton: Morphological changes in pre- and fully developed lung cancer.

Actin, a primary component of the cell cytoskeleton can have multiple isoforms, each of which can have specific properties uniquely suited for their purpose. These monomers are then bound together to form polymeric filaments utilizing adenosine triphosphate hydrolysis as a source of energy. Proteins, such as Arp2/3, VASP, formin, profilin, and cofilin, serve important roles in the polymerization process. These filaments can further be linked to form stress fibers by proteins called actin-binding proteins, such as α-actinin, myosin, fascin, filamin, zyxin, and epsin. These stress fibers are responsible for mechanotransduction, maintaining cell shape, cell motility, and intracellular cargo transport. Cancer metastasis, specifically epithelial mesenchymal transition (EMT), which is one of the key steps of the process, is accompanied by the formation of thick stress fibers through the Rho-associated protein kinase, MAPK/ERK, and Wnt pathways. Recently, with the advent of "field cancerization," pre-malignant cells have also been demonstrated to possess stress fibers and related cytoskeletal features. Analytical methods ranging from western blot and RNA-sequencing to cryo-EM and fluorescent imaging have been employed to understand the structure and dynamics of actin and related proteins including polymerization/depolymerization. More recent methods involve quantifying properties of the actin cytoskeleton from fluorescent images and utilizing them to study biological processes, such as EMT. These image analysis approaches exploit the fact that filaments have a unique structure (curvilinear) compared to the noise or other artifacts to separate them. Line segments are extracted from these filament images that have assigned lengths and orientations. Coupling such methods with statistical analysis has resulted in development of a new reporter for EMT in lung cancer cells as well as their drug responses.

Mutations in the monkeypox virus replication complex: Potential contributing factors to the 2022 outbreak

Attributes contributing to the current monkeypox virus (MPXV) outbreak remain unknown. It has been established that mutations in viral proteins may alter phenotype and pathogenicity. To assess if mutations in the MPXV DNA replication complex (RC) contribute to the outbreak, we conducted a temporal analysis of available MPXV sequences to identify mutations, generated a DNA replication complex (RC) using structures of related viral and eukaryotic proteins, and structure prediction method AlphaFold. Ten mutations within the RC were identified and mapped onto the RC to infer role of mutations. Two mutations in F8L (RC catalytic subunit), and two in G9R (a processivity factor) were ∼100% prevalent in the 2022 sequences. F8L mutation L108F emerged in 2022, whereas W411L emerged in 2018, and persisted in 2022. L108 is topologically located to enhance DNA binding affinity of F8L. Therefore, mutation L108F can change the fidelity, sensitivity to nucleoside inhibitors, and processivity of F8L. Surface exposed W411L likely affects the binding of regulatory factor(s). G9R mutations S30L and D88 N in G9R emerged in 2022, and may impact the interaction of G9R with E4R (uracil DNA glycosylase). The remaining six mutations that appeared in 2001, reverted to the first (1965 Rotterdam) isolate. Two nucleoside inhibitors brincidofovir and cidofovir have been approved for MPXV treatment. Cidofovir resistance in vaccinia virus is achieved by A314T and A684V mutations. Both A314 and A684 are conserved in MPXV. Therefore, resistance to these drugs in MPXV may arise through similar mechanisms.

D-StructMAn: Containerized structural annotation on the scale from genetic variants to whole proteomes.

BackgroundStructural annotation of genetic variants in the context of intermolecular interactions and protein stability can shed light onto mechanisms of disease-related phenotypes. Three-dimensional structures of related proteins in complexes with other proteins, nucleic acids, or ligands enrich such functional interpretation, since intermolecular interactions are well conserved in evolution.ResultsWe present d-StructMAn, a novel computational method that enables structural annotation of local genetic variants, such as single-nucleotide variants and in-frame indels, and implements it in a highly efficient and user-friendly tool provided as a Docker container. Using d-StructMAn, we annotated several very large sets of human genetic variants, including all variants from ClinVar and all amino acid positions in the human proteome. We were able to provide annotation for more than 46% of positions in the human proteome representing over 60% proteins.Conclusionsd-StructMAn is the first of its kind and a highly efficient tool for structural annotation of protein-coding genetic variation in the context of observed and potential intermolecular interactions. d-StructMAn is readily applicable to proteome-scale datasets and can be an instrumental building machine-learning tool for predicting genotype-to-phenotype relationships.

PCN-Miner: an open-source extensible tool for the analysis of Protein Contact Networks.

Protein Contact Network (PCN) is a powerful method for analysing the structure and function of proteins, with a specific focus on disclosing the molecular features of allosteric regulation through the discovery of modular substructures. The importance of PCN analysis has been shown in many contexts, such as the analysis of SARS-CoV-2 Spike protein and its complexes with the Angiotensin Converting Enzyme 2 (ACE2) human receptors. Even if there exist many software tools implementing such methods, there is a growing need for the introduction of tools integrating existing approaches. We present PCN-Miner, a software tool implemented in the Python programming language, able to (i) import protein structures from the Protein Data Bank; (ii) generate the corresponding PCN; (iii) model, analyse and visualize PCNs and related protein structures by using a set of known algorithms and metrics. The PCN-Miner can cover a large set of applications: from clustering to embedding and subsequent analysis. The PCN-Miner tool is freely available at the following GitHub repository: https://github.com/hguzzi/ProteinContactNetworks. It is also available in the Python Package Index (PyPI) repository.

The Role of Mitochondrial Dynamin in Stroke.

Stroke is one of the leading causes of death and disability in the world. However, the pathophysiological process of stroke is still not fully clarified. Mitochondria play an important role in promoting nerve survival and are an important drug target for the treatment of stroke. Mitochondrial dysfunction is one of the hallmarks of stroke. Mitochondria are in a state of continuous fission and fusion, which are termed as mitochondrial dynamics. Mitochondrial dynamics are very important for maintaining various functions of mitochondria. In this review, we will introduce the structure and functions of mitochondrial fission and fusion related proteins and discuss their role in the pathophysiologic process of stroke. A better understanding of mitochondrial dynamin in stroke will pave way for the development of new therapeutic options.

3DLigandSite: structure-based prediction of protein-ligand binding sites.

3DLigandSite is a web tool for the prediction of ligand-binding sites in proteins. Here, we report a significant update since the first release of 3DLigandSite in 2010. The overall methodology remains the same, with candidate binding sites in proteins inferred using known binding sites in related protein structures as templates. However, the initial structural modelling step now uses the newly available structures from the AlphaFold database or alternatively Phyre2 when AlphaFold structures are not available. Further, a sequence-based search using HHSearch has been introduced to identify template structures with bound ligands that are used to infer the ligand-binding residues in the query protein. Finally, we introduced a machine learning element as the final prediction step, which improves the accuracy of predictions and provides a confidence score for each residue predicted to be part of a binding site. Validation of 3DLigandSite on a set of 6416 binding sites obtained 92% recall at 75% precision for non-metal binding sites and 52% recall at 75% precision for metal binding sites. 3DLigandSite is available at https://www.wass-michaelislab.org/3dligandsite. Users submit either a protein sequence or structure. Results are displayed in multiple formats including an interactive Mol* molecular visualization of the protein and the predicted binding sites.

Determination of the Amino Acid Recruitment Order in Early Life by Genome-Wide Analysis of Amino Acid Usage Bias.

The mechanisms shaping the amino acids recruitment pattern into the proteins in the early life history presently remains a huge mystery. In this study, we conducted genome-wide analyses of amino acids usage and genetic codons structure in 7270 species across three domains of life. The carried-out analyses evidenced ubiquitous usage bias of amino acids that were likely independent from codon usage bias. Taking advantage of codon usage bias, we performed pseudotime analysis to re-determine the chronological order of the species emergence, which inspired a new species relationship by tracing the imprint of codon usage evolution. Furthermore, the multidimensional data integration showed that the amino acids A, D, E, G, L, P, R, S, T and V might be the first recruited into the last universal common ancestry (LUCA) proteins. The data analysis also indicated that the remaining amino acids most probably were gradually incorporated into proteogenesis process in the course of two long-timescale parallel evolutionary routes: I→F→Y→C→M→W and K→N→Q→H. This study provides new insight into the origin of life, particularly in terms of the basic protein composition of early life. Our work provides crucial information that will help in a further understanding of protein structure and function in relation to their evolutionary history.

The role of MOZ/KAT6A in hematological malignancies and advances in MOZ/KAT6A inhibitors

Hematological malignancies, unlike solid tumors, are a group of malignancies caused by abnormal differentiation of hematopoietic stem cells. Monocytic leukemia zinc finger protein (MOZ), a member of the MYST (MOZ, Ybf2/Sas3, Sas2, Tip60) family, is a histone acetyltransferase. MOZ is involved in various cellular functions: generation and maintenance of hematopoietic stem cells, development of erythroid cells, B-lineage progenitors and myeloid cells, and regulation of cellular senescence. Studies have shown that MOZ is susceptible to translocation in chromosomal rearrangements to form fusion genes, leading to the fusion of MOZ with other cellular regulators to form MOZ fusion proteins. Different MOZ fusion proteins have different roles, such as in the development and progression of hematological malignancies and inhibition of cellular senescence. Thus, MOZ is an attractive target, and targeting MOZ to design small-molecule drugs can help to treat hematological malignancies. This review summarizes recent progress in biology and medicinal chemistry for the histone acetyltransferase MOZ. In the biology section, MOZ and cofactors, structures of MOZ and related HATs, MOZ and fusion proteins, and roles of MOZ in cancer are discussed. In medicinal chemistry, recent developments in MOZ inhibitors are summarized.

An injectable hydrogel to reverse the adverse microenvironment of diabetic infarcted heart

A library of injectable hydrogels shows the promising outcomes to restore an infarcted heart. However, none of them has been designed to meet diabetic patients. Here, a proof-of-concept research to build an injectable hydrogel to reverse the adverse microenvironment of injured diabetic hearts is reported. A hyper-branched poly (beta amino ester) polymer is abundant in acrylate and phenylboronic acid (PAE-PBA) to achieve a fast crosslinking with thiolated hyaluronic acid (HA-SH) and form a dynamic complexing with the targeted drug. Andrographolide nanoparticles (ADG NPs) to inhibit the over-expressing inflammatory factors and supramolecular nanofibers (IGF-1-F) with a superior bioactivity to insulin-like growth factor 1 (IGF-1) to regulate autophagy and apoptosis are conveniently encapsulated into the hydrogels. After being administered in diabetic infarcted rat hearts, the dynamic borate bond between PBA and ADG were broken and the hydrogel were degraded, accompanying with a controllable release of ADG and IGF-1-F. This functional hydrogel contributed to a remarkable decrease in the expression of inflammatory factors, a sharp inhibition of the infaust autophagy and apoptosis, and an obvious promotion in angiogenesis, demonstrating a strong capability to reverse the adverse microenvironments. Meanwhile, the infarcted area and the fibrosis area were reduced by 17.9% and 33.5%, respectively, accompanying with a high expression of cardiac related protein and well-ordered histological structures, suggesting a favorable restoration in the heart functions. This research presents the first try to explore an injectable hydrogel to reverse the villainous microenvironments of a diabetic infarcted heart, showing prominent implications in myocardial tissue engineering.

Interactive learning modules with 3D printed models improve student understanding of protein structure-function relationships.

Ensuring undergraduate students become proficient in relating protein structure to biological function has important implications. With current two-dimensional (2D) methods of teaching, students frequently develop misconceptions, including that proteins contain a lot of empty space, that bond angles for different amino acids can rotate equally, and that product inhibition is equivalent to allostery. To help students translate 2D images to 3D molecules and assign biochemical meaning to physical structures, we designed three 3D learning modules consisting of interactive activities with 3D printed models for amino acids, proteins, and allosteric regulation with coordinating pre- and post-assessments. Module implementation resulted in normalized learning gains on module-based assessments of 30% compared to 17% in a no-module course and normalized learning gains on a comprehensive assessment of 19% compared to 3% in a no-module course. This suggests that interacting with these modules helps students develop an improved ability to visualize and retain molecular structure and function.

Participation of the IL-10RB Related Cytokines, IL-22 and IFN-λ in Defense of the Airway Mucosal Barrier.

The airway epithelial barrier is a major barrier protecting against clinically significant infections of the lung. Its integrity is often compromised due to mechanical, chemical, or infectious causes. Opportunistic bacterial pathogens are poised to cause parenchymal infection and become difficult to eradicate due to adaptive metabolic changes, biofilm formation, and the acquisition of antimicrobial resistance and fitness genes. Enhancing mucosal defenses by modulating the cytokines that regulate barrier functions, such as interleukin-22 (IL-22) and interferon-λ (IFN-λ), members of the IL-10 family of cytokines, is an attractive approach to prevent these infections that are associated with high morbidity and mortality. These cytokines both signal through the cognate receptor IL-10RB, have related protein structures and common downstream signaling suggesting shared roles in host respiratory defense. They are typically co-expressed in multiple models of infections, but with differing kinetics. IL-22 has an important role in the producing antimicrobial peptides, upregulating expression of junctional proteins in the airway epithelium and working in concert with other inflammatory cytokines such as IL-17. Conversely, IFN-λ, a potent antiviral in influenza infection with pro-inflammatory properties, appears to decrease junctional integrity allowing for bacterial and immune cell translocation. The effects of these cytokines are pleotropic, with pathogen and tissue specific consequences. Understanding how these cytokines work in the mucosal defenses of the respiratory system may suggest potential targets to prevent invasive infections of the damaged lung.

Effect of ultrasound and microwave processing on the structure, in-vitro digestibility and trypsin inhibitor activity of soymilk proteins

Soymilk is becoming popular worldwide due to its nutritional benefits and the increasing demand for plant-based alternatives for cow's milk resulting from lactose intolerance and dairy allergy. However, soymilk proteins have a lower digestibility and contain higher anti-nutrients compared to dairy proteins. In the present study, ultrasound (25 kHz, 400 W, 1–16 min) and microwave (2450 MHz, 70–100 °C, 2–10 min) treatment were applied to evaluate the relationship between conformational changes and in vitro protein digestibility (IVPD) of soymilk proteins as well as the changes of trypsin inhibitors activity. The results revealed that ultrasonication significantly reduced trypsin inhibitor activity up to 52% and improved the digestibility of proteins in soymilk. The digestibility of soymilk significantly increased up to 93% after 10-min microwave processing at 85 °C compared to the untreated samples. Further, a significant loss in α-helix and an increase of β-sheet in the soymilk proteins was observed in ultrasound (16 min) and microwave treatments at 85 °C. The findings of this study demonstrate that ultrasonication and microwave processing showed potential applications in the reduction of trypsin inhibitors activity and improving the digestibility of soymilk through changing the secondary structures of related proteins.

P0539NICOTIFLORIN ATTENUATES RENAL ISCHEMIA/REPERFUSION INJURY THROUGH REDUCING CELL APOPTOSIS

Abstract Background and Aims Renal ischemia/reperfusion (I/R) is the main cause for acute kidney injury, Nicotiflorin can ameliorate ischemia/reperfusion injury in other organs, just like in cerebral ischemic damage. Therefore, this article intends to explore whether Nicotiflorin has protective effects on renal tubular epithelial cell after ischemia-reperfusion. On the one hand, We use C57 mice to establish the Nicotiflorin group, DMSO group, AKI group, sham group and control group to investigate whether Nicotiflorin can ameliorate ischemia-reperfusion injury of kidney. In other hand, we use CCK8 to explore the optimal concentration of Nicotiflorin in renal tubular epithelial cells and find optimal hypoxia oxygenation time, in order to analysis the influence of Nicotiflorin. The results indicate that Nicotiflorin can alleviate ischemia-reperfusion injury by reducing apoptosis of renal tubular epithelial cells. Method In this study, we investigated the protective mechanism of Nicotiflorin on ischemic acute kidney injury by analyzing gene chip in patients with acute kidney injury and proving in vitro and in vivo experiments. The main methods are as follows: (1) Multiple nucleus ischemia-reperfusion model transcriptase data were selected from the NCBI GEO Datasets database and analyzed to screen out related proteins that may be involved in ischemia-reperfusion kidney injury; (2) The tertiary structure of Nicotiflorin and related proteins was obtained from the SWISS-MODEL database and the PubChem compound database. The molecular docking between protein and Nicotiflorin was performed using Autodock software, and the binding energy between Nicotiflorin and the selected protein was analyzed to determine Nicotiflorin binds to each other; (3) We set different groups, such as control group, sham group, AKI group, Nicotiflorin group and DMSO group in animals. The blood function was used to detect renal injury related function indicators 24 hours after modeling. Renal tissue samples were collected for real-time fluorescent RT-PCR, Western blotting and histopathological analysis; (4)Renal tubular epithelial cells were treated with different concentrations of Nicotiflorin, CCK8 was screened for the most appropriate concentration, and the hypoxic and reoxygenated cells were intervened at the concentration to explore the interaction between Nicotiflorin and the docking protein, and to observe the protective mechanism of Nicotiflorin on the kidney Results Conclusion Nicotiflorin binds to ATF3 and promotes the expression of Cyr61 through protein interactions to improve renal ischemia-reperfusion injury.

Structure modeling of γ-aminobutyric acid transporters – Molecular basics of ligand selectivity

γ-Aminobutyric acid transporters are responsible for regulating the GABA level in the synaptic cleft. In this way, they affect GABA-ergic transmission which is important for the proper functioning of the central nervous system. The exact structure of GABA transporters is still unknown, which hinders the design of new, potent and selective inhibitors. For these reasons, we decided to create models of all types of human gamma-aminobutyric acid transporters. They were built based on crystal structures of related proteins from the SLC6 family using homology modeling methods. The reliability of the received models has been confirmed by a number of tools assessing the quality of protein models. To determine the ligand binding mode and indicate the amino acids responsible for selectivity, docking studies and molecular dynamics simulations were performed. The amino acids lining the bottom of the main binding site have a major impact on the selective ligand binding. In addition, an important element is the non-helical fragment of the transmembrane domain 10, and several amino acids within the vestibule of the transporters, which affect its volume. To check whether obtained models are suitable to distinguish active compounds from inactive ones, enrichment plots were prepared. Results suggest that our models may be useful in the search for new inhibitors of GABA transporters of the desired selectivity.

X‐ray Crystal Structure of Agmatinase from Escherichia coli

Agmatinase acts upon the cellular metabolite agmatine to produce putrescine, an important precursor for higher‐order polyamines that are required for cell proliferation, differentiation, and migration. The activity of agmatinase and the role of agmatine have garnered attention due to the importance of agmatine in various medical contexts including: neurological disorders, a possible role for agmatine as a neurotransmitter/neuromodulator, treatment of depression, and even the proposal that the family of metallohydrolases that include agmatinase may find novel biotechnological applications. Here we report the crystal structure of Escherichia coli agmatinase. The structure of E. coli agmatinase exhibits global fold and active site architecture typical of the metal‐dependent ureohydrolase protein superfamily. Moreover, the arrangement of conserved metal ligands and electron density at the active site indicate the presence of two metal ions, which is consistent with reported literature finding E. coli agmatinase to require two Mn2+ ions. Comparisons with the structures of related proteins will be described, along with functional characterization of agmatinase in terms of both enzymatic activity, as well as the requirement and identity of metal ions.

Two independent routes of post-translational chemistry in fluorescent protein FusionRed

The crystal structure of monomeric red fluorescent protein FusionRed (λex/λem 580/608 mn) has been determined at 1.09 Å resolution and revealed two alternative routes of post-translational chemistry, resulting in distinctly different products. The refinement occupancies suggest the 60:40 ratio of the mature Met63-Tyr64-Gly65 chromophore and uncyclized chromophore-forming tripeptide with the protein backbone cleaved between Met63 and the preceding Phe62 and oxidized Cα-Cβ bond of Tyr64. We analyzed the structures of FusionRed and several related red fluorescent proteins, identified structural elements causing hydrolysis of the peptide bond, and verified their impact by single point mutagenesis. These findings advance the understanding of the post-translational chemistry of GFP-like fluorescent proteins beyond the canonical cyclization-dehydration-oxidation mechanism. They also show that impaired cyclization does not prevent chromophore-forming tripeptide from further transformations enabled by the same set of catalytic residues. Our mutagenesis efforts resulted in inhibition of the peptide backbone cleavage, and a FusionRed variant with ~30% improved effective brightness.

Influence of acupuncture plus moxibustion on changes of synaptic structure and expression of synaptic skeleton related genes and proteins in prefrontal cortex of heroin re-addicted rats

To observe the effect of acupuncture plus moxibustion on the synaptic ultrastructure and expression of synaptic skeleton related proteins in the prefrontal cortex (PFC) of heroin re-addicted rats, so as to reveal its mechanisms underlying improvement of heroin addiction. Twenty-four Wister rats (half male and half female) were randomly divi-ded into normal control, model and acupuncture groups (n＝8 in each group). The heroin re-addicted model was established by muscular injection of heroin into the hind limbs for 8 days (incremental 0.8-3.6 mg, once daily for 6 days, and twice daily for 2 days), followed by conventional breeding for 5 days (detoxification), the procedure (addition－detoxification) was repeated 3 cycles. For rats of the acupuncture group, "Baihui" (GV20) was needled with filiform needles which were retained for 30 min, and moxibustion was then applied to bilateral "Shenshu" (BL23) for 30 min. The treatment was conducted once daily during the deto-xification. On the 39th day of experiment, the bilateral prefrontal cortex tissues were sampled for examining the ultrastructure by using transmission electron microscope (TEM) after fixative solution immersion and for determining the expression of genes and proteins of activity-regulated cytoskeleton-associated protein (Arc), microtubule-asso-ciated protein-2 (MAP-2) and microtubule-associated protein Tau (Tau) with quantitative real-time PCR and Western blot, respectively. After modeling, the expression levels of Arc mRNA and protein were significantly up-regulated, and those of MAP-2 and Tau mRNA and proteins ob-viously down-regulated in the model group relevant to the normal control group (P<0.05). Following the intervention, the up-regulated Arc protein and mRNA and the down-regulated MAP-2 and Tau were obviously reversed relevant to the model group (P<0.05). Outcomes of TEM showed unclear pre- and post-membranes of the synapses, narrowing of the synaptic gap and non-uniform of the density of the thickened dense plaque after modeling, which was relatively milder in the acupuncture group. Acupuncture plus moxibustion can improve changes of synaptic ultrastructure in heroin re-addicted rats, which may be related to their effect in regulating the expression of some synaptic skeleton proteins and genes.

Crystal structures of a putative periplasmic cystine-binding protein from Candidatus Liberibacter asiaticus: insights into an adapted mechanism of ligand binding.

The amino acid-binding receptors, a component of ABC transporters, have evolved to cater to different specificities and functions. Of particular interest are cystine-binding receptors, which have shown broad specificity. In the present study, a putative periplasmic cystine-binding protein from Candidatus Liberibacter asiaticus (CLasTcyA) was characterized. Analysis of the CLasTcyA sequence and crystal structures in the ligand-bound state revealed novel features of CLasTcyA in comparison to related proteins. One of the unique features found in CLasTcyA structure was the positioning of the C-terminal extended loop of one chain very close to the substrate-binding site of the adjacent monomer in the asymmetric unit. The presence of a disulphide bond, unique to Candidatus Liberibacter family, holds the C-terminal extended loop in position. Analysis of the substrate-binding pocket of CLasTcyA suggested a broad specificity and a completely different orientation of the bound substrates in comparison to related protein structures. The open conformation for one of the two chains of the asymmetric unit in the Arg-bound structure revealed a limited open state (18.4°) for CLasTcyA as compared to open state of other related proteins (~60°). The strong interaction between Asp126 on helix-α5 of small domain and Arg82 (bigger domain) restricts the degree of opening in ligand-free open state. The dissociation constant of 1.26μm by SPR and 3.7μm by MST exhibited low affinity for the cystine. This is the first structural characterization of an l-cystine ABC transporter from plant pathogen and our results suggest that CLasTcyA may have evolved to cater to its specific needs for its survival in the host.