scholarly journals Silver(I)-Promoted Conversion of Thioamides to Amidines: Divergent Synthesis of a Key Series of Vancomycin Aglycon Residue 4 Amidines That Clarify Binding Behavior to Model Ligands

2012 ◽  
Vol 134 (21) ◽  
pp. 8790-8793 ◽  
Author(s):  
Akinori Okano ◽  
Robert C. James ◽  
Joshua G. Pierce ◽  
Jian Xie ◽  
Dale L. Boger
Keyword(s):  
Binding Behavior ◽  
Vancomycin Aglycon

Computer-aided structural and molecular insights into the mechanisms by which Pseudouridimycin (PUM) disrupts cleft extension in bacterial RNA polymerase to block DNA entry and exit

2020 ◽  
Vol 17 ◽  
Author(s):  
Ali H. Rabbad ◽  
Fisayo A. Olotu ◽  
Mahmoud E. Soliman
Keyword(s):  
Rna Polymerase ◽  
Bacterial Infections ◽  
Entry And Exit ◽  
Dynamic Binding ◽  
Binding Behavior ◽  
Bacterial Rna ◽  
Nucleotide Addition ◽  
Switch Regions ◽  
Cleft Extension ◽  
Key Residues

Background: The ability of Pseudouridimycin (PUM) to occupy the nucleotide addition site of bacterial RNA Polymerase (RNAP) underlies its inhibitory potency as previously reported. PUM has gained high research interest as a broad-spectrum nucleoside analog that has demonstrated exciting potentials in treating drug-resistant bacterial infections. Objective: Herein, we identified, for the first time, a novel complementary mechanism by which PUM elicits its inhibitory effects on bacterial RNAP. Methods: The dynamic binding behavior of PUM to bacterial RNAP was studied using various dynamic analyses approaches. Results and Discussion: Findings revealed that in addition to occupying the nucleotide addition site, PUM also interrupts the unimpeded entry and exit of DNA by reducing the mechanistic extension of the RNAP cleft and perturbing the primary conformations of the switch regions. Moreover, PUM binding reduced the distances between key residues in the β and β’ subunits that extend to accommodate the DNA. Conclusion: This study’s findings present structural insights that would contribute to the structure-based design of potent and selective PUM inhibitors.

ACETATE SORPTION AND DESORPTION ON BOEHMITE SURFACES: THE INFLUENCE OF H2O UPON BINDING BEHAVIOR

2020 ◽  
Author(s):  
Caitlin LeMae Payblas ◽  
◽  
Omar R. Harvey
Keyword(s):  
Binding Behavior

scholarly journals Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model

2021 ◽  
Author(s):  
David A Garcia ◽  
Gregory Fettweis ◽  
Diego M Presman ◽  
Ville Paakinaho ◽  
Christopher Jarzynski ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Single Molecule ◽  
Power Law ◽  
Dwell Time ◽  
Specific Binding ◽  
Power Law Distribution ◽  
Single Molecule Level ◽  
Binding Behavior ◽  
Chromatin Template ◽  
Nuclear Domains

Abstract Single-molecule tracking (SMT) allows the study of transcription factor (TF) dynamics in the nucleus, giving important information regarding the diffusion and binding behavior of these proteins in the nuclear environment. Dwell time distributions obtained by SMT for most TFs appear to follow bi-exponential behavior. This has been ascribed to two discrete populations of TFs—one non-specifically bound to chromatin and another specifically bound to target sites, as implied by decades of biochemical studies. However, emerging studies suggest alternate models for dwell-time distributions, indicating the existence of more than two populations of TFs (multi-exponential distribution), or even the absence of discrete states altogether (power-law distribution). Here, we present an analytical pipeline to evaluate which model best explains SMT data. We find that a broad spectrum of TFs (including glucocorticoid receptor, oestrogen receptor, FOXA1, CTCF) follow a power-law distribution of dwell-times, blurring the temporal line between non-specific and specific binding, suggesting that productive binding may involve longer binding events than previously believed. From these observations, we propose a continuum of affinities model to explain TF dynamics, that is consistent with complex interactions of TFs with multiple nuclear domains as well as binding and searching on the chromatin template.

BSA/DNA binding behavior and the photophysicochemical properties of novel water soluble zinc(II)phthalocyanines directly substituted with piperazine groups

2021 ◽  
Author(s):  
Khaoula Khezami ◽  
Kevser Harmandar ◽  
Esra Bağda ◽  
Efkan Bağda ◽  
Gamze Şahin ◽  
...  
Keyword(s):  
Dna Binding ◽  
Water Soluble ◽  
Binding Behavior ◽  
Soluble Zinc

An insight into the binding behavior of graphene oxide and noble metal nanoparticles

2021 ◽  
Vol 129 (12) ◽  
pp. 125302
Author(s):  
Wajeeha Saeed ◽  
Zeeshan Abbasi ◽  
Shumaila Majeed ◽  
Sohail Anjum Shahzad ◽  
Abdul Faheem Khan ◽  
...  
Keyword(s):  
Graphene Oxide ◽  
Metal Nanoparticles ◽  
Noble Metal ◽  
Noble Metal Nanoparticles ◽  
Binding Behavior ◽  
Insight Into

scholarly journals Positron Emission Tomography in the Inflamed Cerebellum: Addressing Novel Targets among G Protein-Coupled Receptors and Immune Receptors

Pharmaceutics ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 925
Author(s):  
Margit Pissarek
Keyword(s):  
G Protein ◽  
Cannabinoid Receptors ◽  
G Protein Coupled Receptors ◽  
Translocator Protein ◽  
Brain Diseases ◽  
Present Contribution ◽  
Binding Behavior ◽  
Positron Emission ◽  
Inflammatory Processes ◽  
G Protein Coupled

Inflammatory processes preceding clinical manifestation of brain diseases are moving increasingly into the focus of positron emission tomographic (PET) investigations. A key role in inflammation and as a target of PET imaging efforts is attributed to microglia. Cerebellar microglia, with a predominant ameboid and activated subtype, is of special interest also regarding improved and changing knowledge on functional involvement of the cerebellum in mental activities in addition to its regulatory role in motor function. The present contribution considers small molecule ligands as potential PET tools for the visualization of several receptors recognized to be overexpressed in microglia and which can potentially serve as indicators of inflammatory processes in the cerebellum. The sphingosine 1 phosphate receptor 1 (S1P1), neuropeptide Y receptor 2 (NPY2) and purinoceptor Y12 (P2Y12) cannabinoid receptors and the chemokine receptor CX3CR1 as G-protein-coupled receptors and the ionotropic purinoceptor P2X7 provide structures with rather classical binding behavior, while the immune receptor for advanced glycation end products (RAGE) and the triggering receptor expressed on myeloid cells 2 (TREM2) might depend for instance on further accessory proteins. Improvement in differentiation between microglial functional subtypes in comparison to the presently used 18 kDa translocator protein ligands as well as of the knowledge on the role of polymorphisms are special challenges in such developments.

Binding behavior of DEHP to albumin: spectroscopic investigation

2012 ◽  
Vol 74 (1-4) ◽  
pp. 231-238 ◽  
Author(s):  
Hua-xin Zhang ◽  
E Liu
Keyword(s):  
Spectroscopic Investigation ◽  
Binding Behavior

scholarly journals Different Binding Behavior to Chitin of Multiple Forms of Glucoamylases from Aspergillus saitoi and Rhizopus sp.

1991 ◽  
Vol 39 (9) ◽  
pp. 2387-2390 ◽  
Author(s):  
Tomoko TAKAHASHI ◽  
Naka MUROI ◽  
Masachika IRIE ◽  
Yoshio IKEGAMI
Keyword(s):  
Multiple Forms ◽  
Binding Behavior ◽  
Rhizopus Sp

Correlation analyses on binding behavior of heavy metals with sediment matrices

2001 ◽  
Vol 35 (10) ◽  
pp. 2417-2428 ◽  
Author(s):  
Kuang-Chung Yu ◽  
Li-Jyur Tsai ◽  
Shih-Hsiung Chen ◽  
Shien-Tsong Ho
Keyword(s):  
Heavy Metals ◽  
Binding Behavior ◽  
Correlation Analyses

scholarly journals Synthesis and Guest-Binding Properties of pH/Reduction Dual-Responsive Cyclophane Dimer

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3097
Author(s):  
Osamu Hayashida ◽  
Yudai Tanaka ◽  
Takaaki Miyazaki
Keyword(s):  
Electrostatic Interaction ◽  
Disulfide Bonds ◽  
Water Soluble ◽  
Guest Molecules ◽  
Binding Behavior ◽  
Dual Responsive ◽  
Guest Binding ◽  
Basic Solutions ◽  
Ph Conditions ◽  
Almost All

A water-soluble cyclophane dimer having two disulfide groups as a reduction-responsive cleavable bond as well as several acidic and basic functional groups as a pH-responsive ionizable group 1 was successfully synthesized. It was found that 1 showed pH-dependent guest-binding behavior. That is, 1 strongly bound an anionic guest, 6-p-toluidinonaphthalene-2-sulfonate (TNS) with binding constant (K/M−1) for 1:1 host-guest complexes of 9.6 × 104 M−1 at pH 3.8, which was larger than those at pH 7.4 and 10.7 (6.0 × 104 and 2.4 × 104 M−1, respectively), indicating a favorable electrostatic interaction between anionic guest and net cationic 1. What is more, release of the entrapped guest molecules by 1 was easily controlled by pH stimulus. Large favorable enthalpies (ΔH) for formation of host-guest complexes were obtained under the pH conditions employed, suggesting that electrostatic interaction between anionic TNS and 1 was the most important driving force for host-guest complexation. Such contributions of ΔH for formation of host-guest complexes decreased along with increased pH values from acidic to basic solutions. Upon addition of dithiothreitol (DTT) as a reducing reagent to an aqueous PBS buffer (pH 7.4) containing 1 and TNS, the fluorescence intensity originating from the bound guest molecules decreased gradually. A treatment of 1 with DTT gave 2, having less guest-binding affinity by the cleavage of disulfide bonds of 1. Consequently, almost all entrapped guest molecules by 1 were released from the host. Moreover, such reduction-responsive cleavage of 1 and release of bound guest molecules was performed more rapidly in aqueous buffer at pH 10.7.

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