Predicting sequence and structural features of effective piRNA target binding sites

2022 ◽  
Author(s):  
Garima Singh ◽  
Bibekanand Mallick
Keyword(s):  
Binding Sites ◽  
Structural Features ◽  
Target Binding

scholarly journals Binding of Calcium to Fibrinogen: Some Related Properties

1977 ◽  
Author(s):  
G. Marguerie
Keyword(s):  
Binding Sites ◽  
Calcium Binding ◽  
Specific Binding ◽  
Equilibrium Dialysis ◽  
Structural Features ◽  
Salt Bridges ◽  
High Affinity ◽  
Direct Titration ◽  
Specific Binding Sites ◽  
Calcium Binding Sites

The calcium binding properties of bovin fibrinogen have been studied using equilibrium dialysis method. At pH 7.5 fibrinogen has 3 specific calcium binding sites of high affinity and several non specific binding sites of low affinity. Direct titration of the calcium induced proton release indicates that the binding center is a chelate. Thermal an acid denaturation is found to be markedly influenced by the presence of Ca++, suggesting that structural features are related to the binding. However the circular dichroism spectra show that no generalized conformational change is induced when Ca++ is bound to the protein.The plasminic digestion of fibrinogen is also found to be specificaly influenced by Ca++. The velocity of the initial cleavages is slightly reduced in the presence of calcium. It is therefore suggested that the C-terminal part of the Aα chain is involved in the binding.Considering the dimeric structure of the fibrinogen molecule, the presence of only 3 calcium binding sites of high affinity suggests the existence of “salt bridges” between the constitutive polypeptide chains.

scholarly journals Structural Features of the Noncatalytic cGMP Binding Sites of Frog Photoreceptor Phosphodiesterase Using cGMP Analogs

1998 ◽  
Vol 273 (10) ◽  
pp. 5557-5565 ◽  
Author(s):  
Marcia C. Hebert ◽  
Frank Schwede ◽  
Bernd Jastorff ◽  
Rick H. Cote
Keyword(s):  
Binding Sites ◽  
Structural Features ◽  
Photoreceptor Phosphodiesterase

scholarly journals Struct-NB: predicting protein-RNA binding sites using structural features

2010 ◽  
Vol 4 (1) ◽  
pp. 21 ◽  
Author(s):  
Fadi Towfic ◽  
Cornelia Caragea ◽  
David C. Gemperline ◽  
Drena Dobbs ◽  
Vasant Honavar
Keyword(s):  
Binding Sites ◽  
Rna Binding ◽  
Structural Features ◽  
Rna Binding Sites

scholarly journals The dynamics of HMG protein–chromatin interactions in living cellsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (1) ◽  
pp. 127-137 ◽  
Author(s):  
Gabi Gerlitz ◽  
Robert Hock ◽  
Tetsuya Ueda ◽  
Michael Bustin
Keyword(s):  
Binding Sites ◽  
Binding Proteins ◽  
Peer Review Process ◽  
High Mobility ◽  
Structural Features ◽  
Chromatin Binding ◽  
Hmg Proteins ◽  
Chromatin Dynamics ◽  
Chromatin Interactions ◽  
Major Factors

The dynamic interaction between nuclear proteins and chromatin leads to the functional plasticity necessary to mount adequate responses to regulatory signals. Here, we review the factors regulating the chromatin interactions of the high mobility group proteins (HMGs), an abundant and ubiquitous superfamily of chromatin-binding proteins in living cells. HMGs are highly mobile and interact with the chromatin fiber in a highly dynamic fashion, as part of a protein network. The major factors that affect the binding of HMGs to chromatin are operative at the level of the single nucleosome. These factors include structural features of the HMGs, competition with other chromatin-binding proteins for nucleosome binding sites, complex formation with protein partners, and post-translational modifications in the protein or in the chromatin-binding sites. The versatile modulation of the interaction between HMG proteins and chromatin plays a role in processes that establish the cellular phenotype.

scholarly journals Self-association configures the NAD+-binding site of plant NLR TIR domains

2021 ◽  
Author(s):  
Hayden Burdett ◽  
Xiahao Hu ◽  
Maxwell X Rank ◽  
Natsumi Maruta ◽  
Bostjan Kobe
Keyword(s):  
Binding Site ◽  
Conformational Changes ◽  
Active Site ◽  
Binding Sites ◽  
Molecular Mechanisms ◽  
Structural Features ◽  
Active Conformation ◽  
Effector Triggered Immunity ◽  
Self Association ◽  
Tir Domains

TIR domains are signalling domains present in plant nucleotide-binding leucine-rich repeat receptors (NLRs), with key roles in plant innate immunity. They are required for the induction of a hypersensitive response (HR) in effector-triggered immunity, but the mechanism by which this occurs is not yet fully understood. It has been recently shown that the TIR domains from several plant NLRs possess NADase activity. The oligomeric structure of TIR-containing NLRs ROQ1 and RPP1 reveals how the TIR domains arrange into an active conformation, but low resolution around the NAD+ binding sites leaves questions unanswered about the molecular mechanisms linking self-association and NADase activity. In this study, a number of crystal structures of the TIR domain from the grapevine NLR RUN1 reveal how self-association and enzymatic activity may be linked. Structural features previously proposed to play roles involve the ″AE interface″ (mediated by helices A and E), the ″BB-loop″ (connecting β-strand B and helix B in the structure), and the ″BE interface″ (mediated by the BB-loop from one TIR and the ″DE surface″ of another). We demonstrate that self-association through the AE interface induces conformational changes in the NAD+-binding site, shifting the BB-loop away from the catalytic site and allowing NAD+ to access the active site. We propose that an intact ″DE surface″ is necessary for production of the signalling product (variant cyclic ADPR), as it constitutes part of the active site. Addition of NAD+ or NADP+ is not sufficient to induce self-association, suggesting that NAD+ binding occurs after TIR self-association. Our study identifies a mechanistic link between TIR self-association and NADase activity.

scholarly journals Structural and Functional Characteristics of ADAMTS-4 and ADAMTS-5: A Review

2020 ◽  
pp. 12-21
Author(s):  
Anastasia Korchagina ◽  
Lyudmila Derevshchikova
Keyword(s):  
Enzymatic Activity ◽  
Binding Sites ◽  
Catalytic Domain ◽  
Structural Features ◽  
Functional Characteristics ◽  
Rich Domain ◽  
Common Diseases ◽  
The Moment ◽  
Cysteine Rich Domain

ADAMTS-4 and -5 are aggrecanases that are involved in the development of osteoarthrosis, one of the most common diseases at the moment, due to which a large number of people suffer annually. By some estimates, 9.6% of men and 18% of women over the age of 60 have symptomatic osteoarthrosis. This review discusses the currently known data on the structural features and enzymatic activity of these enzymes. The structures of ADAMTS-4 and -5 are similar, they contain 7 domain sites: the signal section, the N-terminal prodomain, the catalytic domain, the disintegrin-like domain, the thrombospodin motif, the cysteine-rich domain, and the spacer domain. In addition to all these elements, ADAMTS-5 has an additional thrombospodin motif at the end. ADAMTS-4 and -5 cleaves aggrecan in 5 different binding sites. However, the Glu373-Ala374 site probably plays the most important role in the pathogenesis, since when this bond is broken, the whole aggrecan molecule loses its integrity, which leads to the destruction of cartilage and the development of the disease. In the course of the analysis of the information, the authors have found that the participation of ADAMTS-4 and -5 in the development of osteoarthritis varies greatly depending on the type of organism. The researchers have established that in mice ADAMTS-4 plays the largest role in the destruction of aggrecan, while in humans ADAMTS-5 or both aggrecanases influence the development of osteoarthritis. The revealed differences are not fully described; therefore, this review summarizes the already known results in this area, which will facilitate further research in this direction.

scholarly journals Cefiderocol Activity against Clinical Pseudomonas aeruginosa Isolates Exhibiting Ceftolozane-Tazobactam Resistance

2021 ◽  
Author(s):  
Patricia J Simner ◽  
Stephan Beisken ◽  
Yehudit Bergman ◽  
Andreas E Posch ◽  
Sara E Cosgrove ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Binding Sites ◽  
Whole Genome ◽  
The Novel ◽  
Broth Microdilution ◽  
Mechanisms Of Resistance ◽  
Fold Reduction ◽  
Target Binding

Abstract Objective Mutations in the AmpC-AmpR region are associated with treatment-emergent ceftolozane-tazobactam (TOL-TAZ) and ceftazidime-avibactam (CAZ-AVI) resistance. We sought to determine if these mutations impact susceptibility to the novel cephalosporin-siderophore compound cefiderocol. Methods Thirty-two paired isolates from 16 patients with index P. aeruginosa isolates susceptible to TOL-TAZ and subsequent P. aeruginosa isolates available after TOL-TAZ exposure from January 2019 to December 2020 were included. TOL-TAZ, CAZ-AVI, imipenem-relebactam (IMI-REL), and cefiderocol minimum inhibitory concentrations (MICs) were determined using broth microdilution. Whole genome sequencing of paired isolates was used to identify mechanisms of resistance to cefiderocol that emerged, focusing on putative mechanisms of resistance to cefiderocol or earlier siderophore-antibiotic conjugates based on the previously published literature. Results Analyzing the 16 pairs of P. aeruginosa isolates, ≥4-fold increases in cefiderocol MICs occurred in 4 of 16 isolates. Cefiderocol non-susceptibility criteria was met for only 1 of the 4 isolates, using Clinical and Laboratory Standards Institute criteria. Specific mechanisms identified included the following: AmpC E247K (2 isolates), MexR A66V and L57D (1 isolate each), and AmpD G116D (1 isolate) substitutions. For both isolates with AmpC E247K mutations, ≥4-fold MIC increases occurred for both TOL-TAZ and CAZ-AVI, while a ≥4-fold reduction in IMI-REL MICs was observed. Conclusions Our findings suggest that alterations in the target binding sites of P. aeruginosa derived AmpC β-lactamases have the potential to reduce the activity of three of four novel β-lactams (i.e., ceftolozane-tazobactam, ceftazidime-avibactam, and cefiderocol) and potentially increase susceptibility to imipenem-relebactam. These findings are in need of validation in a larger cohort.

scholarly journals Structural basis of diverse membrane target recognitions by ankyrins

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Chao Wang ◽  
Zhiyi Wei ◽  
Keyu Chen ◽  
Fei Ye ◽  
Cong Yu ◽  
...  
Keyword(s):  
Nervous System ◽  
Plasma Membrane ◽  
Binding Sites ◽  
Cell Adhesion Molecules ◽  
Structural Basis ◽  
Membrane Domains ◽  
Regulatory Domain ◽  
Multiple Target ◽  
Membrane Target ◽  
Target Binding

Ankyrin adaptors together with their spectrin partners coordinate diverse ion channels and cell adhesion molecules within plasma membrane domains and thereby promote physiological activities including fast signaling in the heart and nervous system. Ankyrins specifically bind to numerous membrane targets through their 24 ankyrin repeats (ANK repeats), although the mechanism for the facile and independent evolution of these interactions has not been resolved. Here we report the structures of ANK repeats in complex with an inhibitory segment from the C-terminal regulatory domain and with a sodium channel Nav1.2 peptide, respectively, showing that the extended, extremely conserved inner groove spanning the entire ANK repeat solenoid contains multiple target binding sites capable of accommodating target proteins with very diverse sequences via combinatorial usage of these sites. These structures establish a framework for understanding the evolution of ankyrins' membrane targets, with implications for other proteins containing extended ANK repeat domains.

scholarly journals COVID19 Approved Drug Repurposing: Pocket Similarity Approach

2020 ◽  
Author(s):  
Mohamed Fadlalla
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Drug Repurposing ◽  
Drug Binding ◽  
Drug Binding Site ◽  
Main Protease ◽  
Major Outbreak ◽  
Target Binding ◽  
Approved Drugs

<p>SARS CoV 2 has spread worldwide and caused a major outbreak of coronavirus disease 2019 (COVID-19). To date, no licensed drug or a vaccine is available against COVID19.</p><p>Starting from all of the resolved SARS CoV2 crystal structures, this study aims to find inhibitors for all of the SARS CoV2 proteins. To achieve this, I used PocketMatch to test the similarity of approved drugs binding sites against all of the binding sites found on SARS CoV 2 proteins. After that docking was used to confirm the results.</p><p>I found drugs that inhibit the main protease, Nsp12 and Nsp3. The discovered drugs are either in clinical trials (Sildenafil, Lopinavir, Ritonavir) or have in vitro antiviral activity (Nelfinavir, Indinavir, Amprenavir, depiqulinum , Gemcitabine, Raltitrexed, Aprepitant, montelukast, Ouabain, Raloxifene) whether against SARS CoV 2 or other viruses. In addition to this, further analysis of pockets revealed a steroidal pocket that might open the door to hypotheses on why the mortality of men is higher than women.</p><p>Many of the in silico repurposing studies test binding of the compound to the target using docking. The significance of this study adds to the similarity between the drug binding site and the target binding site. This takes into consideration the dynamic behaviour of the pocket after ligand binding.</p><div><br></div>

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