[3] protein

## Don't show: data(thermo)
thermo$obigt: 1911 aqueous, 3588 total species
## End(Don't show) ## Standard molal entropy of a protein reaction basis("CHNOS")
C H N O S ispecies logact state CO2 1 0 0 2 0 1576 -3 aq H2O 0 2 0 1 0 1 0 liq NH3 0 3 1 0 0 66 -4 aq H2S 0 2 0 0 1 67 -7 aq O2 0 0 0 2 0 3316 -80 gas
# here we provide the reaction coefficients of the # proteins (per protein backbone); subcrt() calculates # the coefficients of the basis species in the reaction s <- subcrt(c("CSG_METTL", "CSG_METJA"), c(-1/530, 1/530), T=seq(0, 350, length.out=50))
protein.obigt: found CSG_METTL (C2484H4000N638O844S7, 530 residues) protein.obigt: found CSG_METJA (C2555H4032N640O865S14, 530 residues) subcrt: 2 species at 50 values of T and P (wet) subcrt: reaction is not balanced; it is missing this composition: C H N O S -0.133962264 -0.060377358 -0.003773585 -0.039622642 -0.013207547 subcrt: adding missing composition from basis definition and restarting... subcrt: 7 species at 50 values of T and P (wet)
# note: this uses the properties of the nonionized proteins ## logfO2-pH potential diagram # with a charged basis, we calculate properties of ionized proteins basis("CHNOS+")
C H N O S Z ispecies logact state CO2 1 0 0 2 0 0 1576 -3 aq H2O 0 2 0 1 0 0 1 0 liq NH3 0 3 1 0 0 0 66 -4 aq H2S 0 2 0 0 1 0 67 -7 aq O2 0 0 0 2 0 0 3316 -80 gas H+ 0 1 0 0 0 1 3 -7 aq
file <- system.file("extdata/protein/DS11.csv", package = "CHNOSZ") aa <- read.csv(file, as.is=TRUE) aa <- aa[grep("transferase", aa$protein), ] ip <- add.protein(aa)
add.protein: added 5 new protein(s) to thermo$protein
a <- affinity(pH=c(0, 14), O2=c(-64, -61), T=75, iprotein=ip)
energy.args: temperature is 75 C energy.args: pressure is Psat energy.args: variable 1 is pH at 128 values from 0 to 14 energy.args: variable 2 is log_f(O2) at 128 values from -64 to -61 subcrt: 27 species at 348.15 K and 1 bar (wet) subcrt: 18 species at 348.15 K and 1 bar (wet)
diagram(a)
balance: from protein length diagram: plotting A/(2.303RT) / n.balance (maximum affinity method for 2-D diagrams) subcrt: 3 species at 348.15 K and 1 bar (wet) subcrt: 2 species at 348.15 K and 1 bar
title(main="Sequences for transferase at Bison Pool")

Image protein1

 

## surface-layer proteins from Methanococcus and others ## as a function of oxygen fugacity, after Dick, 2008, Fig. 5b # use old properties of [Met] (Dick et al., 2006) to reproduce this example data(thermo)
thermo$obigt: 1911 aqueous, 3588 total species
mod.obigt("[Met]", G=-35245, H=-59310)
mod.obigt: updated [Met](aq) [1] 1867
# make our protein list organisms <- c("METSC", "METJA", "METFE", "HALJP", "METVO", "METBU", "ACEKI", "GEOSE", "BACLI", "AERSA") proteins <- c(rep("CSG", 6), rep("SLAP", 4)) proteins <- paste(proteins, organisms, sep="_") # load the basis species and proteins basis("CHNOS+")
C H N O S Z ispecies logact state CO2 1 0 0 2 0 0 1576 -3 aq H2O 0 2 0 1 0 0 1 0 liq NH3 0 3 1 0 0 0 66 -4 aq H2S 0 2 0 0 1 0 67 -7 aq O2 0 0 0 2 0 0 3316 -80 gas H+ 0 1 0 0 0 1 3 -7 aq
species(proteins)
CO2 H2O NH3 H2S O2 H+ ispecies logact state name 1 2812 1066 747 16 -2909.0 0 3589 -3 aq CSG_METSC 2 2555 1042 640 14 -2643.5 0 3590 -3 aq CSG_METJA 3 2815 1071 747 14 -2914.5 0 3591 -3 aq CSG_METFE 4 3669 1367 971 0 -3608.5 0 3592 -3 aq CSG_HALJP 5 2575 1070 645 11 -2668.0 0 3593 -3 aq CSG_METVO 6 1362 519 355 4 -1400.5 0 3594 -3 aq CSG_METBU 7 3584 1431 926 4 -3730.5 0 3595 -3 aq SLAP_ACEKI 8 5676 2320 1489 3 -5904.5 0 3596 -3 aq SLAP_GEOSE 9 3977 1594 1068 2 -4131.0 0 3597 -3 aq SLAP_BACLI 10 2250 861 618 2 -2322.5 0 3598 -3 aq SLAP_AERSA
# calculate affinities; we go to lower logfO2 than Dick, 2008 # and find an interesting convergence of stabilities there a <- affinity(O2=c(-100, -65))
energy.args: temperature is 25 C energy.args: pressure is Psat energy.args: variable 1 is log_f(O2) at 128 values from -100 to -65 subcrt: 16 species at 298.15 K and 1 bar (wet) subcrt: 18 species at 298.15 K and 1 bar (wet)
# try normalize=FALSE to make Fig. 5a in the paper e <- equilibrate(a, normalize=TRUE)
balance: from protein length equilibrate: n.balance is 571 530 571 828 553 278 736 1198 844 481 equilibrate: loga.balance is 0.81888541459401 equilibrate: using 'normalize' for molar formulas equilibrate: using boltzmann method
d <- diagram(e, ylim=c(-5, -1), names=organisms, format.names=FALSE) # add water stability line abline(v=-83.1, lty=2) title(main="Surface-layer proteins, after Dick, 2008") # checking the geometry of the diagram # most preominant along the x-axis stopifnot(organisms[unique(which.pmax(e$loga.equil))] == c("METFE", "METJA", "METVO", "HALJP")) # stability order close to logfO2=-83.1 stopifnot(order(as.data.frame(e$loga.equil)[62,], decreasing=TRUE)==c(2, 6, 7, 5, 3, 1, 9, 8, 10, 4))

Image protein2

 

# reset thermodynamic database data(thermo)
thermo$obigt: 1911 aqueous, 3588 total species
## relative stabilities of bovine proteins ## as a function of temperature along a glutathione redox buffer mod.buffer("GSH-GSSG", c("GSH","GSSG"), logact=c(-3, -7))
mod.buffer: changed state and/or logact of GSH GSSG in GSH-GSSG buffer
basis(c("CO2", "H2O", "NH4+", "SO4-2", "H2", "H+"), c(-1, 0, -4, -4, 999, -7))
C H N O S Z ispecies logact state CO2 1 0 0 2 0 0 1576 -1 aq H2O 0 2 0 1 0 0 1 0 liq NH4+ 0 4 1 0 0 1 18 -4 aq SO4-2 0 0 0 4 1 -2 24 -4 aq H2 0 2 0 0 0 0 64 999 aq H+ 0 1 0 0 0 1 3 -7 aq
basis("H2", "GSH-GSSG")
C H N O S Z ispecies logact state CO2 1 0 0 2 0 0 1576 -1 aq H2O 0 2 0 1 0 0 1 0 liq NH4+ 0 4 1 0 0 1 18 -4 aq SO4-2 0 0 0 4 1 -2 24 -4 aq H2 0 2 0 0 0 0 64 GSH-GSSG aq H+ 0 1 0 0 0 1 3 -7 aq
basis("CO2", "gas")
C H N O S Z ispecies logact state CO2 1 0 0 2 0 0 3308 -1 gas H2O 0 2 0 1 0 0 1 0 liq NH4+ 0 4 1 0 0 1 18 -4 aq SO4-2 0 0 0 4 1 -2 24 -4 aq H2 0 2 0 0 0 0 64 GSH-GSSG aq H+ 0 1 0 0 0 1 3 -7 aq
prot <- c("CYC", "RNAS1", "BPT1", "ALBU", "INS", "PRIO") species(prot, "BOVIN")
CO2 H2O NH4+ SO4-2 H2 H+ ispecies logact state name 1 517 -900 143 4 1094 -135 3589 -3 aq CYC_BOVIN 2 575 -1005 171 12 1191 -147 3590 -3 aq RNAS1_BOVIN 3 284 -517 84 7 603 -70 3591 -3 aq BPT1_BOVIN 4 2934 -5127 781 39 6224 -703 3592 -3 aq ALBU_BOVIN 5 254 -458 65 6 545 -53 3593 -3 aq INS_BOVIN 6 1026 -1783 318 9 2053 -300 3594 -3 aq PRIO_BOVIN
a <- affinity(T=c(0, 200))
energy.args: pressure is Psat energy.args: variable 1 is T at 128 values from 273.15 to 473.15 K affinity: loading buffer species subcrt: 14 species at 128 values of T and P (wet) subcrt: 18 species at 128 values of T and P (wet) buffer: ( GSH-GSSG ) for activity of H2 (active), CO2 (conserved)
# set line colors according to oxidation state of carbon ZC <- ZC(species()$ispecies) col <- ZC.col(ZC) e <- equilibrate(a, normalize=TRUE)
balance: from protein length equilibrate: n.balance is 104 124 58 583 51 217 equilibrate: loga.balance is 0.0557604646877348 equilibrate: using 'normalize' for molar formulas equilibrate: using boltzmann method
d <- diagram(e, col=col, lwd=3) title(main="Bovine proteins, GSH/GSSG redox buffer")

Image protein3