scholarly journals Replacement effects of neutral amino acid residues of different molecular volumes in the retinal binding cavity of bacteriorhodopsin on the dynamics of its primary process

1996 ◽  
Vol 70 (6) ◽  
pp. 2875-2881 ◽  
Author(s):  
S.L. Logunov ◽  
M.A. el-Sayed ◽  
J.K. Lanyi
Cornea ◽  
2013 ◽  
Vol 32 (5) ◽  
pp. 680-688 ◽  
Author(s):  
Cen Li ◽  
Lei Li ◽  
Rui Cheng ◽  
Zhiyu Dai ◽  
Chaoyang Li ◽  
...  

2015 ◽  
Vol 14 (4) ◽  
pp. 792-800 ◽  
Author(s):  
Atiyeh Mahdavi ◽  
Reza H. Sajedi ◽  
Saman Hosseinkhani ◽  
Majid Taghdir

Mnemiopsin, a Ca2+-regulated photoprotein isolated fromMnemiopsis leidyi, belongs to the family of ctenophore photoproteins. While there are no charged amino acid residues in the coelenterazine binding cavity of cnidarian photoproteins, ctenophore photoproteins have a positively charged residue (Arg) in this region.


2014 ◽  
Vol 58 (7) ◽  
pp. 3914-3920 ◽  
Author(s):  
Takuma Oguri ◽  
Takamitsu Furuyama ◽  
Takashi Okuno ◽  
Yoshikazu Ishii ◽  
Kazuhiro Tateda ◽  
...  

ABSTRACTMox-1 is a unique plasmid-mediated class C β-lactamase that hydrolyzes penicillins, cephalothin, and the expanded-spectrum cephalosporins cefepime and moxalactam. In order to understand the unique substrate profile of this enzyme, we determined the X-ray crystallographic structure of Mox-1 β-lactamase at a 1.5-Å resolution. The overall structure of Mox-1 β-lactamase resembles that of other AmpC enzymes, with some notable exceptions. First, comparison with other enzymes whose structures have been solved reveals significant differences in the composition of amino acids that make up the hydrogen-bonding network and the position of structural elements in the substrate-binding cavity. Second, the main-chain electron density is not observed in two regions, one containing amino acid residues 214 to 216 positioned in the Ω loop and the other in the N terminus of the B3 β-strand corresponding to amino acid residues 303 to 306. The last two observations suggest that there is significant structural flexibility of these regions, a property which may impact the recognition and binding of substrates in Mox-1. These important differences allow us to propose that the binding of moxalactam in Mox-1 is facilitated by the avoidance of steric clashes, indicating that a substrate-induced conformational change underlies the basis of the hydrolytic profile of Mox-1 β-lactamase.


2016 ◽  
Vol 15 (5) ◽  
pp. 691-704 ◽  
Author(s):  
Ludmila P. Burakova ◽  
Galina A. Stepanyuk ◽  
Elena V. Eremeeva ◽  
Eugene S. Vysotski

We suggest that in the inner cavity of ctenophore photoproteins coelenterazine is bound as a 2-peroxy anion which is stabilized owing to Coulomb interaction with a guanidinium group of R41 paired with Y204.


1987 ◽  
Vol 57 (01) ◽  
pp. 017-019 ◽  
Author(s):  
Magda M W Ulrich ◽  
Berry A M Soute ◽  
L Johan M van Haarlem ◽  
Cees Vermeer

SummaryDecarboxylated osteocalcins were prepared and purified from bovine, chicken, human and monkey bones and assayed for their ability to serve as a substrate for vitamin K-dependent carboxylase from bovine liver. Substantial differences were observed, especially between bovine and monkey d-osteocalcin. Since these substrates differ only in their amino acid residues 3 and 4, it seems that these residues play a role in the recognition of a substrate by hepatic carboxylase.


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