Peptide models XXIX. cis – trans Isomerism of peptide bonds: ab initio study on small peptide model compound; the 3D-Ramachandran map of formylglycinamide

2000 ◽  
Vol 500 (1-3) ◽  
pp. 97-111 ◽  
Author(s):  
H.A. Baldoni ◽  
G.N. Zamarbide ◽  
R.D. Enriz ◽  
E.A. Jauregui ◽  
Ö. Farkas ◽  
...  
Keyword(s):  
Ab Initio ◽  
Model Compound ◽  
Ab Initio Study ◽  
Small Peptide ◽  
Peptide Bonds ◽  
Ramachandran Map ◽  
Peptide Models

Peptide models. IX. A complete conformational set of For-Ala-Ala-NH2 from ab inito computations

1994 ◽  
Vol 72 (10) ◽  
pp. 2050-2070 ◽  
Author(s):  
András Perczel ◽  
Michael A. McAllister ◽  
Pál Császár ◽  
Imre G. Csizmadia
Keyword(s):  
Ab Initio ◽  
Minimum Energy ◽  
3D Structure ◽  
Geometry Optimization ◽  
Relative Energy ◽  
Field Methods ◽  
Peptide Bonds ◽  
Assignment Method ◽  
Peptide Models ◽  
Structure Assignment

This paper reports the complete set of minimum energy (i.e. stable) conformations of For-Ala-Ala-NH2 (containing three peptide bonds), computed by ab initio geometry optimization. A more confident structure and relative energy comparison of the 49 different relaxed geometries was possible using the HF/3-21G method as compared to empirical (force field) methods. The analysis of the different conformers resulted in a useful structure database, incorporating 30 different β-turns, which will have some relevance to the description of peptide folding. Spectroscopic (e.g. NMR) consequences of the reported ab initio calculations are also discussed, and a 3D-structure assignment method for proteins is provided.

Peptide models XI. Substitution effects on peptide chains. The magnitude of side-chain–backbone interactions in oligopeptides HCO-(NHCHRCO)n-NH2 for R=CH3. An ab initio study

1995 ◽  
Vol 73 (10) ◽  
pp. 1563-1572 ◽  
Author(s):  
M.A. McAllister ◽  
G. Endredi ◽  
J. Ladik ◽  
W. Viviani ◽  
A. Perczel ◽  
...  
Keyword(s):  
Ab Initio ◽  
Stabilization Energy ◽  
Side Chain ◽  
Substitution Effects ◽  
Appreciable Effect ◽  
Ab Initio Study ◽  
Peptide Models ◽  
Stabilization Effect

The stabilization effect of the Me group with respect to H has been determined for peptides of the type HCO-(NH-CHR-CO)n-NH2 for 1 ≤ n ≤ 3. It was found that for the Me group the stabilization energy was in the vicinity of 5.4 kcal/mol. The site of substitution had no appreciable effect on the stabilization energy. The stabilization energy for monomethyl substitution (R=CH3) ranged from 5.21 to 5.60 kcal/mol. For dimethyl substitution the values were between 10.53 and 10.81 kcal/mol, and for trimethyl substitution it was 15.99 kcal/mol. Keywords: stabilization effects of substituents, oligopeptide conformations, ab initio study on HCO-(NHCHRCO)n-NH2.

Peptide models XXIV: An ab initio study on N-formyl-L-prolinamide with trans peptide bond. The existence or non-existence of αL and ϵL conformations

1999 ◽  
Vol 465 (1) ◽  
pp. 79-91 ◽  
Author(s):  
Hector A. Baldoni ◽  
Ana M. Rodriguez ◽  
Miguel A. Zamora ◽  
Graciela N. Zamarbide ◽  
Ricardo D. Enriz ◽  
...  
Keyword(s):  
Ab Initio ◽  
Peptide Bond ◽  
Ab Initio Study ◽  
Peptide Models

An ab initio study of a model compound of penicillins

1999 ◽  
Vol 491 (1-3) ◽  
pp. 177-185 ◽  
Author(s):  
A. Peña-Gallego ◽  
E.M. Cabaleiro-Lago ◽  
A. Fernández-Ramos ◽  
J.M. Hermida-Ramón ◽  
E. Martı́nez-Núñez
Keyword(s):  
Ab Initio ◽  
Model Compound ◽  
Ab Initio Study
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