Permeabilization activated reduction in fluorescence: A novel method to measure kinetics of protein interactions with intracellular structures

The fluorination of lead-like compounds is a common tool in medicinal chemistry to alter molecular properties in various ways and with different goals. We herein present a detailed study of the binding of fluorinated benzenesulfonamides to human Carbonic Anhydrase II by complementing macromolecular X-ray crystallographic observations with thermodynamic and kinetic data collected with the novel method of kinITC. Our findings comprise so far unknown alternative binding modes in the crystalline state for some of the investigated compounds as well as complex thermodynamic and kinetic structure-activity relationships. They suggest that fluorination of the benzenesulfonamide core is especially advantageous in one position with respect to the kinetic signatures of binding and that a higher degree of fluorination does not necessarily provide for a higher affinity or more favorable kinetic binding profiles. Lastly, we propose a relationship between the kinetics of binding and ligand acidity based on a small set of compounds with similar substitution patterns.

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Kinetics of RNA–protein interactions in cells

Trends in Biochemical Sciences ◽

10.1016/j.tibs.2021.07.006 ◽

2021 ◽

Author(s):

Deepak Sharma ◽

Donny D. Licatalosi ◽

Eckhard Jankowsky

Keyword(s):

Protein Interactions ◽

Kinetics Of ◽

In Cells

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Identification of the Disrupted Pathways Associated with Periodontitis Based on Human Pathway Network

Infection International ◽

10.1515/ii-2017-0143 ◽

2016 ◽

Vol 5 (4) ◽

pp. 93-98

Author(s):

Wen Sun ◽

Lin Han ◽

Wenmao Xu ◽

Yazhen Sun

Keyword(s):

Protein Interactions ◽

Threshold Value ◽

Normal Subjects ◽

Protein Protein Interactions ◽

Pathway Network ◽

Differential Expression Genes ◽

Weight Value ◽

Limma Package ◽

Novel Method ◽

Cognitively Normal Subjects

AbstractObjective: The objective of this work is to search for a novel method to explore the disrupted pathways associated with periodontitis (PD) based on the network level.Methods: Firstly, the differential expression genes (DEGs) between PD patients and cognitively normal subjects were inferred based on LIMMA package. Then, the protein-protein interactions (PPI) in each pathway were explored by Empirical Bayesian (EB) co-expression program. Specifically, we determined the 100th weight value as the threshold value of the disrupted pathways of PPI by constructing the randomly model and confirmed the weight value of each pathway. Meanwhile, we dissected the disrupted pathways under the weight value > the threshold value. Pathways enrichment analyses of DEGs were carried out based on Expression Analysis Systematic Explored (EASE) test. Finally, the better method was selected based on the more rich and significant obtained pathways by comparing the two methods.Results: After the calculation of LIMMA package, we estimated 524 DEGs in all. Then we determined 0.115222 as the threshold value of the disrupted pathways of PPI. When the weight value>0.115222, there were 258 disrupted pathways of PPI enriched in. Additionally, we observed those 524 DEGs that were enriched in 4 pathways under EASE=0.1.Conclusion: We proposed a novel network method inferring the disrupted pathway for PD. The disrupted pathways might be underlying biomarkers for treatment associated with PD.

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The Effect of Proline cis-trans Isomerization on the Folding of the C-Terminal SH2 Domain from p85

International Journal of Molecular Sciences ◽

10.3390/ijms21010125 ◽

2019 ◽

Vol 21 (1) ◽

pp. 125

Author(s):

Francesca Troilo ◽

Francesca Malagrinò ◽

Lorenzo Visconti ◽

Angelo Toto ◽

Stefano Gianni

Keyword(s):

Protein Interactions ◽

Specific Interaction ◽

Sh2 Domain ◽

Regulatory Subunit ◽

Wild Type ◽

Protein Protein Interactions ◽

Sh2 Domains ◽

Trans Isomerization ◽

A Site ◽

Kinetics Of

SH2 domains are protein domains that modulate protein–protein interactions through a specific interaction with sequences containing phosphorylated tyrosines. In this work, we analyze the folding pathway of the C-terminal SH2 domain of the p85 regulatory subunit of the protein PI3K, which presents a proline residue in a cis configuration in the loop between the βE and βF strands. By employing single and double jump folding and unfolding experiments, we demonstrate the presence of an on-pathway intermediate that transiently accumulates during (un)folding. By comparing the kinetics of folding of the wild-type protein to that of a site-directed variant of C-SH2 in which the proline was replaced with an alanine, we demonstrate that this intermediate is dictated by the peptidyl prolyl cis-trans isomerization. The results are discussed in the light of previous work on the effect of peptidyl prolyl cis-trans isomerization on folding events.

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Human placental estrogen synthetase (aromatase). Effect of environment on the kinetics of protein-protein and substrate-protein interactions and the production of 19-oxygenated androgen intermediates in the purified reconstituted cytochrome P450 enzyme system

The Journal of Steroid Biochemistry and Molecular Biology ◽

10.1016/0960-0760(91)90050-f ◽

1991 ◽

Vol 39 (3) ◽

pp. 381-394 ◽

Cited By ~ 5

Author(s):

Kandan Sethumadhavan ◽

Francis L. Bellino

Keyword(s):

Cytochrome P450 ◽

Protein Interactions ◽

Enzyme System ◽

Cytochrome P450 Enzyme ◽

Substrate Protein ◽

P450 Enzyme ◽

Cytochrome P450 Enzyme System ◽

Kinetics Of ◽

Estrogen Synthetase

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Kinetics of Protein-Protein Interactions at the Surface of an Optical Biosensor

Analytical Biochemistry ◽

10.1006/abio.1995.1522 ◽

1995 ◽

Vol 231 (1) ◽

pp. 210-217 ◽

Cited By ~ 119

Author(s):

P.R. Edwards ◽

A. Gill ◽

D.V. Pollardknight ◽

M. Hoare ◽

P.E. Buckle ◽

...

Keyword(s):

Protein Interactions ◽

Optical Biosensor ◽

Protein Protein Interactions ◽

Kinetics Of

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Bombardment by Reflection - A Novel Method to Prepare High Quality Hydrogenated Amorphous Germanium by Anodic PCVD

MRS Proceedings ◽

10.1557/proc-467-639 ◽

1997 ◽

Vol 467 ◽

Author(s):

Annette Diez ◽

Twlo P. Drüsedau

Keyword(s):

Atomic Hydrogen ◽

Carrier Mobility ◽

Hydrogen Pressure ◽

Amorphous Germanium ◽

Hydrogen Dilution ◽

Novel Method ◽

Hydrogenated Amorphous ◽

Hydrogenated Amorphous Germanium ◽

Kinetics Of

ABSTRACTDeposition of amorphous germanium by anodic PCVD was performed changing the germane/hydrogen dilution ratio from 1/6 to 1/100. Films deposited under high dilution of germane are of a high mechanical density (92.5 % of bulk) and good optoelectronic properties (electrical conductivity at room temperature σ=10−5 (Ω cm)−1, majority carrier mobility-lifetime product at λ=1200 nm ημ=x 10−7 cm2/V). The quality of the films is increased by deposition at increasing pumping speed for hydrogen (lower hydrogen pressure) keeping the other parameters constant. It is suggested that fast atomic hydrogen originating from a backscattering process at the powered electrode bombard the growing film and contribute to the improved quality of the a-Ge:H. Also, the growth kinetics of the films is changed from linear to parabolic dependence on germane flow interchanging deposition from high to low hydrogen pressure. This effect is rationalized in terms of a contribution of energetic atomic hydrogen to the dissociation of germane.

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