Derivation of class II force fields: V. Quantum force field for amides, peptides, and related compounds

Maple, Jon R.; Hwang, Ming‐Jing; Jalkanen, K. J.; Stockfisch, Thomas P.; Hagler, A. T.

doi:10.1002/(sici)1096-987x(199803)19:4<430::aid-jcc5>3.0.co;2-t

Cited by 130 publications

(92 citation statements)

References 53 publications

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“…Teplow and coworkers (26) have observed a helix intermediate involvement in the A␤ amyloid formation. Kallberg et al (27) have identified a strong likelihood for a helix for residues [16][17][18][19][20][21][22][23]. The C terminus may form a weak helix because of the Gly residues.…”

Section: Discussionmentioning

confidence: 99%

“…All atoms of the system were considered explicitly, and their interactions were computed by using the CFF91 force field with periodic boundary conditions. The potential energy functions include bond stretching, angle bending, torsion, and out-of-plane angle deformation terms and contain cross-terms to describe the couplings between bond-bond, angle-angle, bond-angle, bond-torsion, torsionangle, and angle-angle-torsion (19). The nonbonded interactions include van der Waals interactions and electrostatic interactions.…”

Section: Methodsmentioning

confidence: 99%

“…5). In A␤ [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35] (and A␤ ), there are hydrophobic regions at both ends (residues 16-21 and 30-35), and the central region is rich in polar and charged residues. Because for neither A␤ [16][17][18][19][20][21][22] nor A␤ are the parallel sheet͞parallel layer organizations stable, the parallel sheet͞parallel layer for the A␤ [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35] is also expected to be unstable, unless the central polar͞charged region could stabilize the inter-layer interactions.…”

Section: Methodsmentioning

confidence: 99%

“…9, which is published as supporting information on the PNAS web site, www.pnas.org). Therefore, another type of inter-␤-sheet interaction must be considered to stabilize the possible parallel ␤-sheets in the A␤ [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35] and A␤ fibrils.…”

Section: Methodsmentioning

confidence: 99%

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Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ ₁₆ _– ₂₂ , Aβ _16–35 , and Aβ ₁₀ _– ₃₅ ): Sequence effects

Nussinov

2002

Proc. Natl. Acad. Sci. U.S.A.

406

396

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Previously, we have studied the minimal oligomer size of an aggregate amyloid seed and the mechanism of seed growth with a multilayer ␤-sheet model. Under high temperature simulation conditions, our approach can test the stability of possible amyloid forms. Here, we report our study of oligomers of Alzheimer's amyloid ␤-peptide ( amyloid conformation ͉ ␤-sheet ͉ double-layered sheets ͉ molecular dynamics simulation ͉ protein folding C hanges in sequence or in shape of a protein may lead to a conformational disease. Conformational diseases are typically expressed in the appearance of amyloid fibrils. Understanding amyloid seed formation and elongation at the molecular level presents a major challenge, as it may lead to novel approaches in design and therapy (1). A relatively large number of protein conformational diseases have already been identified (2). Interestingly, at least in proteins related to Alzheimer's disease, prion protein-related encephalopathies, and type II diabetes, it has been discovered that certain short sequence fragments (5-40 residues) contained within the respective proteins can form amyloids, even in isolated peptide form. The human islet amyloid polypeptide (hIAPP), a 37-residue peptide hormone, is implicated in type II diabetes. Fibrils obtained from this hormone have been observed to be toxic to human and to rat islet ␤-cells in vitro (3). Experiments have demonstrated that a hexamer of hIAPP (residues 22-27, NFGAIL) and even a pentamer (residues 23-27, FGAIL) are already sufficient for amyloid formation and cytotoxicity (4). Prion proteins also contain such amyloidogenic peptide-fragments. Several fragments of the Syrian hamster prion protein (ShPrP) have been observed to form amyloids. These include residues 109-122, 178-191, and 202-218 (5). Within these, the most highly amyloidogenic peptide is AGAAAAGA, which corresponds to ShPrP residues 113-120. This fragment is conserved in all species whose PrP sequence has been determined (5). The ␤-peptide (A␤, 42 residues) from Alzheimer's amyloid precursor protein, constitutes a particularly important example and is among the best studied amyloidogenic peptides. A key step in Alzheimer's disease involves proteolytic cleavage of A␤ (6). The fragment consisting of residues 25-35 in A␤ (GSNKGAIIGLM) has been shown to already form large ␤-sheet fibrils, essentially similar to those obtained by the full-length A␤ (refs. 7-11). Other fragments including 1-28, 16-22, and 10-35 have also been well studied (reviewed in ref.12). Although experimental data on the ␤-sheet orientation have been elusive for A␤ 25-35 (12, 13), solid state NMR experiments revealed that A␤ 16 -22 forms an antiparallel ␤-sheet (14), and that A␤ 10 -35 and the whole sequence of 1-40 form parallel ␤-sheet amyloids (15,16). Although the IR spectra of the A␤ 24 -35 amyloid indicates the existence of an antiparallel ␤-sheet (17), x-ray diffraction failed to identify an ordered ␤-crystalline in the 24-35 fragment amyloid (12, 13).That these disease-related short peptides are ...

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ ₁₆ _– ₂₂ , Aβ _16–35 , and Aβ ₁₀ _– ₃₅ ): Sequence effects

Nussinov

2002

Proc. Natl. Acad. Sci. U.S.A.

406

396

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“…Molecular simulation of 1ns of long time were carried out using Valbond Force Field (CVFF) (Maple et al, 1998) and CHARMM forcé field. The three models were run at different temperatures between 1000K and 1700K with the purpose of obtain a wide conformational sample.…”

Section: With T H E G O a L O F S T U D Y I F T H E P S B L O C K Smentioning

confidence: 99%

Molecular Dynamics Simulation of Synthetic Polymers

Sandoval¹

2012

Molecular Dynamics - Studies of Synthetic and Biological Macromolecules

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New out-of-plane angle and bond angle internal coordinates and related potential energy functions for molecular mechanics and dynamics simulations

1999

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With currently used definitions of out-of-plane angle and bond angle internal coordinates, Cartesian derivatives have singularities, at "r2 in the former case and in the latter. If either of these occur during molecular mechanics or dynamics simulations, the forces are not well defined. To avoid such difficulties, we provide new out-of-plane and bond angle coordinates and associated potential energy functions that inherently avoid these singularities. The application of these coordinates is illustrated by ab initio calculations on ammonia, water, and carbon dioxide.

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Derivation of class II force fields: V. Quantum force field for amides, peptides, and related compounds

Cited by 130 publications

References 53 publications

Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ ₁₆ _– ₂₂ , Aβ _16–35 , and Aβ ₁₀ _– ₃₅ ): Sequence effects

Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ ₁₆ _– ₂₂ , Aβ _16–35 , and Aβ ₁₀ _– ₃₅ ): Sequence effects

Molecular Dynamics Simulation of Synthetic Polymers

New out-of-plane angle and bond angle internal coordinates and related potential energy functions for molecular mechanics and dynamics simulations

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Derivation of class II force fields: V. Quantum force field for amides, peptides, and related compounds

Cited by 130 publications

References 53 publications

Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ 16 – 22 , Aβ 16–35 , and Aβ 10 – 35 ): Sequence effects

Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ 16 – 22 , Aβ 16–35 , and Aβ 10 – 35 ): Sequence effects

Molecular Dynamics Simulation of Synthetic Polymers

New out-of-plane angle and bond angle internal coordinates and related potential energy functions for molecular mechanics and dynamics simulations

Contact Info

Product

Resources

About

Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ ₁₆ _– ₂₂ , Aβ _16–35 , and Aβ ₁₀ _– ₃₅ ): Sequence effects

Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ ₁₆ _– ₂₂ , Aβ _16–35 , and Aβ ₁₀ _– ₃₅ ): Sequence effects