Chain Dimension and Effective Potential Energy of Globular Proteins

1978 ◽  
Vol 11 (4) ◽  
pp. 644-647 ◽  
Author(s):  
Ken Nishikawa ◽  
Tatsuo Ooi
Keyword(s):  
Potential Energy ◽  
Effective Potential ◽  
Globular Proteins ◽  
Effective Potential Energy

scholarly journals The enzyme aromatic amine dehydrogenase induces a substrate conformation crucial for promoting vibration that significantly reduces the effective potential energy barrier to proton transfer

2008 ◽  
Vol 5 (suppl_3) ◽  
pp. 225-232 ◽  
Author(s):  
Linus O Johannissen ◽  
Nigel S Scrutton ◽  
Michael J Sutcliffe
Keyword(s):  
Potential Energy ◽  
Proton Transfer ◽  
Aromatic Amine ◽  
Effective Potential ◽  
Energy Barrier ◽  
Transfer Event ◽  
Effective Potential Energy ◽  
Potential Energy Barrier ◽  
Mechanical Methods ◽  
Amine Dehydrogenase

The role of promoting vibrations in enzymic reactions involving hydrogen tunnelling is contentious. While models incorporating such promoting vibrations have successfully reproduced and explained experimental observations, it has also been argued that such vibrations are not part of the catalytic effect. In this study, we have employed combined quantum mechanical/molecular mechanical methods with molecular dynamics and potential energy surface calculations to investigate how enzyme and substrate motion affects the energy barrier to proton transfer for the rate-limiting H-transfer step in aromatic amine dehydrogenase (AADH) with tryptamine as substrate. In particular, the conformation of the iminoquinone adduct induced by AADH was found to be essential for a promoting vibration identified previously—this lowers significantly the ‘effective’ potential energy barrier, that is the barrier which remains to be surmounted following collective, thermally equilibrated motion attaining a quantum degenerate state of reactants and products. When the substrate adopts a conformation similar to that in the free iminoquinone, this barrier was found to increase markedly. This is consistent with AADH facilitating the H-transfer event by holding the substrate in a conformation that induces a promoting vibration.

Effective potential energy surface of HD16O for calculation of highly excited states of nν3 and ν1 + nν3 types

2015 ◽  
Vol 28 (2) ◽  
pp. 133-138 ◽  
Author(s):  
B. A. Voronin ◽  
S. N. Yurchenko ◽  
S. S. Voronina ◽  
A. V. Kozodoev ◽  
J. Tennyson
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Excited States ◽  
Effective Potential ◽  
Energy Surface ◽  
Effective Potential Energy
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