The B(OH)−NH Analog Is a Surrogate for the Amide Bond (CO−NH) in Peptides: An ab Initio Study

Malde, Alpeshkumar K., Khedkar, Santosh A. and Coutinho, Evans C. (2007) The B(OH)−NH Analog Is a Surrogate for the Amide Bond (CO−NH) in Peptides: An ab Initio Study. Journal of Chemical Theory and Computation, 3 2: 619-627. doi:10.1021/ct600256s

Author Malde, Alpeshkumar K.
Khedkar, Santosh A.
Coutinho, Evans C.
Title The B(OH)−NH Analog Is a Surrogate for the Amide Bond (CO−NH) in Peptides: An ab Initio Study
Journal name Journal of Chemical Theory and Computation   Check publisher's open access policy
ISSN 1549-9618
Publication date 2007-03-01
Year available 2006
Sub-type Article (original research)
DOI 10.1021/ct600256s
Open Access Status
Volume 3
Issue 2
Start page 619
End page 627
Total pages 9
Place of publication Washington, D.C.
Publisher American Chemical Society
Language eng
Subject 030701 Quantum Chemistry
Abstract The conformational preferences of N-methyl-methylboronamide (NMB), a B(OH)−NH analog of the amide CO−NH in natural peptides, have been investigated at the Hartree−Fock; Becke's three-parameter exchange functional and the gradient-corrected functional of Lee, Yang, and Parr; and second-order Møller−Plesset levels of theory with the 6-31+G* basis set. The minima, saddle points, and rotation barriers on the potential energy surface of NMB have been located and the energy barriers estimated. Besides the global minimum, there are three local minima within 2.0 kcal mol-1 of the global minimum characterized by specific ω and τ torsion values. The energy barriers for rotation about the “ω angle” are 16.4−18.8 kcal mol-1 and are a consequence of the double-bond character of the B−N bond as revealed by natural bond orbitals calculations. The “ω angle” and the ω rotation barrier are nearly the same as those seen in natural peptides. The τ rotation barriers (B−O bond) are relatively low because of the single-bond character of the B−O bond. Ala-BON, the Ala-dipeptide derived from NMB, has been constructed as a model peptide to study the conformational preferences about the phi and ψ torsion angles. The study reveals a strong preference for α-helix, type-II β-turn, 2.27 ribbon, and antiparallel β-sheet conformations, and mirror images of both type-II β-turn and 2.27 ribbon motifs whose phi and ψ values fall in the “disfavored regions” of the Ramachandran map. Thus, the replacement of the carbonyl group by B−OH retains the geometry and barrier around the “ω angle” and induces a strong preference for regular secondary structure motifs and also structures with positive phi values. This makes the B(OH)−NH analog an important surrogate for the peptide bond, with the additional advantage of stability to proteolytic enzymes.
Keyword Chemistry, Physical
Physics, Atomic, Molecular & Chemical
Q-Index Code C1
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Chemistry and Molecular Biosciences
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