NMR Analysis of Site-Specific Ligand Binding in Oligomeric Proteins. Dynamic Studies on the Interaction of Riboflavin Synthase with Trifluoromethyl-Substituted Intermediates†

AbstractThe mechanism of specific ligand binding by proteins is discussed using the PDZ domain complexing the pentapeptide. This process is critical for clustering the membrane ion channel. The traditional model based on the Beta-sheet extension by complexed pentapeptide is interpreted as a hydrophobic core extension supported by additional Beta-strand generated by complexed pentapeptide. The explanation is based on the fuzzy oil drop model applied to the crystal structure of PDZ-pentapeptide.

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Unpicking allosteric mechanisms of homo-oligomeric proteins by determining their successive ligand binding constants

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2017.0176 ◽

2018 ◽

Vol 373 (1749) ◽

pp. 20170176 ◽

Cited By ~ 7

Author(s):

Ranit Gruber ◽

Amnon Horovitz

Keyword(s):

Mass Spectrometry ◽

Ligand Binding ◽

Single Molecule ◽

Binding Constants ◽

Molecular Machines ◽

Native Mass Spectrometry ◽

Oligomeric Proteins ◽

Allosteric Mechanisms ◽

The Relationship

Advances in native mass spectrometry and single-molecule techniques have made it possible in recent years to determine the values of successive ligand binding constants for large multi-subunit proteins. Given these values, it is possible to distinguish between different allosteric mechanisms and, thus, obtain insights into how various bio-molecular machines work. Here, we describe for ring-shaped homo-oligomers, in particular, how the relationship between the values of successive ligand binding constants is diagnostic for concerted, sequential and probabilistic allosteric mechanisms. This article is part of a discussion meeting issue ‘Allostery and molecular machines’.

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NMR analysis and site-specific protonation constants of streptomycin

Journal of Pharmaceutical and Biomedical Analysis ◽

10.1016/j.jpba.2011.10.009 ◽

2012 ◽

Vol 59 ◽

pp. 78-82 ◽

Cited By ~ 5

Author(s):

Gábor Orgován ◽

Béla Noszál

Keyword(s):

Protonation Constants ◽

Nmr Analysis ◽

Site Specific

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Site-Specific Free Energy Changes in Proteins upon Ligand Binding by Nuclear Magnetic Resonance: Ca2+-Displacement by Ln3+ in a Ca2+-Binding Protein from Entamoeba histolytica

Chemical Biology & Drug Design ◽

10.1111/j.1747-0285.2011.01090.x ◽

2011 ◽

Vol 77 (4) ◽

pp. 272-280

Author(s):

Kousik Chandra ◽

Sourajit M. Mustafi ◽

Subramanian Muthukumar ◽

Kandala V. R. Chary

Keyword(s):

Nuclear Magnetic Resonance ◽

Free Energy ◽

Magnetic Resonance ◽

Ligand Binding ◽

Entamoeba Histolytica ◽

Binding Protein ◽

Site Specific ◽

Specific Free Energy ◽

Nuclear Magnetic

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Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures

Nature ◽

10.1038/355850a0 ◽

1992 ◽

Vol 355 (6363) ◽

pp. 850-852 ◽

Cited By ~ 502

Author(s):

Andrew D. Ellington ◽

Jack W. Szostak

Keyword(s):

Ligand Binding ◽

Dna Molecules ◽

Single Stranded Dna ◽

Specific Ligand

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Bioinspired structural transition of synthetic polymers through biomolecular ligand binding

Chemical Communications ◽

10.1039/c8cc06232c ◽

2018 ◽

Vol 54 (85) ◽

pp. 12006-12009 ◽

Cited By ~ 4

Author(s):

Seigo Suzuki ◽

Toshiki Sawada ◽

Takashi Ishizone ◽

Takeshi Serizawa

Keyword(s):

Ligand Binding ◽

Structural Transition ◽

Synthetic Polymers ◽

Specific Ligand

The bioinspired structural transition of thermoresponsive poly(N-isopropylacrylamide) was demonstrated by specific ligand binding of artificially evolved peptides to the polymer.

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