help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
Biophys. J. BioFAST: First Published March 23, 2007. doi:10.1529/biophysj.106.092650
© 2007 by the Biophysical Society.

A more recent version of this article appeared on June 15, 2007.
This Article
Right arrow Full Text (Rapid PDF)
Right arrow Supplement
Right arrow All Versions of this Article:
biophysj.106.092650v1
92/12/4168    most recent
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by VanBeek, D. B.
Right arrow Articles by Krueger, B. P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by VanBeek, D. B.
Right arrow Articles by Krueger, B. P.

BIOPHYSICAL THEORY AND MODELING

Fretting about FRET: Correlation Between {kappa} and R

Darren B. VanBeek 1, Matthew C. Zwier 1, Justin M. Shorb 1 and Brent P. Krueger 1*

1 Hope College

* To whom correspondence should be addressed. E-mail: kruegerb{at}hope.edu.

Submitted on July 3, 2006
Revised on August 14, 2006
Accepted on 8 January 2007


  Abstract
Molecular dynamics simulations were used to examine the structural dynamics of two fluorescent probes attached to a typical protein, hen egg-white lysozyme (HEWL). The donor probe (D) was attached via a succinimide group, consistent with the commonly-used maleimide conjugation chemistry, and the acceptor probe (A) was bound into the protein as occurs naturally for HEWL and the dye Eosin Y. The <{kappa}2 > is found to deviate significantly from the theoretical value and high correlation between the orientation factor {kappa} and the distance R is observed. The correlation is quantified using several possible fixed A orientations and correlation as high as 0.80 is found between {kappa} and R and as high as 0.68 between {kappa}2 and R. The presence of this correlation highlights the fact that essentially all FRET studies have assumed that {kappa} and R are independent -- an assumption that is clearly not justified in the system studied here. The correlation results in the quantities < {kappa}2 R-6 > and <{kappa}2> <>R-6 > differing by a factor of 1.6. The observed correlation between {kappa} and R is caused by the succinimide linkage between the D and HEWL, which is found to be relatively inflexible.

Key Words: Energy Transfer, Fluorescence, Molecular Dynamics, Simulation




This article has been cited by other articles:


Home page
 Proc. Natl. Acad. Sci. USAHome page
A. Iqbal, S. Arslan, B. Okumus, T. J. Wilson, G. Giraud, D. G. Norman, T. Ha, and D. M. J. Lilley
Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids
PNAS, August 12, 2008; 105(32): 11176 - 11181.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
H. Wang, S. Mao, J. M. Chalovich, and G. Marriott
Tropomyosin Dynamics in Cardiac Thin Filaments: A Multisite Forster Resonance Energy Transfer and Anisotropy Study
Biophys. J., June 1, 2008; 94(11): 4358 - 4369.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
Copyright © 2007 by the Biophysical Society.