Abstract
Although NMR was discovered in 1946, its application to biological systems only started in the late 1960s and early 1970s. The application was very limited due to the poor sensitivity and very low resolution offered by the one-dimensional techniques used at that time. Two major breakthroughs in the 1970s revolutionized the field: Fourier transformation (FT) NMR that allowed rapid recording of NMR signals and two-dimensional NMR spectroscopy that dramatically increased the spectral resolution. These advances in combination with the development of stable magnets at higher fields led to explosive investigations using NMR spectroscopy in the late 1970s and early 1980s, which centered on exploring its potential in determining the 3D structures of macromolecules. Even though X-ray crystallography was already a method of choice for structure determination during that period, it was believed that NMR may provide complementary structural information in the more physiologically relevant solution environment. Moreover, since some biomolecules are difficult to crystallize, NMR could be used as an alternative method for obtaining 3D structures.
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Appendices
Appendix B: sa.inp—Xplor Protocol for Protein Structure Calculation
REMARKS This protocol has very slow cooling with increase of vdw
evaluate ($seed=287346589)
set seed $seed end
!------------------------------
! read in the PSF file and initial structure
param @parallhdg_ILK.pro end
structure @ILK_new.ps f end
coor @ILK_aves_min.pdb
coor copy end
!------------------------------
! set the weights for the experimental energy terms
evaluate ($knoe=25.0) ! noes
evaluate ($asym=0.1) ! slope of NOE potential
evaluate ($kcdi=10.0) ! torsion angles
!------------------------------
! The next statement makes sure the experimental energies are used in the
! calculation, and switches off the unwanted energy terms.
! note that the NMR torsions are only switched on in the cooling stage
! we include the noncrystallographic symmetry right from the start
!-------------------------------
! Read experimental restraints
noe
reset
nrestraints=6000    ! allocate space for NOEs
ceiling 100
set echo off message off end
class     all
set message off echo off end
@ILK_mod1.tbl
@hbond.tbl
set echo on message on end
averaging all center
potential all square
scale all $knoe
sqconstant all 1.0
sqexponent all 2
! soexponent all 1
! rswitch all 1.0
! sqoffset all 0.0
! asymptote all 2.0
end
couplings
potential harmonic
class phi
force 1.0
nres 300
degeneracy 1
coefficients 6.98 -1.38 1.72 -60.0
@dihed_talos.tbl
end
carbon
nres=200
class all
force 0.5
potential harmonic
@rcoil_c13.tbl
@expected_edited_c13.tbl
@shift_qm.tbl
end
evaluate ($rcon=0.003)
parameters
nbonds
atom
nbxmod 3
wmin=0.01 ! warning off
cutnb=4.5 ! nonbonded cutoff
tolerance 0.5
repel=0.9 ! scale factor for vdW radii=1 (L-J radii)
rexp=2 ! exponents in (r^irex - R0^irex)^rexp
irex=2
rcon=$rcon ! actually set the vdW weight
end
end
set message off echo off end
restraints dihed
scale $kcdi
@dihed_talos.tbl
end
set message on echo on end
flags
exclude * include bonds angle impr vdw noe cdih coup carb end
evaluate ($cool_steps=3000)
evaluate ($init_t=2000.01)
vector do (mass=100.0) (all)   ! uniform mass for all atoms
vector do (fbeta=10.0) (all)  ! coupling to heat bath
eval ($endcount=100)
coor copy end
eval ($count=0)
while ($count<$endcount) loop main
evaluate ($count=$count+1)
coor swap end
coor copy end
vector do (x=xcomp) (all)
vector do (y=ycomp) (all)
vector do (z=zcomp) (all)
evaluate ($ini_rad=0.9)  evaluate ($fin_rad=0.80)
evaluate ($ini_con=0.004)  evaluate ($fin_con=4.0)
evaluate ($ini_ang=0.4)  evaluate ($fin_ang=1.0)
evaluate ($ini_imp=0.1)  evaluate ($fin_imp=1.0)
evaluate ($ini_noe=2.0)  evaluate ($fin_noe=30.0)
evaluate ($knoe=$ini_noe)  ! slope of NOE potential
evaluate ($kcdi=10.0)  ! torsion angles
noe
averaging all center
potential all square
scale all $knoe
sqconstant all 1.0
sqexponent all 2
end
restraints dihed
scale $kcdi
end
evaluate ($rcon=1.0)
parameters
nbonds
atom
nbxmod 3
wmin=0.01  ! warning off
cutnb=100  ! nonbonded cutoff
tolerance 45
repel=1.2 ! scale factor for vdW radii=1 (L-J radii)
rexp=2 ! exponents in (r^irex - R0^irex)^rexp
irex=2
rcon=$rcon ! actually set the vdW weight
end
end
constraints
interaction (not name ca) (all)
weights * 1 angl 0.4 impr 0.1 vdw 0 elec 0 end
interaction (name ca) (name ca)
weights * 1 angl 0.4 impr 0.1 vdw 1.0 end
end
dynamics verlet
nstep=1000  !
timestep=0.005  !
iasvel=maxwell  firsttemp=$init_t
tcoupling=true
tbath=$init_t
nprint=50
iprfrq=0
ntrfr=99999999
end
parameters
nbonds
atom
nbxmod 3
wmin=0.01 ! warning off
cutnb=4.5 ! nonbonded cutoff
tolerance 0.5
repel=0.9 ! scale factor for vdW radii=1 (L-J radii)
rexp=2 ! exponents in (r^irex - R0^irex)^rexp
irex=2
rcon=1.0 ! actually set the vdW weight
end
end
evaluate ($kcdi=200)
restraints dihed
scale $kcdi
end
evaluate ($final_t=100) {K}
evaluate ($tempstep=50) {K}
evaluate ($ncycle=($init_t-$final_t)/$tempstep)
evaluate ($nstep=int($cool_steps/$ncycle))
evaluate ($bath=$init_t)
evaluate ($k_vdw=$ini_con)
evaluate ($k_vdwfact=($fin_con/$ini_con)^(1/$ncycle))
evaluate ($radius=$ini_rad)
evaluate ($radfact=($fin_rad/$ini_rad)^(1/$ncycle))
evaluate ($k_ang=$ini_ang)
evaluate ($ang_fac=($fin_ang/$ini_ang)^(1/$ncycle))
evaluate ($k_imp=$ini_imp)
evaluate ($imp_fac=($fin_imp/$ini_imp)^(1/$ncycle))
evaluate ($noe_fac=($fin_noe/$ini_noe)^(1/$ncycle))
evaluate ($knoe=$ini_noe)
vector do (vx=maxwell($bath)) (all)
vector do (vy=maxwell($bath)) (all)
vector do (vz=maxwell($bath)) (all)
evaluate ($i_cool=0)
while ($i_cool<$ncycle) loop cool
evaluate ($i_cool=$i_cool+1)
evaluate ($bath=$bath - $tempstep)
evaluate ($k_vdw=min($fin_con,$k_vdw*$k_vdwfact))
evaluate ($radius=max($fin_rad,$radius*$radfact))
evaluate ($k_ang=$k_ang*$ang_fac)
evaluate ($k_imp=$k_imp*$imp_fac)
evaluate ($knoe=$knoe*$noe_fac)
constraints interaction (all) (all) weights
* 1 angles $k_ang improper $k_imp
end end
parameter nbonds
cutnb=4.5 rcon=$k_vdw nbxmod=3 repel=$radius
end end
noe scale all $knoe end
dynamics verlet
nstep=$nstep timestep=0.005 iasvel=current firsttemp=$bath
tcoupling=true tbath=$bath nprint=$nstep iprfrq=0
ntrfr=99999999
end
end loop cool
mini powell nstep=500 nprint=50 end
{* NOE Data Analysis *}
print threshold=0.5 noe
evaluate ($noe5=$violations)
print threshold=0.0 noe
evaluate ($noe0=$violations)
evaluate ($rms_noe=$result)
{* CDIH Data Analysis *}
print threshold=5.0 cdih
evaluate ($cdih5=$violations)
print threshold=0.0 cdih
evaluate ($cdih0=$violations)
evaluate ($rms_cdih=$result)
{* BOND Data Analysis *}
print thres=0.05 bond
evaluate ($bond5=$violations)
evaluate ($rms_bond=$result)
{* ANGLE Data Analysis *}
print thres=5.0 angle
evaluate ($angle5=$violations)
evaluate ($rms_angle=$result)
{* IMPROPER Data Analysis *}
print thres=5.0 improper
evaluate ($improper5=$violations)
evaluate ($rms_improper=$result)
{* ENERGY Data Analysis *}
energy end
{* J-coupling constant analysis *}
couplings print threshold 1.0 all end
evaluate ($rms_coup=$result)
evaluate ($viol_coup=$violations)
{* Carbon chemical shift analysis *}
carbon print threshold=1.0 end
evaluate ($rms_carbashift=$rmsca)
evaluate ($rms_carbbshift=$rmscb)
evaluate ($viol_carb=$violations)
remarks====================================
remarks noe, cdih, bonds, angles, improp
remarks violations.: $noe5[I5], $cdih5[I5], $bond5[I5], $angle5[I5], $improper5[I5]
remarks RMSD.: $rms_noe[F6.3], $rms_cdih[F6.3], $rms_bond[F6.3], $rms_angle[F6.3], $rms_improper[F6.3]
remarks 0-viol.: $noe0[I5], $cdih0[I5]
remarks coup, carb-a, carb-b
remarks violations: $viol_coup[I5], $viol_carb[I5],
remarks RMSD: $rms_coup[F6.3], $rms_carbashift[F6.3],
$rms_carbbshift[F6.3],
remarks ====================================
remarks overall=$ener
remarks noe=$NOE
remarks dih=$CDIH
remarks vdw=$VDW
remarks bon=$BOND
remarks ang=$ANGL
remarks imp=$IMPR
remarks coup=$COUP
remarks carb=$CARB
remarks prot=$PROT
remarks ======================================
evaluate ($file="ILK_tal_"+encode($count)+".pdb")
write coordinates output=$file end
end loop main
write coordinates output=$filename end
stop
Appendix C: Example of NOE Table
!K1
assign (resid 1 and name HG#) (resid 1 and name HD#) 2.5 0.7 0.2!#A 526 9.18e+05
assign (resid 1 and name HG#) (resid 1 and name HB#) 3.0 1.2 0.3!#A 521 2.31e+05
assign (resid 1 and name HD#) (resid 1 and name HE#) 2.5 0.7 0.2!#A 518 5.72e+05
assign (resid 1 and name HG#) (resid 1 and name HE#) 3.0 1.2 0.3 !m#A 516 4.30e+05
assign (resid 1 and name HG#) (resid 1 and name HA) 4.0 2.2 2.0 !#A 510 2.25e+05
assign (resid 1 and name HD#) (resid 1 and name HA) 4.0 2.2 1.0!#A 509 1.45e+05
assign (resid 1 and name HB#) (resid 1 and name HA) 3.0 1.2 0.3!#A 508 3.20e+05
assign (resid 1 and name HE#) (resid 1 and name HA) 4.0 2.2 1.0!#A 500 8.04e+04
assign (resid 1 and name HA) (resid 2 and name HB) 4.0 2.2 1.0!#A 512 1.24e+05
assign (resid 1 and name HB#) (resid 2 and name HA) 4.0 2.2 2.0!added
!assign (resid 1 and name HG#) (resid 2 and name HA) 4.0 2.2 2.0!added
!assign (resid 1 and name HG#) (resid 3 and name HA#) 4.0 2.2 1.0!#A 513 9.34e+04
!assign (resid 1 and name HG#) (resid 3 and name HN) 4.0 2.2 1.0!added
assign (resid 1 and name HB#) (resid 3 and name HN) 4.0 2.2 1.0!added
assign (resid 1 and name HB#) (resid 3 and name HA#) 4.0 2.2 2.0!added
!assign (resid 1 and name HD#) (resid 3 and name HA#) 4.0 2.2 2.0!added
assign (resid 1 and name HA) (resid 4 and name HB#) 4.0 2.2 1.0!jun
assign (resid 1 and name HB#) (resid 4 and name HN) 4.0 2.2 2.0!m#A 498 8.90e+04
!V2
assign (resid 2 and name HG1#) (resid 2 and name HB) 2.5 0.7 0.2!#A 314 6.73e+05
assign (resid 2 and name HG1#) (resid 2 and name HA) 3.0 1.2 0.3!m#A 267 5.15e+05
assign (resid 2 and name HG1#) (resid 3 and name HN) 4.0 2.2 1.0!#A 601 1.48e+05
assign (resid 2 and name HB) (resid 3 and name HA#) 4.0 2.2 1.0!#A 293 1.42e+05
assign (resid 2 and name HG1#) (resid 3 and name HA#) 4.0 2.2 1.0!m#A 269 2.73e+05
assign (resid 2 and name HA) (resid 3 and name HA#) 4.0 2.2 1.0!m#A 254 2.15e+05
assign (resid 2 and name HG1#) (resid 3 and name HN) 4.0 2.2 2.0!#A 173 2.73e+05
assign (resid 2 and name HB) (resid 3 and name HN) 4.0 2.2 1.0!#A 166 1.49e+05
assign (resid 2 and name HA) (resid 3 and name HN) 3.0 1.2 0.3!m#A 57 5.58e+05
assign (resid 2 and name HB) (resid 4 and name HN) 4.0 2.2 1.0!#A 230 5.67e+04
assign (resid 2 and name HG1#) (resid 4 and name HN) 4.0 2.2 2.0!#A 229 9.28e+04
assign (resid 2 and name HG2#) (resid 4 and name HN) 4.0 2.2 2.0!#A 603 4.72e+04
!assign (resid 2 and name HG2#) (resid 4 and name HE#) 4.0 2.2 2.0!#A 611 1.30e+05
!assign (resid 2 and name HB) (resid 4 and name HD#) 4.0 2.2 2.0!#A 224 7.79e+04
assign (resid 2 and name HA) (resid 4 and name HD#) 4.0 2.2 2.0!#A 187 5.78e+04
assign (resid 2 and name HA) (resid 4 and name HN) 4.0 2.2 1.0!#A 99 1.15e+05
assign (resid 2 and name HB) (resid 5 and name HE#) 4.0 2.2 2.0!#A 440 1.13e+05
assign (resid 2 and name HG1#) (resid 5 and name HD#) 4.0 2.2 2.0!#A 212 1.60e+05
assign (resid 2 and name HG1#) (resid 5 and name HE#) 4.0 2.2 2.0!#A 433 2.33e+05
assign (resid 2 and name HA) (resid 5 and name HD#) 4.0 2.2 2.0!#A 406 9.65e+04
assign (resid 2 and name HB) (resid 5 and name HD#) 4.0 2.2 2.0!#A 220 1.00e+05
assign (resid 2 and name HA) (resid 5 and name HE#) 4.0 2.2 2.0!#A 186 8.51e+04
assign (resid 2 and name HA) (resid 5 and name HB#) 4.0 2.2 1.0!#Jun
!G3
assign (resid 3 and name HA#) (resid 3 and name HN) 2.5 0.7 0.2!#A 58 4.42e+05
assign (resid 3 and name HA#) (resid 4 and name HA) 4.0 2.2 1.0!m#A 257 1.69e+05
assign (resid 3 and name HA#) (resid 4 and name HN) 3.0 1.2 0.3!#A 59 6.34e+05
assign (resid 3 and name HN) (resid 4 and name HE#) 4.0 2.2 1.0!#A 28 3.96e+04
assign (resid 3 and name HN) (resid 4 and name HN) 3.0 1.2 0.3!#MA 4 6.69e+04
assign (resid 3 and name HA#) (resid 5 and name HB1) 4.0 2.2 2.0!m#A 503 6.23e+04
assign (resid 3 and name HA#) (resid 5 and name HE#) 4.0 2.2 2.0!olga
assign (resid 3 and name HA#) (resid 5 and name HN) 4.0 2.2 1.0!#A 78 1.39e+05
assign (resid 3 and name HN) (resid 5 and name HD#) 4.0 2.2 2.0!#A 50 3.75e+04
assign (resid 3 and name HN) (resid 6 and name HN) 4.0 2.2 1.0!#A 20 4.57e+04
assign (resid 3 and name HA#) (resid 6 and name HN) 4.0 2.2 1.0!#A 486 7.65e+04
assign (resid 3 and name HA#) (resid 6 and name HB#) 4.0 2.2 2.0!added
assign (resid 3 and name HA#) (resid 6 and name HG#) 4.0 2.2 2.0!added
!F4
assign (resid 4 and name HA) (resid 4 and name HB2) 2.5 0.7 0.2!#A 242 3.84e+05
assign (resid 4 and name HA) (resid 4 and name HB1) 3.0 1.2 0.3!#A 241 3.46e+05
assign (resid 4 and name HB1) (resid 4 and name HD#) 3.0 1.2 0.3!m#A 204 4.66e+05
assign (resid 4 and name HB2) (resid 4 and name HD#) 3.0 1.2 0.3!m#A 203 4.42e+05
assign (resid 4 and name HA) (resid 4 and name HD#) 4.0 2.2 1.0!m#A 175 4.05e+05
assign (resid 4 and name HB1) (resid 4 and name HN) 3.0 1.2 0.3!#A 102 2.49e+05
assign (resid 4 and name HB2) (resid 4 and name HN) 3.0 1.2 0.3!#A 101 2.48e+05
assign (resid 4 and name HA) (resid 4 and name HN) 3.0 1.2 0.3!#A 60 2.23e+05
assign (resid 4 and name HD#) (resid 4 and name HE#) 2.5 0.7 0.2!#A 46 2.48e+06
assign (resid 4 and name HE#) (resid 4 and name HN) 4.0 2.2 1.0!#A 40 1.05e+05
assign (resid 4 and name HD#) (resid 4 and name HN) 4.0 2.2 1.0!m#A 38 1.77e+05
assign (resid 4 and name HN) (resid 5 and name HB1) 4.0 2.2 1.0!#A 428 6.11e+04
assign (resid 4 and name HD#) (resid 5 and name HB1) 4.0 2.2 1.0!#A 206 9.60e+04
assign (resid 4 and name HA) (resid 5 and name HN) 3.0 1.2 0.3!m#A 61 3.98e+05
assign (resid 4 and name HN) (resid 5 and name HD#) 4.0 2.2 2.0!#A 39 7.34e+04
assign (resid 4 and name HE#) (resid 5 and name HN) 4.0 2.2 1.0!#A 36 1.29e+05
assign (resid 4 and name HD#) (resid 5 and name HN) 4.0 2.2 1.0!#A 35 1.07e+05
assign (resid 4 and name HN) (resid 5 and name HN) 3.0 1.2 0.3!#MA 8 1.34e+05
assign (resid 4 and name HA) (resid 7 and name HN) 4.0 2.2 1.0!#A 392 2.71e+05
assign (resid 4 and name HB1) (resid 7 and name HN) 4.0 2.2 2.0!#A 116 1.09e+05
!assign (resid 4 and name HD#) (resid 7 and name HD#) 4.0 2.2 2.0!added 1.09e+05
assign (resid 4 and name HD#) (resid 8 and name HB2) 4.0 2.2 2.0!added 1.09e+05
assign (resid 4 and name HD#) (resid 17 and name HG#) 4.0 2.2 2.0
!F5
assign (resid 5 and name HA) (resid 5 and name HB1) 3.0 1.2 0.3!#A 240 2.24e+05
assign (resid 5 and name HB2) (resid 5 and name HB1) 2.5 0.7 0.2!#A 232 5.40e+05
assign (resid 5 and name HB2) (resid 5 and name HD#) 3.0 1.2 0.3!m#A 202 5.11e+05
assign (resid 5 and name HB1) (resid 5 and name HD#) 2.5 0.7 0.2!#A 201 4.51e+05
assign (resid 5 and name HA) (resid 5 and name HD#) 3.0 1.2 0.3!#A 176 4.58e+05
assign (resid 5 and name HB1) (resid 5 and name HN) 3.0 1.2 0.3!#A 104 1.68e+05
assign (resid 5 and name HB2) (resid 5 and name HN) 4.0 2.2 1.0!m#A 103 2.72e+05
assign (resid 5 and name HA) (resid 5 and name HN) 3.0 1.2 0.3!#A 64 3.98e+05
assign (resid 5 and name HD#) (resid 5 and name HE#) 2.5 0.7 0.2!#A 45 3.13e+06
assign (resid 5 and name HD#) (resid 5 and name HN) 3.0 1.2 0.3!#A 34 1.97e+05
assign (resid 5 and name HE#) (resid 6 and name HB#) 4.0 2.2 1.0!#A 447 1.20e+05
assign (resid 5 and name HD#) (resid 6 and name HB#) 4.0 2.2 1.0!#A 446 1.23e+05
assign (resid 5 and name HE#) (resid 6 and name HD#) 4.0 2.2 2.0!#A 441 2.27e+05
!assign (resid 5 and name HD#) (resid 6 and name HG#) 4.0 2.2 1.0!#A 221 1.05e+05
assign (resid 5 and name HE#) (resid 6 and name HG#) 4.0 2.2 1.0!#A 214 1.02e+05
assign (resid 5 and name HD#) (resid 6 and name HA) 4.0 2.2 1.0!#A 183 1.27e+05
assign (resid 5 and name HB2) (resid 6 and name HN) 4.0 2.2 1.0!m#A 112 1.86e+05
assign (resid 5 and name HB1) (resid 6 and name HN) 4.0 2.2 1.0!#A 111 1.39e+05
assign (resid 5 and name HA) (resid 6 and name HN) 3.0 1.2 0.3!#A 62 3.22e+05
assign (resid 5 and name HD#) (resid 6 and name HN) 4.0 2.2 1.0!#A 37 1.27e+05
assign (resid 5 and name HE#) (resid 6 and name HN) 4.0 2.2 1.0!#A 33 8.23e+04
INCOMPLETED
Appendix D: Example of Dihedral Angle Restraint Table
!remark phi angle constraints
!!r22
assign (resid 21 and name c and segid b) (resid 22 and name n and segid b)
(resid 22 and name ca and segid b) (resid 22 and name c and segid b)1.0 -64.0 20.0 2
!!23
assign (resid 22 and name c and segid b) (resid 23 and name n and segid b)
(resid 23 and name ca and segid b) (resid 23 and name c and segid b)1.0 -67.0 20.0 2
!!24
assign (resid 23 and name c and segid b) (resid 24 and name n and segid b)
(resid 24 and name ca and segid b) (resid 24 and name c and segid b)1.0 -73.0 20.0 2
!!25
assign (resid 24 and name c and segid b) (resid 25 and name n and segid b)
(resid 25 and name ca and segid b) (resid 25 and name c and segid b)1.0 -79.0 20.0 2
!!26
assign (resid 25 and name c and segid b) (resid 26 and name n and segid b)
(resid 26 and name ca and segid b) (resid 26 and name c and segid b)1.0 -68.0 20.0 2
!!27
assign (resid 26 and name c and segid b) (resid 27 and name n and segid b)
(resid 27 and name ca and segid b) (resid 27 and name c and segid b)1.0 -66.0 20.0 2
!!28
assign (resid 27 and name c and segid b) (resid 28 and name n and segid b)
(resid 28 and name ca and segid b) (resid 28 and name c and segid b)1.0 -94.0 20.0 2
!!29
assign (resid 28 and name c and segid b) (resid 29 and name n and segid b)
(resid 29 and name ca and segid b) (resid 29 and name c and segid b)1.0 -62.0 20.0 2
!!30
assign (resid 29 and name c and segid b) (resid 30 and name n and segid b)
(resid 30 and name ca and segid b) (resid 30 and name c and segid b)1.0 -65.0 20.0 2
!!31
assign (resid 30 and name c and segid b) (resid 31 and name n and segid b)
(resid 31 and name ca and segid b) (resid 31 and name c and segid b)1.0 -63.0 20.0 2
!!32
assign (resid 31 and name c and segid b) (resid 32 and name n and segid b)
(resid 32 and name ca and segid b) (resid 32 and name c and segid b)1.0 -63.0 20.0 2
!!33
assign (resid 32 and name c and segid b) (resid 33 and name n and segid b)
(resid 33 and name ca and segid b) (resid 33 and name c and segid b)1.0 -63.0 20.0 2
!!34
assign (resid 33 and name c and segid b) (resid 34 and name n and segid b)
(resid 34 and name ca and segid b) (resid 34 and name c and segid b)1.0 -64.0 20.0 2
!!35
assign (resid 34 and name c and segid b) (resid 35 and name n and segid b)
(resid 35 and name ca and segid b) (resid 35 and name c and segid b)1.0 -67.0 20.0 2
!!36
assign (resid 35 and name c and segid b) (resid 36 and name n and segid b)
(resid 36 and name ca and segid b) (resid 36 and name c and segid b)1.0 -63.0 20.0 2
!!37
assign (resid 36 and name c and segid b) (resid 37 and name n and segid b)
(resid 37 and name ca and segid b) (resid 37 and name c and segid b)1.0 -64.0 20.0 2
!!38
assign (resid 37 and name c and segid b) (resid 38 and name n and segid b)
(resid 38 and name ca and segid b) (resid 38 and name c and segid b)1.0 -64.0 20.0 2
!!39
assign (resid 38 and name c and segid b) (resid 39 and name n and segid b)
(resid 39 and name ca and segid b) (resid 39 and name c and segid b)1.0 -63.0 20.0 2
!!40
INCOMPLETED
!remark psi angles constraints
!!22
assign (resid 22 and name n and segid b) (resid 22 and name ca and segid b)
(resid 22 and name c and segid b) (resid 23 and name n and segid b)1.0 -41.0 20.0 2
!!23
assign (resid 23 and name n and segid b) (resid 23 and name ca and segid b)
(resid 23 and name c and segid b) (resid 24 and name n and segid b)1.0 -39.0 20.0 2
!!24
assign (resid 24 and name n and segid b) (resid 24 and name ca and segid b)
(resid 24 and name c and segid b) (resid 25 and name n and segid b)1.0 -30.0 20.0 2
!!25
assign (resid 25 and name n and segid b) (resid 25 and name ca and segid b)
(resid 25 and name c and segid b) (resid 26 and name n and segid b)1.0 -33.0 20.0 2
!!26
assign (resid 26 and name n and segid b) (resid 26 and name ca and segid b)
(resid 26 and name c and segid b) (resid 27 and name n and segid b)1.0 -36.0 20.0 2
!!27
assign (resid 27 and name n and segid b) (resid 27 and name ca and segid b)
(resid 27 and name c and segid b) (resid 28 and name n and segid b)1.0 -34.0 20.0 2
!!28
assign (resid 28 and name n and segid b) (resid 28 and name ca and segid b)
(resid 28 and name c and segid b) (resid 29 and name n and segid b)1.0 -9.0 20.0 2
!!29
assign (resid 29 and name n and segid b) (resid 29 and name ca and segid b)
(resid 29 and name c and segid b) (resid 30 and name n and segid b)1.0 -36.0 20.0 2
!!30
assign (resid 30 and name n and segid b) (resid 30 and name ca and segid b)
(resid 30 and name c and segid b) (resid 31 and name n and segid b)1.0 -40.0 20.0 2
!!31
assign (resid 31 and name n and segid b) (resid 31 and name ca and segid b)
(resid 31 and name c and segid b) (resid 32 and name n and segid b)1.0 -42.0 20.0 2
!!32
assign (resid 32 and name n and segid b) (resid 32 and name ca and segid b)
(resid 32 and name c and segid b) (resid 33 and name n and segid b)1.0 -40.0 20.0 2
!!33
assign (resid 33 and name n and segid b) (resid 33 and name ca and segid b)
(resid 33 and name c and segid b) (resid 34 and name n and segid b)1.0 -44.0 20.0 2
!!34
assign (resid 34 and name n and segid b) (resid 34 and name ca and segid b)
(resid 34 and name c and segid b) (resid 35 and name n and segid b)1.0 -42.0 20.0 2
!!35
assign (resid 35 and name n and segid b) (resid 35 and name ca and segid b)
(resid 35 and name c and segid b) (resid 36 and name n and segid b)1.0 -35.0 20.0 2
!!36
assign (resid 36 and name n and segid b) (resid 36 and name ca and segid b)
(resid 36 and name c and segid b) (resid 37 and name n and segid b)1.0 -42.0 20.0 2
!!37
assign (resid 37 and name n and segid b) (resid 37 and name ca and segid b)
(resid 37 and name c and segid b) (resid 38 and name n and segid b)1.0 -40.0 20.0 2
!!38
INCOMPLETED
Appendix E: Example of Chemical Shift Table for Talos
REMARK AlfaIIb fused to MBP in complex with beta3, input for TALOS
DATA SEQUENCE KVGFFKRNRP PLEEDDEEGE
VARS RESID RESNAME ATOMNAME SHIFT
FORMAT %4d %1s %4s %8.3f
1KN 120.93
1KHA 4.08
1KC 176.52
1KCA 56.26
1KCB 32.81
2VN 117.94
2VHA 4.15
2VC 176.47
2VCA 62.48
2VCB 32.55
3GN 109.71
3GHA 3.88
3GC 173.63
3GCA 45.15
4FN 118.02
4FHA 4.56
4FC 175.36
4FCA57.93
4FCB 39.55
5FN 118.99
5FHA 4.58
5FC 175.12
5FCA 57.51
5F CB 39.60
6KN 120.89
6KHA 4.21
6KC 175.94
6KCA 56.20
6KCB 33.00
7 RN 119.97
7 RHA 4.28
7 RC 175.84
7 RCA 55.98
7 RCB 30.90
8NN 118.01
8NHA 4.66
8NC 175.17
8NCA 53.14
8NCB 38.78
9 RN 119.81
9 RHA 4.62
9 RCA 55.37
9 RCB 30.19
10 PHA 4.67
11 PHA 4.39
11 PC 176.81
11 PCA 63.10
11 PCB 31.84
12LN 119.06
12LHA 4.33
12LC 174.45
12LCA 55.18
12LCB 42.19
13 EN 119.81
13 EHA 4.29
13 EC 176.23
13 ECA 56.30
13 ECB 29.93
14 EN 119.17
14 EHA 4.30
14 EC 177.34
14 ECA 56.30
14 ECB 29.93
15 DN 119.13
15 DHA 4.63
15 DC 175.70
15 DCA 53.91
15 DCB 40.64
16 DN 119.14
16 DHA 4.61
16 DC 175.99
16 DCA 53.92
16 DCB 40.67
17 EN 119.02
17 EHA 4.30
17 EC 176.37
17 ECA 56.29
17 ECB 29.86
18 EN 119.40
18 EHA 4.30
18 EC 176.81
18 ECA 56.38
18 ECB 29.80
19GN 108.49
19GHA 3.96
19GC 173.15
19GCA 45.20
20 EN 123.55
20 EHA 4.16
20 ECA 57.45
20 ECB 30.62
Appendix F: Example of Hydrogen Bond Table
assign (resid 2 and name o) (resid 6 and name n) 3.0 0.7 0.5
assign (resid 2 and name o) (resid 6 and name hn) 2.5 0.7 0.5
assign (resid 3 and name o) (resid 7 and name n) 3.0 0.7 0.5
assign (resid 3 and name o) (resid 7 and name hn) 2.5 0.7 0.5
assign (resid 4 and name o) (resid 8 and name n) 3.0 0.7 0.5
assign (resid 4 and name o) (resid 8 and name hn) 2.5 0.7 0.5
assign (resid 5 and name o) (resid 9 and name n) 3.0 0.7 0.5
assign (resid 5 and name o) (resid 9 and name hn) 2.5 0.7 0.5
Appendix G: Example of Input File To Generate A Random-Coil Coordinates
remarks file nmr/generate_template.inp
remarks Generates a "template" coordinate set. This produces
remarks an arbitrary extended conformation with ideal geometry.
remarks
remarks Author: Axel T. Brunger
topology reset @topallhdg_new.pro end
parameter reset @parallhdg_new.pro end
{====>}
structure @alfa_RQ.psf end {*Read structure file.*}
vector ident (x) (all)
vector do (x=x/10.) (all)
vector do (y=random(0.5)) (all)
vector do (z=random(0.5)) (all)
vector do (fbeta=50) (all) {*Friction coefficient, in 1/ps.*}
vector do (mass=100) (all){*Heavy masses, in amus.*}
parameter
nbonds
cutnb=5.5 rcon=20. nbxmod=−2 repel=0.9 wmin=0.1 tolerance=1.
rexp=2 irexp=2 inhibit=0.25
end
end
flags exclude * include bond angle vdw end
minimize powell nstep=50 nprint=10 end
flags include impr end
minimize powell nstep=50 nprint=10 end
dynamics verlet
nstep=50 timestep=0.001 iasvel=maxwell firsttemp=300.
tcoupling=true tbath=300. nprint=50 iprfrq=0
end
parameter
nbonds
rcon=2. nbxmod=−3 repel=0.75
end
end
minimize powell nstep=100 nprint=25 end
dynamics verlet
nstep=500 timestep=0.005 iasvel=maxwell firsttemp=300.
tcoupling=true tbath=300. nprint=100 iprfrq=0
end
flags exclude vdw elec end
vector do (mass=1.) (name h*)
hbuild selection=(name h*) phistep=360 end
flags include vdw elec end
minimize powell nstep=200 nprint=50 end
{*Write coordinates.*}
remarks produced by nmr/generate_template.inp
write coordinates output=alfa_RQ_00.pdb end
stop
Appendix H: Example of Input File to Generate a Geometric PSF File
remarks file nmr/generate.inp
remarks Generate structure file for a protein
remarks using the SA parameter and topology files.
topology
@../topallhdg_new.pro
end{*Read topology file *}
segment{*Generate protein *}
name=" "{*This name has to match the *}
{*four characters in columns 73 *}
{*through 76 in the coordinate *}
{*file, in XPLOR this name is *}
{*name is referred to as SEGId. *}
chain
@TOPPAR:toph19.pep {*Read peptide bond file *}
sequence LYS VAL GLY PHE PHE LYS GLN ASN ARG PRO
PRO LEU GLU GLU ASP ASP GLU GLU GLY GLU
end
end
end
write structure output=alfa_RQ.psf end
stop
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Teng, Q. (2013). Protein Structure Determination from NMR Data. In: Structural Biology. Springer, Boston, MA. https://doi.org/10.1007/978-1-4614-3964-6_7
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DOI: https://doi.org/10.1007/978-1-4614-3964-6_7
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