Journal ArticleDOI
Location of proline derivatives in conformational space. I. Conformational calculations; optical activity and NMR experiments.
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In order to develop methods of analysis applicable to the determination of the conformation of biological polymers in solution, a series of proline derivatives was studied and qualitative theoretical considerations enabled molecular groups to be located.Abstract:
In order to develop methods of analysis applicable to the determination of the conformation of biological polymers in solution, a series of proline derivatives was studied. The steric constraints of the pyrrolidine ring limit these compounds to a relatively small set of conformations. This set was further reduced by eliminating conformations with large computed conformational energy. Computations revealed that the conformational energy of the proline derivatives fits into one of three classes, depending on the bulk and the polarity of the C-terminal group. Three analogous classes of optical activity were observed. The optical activity data were analyzed in terms of conformations computed to be of low energy. In some cases qualitative theoretical considerations enabled molecular groups to be located. For example, solvent-dependent isomerization of the carboxyl hydrogen of N-acetyl-L-proline was detected. Nuclear magnetic resonance provided an experimental measure of the fraction of molecules which had cis unsymmetrically-substituted tertiary amide groups. This information aided and confirmed the other measures of molecular conformation.read more
Citations
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Journal ArticleDOI
Development of ordered structures in sequential copolypeptides containing L-proline and -hydroxy-L-proline.
Mattice Wl,Mandelkern L +1 more
Journal ArticleDOI
Comparative conformational study of N-acetyl-N′-methylprolineamide with different basis sets
Young Kee Kang,Hae Sook Park +1 more
TL;DR: In this article, the results on conformational free energies of N-acetyl-N′-methylprolineamide (Ac-Pro-NHMe) calculated using the ab initio and density functional methods with the reaction field theory at HF and B3LYP levels of theory with 6-31G(d,p) and 6- 31+g(d) basis sets to investigate the effects of two different basis sets on the structure, cis-trans equilibrium, and rotational barrier of the proline dipeptide.
Journal ArticleDOI
Unperturbed dimensions of sequential copolypeptides containing glycine, L-alanine, L-proline, and -hydroxy-L-proline.
Mattice Wl,Mandelkern L +1 more
Journal ArticleDOI
A matrix isolation study on Ac–l-Pro–NH2: a frequent structural element of β- and γ-turns of peptides and proteins
TL;DR: In this article, the residual conformational flexibility of Ac- l -Pro-NH 2 using matrix isolation IR and VCD spectroscopy in Ar and Kr matrices was analyzed by the help of quantum chemical calculations.
Journal ArticleDOI
Structure and Self Assembly of a Retrovirus (FeLV) Proline Rich Neutralization Domain
TL;DR: The conclusion is that PRN60 forms a beta-turn helix and that this region of FeLV-gp70 is a separate folding domain of the retroviral surface unit glycoprotein.
References
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Book ChapterDOI
Conformation of Polypeptides and Proteins
TL;DR: This chapter considers the parameters that are required for an adequate description of a polypeptide chain and the mathematical method of utilizing these parameters for calculating the coordinates of all the atoms in a suitable frame of reference so that all the interatomic distances, and bond angles, can be calculated and their consequences worked out.
Journal ArticleDOI
Theory and Applications of Ultraviolet Spectroscopy
Journal ArticleDOI
cis and trans Configurations of the Peptide Bond in N-Monosubstituted Amides by Nuclear Magnetic Resonance
Journal ArticleDOI
The rotatory properties of molecules containing two peptide groups: theory.
Journal ArticleDOI
Conformational Analysis of Macromolecules. IV. Helical Structures of Poly‐L‐Alanine, Poly‐L‐Valine, Poly‐β‐Methyl‐L‐Aspartate, Poly‐γ‐Methyl‐L‐Glutamate, and Poly‐L‐Tyrosine
Abstract: Energy calculations have been carried out for several isolated (single‐stranded) homopolymer polyamino acids in order to find the most stable regular (helical) conformations. The energy was expressed as a function of the dihedral angels φ, ψ, and the set of χi's, for rotations about the N–Cα and Cα–C′ bonds of the backbone, and the j single bonds of the side chain, respectively. Torsional, nonbonded, hydrogen‐bonded, and dipole—dipole interaction energy contributions were included. For regular structures, the set of φ, ψ, and the χi's is the same in every residue. Energy contours (expressed in kilocalories per mole of monomer) were plotted on ψ‐vs‐φ diagrams at fixed values of the χi's or on χ2‐vs‐χ1 diagrams at fixed φ and ψ (and, in some cases, χ3). In addition, the energy was minimized with respect to all of the dihedral angles of the backbone and side chain in the neighborhood of the minima of the contour diagrams, using various minimization procedures, in order to locate the local minima precisely. For poly‐L‐alanine the left‐ and right‐handed α‐helical conformations are those of lowest energy, the right‐handed one being more stable than the left‐handed one by 0.4 kcal/mole. Similar results were obtained for poly‐L‐valine, the right‐handed α helix being more stable than the left‐handed one by 0.5 kcal/mole. In this case, the valyl side chain was found to be rotated around the Cα–Cβ bond by about 10°—15° away from a minimum of the side‐chain torsional‐potential‐energy function. This prediction was verified by recent experiments showing the existence of the α‐helical conformation in a block copolymer of D,L‐lysine, and L‐valine in 98% aqueous methyl alcohol solution. For poly‐β‐methyl‐L‐aspartate, analysis of the energy contributions indicated that, whereas the nonbonded energy would favor the right‐handed form, the interaction of the dipole of the side‐chain ester group with the dipole of the backbone amide group is more repulsive in the right‐handed than in the left‐handed α helix, thereby destabilizing the right‐handed form. In order to demonstrate the importance of this dipole‐dipole interaction, the calculations were repeated for several values of the dielectric constant and of the parameters for the nonbonded interaction potential function. As a result of these calculations, it is suggested that the existence of this polyamino acid in the left‐handed α‐helical form is due to the dipole—dipole interaction between the side chain and the backbone. In contrast, poly‐γ‐methyl‐L‐glutamate was found to have a lower energy in the right‐handed α‐helical form than in the left‐handed one. In this polyamino acid, both the nonbonded and the dipole—dipole interaction energies favor the right‐handed form, i.e., the additional methylene group in the glutamic acid side chain alters the relative orientations of the side‐chain and backbone dipoles so as to lead to a stronger stabilization energy in the right‐handed α helix. Poly‐L‐tyrosine was found to have a lower energy in the right‐handed α‐helical form than in the left‐handed one, the difference in energy between the two forms being 1.8 kcal/mole. The main contribution to the stabilization of the right‐handed form is from the nonbonded energy. In summary, in all the cases examined here, the nonbonded interaction energy would favor the right‐handed α helix over the left‐handed one. However, the dipole—dipole interaction between the side chain and the backbone is apparently of sufficient importance, in the case of the aspartate polymer, to reverse the screw sense.