Reversible peptide folding: Dependence on molecular force field used

Damm, Wolfgang; Gunsteren, Wilfred F. van

doi:10.1002/(sici)1096-987x(20000715)21:9<774::aid-jcc6>3.0.co;2-5

Cited by 21 publications

(13 citation statements)

References 55 publications

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“…The substituted polyglycolides are used for different applications and in different environment therefore, Molecular Dynamic (MD) simulation study in water has been carried out with the help of GROMACS software [56] on the desktop computer, dual Intel Pentium 4, 3.0 GHz. It is worth mentioning that the simulation results obtained by GROMOS force field are found to be in good agreement with the experiment for peptides & peptoids [57]. The starting geometry for simulation studies has been taken from QM results for all these molecules.…”

Section: Methodssupporting

confidence: 56%

Conformational behavior of stereo regular substituted polyglycolides is side chain dependent

Nandel¹,

Garla²

2011

JBPC

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Substituted polyglycolides having two asymmetric centers are attractive alternatives to materials derived from petroleum because of their biocompatibility and biodegradability. The conformational behavior of various substituted polyglycolides has been investigated by both quantum mechanical and molecular dynamics approaches. Polymethylglycolide (polylactide) and polyphenylmethylglycolide in RS or SR forms are predicted to adopt 27 ribbon type structures with φ, ψ values of ±30, ±50 or +30 or +50 respectively stabilised by carbonyl-carbonyl interactions. Isopropylglycolide and isobutyl-glycolide having branching at β & γ positions respectively in their side chains can be realized in all SS form with φ, ψ values lying in right handed helical region. In addition to carbonyl-carbonyl interactions, the hydrophobic interactions between the side chains in isopropylgly-colide the C-H-O interactions also contributes to the stability. With cyclic side chains directly attached to Cα of backbone, polyphenylglycolide (polymandelide) and polycyclohexylglycolide are found to adopt left handed helical structure without hydrogen bonds in RR form, stabilised by stacking interactions and hydrophobic interactions respectively. In all the forms of polyphenylglycolide & polycyclohexylglycolide, the cyclic side chains are found to be locked into unfavourable gauche plus conformation. The stability of substituted polyglycolides has been analyzed in terms of various interactions. The carbonyl-carbonyl interactions in all the conformations of all forms of substituted polyglycolides are found to be of highly shielded parallel motif with only one short carbon-oxygen interaction. Simulation studies of substituted polyglycolides in water give a good insight of the approach of water molecules to the backbone

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Section: Methodssupporting

confidence: 56%

Conformational behavior of stereo regular substituted polyglycolides is side chain dependent

Nandel¹,

Garla²

2011

JBPC

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“…678 [9 ± 11]. Only after modifying the force field, van Gunsteren and co-workers were able to explain a melting temperature > 878 [35]. However, the information content of NMR and CD spectroscopy has been questioned recently in particular for very small peptides, which undergo extremely rapid conformational jumps.…”

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confidence: 99%

On the Thermal Stability of -Peptides: A Two-Dimensional Vibrational Spectroscopy Study

Hamm

Woutersen

Rueping³

2002

HCA

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Professor Dieter Seebach in Bewunderung und mit den besten W¸nschen zum 65. Geburtstag gewidmet.A temperature-dependent 2D-IR study of the amide-I band of a b-peptide forming a 12/10/12/10 helix is presented. Cross-relaxation of a spectrally separated marker amide-I mode, which could be assigned with the help of the NMR structure of the molecule, can be used as measure of conformational flexibility of the molecule. We find that the conformational flexibility of the N-terminal part of the helix increases slightly upon increasing the temperature from 08 to 808. The cross-peaks in the 2D-IR spectrum, and hence the connectivity of the corresponding peptide units, do not change, suggesting that the N-terminal part of the helix remains essentially intact at 808. This conclusion is in agreement with previous NMR and CD measurements.Introduction. ± Protein folding is the process of transferring information from one dimension into three dimensions, where the information that determines the molecular structure of a protein is encoded in its amino acid sequence. Understanding the mechanism by which the amino acid sequence of a protein folds into its unique native conformation is one of the biggest challenges in biophysical chemistry.The major degrees of freedom of the polypeptide chain are two s-bonds in each amino acid, which can freely rotate. The amide group (i.e., ÀCOÀNHÀ ) itself is close to planar since the CÀN bond has partial double-bond character. The free-energy surface of the two-dimensional configuration space of each amino acid has been extensively studied. A complicated balance of different forces results in two main local free-energy minima, which are of almost equal depth. Because of the large dimensionality of the problem in polypeptides and proteins, and because of the

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“…94, 169–174 (A) Various force fields were tested by Lindorff-Larsen et al . 95 and a score based on the performance of the force field against the chosen model systems was devised such that the lower score indicates better agreement with experimental data.…”

Section: Figurementioning

confidence: 99%

Microsecond folding experiments and simulations: a match is made

Prigozhin

Gruebele

2013

Phys. Chem. Chem. Phys.

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For the past two decades, protein folding experiments have been speeding up from the second or millisecond time scale to the microsecond time scale, and full-atom simulations have been extended from the nanosecond to the microsecond and even millisecond time scale. Where the two meet, it is now possible to compare results directly, allowing force fields to be validated and refined, and allowing experimental data to be interpreted in atomistic detail. In this perspective we compare recent experiments and simulations on the microsecond time scale, pointing out the progress that has been made in determining native structures from physics-based simulations, refining experiments and simulations to provide more quantitative underlying mechanisms, and tackling the problems of multiple reaction coordinates, downhill folding, and complex underlying structure of unfolded or misfolded states.

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Reversible peptide folding: Dependence on molecular force field used

Cited by 21 publications

References 55 publications

Conformational behavior of stereo regular substituted polyglycolides is side chain dependent

Conformational behavior of stereo regular substituted polyglycolides is side chain dependent

On the Thermal Stability of -Peptides: A Two-Dimensional Vibrational Spectroscopy Study

Microsecond folding experiments and simulations: a match is made

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