Recognition of the cell-wall binding site of the vancomycin-group antibiotics by unnatural structural motifs: 1H NMR studies of the effects of ligand binding on antibiotic dimerisation

1994 ◽  
pp. 659 ◽  
Author(s):  
Patrick Groves ◽  
Mark S. Searle ◽  
Ines Chicarelli-Robinson ◽  
Dudley H. Williams
Keyword(s):  
Cell Wall ◽  
Ligand Binding ◽  
Binding Site ◽  
1H Nmr ◽  
Nmr Studies ◽  
Structural Motifs ◽  
Cell Wall Binding ◽  
Vancomycin Group

scholarly journals Structural Investigations on the SH3b Domains of Clostridium perfringens Autolysin through NMR Spectroscopy and Structure Simulation Enlighten the Cell Wall Binding Function

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5716
Author(s):  
Yubao Shan ◽  
Xiaoling He ◽  
Zi Wang ◽  
Xiali Yue ◽  
Jiang Zhu ◽  
...  
Keyword(s):  
Cell Wall ◽  
Nmr Spectroscopy ◽  
Ligand Binding ◽  
Clostridium Perfringens ◽  
Catalytic Domain ◽  
Peptide Ligand ◽  
Structural Investigations ◽  
Cell Wall Binding ◽  
Potential Ligand ◽  
And Function

Clostridium perfringens autolysin (CpAcp) is a peptidoglycan hydrolase associated with cell separation, division, and growth. It consists of a signal peptide, ten SH3b domains, and a catalytic domain. The structure and function mechanisms of the ten SH3bs related to cell wall peptidoglycan binding remain unclear. Here, the structures of CpAcp SH3bs were studied through NMR spectroscopy and structural simulation. The NMR structure of SH3b6 was determined at first, which adopts a typical β-barrel fold and has three potential ligand-binding pockets. The largest pocket containing eight conserved residues was suggested to bind with peptide ligand in a novel model. The structures of the other nine SH3bs were subsequently predicted to have a fold similar to SH3b6. Their ligand pockets are largely similar to those of SH3b6, although with varied size and morphology, except that SH3b1/2 display a third pocket markedly different from those in other SH3bs. Thus, it was supposed that SH3b3-10 possess similar ligand-binding ability, while SH3b1/2 have a different specificity and additional binding site for ligand. As an entirety, ten SH3bs confer a capacity for alternatively binding to various peptidoglycan sites in the cell wall. This study presents an initial insight into the structure and potential function of CpAcp SH3bs.

Chromosomal mutants of Saccharomyces cerevisiae affecting the cell wall binding site for killer factor

1978 ◽  
Vol 24 (3) ◽  
pp. 228-237 ◽  
Author(s):  
Karen Al-Aidroos ◽  
H. Bussey
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Wall ◽  
Binding Site ◽  
Functional Groups ◽  
Cell Wall Binding ◽  
Mutant Strains

Fifty-two killer, factor-resistant, nuclear mutants were isolated from sensitive strains of yeast and assorted into three functional groups. All but one mutant owed their resistance to an alteration in the cell wall binding site for killer. In several mutant strains, an alteration at the site of killer binding was associated with a change in the susceptibility of the cell wall to degradation by glusulase. The killer-binding site could be inactivated by periodate but not by promise treatment. The nature of the site is discussed.

scholarly journals 1H NMR Studies of the 5-(Hydroxymethyl)-2'-Deoxyuridine Containing TF1 Binding Site

1996 ◽  
Vol 24 (14) ◽  
pp. 2740-2745 ◽  
Author(s):  
L. B. Pasternack ◽  
J. Bramham ◽  
L. Mayol ◽  
A. Galeone ◽  
X. Jia ◽  
...  
Keyword(s):  
Binding Site ◽  
1H Nmr ◽  
Nmr Studies

Solid state 1H NMR studies of cell wall materials of potatoes

1999 ◽  
Vol 55 (4) ◽  
pp. 883-894 ◽  
Author(s):  
Huiru Tang ◽  
Peter S Belton ◽  
Annie Ng ◽  
Keith W Waldron ◽  
Peter Ryden
Keyword(s):  
Cell Wall ◽  
Solid State ◽  
1H Nmr ◽  
Nmr Studies ◽  
Wall Materials ◽  
Cell Wall Materials

(16)-beta-D-glucan as the cell wall binding site for Debaryomyces hansenii killer toxin

2002 ◽  
Vol 34 (2) ◽  
pp. 95-99 ◽  
Author(s):  
A. Santos ◽  
D. Marquina ◽  
J. Barroso ◽  
J.M. Peinado
Keyword(s):  
Cell Wall ◽  
Binding Site ◽  
Debaryomyces Hansenii ◽  
Killer Toxin ◽  
Cell Wall Binding

scholarly journals Ligand binding remodels protein side chain conformational heterogeneity

2021 ◽  
Author(s):  
Stephanie A. Wankowicz ◽  
Saulo H.P. de Oliveira ◽  
Daniel W. Hogan ◽  
Henry van den Bedem ◽  
James S. Fraser
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Conformational Changes ◽  
Biological Function ◽  
Side Chain ◽  
Conformational Heterogeneity ◽  
X Ray Diffraction ◽  
Nmr Studies ◽  
Static Structure ◽  
X Ray

ABSTRACTWhile protein conformational heterogeneity plays an important role in many aspects of biological function, including ligand binding, its impact has been difficult to quantify. Macromolecular X-ray diffraction is commonly interpreted with a static structure, but it can provide information on both the anharmonic and harmonic contributions to conformational heterogeneity. Here, through multiconformer modeling of time- and space-averaged electron density, we measure conformational heterogeneity of 743 stringently matched pairs of crystallographic datasets that reflect unbound/apo and ligand-bound/holo states. When comparing the conformational heterogeneity of side chains, we observe that when binding site residues become more rigid upon ligand binding, distant residues tend to become more flexible, especially in non-solvent exposed regions. Among ligand properties, we observe increased protein flexibility as the number of hydrogen bonds decrease and relative hydrophobicity increases. Across a series of 13 inhibitor bound structures of CDK2, we find that conformational heterogeneity is correlated with inhibitor features and identify how conformational changes propagate differences in conformational heterogeneity away from the binding site. Collectively, our findings agree with models emerging from NMR studies suggesting that residual side chain entropy can modulate affinity and point to the need to integrate both static conformational changes and conformational heterogeneity in models of ligand binding.

1H NMR studies of the high-affinity Rev binding site of the Rev responsive element of HIV-1 mRNA: base pairing in the core binding element

Biochemistry ◽  
1994 ◽  
Vol 33 (18) ◽  
pp. 5357-5366 ◽  
Author(s):  
Robert D. Peterson ◽  
David P. Bartel ◽  
Jack W. Szostak ◽  
Suzanna J. Horvath ◽  
Juli Feigon
Keyword(s):  
Binding Site ◽  
1H Nmr ◽  
Base Pairing ◽  
Nmr Studies ◽  
High Affinity ◽  
The Core ◽  
Responsive Element ◽  
Hiv 1

Constraints of Opsin Structure on the Ligand-binding Site: Studies with Ring-fused Retinals¶

2002 ◽  
Vol 76 (6) ◽  
pp. 606 ◽  
Author(s):  
Takahiro Hirano ◽  
In Taek Lim ◽  
Don Moon Kim ◽  
Xiang-Guo Zheng ◽  
Kazuo Yoshihara ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Ligand Binding Site
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