Atropisomerism of the Asn α Radicals Revealed by Ramachandran Surface Topology Kla ́ ra Z. Gerlei, † Imre Ja ́ kli, ‡,§ Mila ́ n Sző ri, † Svend J. Knak Jensen, ∥ Be ́ la Viskolcz, † Imre G. Csizmadia, †,§,⊥ and Andra ́ s Perczel* ,‡,§,∇ † Department of Chemical Informatics, Faculty of Education, University of Szeged, 6726 Szeged, Hungary ‡ Protein Modeling Group HAS-ELTE, Institute of Chemistry, Eö tvö s Lora ́ nd University, Pa ́ zma ́ ny Pé ter se ́ ta ́ ny 1/A, H-1117 Budapest, Hungary § Open Laboratory of Protein Science, Institute of Chemistry, Eö tvö s Lora ́ nd University, Pa ́ zma ́ ny Pe ́ ter sé ta ́ ny 1/A, H-1117 Budapest, Hungary ∥ Department of Chemistry, Langelandsgade 140, University of Aarhus, DK-8000 Aarhus C, Denmark ⊥ Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6 ∇ Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eö tvö s Lora ́ nd University, Pa ́ zma ́ ny Pé ter sé ta ́ ny 1/A, H-1117 Budapest, Hungary * S Supporting Information ABSTRACT: C radicals are typically trigonal planar and thus achiral, regardless of whether they originate from a chiral or an achiral C-atom (e.g., C−H+ • OH → C• + H 2 O). Oxidative stress could initiate radical formation in proteins when, for example, the H-atom is abstracted from the Cα-carbon of an amino acid residue. Electronic structure calculations show that such a radical remains achiral when formed from the achiral Gly, or the chiral but small Ala residues. However, when longer side-chain containing proteogenic amino acid residues are studied (e.g., Asn), they provide radicals of axis chirality, which in turn leads to atropisomerism observed for the first time for peptides. The two enantiomeric extended backbone structures, •β L and •β D , interconvert via a pair of enantiotopic reaction paths, monitored on a 4D Ramachandran surface, with two distinct transition states of very different Gibbs-free energies: 37.4 and 67.7 kJ/mol, respectively. This discovery requires the reassessment of our understanding on radical formation and their conformational and stereochemical behavior. Furthermore, the atropisomerism of proteogenic amino acid residues should affect our understanding on radicals in biological systems and, thus, reframes the role of the D-residues as markers of molecular aging. ■ INTRODUCTION It has been discovered recently that, despite the belief that living cells are solely composed of L-α-amino acids, D-residues also occur in human tissues. Furthermore, the percentage of D- amino acid residues increases with aging of the organism. 1 The role of free radicals in biological systems has been recognized both in essential biochemical reactions 2 and in the destructive oxidative stress. 3 Numerous diseases, such as Alzheimer’s, Parkinson’s, type II diabetes, vascular dementia, 4−6 as well as aging, 7−9 are attributed to oxidative stress. 10−17 To understand the molecular basis of such diseases, it is essential to characterize the associated free radicals, their stereochemical behavior, arising from the interaction of reactive oxygen species (O 2 −• , H 2 O 2 , and HO•) with proteogenic amino acid residues. 18,19 In general, atropisomerism is a manifestation of conforma- tional changes, as shown in Scheme 1. The clockwise (P or +) and the counter-clockwise (M or −) torsion amounts to axis chirality. In the case of symmetric molecular structures (like X− Received: July 17, 2013 Revised: September 7, 2013 Published: September 9, 2013 Scheme 1. Definition for Atropisomerism in Symmetric Molecular Structures as Non-Superimposable Mirror Images Article pubs.acs.org/JPCB © 2013 American Chemical Society 12402 dx.doi.org/10.1021/jp4070906 | J. Phys. Chem. B 2013, 117, 12402−12409