Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center

Nizar N Batada; Kenneth D Westover; David A Bushnell; Michael Levitt; Roger D Kornberg

doi:10.1073/pnas.0408168101

Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center

Nizar N Batada, Kenneth D Westover, David A Bushnell, Michael Levitt, Roger D Kornberg

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

Abstract / Description of output

Nucleoside triphosphates (NTPs) diffuse to the active center of RNA polymerase II through a funnel-shaped opening that narrows to a negatively charged pore. Computer simulation shows that the funnel and pore reduce the rate of diffusion by a factor of approximately 2 x 10(-7). The resulting limitation on the rate of RNA synthesis under conditions of low NTP concentration may be overcome by NTP binding to an entry site adjacent to the active center. Binding to the entry site greatly enhances the lifetime of an NTP in the active center region, and it prevents "backtracking" and the consequent occlusion of the active site.

Original language	English
Pages (from-to)	17361-4
Number of pages	4
Journal	Proceedings of the National Academy of Sciences (PNAS)
Volume	101
Issue number	50
DOIs	https://doi.org/10.1073/pnas.0408168101
Publication status	Published - 14 Dec 2004

Keywords / Materials (for Non-textual outputs)

Binding Sites
Computer Simulation
Diffusion
Dinucleoside Phosphates
Models, Molecular
Protein Structure, Tertiary
RNA Polymerase II
Static Electricity
Thermodynamics

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10.1073/pnas.0408168101

Cite this

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title = "Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center",

abstract = "Nucleoside triphosphates (NTPs) diffuse to the active center of RNA polymerase II through a funnel-shaped opening that narrows to a negatively charged pore. Computer simulation shows that the funnel and pore reduce the rate of diffusion by a factor of approximately 2 x 10(-7). The resulting limitation on the rate of RNA synthesis under conditions of low NTP concentration may be overcome by NTP binding to an entry site adjacent to the active center. Binding to the entry site greatly enhances the lifetime of an NTP in the active center region, and it prevents {"}backtracking{"} and the consequent occlusion of the active site.",

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author = "Batada, {Nizar N} and Westover, {Kenneth D} and Bushnell, {David A} and Michael Levitt and Kornberg, {Roger D}",

year = "2004",

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doi = "10.1073/pnas.0408168101",

language = "English",

volume = "101",

pages = "17361--4",

journal = "Proceedings of the National Academy of Sciences (PNAS)",

issn = "0027-8424",

publisher = "National Academy of Sciences",

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TY - JOUR

T1 - Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center

AU - Batada, Nizar N

AU - Westover, Kenneth D

AU - Bushnell, David A

AU - Levitt, Michael

AU - Kornberg, Roger D

PY - 2004/12/14

Y1 - 2004/12/14

N2 - Nucleoside triphosphates (NTPs) diffuse to the active center of RNA polymerase II through a funnel-shaped opening that narrows to a negatively charged pore. Computer simulation shows that the funnel and pore reduce the rate of diffusion by a factor of approximately 2 x 10(-7). The resulting limitation on the rate of RNA synthesis under conditions of low NTP concentration may be overcome by NTP binding to an entry site adjacent to the active center. Binding to the entry site greatly enhances the lifetime of an NTP in the active center region, and it prevents "backtracking" and the consequent occlusion of the active site.

AB - Nucleoside triphosphates (NTPs) diffuse to the active center of RNA polymerase II through a funnel-shaped opening that narrows to a negatively charged pore. Computer simulation shows that the funnel and pore reduce the rate of diffusion by a factor of approximately 2 x 10(-7). The resulting limitation on the rate of RNA synthesis under conditions of low NTP concentration may be overcome by NTP binding to an entry site adjacent to the active center. Binding to the entry site greatly enhances the lifetime of an NTP in the active center region, and it prevents "backtracking" and the consequent occlusion of the active site.

KW - Binding Sites

KW - Computer Simulation

KW - Diffusion

KW - Dinucleoside Phosphates

KW - Models, Molecular

KW - Protein Structure, Tertiary

KW - RNA Polymerase II

KW - Static Electricity

KW - Thermodynamics

U2 - 10.1073/pnas.0408168101

DO - 10.1073/pnas.0408168101

M3 - Article

C2 - 15574497

SN - 0027-8424

VL - 101

SP - 17361

EP - 17364

JO - Proceedings of the National Academy of Sciences (PNAS)

JF - Proceedings of the National Academy of Sciences (PNAS)

IS - 50

ER -

Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center

Abstract / Description of output

Keywords / Materials (for Non-textual outputs)

Access to Document

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