PEPCAT?A new tool for conformational analysis of peptides

O'Donohue, M.; Minasian, E.; Leach, S. J.; Burgess, Antony W.; Treutlein, Herbert

doi:10.1002/(sici)1096-987x(20000430)21:6<446::aid-jcc4>3.0.co;2-s

Cited by 7 publications

(4 citation statements)

References 34 publications

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“…Structural Analysis. The program PEPCAT (PEPtide Conformational Analysis Tool) 36 was used to carry out a cluster analysis of apoC-II 56-76 structures generated during the simulations to monitor the effects of oxidation and mutation of the peptide. PEPCAT is particularly useful in monitoring changes in the specific elements of the secondary structure of proteins.…”

Section: Resultsmentioning

confidence: 99%

Effect of Oxidation and Mutation on the Conformational Dynamics and Fibril Assembly of Amyloidogenic Peptides Derived from Apolipoprotein C-II

et al. 2009

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The oxidation of methionine residues in proteins can inhibit the self-assembly of proteins to form amyloid fibrils. For human apolipoprotein (apo) C-II the oxidation of methionine at position 60 inhibits fibril formation by the mature protein and by the core peptides apoC-II(56-76) and apoC-II(60-70). To investigate the molecular nature of these effects, we carried out fully solvated, all-atom molecular dynamics simulations of the structural changes in apoC-II(56-76) associated with substitutions of oxidized methionine (Met ox) at position 60. The results with apoC-II(56-76) (Met ox) showed less flexibility in structure, leading to a perturbation of the hydrophobic core. Valine substitution at position 60 showed an increased tendency to explore a wide range of conformational space, whereas the behavior of the Gln substitution mutant was similar to the wild-type peptide. These simulations are consistent with kinetic measurements which showed that a Met60Gln substitution within apoC-II(56-76) had little effect on the rate of fibril formation whereas substitution of Met ox or Val at position 60 lead to significant inhibition of peptide fibril formation. The effects of amino acid modification and substitutions on the kinetics of peptide fibril formation differ from the effects observed with full-length apoC-II inferring that additional mechanisms are involved in fibril formation by mature apoC-II.

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Section: Resultsmentioning

confidence: 99%

Effect of Oxidation and Mutation on the Conformational Dynamics and Fibril Assembly of Amyloidogenic Peptides Derived from Apolipoprotein C-II

et al. 2009

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“…PEPCAT Analysis. PEPCAT is a peptide analysis tool that classifies a trajectory into conformational states based on a set of chosen geometric descriptors . In this work, conformational analyses were performed using PEPCAT on systems S4, O4, S5, and O5, along with the reference systems to investigate the conformational dynamics of each system.…”

Section: Resultsmentioning

confidence: 99%

Electric Field Effects on Insulin Chain-B Conformation

et al. 2005

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The response of proteins to different forms of stress continues to be a topic of major interest, especially with the proliferation of electromagnetic devices conjectured to have detrimental effects on human health. In this paper, we have performed molecular dynamics simulations on insulin chain-B under the influence of both static and oscillating electric fields, ranging from 10(7) to 10(9) V/m. We have found that both variants have an effect on the normal behavior of the protein, with oscillating fields being more disruptive to the structure as compared to static fields of similar effective strength. The application of a static field had a stabilizing effect on the secondary structure, restricting the inherent flexibility that is crucial for insulin's biological activity.

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“…This analysis was performed in a similar way to the one described by O'Donohue et al (2000). In brief, the dihedral space of every rotable bond of the lysine side chains were partitioned in three regions: t ( > 120°and < ∼120), g+ (0°< Յ 120°), and g−(−120°< Յ 0°).…”

Section: Conformational Analysis Of the Lysine Side Chainsmentioning

confidence: 99%

Energetic and entropic contributions to the interactions between like‐charged groups in cationic peptides: A molecular dynamics simulation study

Villarreal¹,

Montich²

2002

Protein Science

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The interaction between like-charged amino acid residues has been proposed to stabilize the folded state of peptides and proteins, and to modulate the substrate binding and the action mechanism of enzymes. We have used an alanine-and lysine-based peptide as a model system to study the interaction between like charges, and we have performed a 16-nsec molecular dynamics simulation in solution. The calculated potential of mean force for the approach of the lysine's N atoms showed a minimum at a distance of 0.7 nm, in agreement with the separation probabilities obtained from analysis of protein crystal structures. The analysis of the individual energy components showed that the solvent polarization pays for the approach of the like charges and that the van der Waals energies do not contribute significantly. The entropic contributions have been divided in conformational and desolvation terms. Both terms favor the formation of the charge pair. A 10-fold increase in counterion concentration was observed-with respect to its bulk concentration-next to the peptide charges, which helps to stabilize the peptide charges at a close distance.

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PEPCAT?A new tool for conformational analysis of peptides

Cited by 7 publications

References 34 publications

Effect of Oxidation and Mutation on the Conformational Dynamics and Fibril Assembly of Amyloidogenic Peptides Derived from Apolipoprotein C-II

Effect of Oxidation and Mutation on the Conformational Dynamics and Fibril Assembly of Amyloidogenic Peptides Derived from Apolipoprotein C-II

Electric Field Effects on Insulin Chain-B Conformation

Energetic and entropic contributions to the interactions between like‐charged groups in cationic peptides: A molecular dynamics simulation study

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