ISSN:
1573-5001
Keywords:
conformational equilibrium
;
empirical force fields
;
maximum entropy method
;
molecular dynamics
;
Monte Carlo methods
;
opioid peptides
Source:
Springer Online Journal Archives 1860-2000
Topics:
Biology
,
Chemistry and Pharmacology
Notes:
Abstract A method is proposed to determine the conformational equilibrium of flexible polypeptides in solution, using the data provided by NMR spectroscopy and theoretical conformational calculations. The algorithm consists of the following three steps: (i) search of the conformational space in order to find conformations with reasonably low energy; (ii) simulation of the NOE spectrum and vicinal coupling constants for each of the low energy conformations; and (iii) determining the statistical weights of the conformations, by means of the maximum-entropy method, in order to obtain the best fit of the averaged NOE intensities and coupling constants to the experimental quantities. The method has been applied to two cyclic enkephalin analogs: DNS1-c-[d-A2bu2,Trp4,Leu5]enkephalin (ENKL) and DNS1-c-[d-A2bu2,Trp4,d-Leu5]enkephalin (ENKD). NMR measurements were carried out in deuterated dimethyl sulfoxide. Two techniques were used in conformational search: the electrostatically driven Monte Carlo method (EDMC), which results in extensive search of the conformational space, but gives only energy minima, and the molecular dynamics method (MD), which results in a more accurate, but also more confined search. In the case of EDMC calculations, conformational energy was evaluated using the ECEPP/3 force field augmented with the SRFOPT solvation-shell model, while in the case of MD the AMBER force field was used with explicit solvent molecules. Both searches and subsequent fitting of conformational weights to NMR data resulted in similar conformations of the cyclic part of the peptides studied. For both ENKL and ENKD a common feature of the low-energy solution conformations is the presence of a type II′ or type IV β-turn at residues 3 and 4; the ECEPP/3 force field also gives a remarkable content of type III β-turn. These β-turns are tighter in the case of ENKL, which is reflected in different distributions of the d-A2bu(NγH)...d-A2bu(CO) and d-A2bu(NγH)...Gly3(CO) hydrogen-bonding distances, indicating that the d-A2bu(NγH) amide proton is more shielded from the solvent than in the case of ENKD. This finding conforms with the results of temperature coefficient data of the d-A2bu(NγH) proton. It has also been found that direct (MD) or Boltzmann (EDMC) averages of the observables do not exactly conform with the measured values, even when explicit solvent molecules are included. This suggests that improving force-field parameters might be necessary in order to obtain reliable conformational ensembles in computer simulations, without the aid of experimental data.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1023/A:1008349424452
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