Hamiltonian path analysis of viral genomes

Reidun Twarock; German Leonov; Peter Stockley

doi:10.1038/s41467-018-03713-y

Hamiltonian path analysis of viral genomes

Reidun Twarock, German Leonov, Peter Stockley

Research output: Contribution to journal › Article › peer-review

Abstract

Cryo-electron microscopy (EM) is undergoing a revolution, enabling the study of viral pathogens in unprecedented detail. The asymmetric EM reconstruction of bacteriophage MS2 at medium resolution (8.7 Å) by Koning et al.1, and the subsequent reconstruction at even higher resolution (3.6 Å) by Dai et al.2 revealed the structures of both the protein shell and the asym- metric genomic RNA and the unique maturation protein (A). It is the start of a wave of such structural data for viruses, and calls for the development of new analytical tools to describe the results. One approach is Hamiltonian path analysis (HPA) that we introduced to describe repeated, sequence-specific contacts between the MS2 genome and its protein shell3. Here, we describe how HPA is consistent with the new structures and, in turn, how it extends our understanding beyond the structural data alone.

Original language	English
Pages (from-to)	2021-2023
Number of pages	3
Journal	Nature Communications
Volume	9
DOIs	https://doi.org/10.1038/s41467-018-03713-y
Publication status	Published - 22 May 2018

Bibliographical note

Keywords

Virus Assembly
Hamiltonian path;
graph theory

Access to Document

10.1038/s41467-018-03713-y

Hamiltonian path analysis of viral genomes
© The Author(s) 2018
Final published version, 1.67 MBLicence: CC BY

Cite this

@article{9a58f9c558554b77b1b32db3d2765cf3,

title = "Hamiltonian path analysis of viral genomes",

abstract = "Cryo-electron microscopy (EM) is undergoing a revolution, enabling the study of viral pathogens in unprecedented detail. The asymmetric EM reconstruction of bacteriophage MS2 at medium resolution (8.7 {\AA}) by Koning et al.1, and the subsequent reconstruction at even higher resolution (3.6 {\AA}) by Dai et al.2 revealed the structures of both the protein shell and the asym- metric genomic RNA and the unique maturation protein (A). It is the start of a wave of such structural data for viruses, and calls for the development of new analytical tools to describe the results. One approach is Hamiltonian path analysis (HPA) that we introduced to describe repeated, sequence-specific contacts between the MS2 genome and its protein shell3. Here, we describe how HPA is consistent with the new structures and, in turn, how it extends our understanding beyond the structural data alone.",

keywords = "Virus Assembly, Hamiltonian path;, graph theory",

author = "Reidun Twarock and German Leonov and Peter Stockley",

note = "{\textcopyright} The Author(s) 2018",

year = "2018",

month = may,

day = "22",

doi = "10.1038/s41467-018-03713-y",

language = "English",

volume = "9",

pages = "2021--2023",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

}

TY - JOUR

T1 - Hamiltonian path analysis of viral genomes

AU - Twarock, Reidun

AU - Leonov, German

AU - Stockley, Peter

PY - 2018/5/22

Y1 - 2018/5/22

N2 - Cryo-electron microscopy (EM) is undergoing a revolution, enabling the study of viral pathogens in unprecedented detail. The asymmetric EM reconstruction of bacteriophage MS2 at medium resolution (8.7 Å) by Koning et al.1, and the subsequent reconstruction at even higher resolution (3.6 Å) by Dai et al.2 revealed the structures of both the protein shell and the asym- metric genomic RNA and the unique maturation protein (A). It is the start of a wave of such structural data for viruses, and calls for the development of new analytical tools to describe the results. One approach is Hamiltonian path analysis (HPA) that we introduced to describe repeated, sequence-specific contacts between the MS2 genome and its protein shell3. Here, we describe how HPA is consistent with the new structures and, in turn, how it extends our understanding beyond the structural data alone.

AB - Cryo-electron microscopy (EM) is undergoing a revolution, enabling the study of viral pathogens in unprecedented detail. The asymmetric EM reconstruction of bacteriophage MS2 at medium resolution (8.7 Å) by Koning et al.1, and the subsequent reconstruction at even higher resolution (3.6 Å) by Dai et al.2 revealed the structures of both the protein shell and the asym- metric genomic RNA and the unique maturation protein (A). It is the start of a wave of such structural data for viruses, and calls for the development of new analytical tools to describe the results. One approach is Hamiltonian path analysis (HPA) that we introduced to describe repeated, sequence-specific contacts between the MS2 genome and its protein shell3. Here, we describe how HPA is consistent with the new structures and, in turn, how it extends our understanding beyond the structural data alone.

KW - Virus Assembly

KW - Hamiltonian path;

KW - graph theory

U2 - 10.1038/s41467-018-03713-y

DO - 10.1038/s41467-018-03713-y

M3 - Article

SN - 2041-1723

VL - 9

SP - 2021

EP - 2023

JO - Nature Communications

JF - Nature Communications

ER -