Selenium in Proteins: Conformational Changes Induced by Se Substitution on Methionine, as Studied in Isolated Model Peptides by Optical Spectroscopy and Quantum Chemistry
Abstract
:1. Introduction
2. Methods
3. Conformational Landscapes
- The folded backbone forms are additionally stabilized by a side-chain/main chain intra-residue H-bond, forming a 6-membered ring, where the side-chain heteroatom Se plays the role of proton acceptor. According to the terminology used previously [21], based on the H-bonding status of the successive NH bonds along the backbone, these conformations belong to a 6δ-π-10 folded backbone family: the number stands for the length of the ring formed by the H-bond concerned, the δ superscript for a backbone–side-chain H-bond bridging an NH bond with a side-chain acceptor in a δ position relative to the main chain, and π for an NH–π interaction with Phe ring. The structural analysis shows that the intra- residue 6δ H-bond can take place with a specific side-chain folding, described by a gauche+ (g+) and gauche- (g−) orientation of the χ1 and χ2 dihedrals (i.e., the N-Cα-Cβ-Cγ and Cα-Cβ-Cγ-Se dihedrals), respectively. Two possible orientations of the terminal methyl group of the Sem side-chain (described by the Cβ-Cγ-Se-Cε χ3 dihedral) can take place: gauche− and anti (a), respectively, which give rise to significantly different H-bond lengths and strengths (see below). For the sake of simplicity, the Sem side-chain conformation is thus identified by the orientation of the terminal group (g− or a). Similarly, the Phe side-chain can take three possible orientations (g+, g− or a) depending on the χ1 dihedral, but in the present case, g+ conformations are favored by the formation of an intra-residue NH–π H-bond. For the sake of identification, conformations have thus been labeled with the Sem and Phe side-chains’ orientations, given as indices on the symbol (5, 7, 6δ, 7δ, π, or f (for free)) that indicates the H-bonding status of the NH group of the corresponding residue.The extended and semi-extended forms correspond to the succession of local conformational preferences of the basic peptide backbone, found with Ala or residues, i.e., the so-called C5 or C7 structures corresponding to β-sheet or γ-turns, respectively, the latter folding existing under two chiral forms, the inverse and direct γ-turns, labeled L or D, respectively. The key point here is the fact that the presence of the Sem side-chain does locally stabilize an extended C5 backbone conformation, thanks to the formation of a 7δ inter-residue H-bond. Again the Sem side-chain end adopts conformations where such a bond can form (χ1 and χ2 with a and g+ orientations, respectively), but the orientation of the terminal methyl group of the Sem side-chain (described by the χ3 dihedral) can occur either in an a or a g+ orientation. As a consequence, the semi-extended and extended forms (Figure 1) exhibit a 5-7δ-7 and a 5-7δ/5-π backbone, respectively, the 7δ/5 notation standing for a second NH group simultaneously involved in 7δ and C5 interactions. Finally, depending on the Phe side-chain orientation, additional π H-bonds can form. In semi-extended forms with a Phe g+ orientation, the second NH group is simultaneously involved in a 7δ H-bond and a π interaction with the Phe side-chain (notation 7δ/πg+ in Figure 1), without strongly affecting the overall backbone structure, the 7δ H-bonds and their relative strengths.
4. Experimental Results and Assignments
4.1. UV Spectroscopy
4.2. IR Spectroscopy
Conformational Population of Ac-Sem-Phe-NH2
5. Discussion
5.1. Revisiting the Spectroscopy of Ac-Met-Phe-NH2
5.2. Comparing the H-Bonding Patterns of Sem and Met
5.3. General Considerations from NBO Analysis
6. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
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Goldsztejn, G.; Mundlapati, V.R.; Brenner, V.; Gloaguen, E.; Mons, M. Selenium in Proteins: Conformational Changes Induced by Se Substitution on Methionine, as Studied in Isolated Model Peptides by Optical Spectroscopy and Quantum Chemistry. Molecules 2022, 27, 3163. https://doi.org/10.3390/molecules27103163
Goldsztejn G, Mundlapati VR, Brenner V, Gloaguen E, Mons M. Selenium in Proteins: Conformational Changes Induced by Se Substitution on Methionine, as Studied in Isolated Model Peptides by Optical Spectroscopy and Quantum Chemistry. Molecules. 2022; 27(10):3163. https://doi.org/10.3390/molecules27103163
Chicago/Turabian StyleGoldsztejn, Gildas, Venkateswara Rao Mundlapati, Valérie Brenner, Eric Gloaguen, and Michel Mons. 2022. "Selenium in Proteins: Conformational Changes Induced by Se Substitution on Methionine, as Studied in Isolated Model Peptides by Optical Spectroscopy and Quantum Chemistry" Molecules 27, no. 10: 3163. https://doi.org/10.3390/molecules27103163