keyword
https://read.qxmd.com/read/37777712/dgdta-dynamic-graph-attention-network-for-predicting-drug-target-binding-affinity
#21
JOURNAL ARTICLE
Haixia Zhai, Hongli Hou, Junwei Luo, Xiaoyan Liu, Zhengjiang Wu, Junfeng Wang
BACKGROUND: Obtaining accurate drug-target binding affinity (DTA) information is significant for drug discovery and drug repositioning. Although some methods have been proposed for predicting DTA, the features of proteins and drugs still need to be further analyzed. Recently, deep learning has been successfully used in many fields. Hence, designing a more effective deep learning method for predicting DTA remains attractive. RESULTS: Dynamic graph DTA (DGDTA), which uses a dynamic graph attention network combined with a bidirectional long short-term memory (Bi-LSTM) network to predict DTA is proposed in this paper...
September 30, 2023: BMC Bioinformatics
https://read.qxmd.com/read/37770930/integrin-signaling-in-cancer-bidirectional-mechanisms-and-therapeutic-opportunities
#22
REVIEW
Siyi Li, Chibuzo Sampson, Changhao Liu, Hai-Long Piao, Hong-Xu Liu
Integrins are transmembrane receptors that possess distinct ligand-binding specificities in the extracellular domain and signaling properties in the cytoplasmic domain. While most integrins have a short cytoplasmic tail, integrin β4 has a long cytoplasmic tail that can indirectly interact with the actin cytoskeleton. Additionally, 'inside-out' signals can induce integrins to adopt a high-affinity extended conformation for their appropriate ligands. These properties enable integrins to transmit bidirectional cellular signals, making it a critical regulator of various biological processes...
September 28, 2023: Cell Communication and Signaling: CCS
https://read.qxmd.com/read/37737847/bidirectional-charge-transfer-at-the-heme-iron-in-reversible-and-quasi-irreversible-cytochrome-p450-inhibition
#23
JOURNAL ARTICLE
Hajime Hirao, Enhua Zhang
The coordination bonding between inhibitor ligands and heme iron plays a critical role in disrupting the essential catalytic functions of cytochrome P450 enzymes (P450s). Despite its intrinsic importance and consequential implications for human health, our current understanding of coordination bonding in P450 inhibition remains limited. To address this knowledge gap, we conducted a systematic theoretical analysis of the complexes between a ferric or a ferrous heme model and representative inhibitor ligands...
September 22, 2023: Inorganic Chemistry
https://read.qxmd.com/read/37737630/iron-ions-regulate-antifungal-hsaf-biosynthesis-in-lysobacter-enzymogenes-by-manipulating-the-dna-binding-affinity-of-the-ferric-uptake-regulator-fur
#24
JOURNAL ARTICLE
Bao Tang, Bo Wang, Zhizhou Xu, Rouxian Hou, Min Zhang, Xian Chen, Youzhou Liu, Fengquan Liu
Heat-stable antifungal factor (HSAF), produced by Lysobacter enzymogenes OH11, is regarded as a potential biological pesticide due to its broad-spectrum antifungal activity and novel mode of action. However, the current production of HSAF is low and cannot meet the requirements for large-scale production. Herein, we discovered that iron ions greatly promoted HSAF production, and the ferric uptake regulator (Fur) was involved in this regulatory process. Fur was also found to participate in the regulation of iron homeostasis in OH11 via the classic inhibition mechanism of Holo -Fur...
September 22, 2023: Microbiology Spectrum
https://read.qxmd.com/read/37669908/engineered-dnazyme-enables-homogeneous-detection-of-cereulide-via-polychromic-fluorescence-modality
#25
JOURNAL ARTICLE
Jingnan Meng, Haoran Shen, Lin Luo, Xi Zeng, Juan Wang, Yingju Liu, Zhen-Lin Xu
Cereulide, the exotoxin of emetic Bacillus cereus , has garnered considerable attention due to its capacity to produce foodborne poisonings and great chemical stability. Herein, a G-quadruplex-hemin DNAzyme-based biosensor was developed to detect cereulide in the homogeneous solution. Due to the special ring structure and high affinity to K+ , cereulide can be attracted and intercalated into the G-quadruplex; thus, the properties of the G4 DNAzyme can be altered. The melting temperature ( T m ) of the G4 DNAzyme in the presence or absence of cereulide was 58...
September 5, 2023: Analytical Chemistry
https://read.qxmd.com/read/37633566/legionella-pneumophila-macrophage-infectivity-potentiator-protein-appendage-domains-modulate-protein-dynamics-and-inhibitor-binding
#26
JOURNAL ARTICLE
C Wiedemann, J J Whittaker, V H Pérez Carrillo, B Goretzki, M Dajka, F Tebbe, J-M Harder, P R Krajczy, B Joseph, F Hausch, A Guskov, U A Hellmich
Macrophage infectivity potentiator (MIP) proteins are widespread in human pathogens including Legionella pneumophila, the causative agent of Legionnaires' disease and protozoans such as Trypanosoma cruzi. All MIP proteins contain a FKBP (FK506 binding protein)-like prolyl-cis/trans-isomerase domain that hence presents an attractive drug target. Some MIPs such as the Legionella pneumophila protein (LpMIP) have additional appendage domains of mostly unknown function. In full-length, homodimeric LpMIP, the N-terminal dimerization domain is linked to the FKBP-like domain via a long, free-standing stalk helix...
August 24, 2023: International Journal of Biological Macromolecules
https://read.qxmd.com/read/37622838/vanadium-as-auxiliary-for-fe-v-dual-atom-electrocatalyst-in-lithium-sulfur-batteries-3d-in-2d-morphology-inducer-and-coordination-structure-regulator
#27
JOURNAL ARTICLE
Lubin Yang, Yukun Pan, Zhiqiang Zhou, Yongzheng Zhang, Jie Xu, Cheng Ma, Yayun Zhang, Jitong Wang, Wenming Qiao, Licheng Ling
The undesirable shuttling behavior, the sluggish redox kinetics of liquid-solid transformation, and the large energy barrier for decomposition of Li2 S have been the recognized problems impeding the practical application of lithium-sulfur batteries. Herein, inspired by the spectacular catalytic activity of the Fe/V center in bioenzyme for nitrogen/sulfur fixation, we design an integrated electrocatalyst comprising N-bridged Fe-V dual-atom active sites (Fe/V-N7 ) dispersed on ingenious "3D in 2D" carbon nanosheets (denoted as DAC), in which vanadium induces the laminar structure and regulates the coordination configuration of active centers simultaneously, realizing the redistribution of the 3d-orbital electrons of Fe centers...
August 25, 2023: ACS Nano
https://read.qxmd.com/read/37463200/changing-protein-dna-interactions-promote-orc-binding-site-exchange-during-replication-origin-licensing
#28
JOURNAL ARTICLE
Annie Zhang, Larry J Friedman, Jeff Gelles, Stephen P Bell
During origin licensing, the eukaryotic replicative helicase Mcm2-7 forms head-to-head double hexamers to prime origins for bidirectional replication. Recent single-molecule and structural studies revealed that one molecule of the helicase loader ORC (origin recognition complex) can sequentially load two Mcm2-7 hexamers to ensure proper head-to-head helicase alignment. To perform this task, ORC must release from its initial high-affinity DNA-binding site and "flip" to bind a weaker, inverted DNA site. However, the mechanism of this binding-site switch remains unclear...
July 25, 2023: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/37443315/cryo-em-structures-of-full-length-integrin-%C3%AE-iib%C3%AE-3-in-native-lipids
#29
JOURNAL ARTICLE
Brian D Adair, Jian-Ping Xiong, Mark Yeager, M Amin Arnaout
Platelet integrin αIIbβ3 is maintained in a bent inactive state (low affinity to physiologic ligand), but can rapidly switch to a ligand-competent (high-affinity) state in response to intracellular signals ("inside-out" activation). Once bound, ligands drive proadhesive "outside-in" signaling. Anti-αIIbβ3 drugs like eptifibatide can engage the inactive integrin directly, inhibiting thrombosis but inadvertently impairing αIIbβ3 hemostatic functions. Bidirectional αIIbβ3 signaling is mediated by reorganization of the associated αIIb and β3 transmembrane α-helices, but the underlying changes remain poorly defined absent the structure of the full-length receptor...
July 13, 2023: Nature Communications
https://read.qxmd.com/read/37405648/a-two-step-golden-gate-cloning-procedure-for-the-generation-of-natively-paired-ysd-fab-libraries
#30
JOURNAL ARTICLE
Lena Vollmer, Simon Krah, Stefan Zielonka, Desislava Yanakieva
In vitro antibody display libraries have emerged as powerful tools for a streamlined discovery of novel antibody binders. While in vivo antibody repertoires are matured and selected as a specific pair of variable heavy and light chains (VH and VL) with optimal specificity and affinity, during the recombinant generation of in vitro libraries, the native sequence pairing is not maintained. Here we describe a cloning method that combines the flexibility and versatility of in vitro antibody display with the advantages of natively paired VH-VL antibodies...
2023: Methods in Molecular Biology
https://read.qxmd.com/read/37398123/changing-protein-dna-interactions-promote-orc-binding-site-exchange-during-replication-origin-licensing
#31
Annie Zhang, Larry J Friedman, Jeff Gelles, Stephen P Bell
UNLABELLED: During origin licensing, the eukaryotic replicative helicase Mcm2-7 forms head-to-head double hexamers to prime origins for bidirectional replication. Recent single-molecule and structural studies revealed that one molecule of the helicase loader ORC can sequentially load two Mcm2-7 hexamers to ensure proper head-to-head helicase alignment. To perform this task, ORC must release from its initial high-affinity DNA binding site and "flip" to bind a weaker, inverted DNA site...
June 16, 2023: bioRxiv
https://read.qxmd.com/read/37267105/distinct-bidirectional-regulation-of-lfa1-and-%C3%AE-4%C3%AE-7-by-rap1-and-integrin-adaptors-in-t%C3%A2-cells-under-shear-flow
#32
JOURNAL ARTICLE
Yuji Kamioka, Yoshihiro Ueda, Naoyuki Kondo, Keizo Tokuhiro, Yoshiki Ikeda, Wolfgang Bergmeier, Tatsuo Kinashi
Bidirectional control of integrin activation plays crucial roles in cell adhesive behaviors, but how integrins are specifically regulated by inside-out and outside-in signaling has not been fully understood. Here, we report distinct bidirectional regulation of major lymphocyte homing receptors LFA1 and α4β7 in primary T cells. A small increase of Rap1 activation in L-selectin-mediated tether/rolling was boosted by the outside-in signaling from ICAM1-interacting LFA1 through subsecond, simultaneous activation of Rap1 GTPase and talin1, but not kindlin-3, resulting in increased capture and slowing...
June 1, 2023: Cell Reports
https://read.qxmd.com/read/37215084/fhods-nuclear-tethered-formins-for-nuclear-mechanotransduction
#33
REVIEW
Susumu Antoku, Thomas U Schwartz, Gregg G Gundersen
In this review, we discuss FHOD formins with a focus on recent studies that reveal a new role for them as critical links for nuclear mechanotransduction. The FHOD family in vertebrates comprises two structurally related proteins, FHOD1 and FHOD3 . Their similar biochemical properties suggest overlapping and redundant functions. FHOD1 is widely expressed, FHOD3 less so, with highest expression in skeletal ( FHOD1 ) and cardiac ( FHOD3 ) muscle where specific splice isoforms are expressed. Unlike other formins, FHODs have strong F-actin bundling activity and relatively weak actin polymerization activity...
2023: Frontiers in Cell and Developmental Biology
https://read.qxmd.com/read/37147776/furnishing-continuous-efficient-bidirectional-polysulfide-conversion-for-long-life-and-high-loading-lithium-sulfur-batteries-via-the-built-in-electric-field
#34
JOURNAL ARTICLE
Yilun Ren, Yujie Ma, Biao Wang, Shaozhong Chang, Qingxi Zhai, Hao Wu, Yuming Dai, Yurong Yang, Shaochun Tang, Xiangkang Meng
Most catalysts cannot accelerate uninterrupted conversion of polysulfides, resulting in poor long-cycle and high-loading performance of lithium-sulfur (Li-S) batteries. Herein, rich p-n junction CoS2 /ZnS heterostructures embedded on N-doped carbon nanosheets are fabricated by ion-etching and vulcanization as a continuous and efficient bidirectional catalyst. The p-n junction built-in electric field in the CoS2 /ZnS heterostructure not only accelerates the transformation of lithium polysulfides (LiPSs), but also promotes the diffusion and decomposition for Li2 S the from CoS2 to ZnS avoiding the aggregation of lithium sulfide (Li2 S)...
May 5, 2023: Small
https://read.qxmd.com/read/37125765/atomically-dispersed-fe-n-4-and-ni-n-4-independent-sites-enable-bidirectional-sulfur-redox-electrocatalysis
#35
JOURNAL ARTICLE
Jin-Lin Yang, Peihua Yang, Da-Qian Cai, Zhe Wang, Hong Jin Fan
Single-atom catalysts (SACs) with high atom utilization and outstanding catalytic selectivity are useful for improving battery performance. Herein, atomically dispersed Ni-N4 and Fe-N4 dual sites coanchored on porous hollow carbon nanocages (Ni-Fe-NC) are fabricated and deployed as the sulfur host for Li-S battery. The hollow and conductive carbon matrix promotes electron transfer and also accommodates volume fluctuation during cycling. Notably, the high d band center of Fe in Fe-N4 site demonstrates strong polysulfide affinity, leading to an accelerated sulfur reduction reaction...
April 26, 2023: Nano Letters
https://read.qxmd.com/read/36939283/chronic-basal-forebrain-activation-improves-spatial-memory-boosts-neurotrophin-receptor-expression-and-lowers-bace1-and-a%C3%AE-42-levels-in-the-cerebral-cortex-in-mice
#36
JOURNAL ARTICLE
Jacob Kumro, Ashutosh Tripathi, Yun Lei, Jeremy Sword, Patrick Callahan, Alvin Terry, Xin-Yun Lu, Sergei A Kirov, Anilkumar Pillai, David T Blake
The etiology of Alzheimer's dementia has been hypothesized in terms of basal forebrain cholinergic decline, and in terms of reflecting beta-amyloid neuropathology. To study these different biological elements, we activated the basal forebrain in 5xFAD Alzheimer's model mice and littermates. Mice received 5 months of 1 h per day intermittent stimulation of the basal forebrain, which includes cholinergic projections to the cortical mantle. Then, mice were behaviorally tested followed by tissue analysis. The 5xFAD mice performed worse in water-maze testing than littermates...
March 20, 2023: Cerebral Cortex
https://read.qxmd.com/read/36869836/scgad-a-new-task-and-end-to-end-framework-for-generalized-cell-type-annotation-and-discovery
#37
JOURNAL ARTICLE
Yuyao Zhai, Liang Chen, Minghua Deng
The rapid development of single-cell RNA sequencing (scRNA-seq) technology allows us to study gene expression heterogeneity at the cellular level. Cell annotation is the basis for subsequent downstream analysis in single-cell data mining. As more and more well-annotated scRNA-seq reference data become available, many automatic annotation methods have sprung up in order to simplify the cell annotation process on unlabeled target data. However, existing methods rarely explore the fine-grained semantic knowledge of novel cell types absent from the reference data, and they are usually susceptible to batch effects on the classification of seen cell types...
March 3, 2023: Briefings in Bioinformatics
https://read.qxmd.com/read/36769244/er-pm-junctions-on-gabaergic-interneurons-are-organized-by-neuregulin-2-vap-interactions-and-regulated-by-nmda-receptors
#38
JOURNAL ARTICLE
Detlef Vullhorst, Mara S Bloom, Neha Akella, Andres Buonanno
Neuregulins (NRGs) signal via ErbB receptors to regulate neural development, excitability, synaptic and network activity, and behaviors relevant to psychiatric disorders. Bidirectional signaling between NRG2/ErbB4 and NMDA receptors is thought to homeostatically regulate GABAergic interneurons in response to increased excitatory neurotransmission or elevated extracellular glutamate levels. Unprocessed proNRG2 forms discrete clusters on cell bodies and proximal dendrites that colocalize with the potassium channel Kv2...
February 2, 2023: International Journal of Molecular Sciences
https://read.qxmd.com/read/36753279/strategies-and-best-practices-to-improve-diversity-equity-and-inclusion-among-us-graduate-medical-education-programs
#39
JOURNAL ARTICLE
Dowin Boatright, Maya London, Arra Jane Soriano, Marjorie Westervelt, Stephany Sanchez, Jed D Gonzalo, William McDade, Tonya L Fancher
IMPORTANCE: Closing the diversity gap is critical to ensure equity in medical education and health care quality. Nevertheless, evidence-based strategies and best practices to improve diversity, equity, and inclusion (DEI) in the biomedical workforce remain poorly understood and underused. To improve the culture of DEI in graduate medical education (GME), in 2020 the Accreditation Council of Graduate Medical Education (ACGME) launched the Barbara Ross-Lee, DO, Diversity, Equity, and Inclusion Award to recognize exceptional DEI efforts in US residency programs...
February 1, 2023: JAMA Network Open
https://read.qxmd.com/read/36749013/optimal-gap-affine-alignment-in-o-s-space
#40
JOURNAL ARTICLE
Santiago Marco-Sola, Jordan M Eizenga, Andrea Guarracino, Benedict Paten, Erik Garrison, Miquel Moreto
MOTIVATION: Pairwise sequence alignment remains a fundamental problem in computational biology and bioinformatics. Recent advances in genomics and sequencing technologies demand faster and scalable algorithms that can cope with the ever-increasing sequence lengths. Classical pairwise alignment algorithms based on dynamic programming are strongly limited by quadratic requirements in time and memory. The recently proposed wavefront alignment algorithm (WFA) introduced an efficient algorithm to perform exact gap-affine alignment in O(ns) time, where s is the optimal score and n is the sequence length...
February 3, 2023: Bioinformatics
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