CALCON
1) How to use
Concentration values
"p" at the begining of concenbtration values (x) indicates the values are given as -log(x).
For example, p 6.0 means 0.000001. A space is allowed after "p", but put no space before "p".
2) Ionic strength
Correction of binding constant is executed for each of Mg, Ca, ATP, EGTA, EDTA, ADP, PO4
and their conbinatoins. Ions (e.g. NaOH) used for the pH adjustment of ATP, ETGA, EDTA etc,
if any, are neglected. Each binding constant used in the program can be defined independently.
Ioninc strength correction, in the case of Tris-HCl, we estimated total HCl using the following
equation, putting, [Tris] = 20 mM,
[HCl] / mM = (218.44 - 23.81 * pH) * 0.4,
the estimation of error of which would be less than 1 mM. For details, please have a look at
TRIS-HCL.TXT as well as TRIS-HCL.WJ2.
3) Binding constants
Binding constants used in the program are derived from the same references for each
cations after correcting the defined ioninc strength. Details are describes in the program,
"procedure logGamma". This variable is log of γ, ion activity (effective concentration) of ions.
Binding constants used.
For ATP
H+ 4.11
Mg++ 4.22 {3.84}
2.24 {2.09} { Mg + HATP <-> MgHATP }
0 {1.58} { Mg + H2ATP <-> MgH2ATP }
Ca++ 3.98
2.13 { Ca + HATP <-> CaHATP }
For EGTA (GEDTA)
H 9.46 8.85 2.65 2.0
Mg 5.2 3.4
Ca 10.97 5.3
Foe EDTA
H 10.26 6.16 2.67 1.99
Mg 8.69 2.28
Ca 10.59 3.51
For ADP
H 6.44 3.93
Mg 3.17 1.64
Ca 2.86 1.58
For phosphate (PO_4^3-)
H 11.591 {12.203 at 0 ionic str.}
6.718 { 7.207 at 0 ionic str.}
1.91; { 2.161 at 0 ionic str.}
Mg 0 2.02; {1.88 at 0.2 KCl}{ Mg + HPO4 <-> MgHPO4 }
Ca 0 1.84; {1.70 at 0.2 KCl}{ Ca + HPO4 <-> CaHPO4 }
<Japanese>
プログラム開発経緯
Shinji Kamimura created CALCON using BASIC in May 1982.
- Turbo Pascal versions -
1995-07-12 ver 0.1 Started
1995-07-13 ver 0.2 Ionic strength correction
1995-07-16 ver 0.3 Add ADP and PO4
1995-09-08 ver 0.5 Corrected an error in the ionic strength correction
1995-09-22 ver 1.0 Stopped developping
1995-09-30 ver 1.2 Rewrote using OOP (uploaded to Nifty on 95-10-28)
- Turbo Vision versions -
1995-10-04 ver 2.0 Ported all functions to Turbo Vision
1995-10-15 ver 2.1 Help system
1995-10-17 ver 2.2 Rewrote 'Main' using Turbo Vision (except InputLine)
1995-10-20 ver 2.3 Completed porting to Turbo Vision
1995-10-22 ver 2.31 made interface of 'Change/Restore Constants'
1995-10-23 ver 2.32 implemented 'Restore Constants'
1995-10-24 ver 2.4 Implemented 'ChangeConst' (uploaded to Nifty on 95-10-28)
1995-10-25 ver 2.41 made interface of 'pH buffer'
1995-10-27 ver 2.42 implemented 'pH buffer'
1995-10-28 ver 2.43 improved documents and source
1995-10-30 ver 2.44 check input value (SetParam)
1995-11-01 ver 2.45 split source (move TSolution to ccndumb.pas)
1995-11-03 ver 2.46 trivial changes
- Windows versions -
1995-10-15 ver 0.1 Ported from ver 1.2 by Go Nakayama
1995-10-21 ver 0.2
1995-11-03 ver 0.3 Made interface of 'Change?Restore Constants'
使用法
~~~~~~
o 濃度の入力
濃度を入力するとき，１文字目に小文字の p を入力すると，p に続けて入力した数値 x は逆数の対数 -log(x) であると解釈されます。すなわち，p 6.0 は 0.000001 と同じです。p の後の空白は必要ありませんが p の前に空白を入れてはいけません。
アルゴリズム
~~~~~~~~~~~~
オリジナルは，David A. Goldstein (1979) Biophys. J. 26:235-242 です。
イオン強度による結合定数の補正もしています。
o イオン強度
イオン強度は Mg, Ca, ATP, EGTA, EDTA, ADP, PO4 およびそれらの組み合わせのみに
ついて計算してあります。ATP, EGTA, EDTA などを pH 7 にするために加えた NaOH は
含みません。また，結合定数の補正にはユーザーが指定した値を使います。
o 結合定数，キレート安定度定数
結合定数の値は Sillen and Martell (1964) に依っています（表１参照）。
表１．結合定数（酸解離定数，キレート安定度定数）
ATP
H+ 4.11
Mg++ 4.22 {3.84}
2.24 {2.09} { Mg + HATP <-> MgHATP }
- {1.58} { Mg + H2ATP <-> MgH2ATP }
Ca++ 3.98
2.13 { Ca + HATP <-> CaHATP }
EGTA (GEDTA)
H 9.46 8.85 2.65 2.0
Mg 5.2 3.4
Ca 10.97 5.3
EDTA
H 10.26 6.16 2.67 1.99
Mg 8.69 2.28
Ca 10.59 3.51
ADP
H 6.44 3.93
Mg 3.17 1.64
Ca 2.86 1.58
PO_4^3-
H 11.591 {12.203 at 0 ionic str.}
6.718 { 7.207 at 0 ionic str.}
1.91; { 2.161 at 0 ionic str.}
Mg - 2.02; {1.88 at 0.2 M KCl}{ Mg + HPO4 <-> MgHPO4 }
Ca - 1.84; {1.70 at 0.2 M KCl}{ Ca + HPO4 <-> CaHPO4 }
著作権・開発環境・コンパイラ
~~~~~~~~~~~~~~~~~~~~
このプログラムはフリーソフトです。非営利目的の複製・配布は自由です。
Copyright (C) 1995 by Takeshi Tojo (ss46351@komaba.ecc.u-tokyo.ac,jp)
このプログラムは
TURBO Pascal 6.0 Copyright (c) Borland International, Inc.
を用いて
EPSON PC-386GS + EPSON MS-DOS 6.2 および
NEC PC-9801DA + NEC MS-DOS 5.00
上で開発しました。