scholarly journals Characterization of a Buried Neutral Histidine inBacillus circulansXylanase:  Internal Dynamics and Interaction with a Bound Water Molecule†

Biochemistry ◽  
1998 ◽  
Vol 37 (7) ◽  
pp. 1810-1818 ◽  
Author(s):  
Gregory P. Connelly ◽  
Lawrence P. McIntosh
Keyword(s):  
Water Molecule ◽  
Bound Water ◽  
Internal Dynamics

Dynamic Characterization of the Water Binding Loop in the P-Type Cardiotoxin:  Implication for the Role of the Bound Water Molecule†

Biochemistry ◽  
2001 ◽  
Vol 40 (43) ◽  
pp. 12782-12794 ◽  
Author(s):  
Shih-Che Sue ◽  
Harold C. Jarrell ◽  
Jean-Robert Brisson ◽  
Wen-guey Wu
Keyword(s):  
Water Molecule ◽  
Bound Water ◽  
Dynamic Characterization ◽  
Water Binding ◽  
P Type ◽  
Binding Loop

scholarly journals How wide is the window opened by high-resolution relaxometry on the internal dynamics of proteins in solution?

2021 ◽  
Vol 75 (2-3) ◽  
pp. 119-131
Author(s):  
Albert A. Smith ◽  
Nicolas Bolik-Coulon ◽  
Matthias Ernst ◽  
Beat H. Meier ◽  
Fabien Ferrage
Keyword(s):  
Nuclear Magnetic Resonance ◽  
High Resolution ◽  
High Field ◽  
Rotational Diffusion ◽  
Relaxation Data ◽  
Internal Dynamics ◽  
Nmr Relaxometry ◽  
Analysis Of Dynamics

AbstractThe dynamics of molecules in solution is usually quantified by the determination of timescale-specific amplitudes of motions. High-resolution nuclear magnetic resonance (NMR) relaxometry experiments—where the sample is transferred to low fields for longitudinal (T1) relaxation, and back to high field for detection with residue-specific resolution—seeks to increase the ability to distinguish the contributions from motion on timescales slower than a few nanoseconds. However, tumbling of a molecule in solution masks some of these motions. Therefore, we investigate to what extent relaxometry improves timescale resolution, using the “detector” analysis of dynamics. Here, we demonstrate improvements in the characterization of internal dynamics of methyl-bearing side chains by carbon-13 relaxometry in the small protein ubiquitin. We show that relaxometry data leads to better information about nanosecond motions as compared to high-field relaxation data only. Our calculations show that gains from relaxometry are greater with increasing correlation time of rotational diffusion.

scholarly journals Successive light-induced two electron transfers in a Ru–Fe supramolecular assembly: from Ru–Fe(ii)–OH2 to Ru–Fe(iv)–oxo

2015 ◽  
Vol 6 (4) ◽  
pp. 2323-2327 ◽  
Author(s):  
Christian Herrero ◽  
Annamaria Quaranta ◽  
Marie Sircoglou ◽  
Katell Sénéchal-David ◽  
Aurélie Baron ◽  
...  
Keyword(s):  
Water Molecule ◽  
Visible Light ◽  
Bound Water ◽  
Supramolecular Assembly ◽  
Light Activation ◽  
Visible Light Activation ◽  
Electron Transfers

A RuII–FeII chromophore–catalyst assembly performs the visible-light activation of a metal-bound water molecule to form a metal oxo species responsible for the oxidation of a substrate.

Low-temperature FTIR spectroscopy provides evidence for protein-bound water molecules in eubacterial light-driven ion pumps

2018 ◽  
Vol 20 (5) ◽  
pp. 3165-3171 ◽  
Author(s):  
Yurika Nomura ◽  
Shota Ito ◽  
Miwako Teranishi ◽  
Hikaru Ono ◽  
Keiichi Inoue ◽  
...  
Keyword(s):  
Low Temperature ◽  
Water Molecule ◽  
Ftir Spectroscopy ◽  
Proton Pump ◽  
Bound Water ◽  
Water Molecules ◽  
Ion Pumps ◽  
Functional Determinant ◽  
Ftir Study ◽  
Hydrogen Bonded

The present FTIR study showed that eubacterial light-driven H+, Na+ and Cl− pump rhodopsins contain strongly hydrogen-bonded water molecule, the functional determinant of light-driven proton pump. This explains well the asymmetric functional conversions of light-driven ion pumps.

scholarly journals Mutagenesis and crystallographic studies of the catalytic residues of the papain family protease bleomycin hydrolase: new insights into active-site structure

2006 ◽  
Vol 401 (2) ◽  
pp. 421-428 ◽  
Author(s):  
Paul A. O'Farrell ◽  
Leemor Joshua-Tor
Keyword(s):  
Water Molecule ◽  
Active Site ◽  
Bound Water ◽  
Active Site Residues ◽  
Site Structure ◽  
Active Site Cysteine ◽  
C Terminus ◽  
Bleomycin Hydrolase ◽  
Active Site Mutants

Bleomycin hydrolase (BH) is a hexameric papain family cysteine protease which is involved in preparing peptides for antigen presentation and has been implicated in tumour cell resistance to bleomycin chemotherapy. Structures of active-site mutants of yeast BH yielded unexpected results. Replacement of the active-site asparagine with alanine, valine or leucine results in the destabilization of the histidine side chain, demonstrating unambiguously the role of the asparagine residue in correctly positioning the histidine for catalysis. Replacement of the histidine with alanine or leucine destabilizes the asparagine position, indicating a delicate arrangement of the active-site residues. In all of the mutants, the C-terminus of the protein, which lies in the active site, protrudes further into the active site. All mutants were compromised in their catalytic activity. The structures also revealed the importance of a tightly bound water molecule which stabilizes a loop near the active site and which is conserved throughout the papain family. It is displaced in a number of the mutants, causing destabilization of this loop and a nearby loop, resulting in a large movement of the active-site cysteine. The results imply that this water molecule plays a key structural role in this family of enzymes.

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