The Folding of Acetyl(Ala)₂₈NH₂and Acetyl(Ala)₄₀NH₂Extended Strand Peptides into Antiparallel β-Sheets. A Density Functional Theory Study of β-Sheets with β-Turns

Abstract

We report ONIOM calculations using B3LYP/D95** and AM1 on β-sheet formation from acetyl(Ala)NNH2 (N=28 or 40). The sheets contain from one to four β-turns for N=28 and up to six for N=40. We have obtained four types of geometrically optimized structures. All contain only β-turns. They differ from each other in the types of β-turns formed. The unsolvated sheets containing two turns are most stable. Aqueous solvation (using the SM5.2 and CPCM methods) reduces the stabilities of the folded structures compared to the extended strands.

3D Structures and Redox Potentials of Cu2+–Aβ(1–16) Complexes at Different pH: A Computational Study

“…Because of the size of the system and thus of the computational cost, reoptimizations to find the true minima were not carried out. Instead, and because the imaginary frequencies were all quite small, their contribution to the molar enthalpy was considered to be RT , as for a low-frequency vibration, and their contribution to the entropy was estimated considering a frequency of 10 cm –1 for each imaginary one, as done previously …”

“…Instead, and because the imaginary frequencies were all quite small, their contribution to the molar enthalpy was considered to be RT, as for a low-frequency vibration, and their contribution to the entropy was estimated considering a frequency of 10 cm −1 for each imaginary one, as done previously. 59 Open-shell calculations were based on an unrestricted formalism. All electronic structure calculations have been performed with the Gaussian 09 set of programs.…”

Capping Amyloid β-Sheets of the Tau-Amyloid Structure VQIVYK with Hexapeptides Designed To Arrest Growth. An ONIOM and Density Functional Theory Study

“…As in previous optimizations of alanine β-sheets, we have often found C 7 cyclic H-bonding near the termini of the sheets. 4 , 16 We have indicated structures containing a C 7 interaction in the relevant entries of the tables.…”

“…As in the past, we have corrected the enthalpies by RT, which would be appropriate for a low frequency. 16 …”

“…The current procedure also gave relative energies that agreed well with complete DFT optimizations for a series of five small 3 10 -helical peptides. 18 We have used this procedure with success for several previous studies of peptide structures, 3 , 4 , 16 , 18 − 24 and have shown it to compare favorably with other functional/basis set combinations for calculations on the gas phase water dimer. 25 …”