1887
banner image
No data available.
Please log in to see this content.
You have no subscription access to this content.
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
Monte Carlo-based linear Poisson-Boltzmann approach makes accurate salt-dependent solvation free energy predictions possible
Rent:
Rent this article for
USD
10.1063/1.2803189
    + View Affiliations - Hide Affiliations
    Affiliations:
    1 Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
    2 Department of Computer Science and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
    3 Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
    a) Permanent address: Institute of Computational Mathematics and Mathematical Geophysics, Novosibirsk, Russia. Electronic mail: simonov@scs.fsu.edu
    b) Electronic mail: mascagni@fsu.edu
    c) Author to whom correspondence should be addressed. Electronic mail: mfenley@sb.fsu.edu
    J. Chem. Phys. 127, 185105 (2007); http://dx.doi.org/10.1063/1.2803189
/content/aip/journal/jcp/127/18/10.1063/1.2803189
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/18/10.1063/1.2803189

Figures

Image of FIG. 1.
FIG. 1.

(Color) The surface electrostatic potential of the arginine-rich peptide motif (ARM) P22 transcriptional antitermination N peptide [left figure (A), PDB ID: 1A4T, model 1] and N-terminal peptide of the N protein (N36) from bacteriophage [right figure (B), PDB ID: 1QFQ, model 1]. The RNA binding partner is represented as a stick diagram. Note that the major groove side of the RNA binds to the positive surface (green) of the ARM peptide. Moreover, the P22 transcriptional antitermination N peptide (left figure) has a more pronounced and larger positive electrostatic potential patch when compared to N-terminal peptide of the N protein (N36) from bacteriophage (right figure). The interior and dielectric constants were set to 2 and 80, respectively. The NaCl concentration was fixed at . The surface electrostatic potential maps were generated with the highly accurate and fast multipole accelerated boundary element implementation of the linear Poisson-Boltzmann solver (Ref. 37). The color scheme used in these maps is as follows: yellow is the most negative and green is the most positive . White is neutral. Red and blue represent negative and positive potentials, respectively.

Image of FIG. 2.
FIG. 2.

(Color online) Dependence of the computed electrostatic solvation free energy (in kcal/mol) for the peptide A (PDB ID: 1A4T, model 1) on the number of samples. The calculated confidence interval is given by the green curves.

Image of FIG. 3.
FIG. 3.

(Color online) Salt-dependent part of the electrostatic solvation free energy (in kcal/mol) for ARM peptides [PDB IDs: (A) 1A4T, (B) 1QFQ, (C) 1HJI, and (D) 1NYB; see text for details about these peptides] with different total charges and surface charge densities. Error bars give the calculated statistical confidence intervals for (A) and (B).

Image of FIG. 4.
FIG. 4.

(Color online) Difference in solvation free energy (relative to a reference salt concentration of NaCl), as defined in text above, for two 19-mer ARM peptides: P22 transcriptional antitermination N peptide (PDB ID: 1A4T, model 1) and N-terminal peptide of the N protein (N36) from bacteriophage (PDB ID: 1QFQ, model 1). The interior and dielectric constants were set to 1 and 78.5, respectively. The van der Waals surface is employed to define the dielectric interface separating the molecular interior region from the solvent region. All BEM linear PB calculations were performed with the highly accurate and fast multipole accelerated boundary element implementation of the linear Poisson-Boltzmann equation (Ref. 37). Error bars give the calculated statistical confidence intervals for the Monte Carlo results.

Tables

Generic image for table
Table I.

Dependence of the electrostatic solvation free energy (in kcal/mol) on salt concentration . Peptide A (PDB ID: 1A4T). Total . is the difference between the computed reaction-field energy for the given dielectric constants and the reference value of for .

Generic image for table
Table II.

Dependence of the electrostatic solvation free energy (in kcal/mol) on salt concentration . Peptide B (PDB ID: 1QFQ). Total . is the difference between the computed reaction-field energy for the given dielectric constants and the reference value of for .

Loading

Article metrics loading...

/content/aip/journal/jcp/127/18/10.1063/1.2803189
2007-11-13
2014-04-20
Loading

Full text loading...

This is a required field
Please enter a valid email address
752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Monte Carlo-based linear Poisson-Boltzmann approach makes accurate salt-dependent solvation free energy predictions possible
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/18/10.1063/1.2803189
10.1063/1.2803189
SEARCH_EXPAND_ITEM