scholarly journals Intravital Imaging of Vascular Transmigration by the Lyme Spirochete: Requirement for the Integrin Binding Residues of the B. burgdorferi P66 Protein

2015 ◽  
Vol 11 (12) ◽  
pp. e1005333 ◽  
Author(s):  
Devender Kumar ◽  
Laura C. Ristow ◽  
Meiqing Shi ◽  
Priyanka Mukherjee ◽  
Jennifer A. Caine ◽  
...  
Keyword(s):  
Intravital Imaging ◽  
Binding Residues ◽  
Lyme Spirochete

An Insight into Oligopeptide Transporter 3 (OPT3) family proteins

2020 ◽  
Vol 27 ◽  
Author(s):  
Fırat Kurt
Keyword(s):  
Stress Responses ◽  
Chelating Agent ◽  
Biological Processes ◽  
Biotic And Abiotic Stress ◽  
Oligopeptide Transporter ◽  
Binding Residues ◽  
Fe Homeostasis ◽  
Proteins Interactions ◽  
Insight Into ◽  
Selection Of

: Oligopeptide transporter 3 (OPT3) proteins are one of the subsets of OPT clade, yet little is known about these transporters. Therefore, homolog OPT3 proteins in several plant species were investigated and characterized using bioinformatical tools. Motif and co-expression analyses showed that OPT3 proteins may be involved in both biotic and abiotic stress responses as well as growth and developmental processes. AtOPT3 usually seemed to take part in Fe homeostasis whereas ZmOPT3 putatively interacted with proteins involved in various biological processes from plant defense system to stress responses. Glutathione (GSH), as a putative alternative chelating agent, was used in the AtOPT3 and ZmOPT3 docking analyses to identify their putative binding residues. The information given in this study will contribute to the understanding of OPT3 proteins’ interactions in various pathways and to the selection of potential ligands for OPT3s.

Computational Biology Tools for Identifying Specific Ligand Binding Residues for Novel Agrochemical and Drug Design

2015 ◽  
Vol 16 (8) ◽  
pp. 701-717 ◽  
Author(s):  
Izabella Pena Neshich ◽  
Leticia Nishimura ◽  
Fabio de Moraes ◽  
Jose Salim ◽  
Fabian Villalta-Romero ◽  
...  
Keyword(s):  
Drug Design ◽  
Computational Biology ◽  
Ligand Binding ◽  
Binding Residues ◽  
Specific Ligand

scholarly journals A Porthole over AKI: Cell Dynamics in Damage and Repair

Nephron ◽  
2020 ◽  
Vol 144 (12) ◽  
pp. 650-654
Author(s):  
Luca Bordoni ◽  
Donato Sardella ◽  
Ina Maria Schiessl
Keyword(s):  
Acute Kidney Injury ◽  
Renal Cell ◽  
Kidney Injury ◽  
Cell Types ◽  
Cell Interactions ◽  
Intravital Imaging ◽  
Cell Dynamics ◽  
Powerful Technique ◽  
Increased Risk ◽  
Cell Crosstalk

Acute kidney injury (AKI) is associated with an increased risk of CKD. Injury-induced multifaceted renal cell-to-cell crosstalk can either lead to successful self-repair or chronic fibrosis and inflammation. In this mini-review, we will discuss critical renal cell types acting as victims or executioners in AKI pathology and introduce intravital imaging as a powerful technique to further dissect these cell-to-cell interactions.

scholarly journals GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues

2021 ◽  
Author(s):  
Ying Xia ◽  
Chun-Qiu Xia ◽  
Xiaoyong Pan ◽  
Hong-Bin Shen
Keyword(s):  
Neural Networks ◽  
Nucleic Acid ◽  
Biological Activities ◽  
New Drugs ◽  
Superior Performance ◽  
Nucleic Acid Binding ◽  
Hierarchical Graph ◽  
Binding Residue ◽  
Binding Residues ◽  
Graph Neural Networks

Abstract Knowledge of the interactions between proteins and nucleic acids is the basis of understanding various biological activities and designing new drugs. How to accurately identify the nucleic-acid-binding residues remains a challenging task. In this paper, we propose an accurate predictor, GraphBind, for identifying nucleic-acid-binding residues on proteins based on an end-to-end graph neural network. Considering that binding sites often behave in highly conservative patterns on local tertiary structures, we first construct graphs based on the structural contexts of target residues and their spatial neighborhood. Then, hierarchical graph neural networks (HGNNs) are used to embed the latent local patterns of structural and bio-physicochemical characteristics for binding residue recognition. We comprehensively evaluate GraphBind on DNA/RNA benchmark datasets. The results demonstrate the superior performance of GraphBind than state-of-the-art methods. Moreover, GraphBind is extended to other ligand-binding residue prediction to verify its generalization capability. Web server of GraphBind is freely available at http://www.csbio.sjtu.edu.cn/bioinf/GraphBind/.

scholarly journals Monitoring the dynamics of Src activity in response to anti-invasive dasatinib treatment at a subcellular level using dual intravital imaging

2014 ◽  
Vol 8 (5) ◽  
pp. 478-486 ◽  
Author(s):  
Max Nobis ◽  
Ewan J McGhee ◽  
David Herrmann ◽  
Astrid Magenau ◽  
Jennifer P Morton ◽  
...  
Keyword(s):  
Intravital Imaging ◽  
Subcellular Level ◽  
Dasatinib Treatment

scholarly journals ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Yuning Chen ◽  
Ya-Nan Zhang ◽  
Renhong Yan ◽  
Guifeng Wang ◽  
Yuanyuan Zhang ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
Broad Spectrum ◽  
Management Strategy ◽  
Spectrum Management ◽  
Clinical Development ◽  
Severe Toxicity ◽  
Converting Enzyme ◽  
Angiotensin Converting Enzyme 2 ◽  
Binding Residues

AbstractThe evolution of coronaviruses, such as SARS-CoV-2, makes broad-spectrum coronavirus preventional or therapeutical strategies highly sought after. Here we report a human angiotensin-converting enzyme 2 (ACE2)-targeting monoclonal antibody, 3E8, blocked the S1-subunits and pseudo-typed virus constructs from multiple coronaviruses including SARS-CoV-2, SARS-CoV-2 mutant variants (SARS-CoV-2-D614G, B.1.1.7, B.1.351, B.1.617.1, and P.1), SARS-CoV and HCoV-NL63, without markedly affecting the physiological activities of ACE2 or causing severe toxicity in ACE2 “knock-in” mice. 3E8 also blocked live SARS-CoV-2 infection in vitro and in a prophylactic mouse model of COVID-19. Cryo-EM and “alanine walk” studies revealed the key binding residues on ACE2 interacting with the CDR3 domain of 3E8 heavy chain. Although full evaluation of safety in non-human primates is necessary before clinical development of 3E8, we provided a potentially potent and “broad-spectrum” management strategy against all coronaviruses that utilize ACE2 as entry receptors and disclosed an anti-coronavirus epitope on human ACE2.

scholarly journals Identification of binding residues between periplasmic adapter protein (PAP) and RND efflux pumps explains PAP-pump promiscuity and roles in antimicrobial resistance

2019 ◽  
Vol 15 (12) ◽  
pp. e1008101 ◽  
Author(s):  
Helen E. McNeil ◽  
Ilyas Alav ◽  
Ricardo Corona Torres ◽  
Amanda E. Rossiter ◽  
Eve Laycock ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Efflux Pumps ◽  
Adapter Protein ◽  
Rnd Efflux Pumps ◽  
Binding Residues
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