Alanine conformational studies

A Conformational Study of the l-Alanine Residue in Polypeptides by Ab Initio UC NMR Shielding Calculation... 

R. D. Brown, A.P. Pierlot, MiUimeter-wave spectroscopy of biomolecules alanine, J. Am. Chem. Soc. 115 (1993) 9687 S.G. Stepanian, l.D. Reva, E.D. Radchenko, L. Adamowicz, Conformational Behavior of a-Alanine. Matrix-Isolation Infrared and Theoretical DFT and ab Initio Study, J. Phys. Chem. A 102 (1998) 4623 B. Lambie, R. Ramaekers, G. Maes, On the contribution of intramolecular H-bonding entropy to the conformational stability of alanine conformations, Spectrochim. Acta A 59 (2003) 1387. 

Fig.l Structures and designation of the a-alanine conformers, Forms I and Ila were already known before. Conformer VI was generated and characterized for the first time in the studies of Bazso eta/. and Nunes eta/. Adapted with permission from C. M. Nunes, L. Lapinski, R. Fausto and I. Reva, J. Chem. Phys., 2013,138,125101 Copyright 2013, AIR Publishing LLC,... 

V. Renugopalakrishnan Could you comment on the conformation of L-alanine dipeptide in water What values do you observe for 0 and Have you conducted conformational studies using your method in non-aqueous solvents ... 

Rittner et al. have performed the conformational study of alanine and valine methyl esters (Fig. 2a), which do not show zwitterionic structures... 

The conformational studies of alanine and valine methyl esters, which do not show zwitterionic structures in solution, has been studied by Rittner and co-workers. by NMR and theoretical calculations. The Vhh couplings have been measured for valine methyl ester in solvents of different dielectrical constants (a) and compared with the theoretically calculated J values for the predicted conformers. An analysis of the obtained data has led the authors to the conclusion that the interplay between steric hindrance and hyperconjugation is the responsible force for determining the conformational preferences of alanine and valine methyl esters. 

Synthetic polypeptides consist of repeating sequences of certain amino acids and their structures are not as complicated as those of proteins. Eor this reason, synthetic polypeptides are sometimes used as model compounds for proteins. Their preferred conformations are classified as a helix, P sheet, 0) helix and so on. High-resolution solid-state C NMR spectroscopy has proved to be a very powerful tool for determining the structure of polypeptides in the crystalline state. Eor example, C CP MAS NMR spectra of solid poly(L-alanine) ([Ala] J show the Ca, Cp and C=0 carbon signals to be well resolved between the a helix and P sheet forms. The chemical shifts of the Ca and C=0 carbons of the a helix are displaced sig nilicantly to high frequency by 4.2 and 4.6 ppm, re spectively, relative to those of the P sheet form, while the shift of the Cp carbon of the a heUx is displaced to low frequency by about 5 ppm with respect to that of the P sheet. Eor this reason, the value of the C shift can be used to describe the local conformation. In addition, the C shifts of randomly coiled [Ala] in trifluoroacetic acid solution have values between those of the a helix and P sheet forms. The absolute C shifts of the Ca and Cp carbons are affected by the chemical structure of the individual amino acid residues and can be used effectively for conformational studies of particular amino acid residues in polypeptides and proteins. On the other hand, the C=0 shifts do not seem to be affected by residue structure and can be used for diagnosing the main chain conformation. 

Before analyzing in detail the conformational behaviour of y9-peptides, it is instructive to look back into the origins and the context of this discovery. The possi-bihty that a peptide chain consisting exclusively of y9-amino acid residues may adopt a defined secondary structure was raised in a long series of studies which began some 40 years ago, on y9-amino acid homopolymers (nylon-3 type polymers), such as poly(/9-alanine) 3 [14, 15], poly(y9-aminobutanoic acid) 4 [16-18], poly(a-dialkyl-/9-aminopropanoic acid) 5 ]19], poly(y9-L-aspartic acid) 6 ]20, 21], and poly-(a-alkyl-/9-L-aspartate) 7 [22-36] (Fig. 2.1). 

In one of the very first realistic computational studies of PECD effects, performed for the amino acid alanine [51], it was noted that different results were obtained at each of three fixed geometries corresponding to low lying conformations identified in previous structure investigations [69-71]. A later combined experimental-theoretical study of PECD in 3-hydroxytetrahydrofuran [61] further looked at the influence of presumed conformation and concluded that while the predicted cross-section, a, and p parameters were mildly affected by conformation, the chiral parameters were much more strongly... 

Stepanian, S. G., Reva, D., Radchenko, E. D., Adamowicz, L., 1998b, Conformational Behavior of Alanine. Matrix-Isolation Infrared and Theoretical DFT and ab Initio Study , J. Phys. Chem. A, 102, 4623. 

Kikuchi, O., T. Natsui, and T. Kozaki. 1990a. MNDO Effective Charge Model Study of Conformations of Zwitterionic and Neutral Forms of Glycine, Alanine and Serine in the Gas Phase and in Solution. J. Mol. Struct. (Theochem) 207, 103-114. 

Siam, K., V. J. Klimkowski, J. D. Ewbank, C. Van Alsenoy, and L. Schafer. 1984. Ab Initio Studies of Structural Features Not Easily Amenable to Experiment Part 39. Conformational analysis of glycine and alanine. J. Mol. Struct. (Theochem) 110, 171-182. 

Van Alsenoy, C., M. Cao, S. Q. Newton, B. Teppen, A. Perczel, I. G. Csizmadia, F. A. Momany, and L. Schafer. 1993. Conformational Analysis and Structural Study by Ab Initio Gradient Geometry Optimizations of the Model Tripeptide N-formyl L-alanyl L-alanine Amide. J. Mol. Struct. (Theochem) 286,149-163. 

Many of the conformational properties of peptide systems, including protein conformation, can be approximated in terms of the local interactions encountered in dipeptides, where the two torsional angles 4> (N-C(a)) and < i (C(a)-C ) are the main conformational variables. N-acetyl N -methyl alanine amide, shown in Fig. 7.11, is a model dipeptide that has been the subject of numerous computational studies. 

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