Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle

Suna P. Gulay, Sujal Bista, Amitabh Varshney, Serdal Kirmizialtin, Karissa Y. Sanbonmatsu, Jonathan D. Dinman

Research output: Contribution to journalArticle

Abstract

Chemical modification was used to quantitatively determine the flexibility of nearly the entire rRNA component of the yeast ribosome through 8 discrete stages of translational elongation, revealing novel observations at the gross and fine-scales. These include (i) the bulk transfer of energy through the intersubunit bridges fromthe large to the small subunit after peptidyltransfer, (ii) differences in the interaction of the sarcin ricin loop with the two elongation factors and (iii) networked information exchange pathways that may functionally facilitate intra- and intersubunit coordination, including the 5.8S rRNA. These analyses reveal hot spots of fluctuations that set the stage for large-scale conformational changes essential for translocation and enable the first molecular dynamics simulation of an 80S complex. Comprehensive datasets of rRNA base flexibilities provide a unique resource to the structural biology community that can be computationally mined to complement ongoing research toward the goal of understanding the dynamic ribosome.

Original languageEnglish (US)
Pages (from-to)4958-4971
Number of pages14
JournalNucleic Acids Research
Volume45
Issue number8
DOIs
StatePublished - Jan 1 2017

Fingerprint

Ribosomes
Yeasts
Peptide Elongation Factors
Ricin
Energy Transfer
Molecular Dynamics Simulation
Research
Datasets

ASJC Scopus subject areas

  • Genetics

Cite this

Gulay, S. P., Bista, S., Varshney, A., Kirmizialtin, S., Sanbonmatsu, K. Y., & Dinman, J. D. (2017). Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle. Nucleic Acids Research, 45(8), 4958-4971. https://doi.org/10.1093/nar/gkx112

Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle. / Gulay, Suna P.; Bista, Sujal; Varshney, Amitabh; Kirmizialtin, Serdal; Sanbonmatsu, Karissa Y.; Dinman, Jonathan D.

In: Nucleic Acids Research, Vol. 45, No. 8, 01.01.2017, p. 4958-4971.

Research output: Contribution to journalArticle

Gulay, SP, Bista, S, Varshney, A, Kirmizialtin, S, Sanbonmatsu, KY & Dinman, JD 2017, 'Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle', Nucleic Acids Research, vol. 45, no. 8, pp. 4958-4971. https://doi.org/10.1093/nar/gkx112
Gulay, Suna P. ; Bista, Sujal ; Varshney, Amitabh ; Kirmizialtin, Serdal ; Sanbonmatsu, Karissa Y. ; Dinman, Jonathan D. / Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle. In: Nucleic Acids Research. 2017 ; Vol. 45, No. 8. pp. 4958-4971.
@article{01a3bc8d1f534fccb5a63694c3202301,
title = "Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle",
abstract = "Chemical modification was used to quantitatively determine the flexibility of nearly the entire rRNA component of the yeast ribosome through 8 discrete stages of translational elongation, revealing novel observations at the gross and fine-scales. These include (i) the bulk transfer of energy through the intersubunit bridges fromthe large to the small subunit after peptidyltransfer, (ii) differences in the interaction of the sarcin ricin loop with the two elongation factors and (iii) networked information exchange pathways that may functionally facilitate intra- and intersubunit coordination, including the 5.8S rRNA. These analyses reveal hot spots of fluctuations that set the stage for large-scale conformational changes essential for translocation and enable the first molecular dynamics simulation of an 80S complex. Comprehensive datasets of rRNA base flexibilities provide a unique resource to the structural biology community that can be computationally mined to complement ongoing research toward the goal of understanding the dynamic ribosome.",
author = "Gulay, {Suna P.} and Sujal Bista and Amitabh Varshney and Serdal Kirmizialtin and Sanbonmatsu, {Karissa Y.} and Dinman, {Jonathan D.}",
year = "2017",
month = "1",
day = "1",
doi = "10.1093/nar/gkx112",
language = "English (US)",
volume = "45",
pages = "4958--4971",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "8",

}

TY - JOUR

T1 - Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle

AU - Gulay, Suna P.

AU - Bista, Sujal

AU - Varshney, Amitabh

AU - Kirmizialtin, Serdal

AU - Sanbonmatsu, Karissa Y.

AU - Dinman, Jonathan D.

PY - 2017/1/1

Y1 - 2017/1/1

N2 - Chemical modification was used to quantitatively determine the flexibility of nearly the entire rRNA component of the yeast ribosome through 8 discrete stages of translational elongation, revealing novel observations at the gross and fine-scales. These include (i) the bulk transfer of energy through the intersubunit bridges fromthe large to the small subunit after peptidyltransfer, (ii) differences in the interaction of the sarcin ricin loop with the two elongation factors and (iii) networked information exchange pathways that may functionally facilitate intra- and intersubunit coordination, including the 5.8S rRNA. These analyses reveal hot spots of fluctuations that set the stage for large-scale conformational changes essential for translocation and enable the first molecular dynamics simulation of an 80S complex. Comprehensive datasets of rRNA base flexibilities provide a unique resource to the structural biology community that can be computationally mined to complement ongoing research toward the goal of understanding the dynamic ribosome.

AB - Chemical modification was used to quantitatively determine the flexibility of nearly the entire rRNA component of the yeast ribosome through 8 discrete stages of translational elongation, revealing novel observations at the gross and fine-scales. These include (i) the bulk transfer of energy through the intersubunit bridges fromthe large to the small subunit after peptidyltransfer, (ii) differences in the interaction of the sarcin ricin loop with the two elongation factors and (iii) networked information exchange pathways that may functionally facilitate intra- and intersubunit coordination, including the 5.8S rRNA. These analyses reveal hot spots of fluctuations that set the stage for large-scale conformational changes essential for translocation and enable the first molecular dynamics simulation of an 80S complex. Comprehensive datasets of rRNA base flexibilities provide a unique resource to the structural biology community that can be computationally mined to complement ongoing research toward the goal of understanding the dynamic ribosome.

UR - http://www.scopus.com/inward/record.url?scp=85020190334&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85020190334&partnerID=8YFLogxK

U2 - 10.1093/nar/gkx112

DO - 10.1093/nar/gkx112

M3 - Article

C2 - 28334755

AN - SCOPUS:85020190334

VL - 45

SP - 4958

EP - 4971

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 8

ER -