A test of ligand field molecular mechanics as an efficient alternative to QM/MM for modelling metalloproteins: the structures of oxidised type I copper centres

2006 ◽  
pp. 2551 ◽  
Author(s):  
Robert James Deeth
Keyword(s):  
Molecular Mechanics ◽  
Ligand Field ◽  
Type I ◽  
Efficient Alternative

Integration of Ligand Field Molecular Mechanics in Tinker

2015 ◽  
Vol 55 (6) ◽  
pp. 1282-1290 ◽  
Author(s):  
Marco Foscato ◽  
Robert J. Deeth ◽  
Vidar R. Jensen
Keyword(s):  
Molecular Mechanics ◽  
Ligand Field

Effect of a hydrophobic amino acid at position (i −1) on the stability of β-turns in hydrophilic pentapeptides as studied by NMR and molecular mechanics

1995 ◽  
Vol 73 (7) ◽  
pp. 972-980
Author(s):  
Xiaohong Liu ◽  
Serafin Fraga ◽  
Albin Otter ◽  
George Kotovych ◽  
Paul G. Scott
Keyword(s):  
Amino Acid ◽  
Molecular Mechanics ◽  
Ideal Type ◽  
Type I ◽  
Hydrophobic Amino Acid ◽  
Molecular Mechanics Calculations ◽  
Nmr Data ◽  
Nmr Study ◽  
Protected Tetrapeptide ◽  
The Stability

A detailed NMR study of the peptide NAc-FDEKA-NH2 in aqueous and in CD3OH/H2O solutions as well as the N-acetylpentapeptide amides YDEKA, VDEKA, GDEKA, and the protected tetrapeptide NAc-DEKA-NH2 in methanolic solutions indicates the importance of the first amino acid (at i −1) on stabilizing the type I β-turn. The data illustrate the hydrophobic stabilization of this turn, which is present in FDEKA, YDEKA, and VDEKA. For GDEKA and DEKA, the NMR data indicate that this turn is not present. Molecular mechanics calculations support this conclusion and indicate that for FDEKA and GDEKA the type I β-turn is distorted in both the vacuum and the solvated structures. For the solvated structures, the Cα(i) − Cα(i + 3) distance is 4.87 Å for FDEKA and 6.00 Å for GDEKA, which are to be compared with the value of 4.64 Å for an ideal type I β-turn, i.e., the distortion is far greater in GDEKA than in FDEKA. The calculations can be interpreted to indicate the presence of two major conformations in solution. Keywords: β-turns, FDEKA, pentapeptide.

Modeling of the Various Minima on the Potential Energy Surface of Bispidine Copper(II) Complexes: A Further Test for Ligand Field Molecular Mechanics

2008 ◽  
Vol 47 (20) ◽  
pp. 9518-9527 ◽  
Author(s):  
Alexander Bentz ◽  
Peter Comba ◽  
Robert J. Deeth ◽  
Marion Kerscher ◽  
Björn Seibold ◽  
...  
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Molecular Mechanics ◽  
Energy Surface ◽  
Ligand Field
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