PMID- 21751805
OWN - NLM
STAT- MEDLINE
DCOM- 20111205
LR  - 20211020
IS  - 1520-5207 (Electronic)
IS  - 1520-6106 (Print)
IS  - 1520-5207 (Linking)
VI  - 115
IP  - 32
DP  - 2011 Aug 18
TI  - Theoretical assessment of the oligolysine model for ionic interactions in 
      protein-DNA complexes.
PG  - 9864-72
LID - 10.1021/jp204915y [doi]
AB  - The observed salt dependence of charged ligand binding to polyelectrolytes, such 
      as proteins to DNA or antithrombin to heparin, is often interpreted by means of 
      the "oligolysine model." We review this model as derived entirely within the 
      framework of the counterion condensation theory of polyelectrolytes with no 
      introduction of outside assumptions. We update its comparison with experimental 
      data on the structurally simple systems for which it was originally intended. We 
      then compute the salt dependence of the binding free energy for a variety of 
      protein-DNA complexes with nonlinear Poisson-Boltzmann (NLPB) simulation methods. 
      The results of the NLPB calculations confirm the central prediction of the 
      oligolysine model that the net charge density of DNA remains invariant to protein 
      binding. Specifically, when a cationic protein residue penetrates the layer of 
      counterions condensed on DNA, a counterion is released to bulk solution, and when 
      an anionic protein residue penetrates the condensed counterion layer, an 
      additional counterion is condensed from bulk solution. We also conclude, however, 
      that the cumulative effect of charged protein residues distant from the binding 
      interface makes a significant contribution to the salt dependence of binding, an 
      observation not accommodated by the oligolysine model.
FAU - Fenley, Marcia O
AU  - Fenley MO
AD  - Institute of Molecular Biophysics+, Florida State University, Tallahassee, 
      Florida 32306, USA. mfenley@sb.fsu.edu
FAU - Russo, Cristina
AU  - Russo C
FAU - Manning, Gerald S
AU  - Manning GS
LA  - eng
GR  - R44 GM073391/GM/NIGMS NIH HHS/United States
GR  - R44 GM073391-03/GM/NIGMS NIH HHS/United States
GR  - HHMI/Howard Hughes Medical Institute/United States
GR  - 5R44GM073391-03/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20110726
PL  - United States
TA  - J Phys Chem B
JT  - The journal of physical chemistry. B
JID - 101157530
RN  - 0 (Ions)
RN  - 0 (Proteins)
RN  - 9007-49-2 (DNA)
RN  - K3Z4F929H6 (Lysine)
SB  - IM
MH  - DNA/*chemistry
MH  - Ions/chemistry
MH  - Lysine/analogs & derivatives/*chemistry
MH  - Models, Molecular
MH  - Proteins/*chemistry
MH  - Static Electricity
PMC - PMC3156561
MID - NIHMS314269
EDAT- 2011/07/15 06:00
MHDA- 2011/12/13 00:00
PMCR- 2012/08/18
CRDT- 2011/07/15 06:00
PHST- 2011/07/15 06:00 [entrez]
PHST- 2011/07/15 06:00 [pubmed]
PHST- 2011/12/13 00:00 [medline]
PHST- 2012/08/18 00:00 [pmc-release]
AID - 10.1021/jp204915y [doi]
PST - ppublish
SO  - J Phys Chem B. 2011 Aug 18;115(32):9864-72. doi: 10.1021/jp204915y. Epub 2011 Jul 
      26.