scholarly journals How Active-Site Protonation State Influences the Reactivity and Ligation of the Heme in Chlorite Dismutase

2010 ◽  
Vol 132 (16) ◽  
pp. 5711-5724 ◽  
Author(s):  
Bennett R. Streit ◽  
Béatrice Blanc ◽  
Gudrun S. Lukat-Rodgers ◽  
Kenton R. Rodgers ◽  
Jennifer L. DuBois
Keyword(s):  
Active Site ◽  
Protonation State ◽  
Chlorite Dismutase

Distinguishing two groups of flavin reductases by analyzing the protonation state of an active site carboxylic acid

2011 ◽  
Vol 79 (7) ◽  
pp. 2076-2085 ◽  
Author(s):  
Verónica I. Dumit ◽  
Néstor Cortez ◽  
G. Matthias Ullmann
Keyword(s):  
Carboxylic Acid ◽  
Active Site ◽  
Protonation State

Catalytic Roles of Active-Site Amino Acid Residues of Coenzyme B12-Dependent Diol Dehydratase:  Protonation State of Histidine and Pull Effect of Glutamate

2004 ◽  
Vol 126 (49) ◽  
pp. 16207-16216 ◽  
Author(s):  
Takashi Kamachi ◽  
Tetsuo Toraya ◽  
Kazunari Yoshizawa
Keyword(s):  
Amino Acid ◽  
Active Site ◽  
Coenzyme B12 ◽  
Amino Acid Residues ◽  
Protonation State ◽  
Diol Dehydratase

scholarly journals X-ray crystallographic studies on the hydrogen isotope effects of green fluorescent protein at sub-ångström resolutions

2019 ◽  
Vol 75 (12) ◽  
pp. 1096-1106 ◽  
Author(s):  
Yang Tai ◽  
Kiyofumi Takaba ◽  
Yuya Hanazono ◽  
Hoang-Anh Dao ◽  
Kunio Miki ◽  
...  
Keyword(s):  
Green Fluorescent Protein ◽  
Active Site ◽  
Hydrogen Isotope ◽  
Fluorescent Protein ◽  
Isotope Effects ◽  
Protonation State ◽  
X Ray ◽  
Two Samples ◽  
Deuterated Proteins ◽  
Green Fluorescent

Hydrogen atoms are critical to the nature and properties of proteins, and thus deuteration has the potential to influence protein function. In fact, it has been reported that some deuterated proteins show different physical and chemical properties to their protiated counterparts. Consequently, it is important to investigate protonation states around the active site when using deuterated proteins. Here, hydrogen isotope effects on the S65T/F99S/M153T/V163A variant of green fluorescent protein (GFP), in which the deprotonated B form is dominant at pH 8.5, were investigated. The pH/pD dependence of the absorption and fluorescence spectra indicates that the protonation state of the chromophore is the same in protiated GFP in H2O and protiated GFP in D2O at pH/pD 8.5, while the pK a of the chromophore became higher in D2O. Indeed, X-ray crystallographic analyses at sub-ångström resolution revealed no apparent changes in the protonation state of the chromophore between the two samples. However, detailed comparisons of the hydrogen OMIT maps revealed that the protonation state of His148 in the vicinity of the chromophore differed between the two samples. This indicates that protonation states around the active site should be carefully adjusted to be the same as those of the protiated protein when neutron crystallographic analyses of proteins are performed.

Compound I of Nitric Oxide Synthase:  The Active Site Protonation State

2007 ◽  
Vol 129 (11) ◽  
pp. 3182-3188 ◽  
Author(s):  
Kyung-Bin Cho ◽  
Etienne Derat ◽  
Sason Shaik
Keyword(s):  
Nitric Oxide ◽  
Nitric Oxide Synthase ◽  
Active Site ◽  
Protonation State ◽  
Compound I ◽  
Oxide Synthase

Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors

2014 ◽  
Vol 70 (2) ◽  
pp. 461-470 ◽  
Author(s):  
Petr Pachl ◽  
Milan Fábry ◽  
Ivan Rosenberg ◽  
Ondřej Šimák ◽  
Pavlína Řezáčová ◽  
...  
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Specific Inhibitor ◽  
Detailed Comparison ◽  
Atomic Resolution ◽  
Phosphate Anion ◽  
Protonation State ◽  
Interatomic Distances ◽  
Enzyme Active Site ◽  
Resolution Structure

The human 5′(3′)-deoxyribonucleotidases catalyze the dephosphorylation of deoxyribonucleoside monophosphates to the corresponding deoxyribonucleosides and thus help to maintain the balance between pools of nucleosides and nucleotides. Here, the structures of human cytosolic deoxyribonucleotidase (cdN) at atomic resolution (1.08 Å) and mitochondrial deoxyribonucleotidase (mdN) at near-atomic resolution (1.4 Å) are reported. The attainment of an atomic resolution structure allowed interatomic distances to be used to assess the probable protonation state of the phosphate anion and the side chains in the enzyme active site. A detailed comparison of the cdN and mdN active sites allowed the design of a cdN-specific inhibitor.

Effects of protonation state of Asp181 and position of active site water molecules on the conformation of PTP1B

2013 ◽  
Vol 81 (5) ◽  
pp. 788-804 ◽  
Author(s):  
Ahmet Özcan ◽  
Elif Ozkirimli Olmez ◽  
Burak Alakent
Keyword(s):  
Active Site ◽  
Water Molecules ◽  
Protonation State ◽  
Site Water
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