scholarly journals Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration

Structure ◽  
2011 ◽  
Vol 19 (4) ◽  
pp. 523-533 ◽  
Author(s):  
Timothy D. Fenn ◽  
Michael J. Schnieders ◽  
Marat Mustyakimov ◽  
Chuanjie Wu ◽  
Paul Langan ◽  
...  
2020 ◽  
Vol 65 (6) ◽  
pp. 1058-1064
Author(s):  
С.В. Пастон ◽  
◽  
А.М. Поляничко ◽  
О.В. Шуленина ◽  
Д.Н. Осинникова ◽  
...  

The aqueous environment and ionic surrounding are the most important factors determining the conformation of DNA and its functioning in the cell. The specificity of the interaction between DNA and cations is especially pronounced with a decrease in water activity. In this work, we studied the B-A transition in high molecular weight DNA with a decrease of humidity in the film with different contents of Na+ ions using FTIR spectroscopy. The IR spectrum of DNA is not only very sensitive to the state of its secondary structure, but also allows us to estimate the amount of water bound to DNA. Upon dehydration of the DNA film, changes characteristic of the B-A transition were observed in the IR absorption spectrum. Using thermogravimetric analysis, it was shown that the degree of DNA hydration reaches the saturation level at a relative humidity of 60% and decreases slightly upon further drying. It has been established that with increasing Na+ concentration, the amount of water strongly bound to DNA decreases. Along with it, sodium ions destroy the hydration shell of DNA and are able to interact directly with phosphate groups.


2008 ◽  
Vol 18 (5) ◽  
pp. 593-600 ◽  
Author(s):  
Matthew P Blakeley ◽  
Paul Langan ◽  
Nobuo Niimura ◽  
Alberto Podjarny

ACS Catalysis ◽  
2018 ◽  
Vol 8 (9) ◽  
pp. 8058-8069 ◽  
Author(s):  
Zhihong Li ◽  
Xiaoshuai Zhang ◽  
Qingqing Wang ◽  
Chunran Li ◽  
Nianying Zhang ◽  
...  

Nature ◽  
1972 ◽  
Vol 235 (5337) ◽  
pp. 328-329 ◽  
Author(s):  
JACQUES J. VERBIST ◽  
MOGENS S. LEHMANN ◽  
THOMAS F. KOETZLE ◽  
WALTER C. HAMILTON

2008 ◽  
Vol 64 (a1) ◽  
pp. C247-C248
Author(s):  
N. Shimizu ◽  
H. Yoshikawa ◽  
M. Adachi ◽  
T. Tamada ◽  
K. Hidaka ◽  
...  

2014 ◽  
Vol 70 (a1) ◽  
pp. C1207-C1207
Author(s):  
Leighton Coates

β-lactam antibiotics have been used effectively over several decades against many types of highly virulent bacteria. The predominant cause of resistance to these antibiotics in Gram-negative bacterial pathogens is the production of serine β-lactamase enzymes. A key aspect of the class A serine β-lactamase mechanism that remains unresolved and controversial is the identity of the residue acting as the catalytic base during the acylation reaction. Multiple mechanisms have been proposed for the formation of the acyl-enzyme intermediate that are predicated on understanding the protonation states and hydrogen-bonding interactions among the important residues involved in substrate binding and catalysis of these enzymes. For resolving a controversy of this nature surrounding the catalytic mechanism, neutron crystallography is a powerful complement to X-ray crystallography that can explicitly determine the location of deuterium atoms in proteins, thereby directly revealing the hydrogen-bonding interactions of important amino acid residues. Neutron crystallography was used to unambiguously reveal the ground-state active site protonation states and the resulting hydrogen-bonding network in two ligand-free Toho-1 β-lactamase mutants which provided remarkably clear pictures of the active site region prior to substrate binding and subsequent acylation [1,2] and an acylation transition-state analog, benzothiophene-2-boronic acid (BZB), which was also isotopically enriched with 11B. The neutron structure revealed the locations of all deuterium atoms in the active site region and clearly indicated that Glu166 is protonated in the BZB transition-state analog complex. As a result, the complete hydrogen-bonding pathway throughout the active site region could then deduced for this protein-ligand complex that mimics the acylation tetrahedral intermediate [3].


2013 ◽  
Vol 55 (1) ◽  
pp. 47-51
Author(s):  
Taro TAMADA ◽  
Motoyasu ADACHI ◽  
Kazuo KURIHARA ◽  
Ryota KUROKI

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