An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial t...

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Main Author: Ranjan V. Mannige
Format: Article
Language:English
Published: PeerJ Inc. 2017-05-01
Series:PeerJ
Subjects:
Online Access:https://peerj.com/articles/3327.pdf
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spelling doaj-98e04ef094ba4a818aff77afa417717c2020-11-24T20:59:08ZengPeerJ Inc.PeerJ2167-83592017-05-015e332710.7717/peerj.3327An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)Ranjan V. Mannige0Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesThe Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing the φ and ψ values of a peptide (e.g., is the regular peptide defined by φ = ψ =  − 100°  left-handed or right-handed?). This report provides a new metric for backbone handedness (h) based on interpreting a peptide backbone as a helix with axial displacement d and angular displacement θ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral angles φ, ψ and ω. In particular, h equals sin(θ)d∕|d|, with range [−1, 1] and negative (or positive) values indicating left(or right)-handedness. The metric h is used to characterize the handedness of every region of the Ramachandran plot for both cis (ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ, ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based on d and θ that serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone including cis and trans backbones. The intuitiveness arises from the fact that d and θ provide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity.https://peerj.com/articles/3327.pdfRamachandran plotPeptide backboneBackbone chiralityBackbone handednessMiyazawaPeptide helix
collection DOAJ
language English
format Article
sources DOAJ
author Ranjan V. Mannige
spellingShingle Ranjan V. Mannige
An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)
PeerJ
Ramachandran plot
Peptide backbone
Backbone chirality
Backbone handedness
Miyazawa
Peptide helix
author_facet Ranjan V. Mannige
author_sort Ranjan V. Mannige
title An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)
title_short An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)
title_full An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)
title_fullStr An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)
title_full_unstemmed An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)
title_sort exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)
publisher PeerJ Inc.
series PeerJ
issn 2167-8359
publishDate 2017-05-01
description The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing the φ and ψ values of a peptide (e.g., is the regular peptide defined by φ = ψ =  − 100°  left-handed or right-handed?). This report provides a new metric for backbone handedness (h) based on interpreting a peptide backbone as a helix with axial displacement d and angular displacement θ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral angles φ, ψ and ω. In particular, h equals sin(θ)d∕|d|, with range [−1, 1] and negative (or positive) values indicating left(or right)-handedness. The metric h is used to characterize the handedness of every region of the Ramachandran plot for both cis (ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ, ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based on d and θ that serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone including cis and trans backbones. The intuitiveness arises from the fact that d and θ provide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity.
topic Ramachandran plot
Peptide backbone
Backbone chirality
Backbone handedness
Miyazawa
Peptide helix
url https://peerj.com/articles/3327.pdf
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