Molecular Recognition Kinetics of Nonsurface Active Pyrimidine Derivatives Dissolved in the Aqueous Subphase by an Amphiphilic Melamine Type Monolayer:  A Theoretical Approach

2005 ◽  
Vol 109 (29) ◽  
pp. 14137-14143 ◽  
Author(s):  
V. B. Fainerman ◽  
D. Vollhardt ◽  
E. V. Aksenenko ◽  
F. Liu
Keyword(s):  
Molecular Recognition ◽  
Theoretical Approach ◽  
Pyrimidine Derivatives ◽  
Aqueous Subphase ◽  
Kinetics Of

scholarly journals Activation of Bacterial Histidine Kinases: Insights into the Kinetics of the cis Autophosphorylation Mechanism

mSphere ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Gaurav D. Sankhe ◽  
Narendra M. Dixit ◽  
Deepak K. Saini
Keyword(s):  
Mathematical Model ◽  
Theoretical Approach ◽  
Reaction Rates ◽  
Antibacterial Drug ◽  
Histidine Kinases ◽  
Content Type ◽  
Two Component ◽  
Kinetics Of ◽  
Best Fit ◽  
Step Mechanism

ABSTRACT Two-component signaling systems (TCSs) are central to bacterial adaptation. However, the mechanisms underlying the reactions involving TCS proteins and their reaction rates are largely undetermined. Here, we employed a combined experimental and theoretical approach to elucidate the kinetics of autophosphorylation of three histidine kinases (HKs) of Mycobacterium tuberculosis , viz. , MtrB, PrrB, and PhoR, all known to play a role in regulating its virulence. Using wild-type and mutant proteins, we performed dimerization assays, thermophoretic-affinity measurements, and competition-based phosphorylation assays to establish that for HK, MtrB autophosphorylation occurs in cis , similar to what has been proposed for the PhoR and PrrB HKs. Next, to determine the kinetics of cis autophosphorylation, we used a quantitative high-throughput assay and identified a two-step mechanism of HK activation, involving (i) the reversible association of HK with ATP, followed by (ii) its phosphorylation. We developed a mathematical model based on this two-step cis mechanism that captured the experimental data. Best-fit parameter values yielded estimates of the extent of HK-ATP association and the rates of HK autophosphorylation, allowing quantification of the propensity of HK autophosphorylation. Our combined experimental and theoretical approach presents a facile, scalable tool to quantify reactions involving bacterial TCS proteins, useful in antibacterial drug development strategies. IMPORTANCE Two-component systems consisting of an input-sensing histidine kinase (HK) and an output-generating response regulator (RR) are one of the key apparatuses utilized by bacteria for adapting to the extracellular milieu. HK autophosphorylation is shown to occur primarily in trans (intermolecular) and more recently shown to occur in cis (intramolecular). Although the catalysis of HK activation remains universal, the reaction scheme for evaluation of the kinetic parameter differs between these designs and cis mode largely remains unexplored. We combined experimental and theoretical approach to unravel two-step mechanism of activation of three cis mode HKs of M. tuberculosis . The new mathematical model yields best-fit parameters to estimate the rates of HK-ATP association and HK autophosphorylation.

Molecular Recognition of Dissolved Pyrimidine Derivatives by a Dialkyl Melamine-Type Monolayer

ChemPhysChem ◽  
2005 ◽  
Vol 6 (7) ◽  
pp. 1246-1250 ◽  
Author(s):  
Dieter Vollhardt ◽  
Fang Liu ◽  
Rainer Rudert
Keyword(s):  
Molecular Recognition ◽  
Pyrimidine Derivatives

scholarly journals Kinetics of molecular recognition mediated nanoparticle self-assembly

Nano Research ◽  
2009 ◽  
Vol 2 (1) ◽  
pp. 78-84 ◽  
Author(s):  
Chinmay Soman ◽  
Todd Giorgio
Keyword(s):  
Molecular Recognition ◽  
Self Assembly ◽  
Kinetics Of

Universal statistical fluctuations in thermodynamics and kinetics of single molecular recognition

2016 ◽  
Vol 18 (12) ◽  
pp. 8570-8578
Author(s):  
Xiliang Zheng ◽  
Jin Wang
Keyword(s):  
Molecular Recognition ◽  
Statistical Distributions ◽  
Thermodynamics And Kinetics ◽  
Statistical Fluctuations ◽  
Kinetics Of

We investigated the main universal statistical distributions of single molecular recognition.

scholarly journals On the role of aromatic-sugar interactions in the molecular recognition of carbohydrates: A 3D view by using NMR

2008 ◽  
Vol 80 (8) ◽  
pp. 1827-1835 ◽  
Author(s):  
M. Dolores Díaz ◽  
María del Carmen Fernández-Alonso ◽  
Gabriel Cuevas ◽  
F. Javier Cañada ◽  
Jesús Jiménez-Barbero
Keyword(s):  
Molecular Recognition ◽  
Computational Methods ◽  
Theoretical Approach ◽  
Different Levels

This revision describes an up-to-date review of our efforts to investigate the interaction of carbohydrates with aromatic moieties at different levels of complexity. Protein-sugar interactions have been studied using NMR experiments on a variety of hevein/chitooligosaccharide systems. In addition, NMR and computational methods have also been used to evaluate the interaction of simple aromatic entities with simple monosaccharides. In between, the stacking features of aromatic-containing glycomolecules have also been described by using an analogous experimental-theoretical approach.

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