locally enhanced sampling
Recently Published Documents


TOTAL DOCUMENTS

21
(FIVE YEARS 0)

H-INDEX

9
(FIVE YEARS 0)

2020 ◽  
Vol 153 (12) ◽  
pp. 121103
Author(s):  
Victor Ovchinnikov ◽  
Simone Conti ◽  
Martin Karplus


F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 65
Author(s):  
Kevin Trujillo ◽  
Tasso Papagiannopoulos ◽  
Kenneth W. Olsen

Like many hemoglobins, the structure of the dimeric hemoglobin from the clam Scapharca inaequivalvis is a “closed bottle” since there is no direct tunnel from the oxygen binding site on the heme to the solvent.  The proximal histidine faces the dimer interface, which consists of the E and F helicies.  This is significantly different from tetrameric vertebrate hemoglobins and brings the heme groups near the subunit interface. The subunit interface is also characterized by an immobile, hydrogen-bonded network of water molecules.  Although there is data which is consistent with the histidine gate pathway for ligand escape, these aspects of the structure would seem to make that pathway less likely. Locally enhanced sampling molecular dynamics are used here to suggest alternative pathways in the wild-type and six mutant proteins. In most cases the point mutations change the selection of exit routes observed in the simulations. Exit via the histidine gate is rarely seem although oxygen molecules do occasionally cross over the interface from one subunit to the other. The results suggest that changes in flexibility and, in some cases, creation of new cavities can explain the effects of the mutations on ligand exit paths.



2012 ◽  
Vol 3 (5) ◽  
pp. 1503 ◽  
Author(s):  
Richard T. Bradshaw ◽  
Pietro G. A. Aronica ◽  
Edward W. Tate ◽  
Robin J. Leatherbarrow ◽  
Ian R. Gould


2009 ◽  
Vol 113 (41) ◽  
pp. 13596-13603 ◽  
Author(s):  
Liang Xu ◽  
Xin Liu ◽  
Weijie Zhao ◽  
Xicheng Wang






2005 ◽  
Vol 45 (supplement) ◽  
pp. S151
Author(s):  
S. Yamasaki ◽  
S. Nakamura ◽  
T. Terada ◽  
K. Shimizu


Sign in / Sign up

Export Citation Format

Share Document