Peptide models XLV: conformational properties of N-formyl-L-methioninamide and its relevance to methionine in proteins.
The conformational space of the most biologically significant backbone folds of a suitable methionine peptide model was explored by density functional computational method. Using a medium [6-31G(d)] and a larger basis set [6-311++G(2d,2p)], the systematic exploration of low-energy backbone structures restricted for the "L-region" in the Ramachandran map of N-formyl-L-methioninamide results in conformers corresponding to the building units of an extended backbone structure (betaL), an inverse gamma-turn (gammaL), or a right-handed helical structure (alphaL). However, no poly-proline II type (epsilonL) fold was found, indicating that this conformer has no intrinsic stability, and highlighting the effect of molecular environment in stabilizing this backbone structure. This is in agreement with the abundance of the epsilonL-type backbone conformation of methionine found in proteins. Stability properties (DeltaE) and distinct backbone-side-chain interactions support the idea that specific intramolecular contacts are operative in the selection of the lowest energy conformers. Apart from the number of different folds, all stable conformers are within a 10 kcal x mol(-1) energy range, indicating the highly flexible behavior of methionine. This conformational feature can be important in supporting catalytic processes, facilitating protein folding and dimerization via metal ion binding. In both of the biological examples discussed (HIV-1 reverse transcriptase and PcoC copper-resistant protein), the conformational properties of Met residues were found to be of key importance. Spatial proximity to other types of residues or the same type of residue seems to be crucial for the structural integrity of a protein, whether Met is buried or exposed.
Láng
András
A
Department of Organic Chemistry, Eötvös Loránd University, Budapest, Hungary.
Csizmadia
Imre G
IG
Perczel
András
A
D000596:Amino Acids / Q000737:chemistry*; D001703:Biophysics / Q000379:methods; D030562:Databases, Protein; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry; D054303:HIV Reverse Transcriptase / Q000737:chemistry; D006860:Hydrogen Bonding; D008715:Methionine / Q000031:analogs & derivatives / Q000737:chemistry*; D008954:Models, Biological; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D009239:N-Formylmethionine / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D011392:Proline / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods; D055672:Static Electricity; D013816:Thermodynamics
D000596:Amino Acids; D029968:Escherichia coli Proteins; C462541:PcoC protein, E coli; D010455:Peptides; D011506:Proteins; D009239:N-Formylmethionine; D011392:Proline; D008715:Methionine; D054303:HIV Reverse Transcriptase; C018594:methioninamide