Water Makes the Difference: Rearrangement of Water Solvation Layer Triggers Non-additivity of Functional Group Contributions in Protein-Ligand Binding

ChemMedChem ◽  
2012 ◽  
Vol 7 (8) ◽  
pp. 1423-1434 ◽  
Author(s):  
Adam Biela ◽  
Michael Betz ◽  
Andreas Heine ◽  
Gerhard Klebe
Keyword(s):  
Ligand Binding ◽  
Functional Group ◽  
Group Contributions ◽  
The Difference

Non-additivity of Functional Group Contributions in Protein–Ligand Binding: A Comprehensive Study by Crystallography and Isothermal Titration Calorimetry

2010 ◽  
Vol 397 (4) ◽  
pp. 1042-1054 ◽  
Author(s):  
Bernhard Baum ◽  
Laveena Muley ◽  
Michael Smolinski ◽  
Andreas Heine ◽  
David Hangauer ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Isothermal Titration Calorimetry ◽  
Functional Group ◽  
Titration Calorimetry ◽  
Group Contributions ◽  
Comprehensive Study

Relationship between the Differences of Odor Detection Threshold Values Measured by Different Methods and some of the Physicochemical Properties

2013 ◽  
Vol 807-809 ◽  
pp. 451-455 ◽  
Author(s):  
Di Fang ◽  
Jie Min Liu ◽  
Qin Yi
Keyword(s):  
Physicochemical Properties ◽  
Functional Group ◽  
Saturated Vapor ◽  
Detection Threshold ◽  
Threshold Values ◽  
Odor Detection ◽  
Linear Relationships ◽  
Odor Detection Threshold ◽  
The Difference ◽  
The Relationship

The amount of sample can enter the nasal cavity depends on the physiochemical characteristics such as distribution, volatility and solubility. It can be suspected that the difference of odor detection threshold (ODT) measured by different methods is related to the physicochemical properties of compounds. To investigate the relationship between ODT differences and the physicochemical properties of compounds, ODT values of four series of organic compounds were measured by triangle odor bag method and gas chromatography and olfactometry method; the results were compared and the absolute differences were calculated. Relationship between ODT differences and the type of functional group and some of the physicochemical properties of compounds was analyzed. The results showed the type of functional group had significant effect on the differences. Certain linear relationships between the logarithmic value of differences and the logarithmic values of saturated vapor pressure and molecular weight were observed.

Functional group contributions to the auger spectra of methyl cyanide and methyl isocyanide

1986 ◽  
Vol 40 (1) ◽  
pp. 69-83 ◽  
Author(s):  
R.R. Rye ◽  
J.T. Yatess ◽  
M.R. Albert
Keyword(s):  
Functional Group ◽  
Group Contributions ◽  
Methyl Cyanide ◽  
Methyl Isocyanide ◽  
Auger Spectra

Corrigendum to “Gas-phase ligand binding to Jacobsen's manganese salen catalyst: Functional group and steric effects” [Int. J. Mass Spectrom. 305 (2011) 40–44]

2012 ◽  
Vol 314 ◽  
pp. 63
Author(s):  
William C. Clodfelter ◽  
Emileigh M. Wong ◽  
Kelly A. Hay ◽  
Scott Gronert
Keyword(s):  
Ligand Binding ◽  
Gas Phase ◽  
Functional Group ◽  
Steric Effects ◽  
Mass Spectrom

Evaluation of Functional Group Contributions to Excess Volumetric Properties of Solvated Molecules

1999 ◽  
Vol 103 (11) ◽  
pp. 1982-1990 ◽  
Author(s):  
Daren M. Lockwood ◽  
Peter J. Rossky
Keyword(s):  
Functional Group ◽  
Volumetric Properties ◽  
Group Contributions ◽  
Solvated Molecules

Steric Effect: Partitioning in Atomic and Functional Group Contributions

2009 ◽  
Vol 113 (15) ◽  
pp. 3698-3702 ◽  
Author(s):  
Miquel Torrent-Sucarrat ◽  
Shubin Liu ◽  
Frank De Proft
Keyword(s):  
Steric Effect ◽  
Functional Group ◽  
Group Contributions

scholarly journals Endogenous Binding of Steroid Molecules to DNA Nucleotides by a Ca2+/PO4- Process to Enable Gene Transcription

2020 ◽  
Author(s):  
Charles Schaper
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Ligand Binding ◽  
Gene Transcription ◽  
Functional Group ◽  
Ring Structure ◽  
Binding Domain ◽  
Ligand Binding Domain ◽  
Steroid Molecule ◽  
First Time

Steroid hormones, such as cortisol, testosterone and estrogen, have powerful control over human physiology, growth, and reproduction, but efforts to deploy its potential, such as with glucocorticoids, a first-line defense of inflammation, are often met with severe side effects. Unfortunately, much is unknown about the basic interaction of steroid molecules with DNA, including its receptors, activators, factors, and the gene transcription procedure. In this research article, a remarkable finding is shown for the first time, in which it is illustrated through structural analysis that the base pairings of the four DNA nucleotides, adenine with thymine (A-T) and cytosine with guanine (C-G), form perfectly the classic four ring structure of the steroid molecule, which indicates the profound result put forth in this article that steroid molecules bind directly to DNA for the purpose of gene transcription. Further, critical to a basic understanding of DNA, it is resolved here of the location of the unusual ``missing" hydrogen bond of the A-T pairing, which has only two internal hydrogen bonds whereas C-G has three hydrogen bonds. It is shown that the third hydrogen bond for A-T is formed when the A-T nucleotide is coupled with corticosteroids, such as cortisol, which has an oxygen functional group that is perfectly positioned to form a hydrogen bond with the accessible oxygen-based functional group of thymine. In addition, to facilitate the binding process, it is shown that Ca2+ ions, which are associated with the ligand binding domain of the steroid receptor prior to its association with DNA, couple the oxygen-based functional groups at each end of the steroid molecule with the PO4- ions of adjacent nucleotides and thus bind the steroid molecule directly to the nucleic acid. The results are further amplified by analysis of the cortisol hormone and the ligand binding domain of the glucocorticoid receptor in its interaction with the A-T nucleotide pairing.

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