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Computational Design of Heterochiral Peptides against a Helical Target
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Section:Abstract
Polypeptides incorporating d-amino acids occasionally occur in nature and are an important class of pharmaceutical molecules. With the use of heterochiral Monte Carlo (HCMC), a method inspired by the de novo design of proteins, we develop peptide scaffolds for interacting with a molecular target, a left-handed α-helix. The HCMC approach concurrently seeks to optimize a peptide sequence, its internal conformation, and its docked conformation with a target surface. Several major classes of interactions are observed: (1) homochiral interactions between two αL helices, (2) heterochiral interactions between an αL and an αR helix, and (3) heterochiral interactions between the αL target and novel nonhelical structures. We explore the application of HCMC to simulating the preferential enantioselectivity of heterochiral complexes. Implications for biomimetic design in molecular recognition are discussed.
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This article has been cited by 5 ACS Journal articles (5 most recent appear below).
Left- and Right-Handed Alpha-Helical Turns in Homo- and Hetero-Chiral Helical Scaffolds
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Nicholas E. Shepherd, Huy N. Hoang, Giovanni Abbenante and David P. FairlieJournal of the American Chemical Society2009 131 (43), 15877-15886Proteins typically consist of right-handed alpha helices, whereas left-handed alpha helices are rare in nature. Peptides of 20 amino acids or less corresponding to protein helices do not form thermodynamically stable alpha helices in water away from ...
Transfer of Noncovalent Chiral Information along an Optically Inactive Helical Peptide Chain: Allosteric Control of Asymmetry of the C-Terminal Site by External Molecule that Binds to the N-Terminal Site
Naoki Ousaka and Yoshihito InaiThe Journal of Organic Chemistry2009 74 (4), 1429-1439Transfer of Noncovalent Chiral Information along an Optically Inactive Helical Peptide Chain: Allosteric Control of Asymmetry of the C-Terminal Site by External Molecule that Binds to the N-Terminal Site
Naoki Ousaka and Yoshihito InaiThe Journal of Organic Chemistry2009 74 (4), 1429-1439This study aims at demonstrating end-to-end transfer of noncovalent chiral information along a peptide chain. The domino-type induction of helical sense is proven by using achiral peptides 1-m of bis-chromophoric sequence with different chain lengths: H-...
Conformationally Constrained Aliphatic−Aromatic Amino-Acid-Conjugated Hybrid Foldamers with Periodic β-Turn Motifs
Deekonda Srinivas, Rajesh Gonnade, Sapna Ravindranathan, and Gangadhar J. SanjayanThe Journal of Organic Chemistry2007 72 (18), 7022-7025Conformationally Constrained Aliphatic−Aromatic Amino-Acid-Conjugated Hybrid Foldamers with Periodic β-Turn Motifs
Deekonda Srinivas, Rajesh Gonnade, Sapna Ravindranathan, and Gangadhar J. SanjayanThe Journal of Organic Chemistry2007 72 (18), 7022-7025In this note, we describe the design, synthesis, and structural studies of novel hybrid foldamers derived from Aib-Pro-Adb building blocks that display repeat β-turn structure motif. The foldamer having a conformationally constrained aliphatic−aromatic ...
BINOL-Based Foldamers
Access to Oligomers with Diverse Structural ArchitecturesPranjal K. Baruah, Rajesh Gonnade, P. R. Rajamohanan, Hans-Jörg Hofmann, and Gangadhar J. SanjayanThe Journal of Organic Chemistry2007 72 (14), 5077-5084BINOL-Based Foldamers
Access to Oligomers with Diverse Structural ArchitecturesPranjal K. Baruah, Rajesh Gonnade, P. R. Rajamohanan, Hans-Jörg Hofmann, and Gangadhar J. SanjayanThe Journal of Organic Chemistry2007 72 (14), 5077-5084In this article, we report on the synthesis and conformation of a new family of aromatic oligoamide foldamers based on binaphthol (BINOL) monomers. A series of oligomers with differing chirality of the individual BINOL building blocks and mixed sequences ...
Induction of a Heterochiral Helix through the Covalent Chiral Domino Effect Originating in the “Schellman Motif”
Naoki Ousaka and Yoshihito InaiJournal of the American Chemical Society2006 128 (46), 14736-14737Induction of a Heterochiral Helix through the Covalent Chiral Domino Effect Originating in the “Schellman Motif”
Naoki Ousaka and Yoshihito InaiJournal of the American Chemical Society2006 128 (46), 14736-14737We report unique phenomena where the transition from a homochiral helix to a heterochiral helix occurs by increasing the chain length of the l-sequence. Peptides composed of the l-Leu sequences with different lengths and the achiral nona-sequence at the C-...
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History
- Published In Issue January 25, 2006
- Received July 5, 2005
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