Gramicidin Permeation Database
File and Filename Format:
1. There is a file for each submission, generally corresponding to one type of data.
2. The accession code (filename) is TPPPPIILLNN(X).
A) T is the measurement type (I=current, of which RevPot is a special case; L=lifetime; B=block; N=noise; F=flux-ratio; V=Doppler velocity).
B) PPPP is the peptide or peptides (gAgM=heterodimers; fWgA= fluorinated gA; WFgA=phenylalanine mutants; fVgA=fluorinated valine mutants).
C) II is the predominant conducting species (BI=biionic conditions).
D) LL is the lipid (MI=mixed; MG=monoglyceride; PC=lecithin).
E) NN is a number differentiating experiments with the same filename parameters.
F) X is any additional pertinent information (eg. urea, sucrose, glycerin).
3. Each file contains reference information, historical information about when the data set was completed and any special circumstances, a set of machine readable standard experimental condition lines, followed my a set of machine readable datapoint lines. These are followed by a set of abbreviation definitions, and then any annotation, such as previous interpretations, precautions, or significant analysis.
Measurement record format:
|
MEAS |
measurement type, value, SD, N |
|
STAT |
number of channels, fraction used |
|
PEPC |
peptides, cis (grounded) side |
|
PEPT |
peptides, trans (charged) side |
|
SOLC |
solvent, cis side |
|
IONC |
number of cis ion types, ion types |
|
CONC |
ion concentrations (molar), cis side |
|
ACTC |
ion activities (molar), cis side |
|
SOLT |
solvent, trans side (free style) |
|
IONT |
number of trans ion types, ion types |
|
CONT |
ion concentrations, trans side |
|
ACTT |
ion activities, trans side |
|
VM |
membrane potential (volts) |
|
TEMP |
temperature (centigrade) |
|
SYMM |
symmetry types (none=0, bilateral=1) |
Explanation of field contents for measurement records:
|
SCC |
single channel current (pA) |
|
MCC |
normalized multichannel current (1.0 at 0.1 V) |
|
RP |
reversal potential (volts) |
|
FR |
flux ratio (unitless) |
|
FREX |
flux ratio exponent: Using n or n' value |
|
SCUF |
single channel unidirectional flux (ions/sec) |
|
MCUF |
normalized multichannel unidirectional flux (1.0 at 0.1 V) |
|
SCN |
single channel noise (fA^2/Hz) |
|
NRO |
single channel noise roll off - 3 DB point (Hz) |
|
ASCL |
average single channel lifetime (s) |
|
SCDR |
single channel lifetime histogram decay rate(s) |
|
MCRR |
multichannel relaxation rate (/s) |
|
SCOF |
single channel occurrence frequency (/s) |
|
BLKF |
average block frequency (/s) |
|
BLKD |
average block duration (s) |
|
DVEL |
Average ion Doppler velocity (Ang/pS) |
|
SD |
interexperimental standard deviation |
|
N |
number of experiments (different bilayers or patches) |
|
STAT |
sampling statistics: for single channel measurements, the total number of channels in the N experiments; fraction in the main peak (serves heterodimer experiments as well as mini-channel studies). For multichannel experiments, an estimate of the number of channels, if available; if the fraction used is not specified, it will be assumed that 100% were used for average. |