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Jasper Landman, Robert C. Brewster, Franz M. Weinert, Rob Phillips, Willem K. Kegel
Self-consistent theory of transcriptional control in complex regulatory architectures
www.plosone.org
www.plosone.org
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2.6022 0 Td
(even)Tj
2.0693 0 Td
(outside)Tj
3.1351 0 Td
(of)Tj
1.0148 0 Td
(its)Tj
1.1452 0 Td
(specific)Tj
-34.5541 -1.2982 Td
(binding)Tj
3.3505 0 Td
(site)Tj
1.5704 0 Td
([)Tj
0.83 0.64 0.02 0 k
(1)Tj
0 g
(,)Tj
0.83 0.64 0.02 0 k
1.2585 0 Td
(45)Tj
0 g
(].)Tj
1.7405 0 Td
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5.9527 0 Td
(the)Tj
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(shown)Tj
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1.0318 0 Td
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(previous)Tj
3.651 0 Td
(work)Tj
2.279 0 Td
([)Tj
0.83 0.64 0.02 0 k
(38)Tj
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(].)Tj
2.075 0 Td
(We)Tj
1.61 0 Td
(have)Tj
-35.1493 -1.3039 Td
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(measure)Tj
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(energies)Tj
3.5036 0 Td
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1.9956 0 Td
(respect)Tj
3.0387 0 Td
(to)Tj
1.0262 0 Td
(the)Tj
1.4683 0 Td
(binding)Tj
3.3506 0 Td
(energy)Tj
2.9083 0 Td
(of)Tj
1.0148 0 Td
(proteins)Tj
3.5149 0 Td
(to)Tj
1.0261 0 Td
(the)Tj
-34.9622 -1.2983 Td
(non-specific)Tj
5.142 0 Td
(genomic)Tj
3.6793 0 Td
(background.)Tj
5.2497 0 Td
(An)Tj
1.4514 0 Td
(added)Tj
2.6645 0 Td
(complication)Tj
5.4765 0 Td
(here)Tj
1.9673 0 Td
(is)Tj
0.8503 0 Td
(that)Tj
1.7745 0 Td
(not)Tj
1.5761 0 Td
(every)Tj
2.347 0 Td
(non-specific)Tj
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(site)Tj
1.5703 0 Td
(has)Tj
1.5421 0 Td
(an)Tj
1.2019 0 Td
(equal)Tj
2.3584 0 Td
(binding)Tj
3.3505 0 Td
(energy.)Tj
3.1351 0 Td
(In)Tj
1.1055 0 Td
(first)Tj
1.8085 0 Td
(approximation)Tj
6.1738 0 Td
(the)Tj
1.4683 0 Td
(occupation)Tj
4.6715 0 Td
(of)Tj
1.0148 0 Td
(a)Tj
0.6576 0 Td
(reservoir)Tj
3.7701 0 Td
(with)Tj
1.9956 0 Td
(a)Tj
-35.824 -1.3039 Td
(Gaussian)Tj
3.8664 0 Td
(distribution)Tj
4.9663 0 Td
(of)Tj
1.0147 0 Td
(binding)Tj
3.3562 0 Td
(energies)Tj
3.5036 0 Td
(is)Tj
0.8448 0 Td
(equal)Tj
2.3584 0 Td
(to)Tj
1.0261 0 Td
(that)Tj
1.7802 0 Td
(of)Tj
1.0148 0 Td
(a)Tj
0.6519 0 Td
(reservoir)Tj
3.7701 0 Td
(of)Tj
1.0148 0 Td
(identical)Tj
3.6566 0 Td
(sites)Tj
1.9333 0 Td
(with)Tj
1.9955 0 Td
(a)Tj
-36.7537 -1.2982 Td
(binding)Tj
3.3505 0 Td
(energy)Tj
2.9083 0 Td
(of)Tj
/F14 1 Tf
0 Tc
1.0148 0 Td
(h)Tj
/F13 1 Tf
()Tj
ET
Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 280.5732 555.8173 cm
BT
/F6 1 Tf
1 TL
-0.0053 Tc
0 0 Td
(ns)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 287.3763 551.3952 cm
BT
/F14 1 Tf
1 TL
0 0 Td
(i)Tj
/F20 1 Tf
-0.004 Tc
0.6009 0 Td
[()]TJ
/F21 1 Tf
0.7937 0 Td
()Tj
/F11 1 Tf
[()]TJ
ET
Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 310.7905 555.8173 cm
BT
/F6 1 Tf
1 TL
-0.0053 Tc
0 0 Td
(2)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 314.3622 551.3952 cm
BT
/F6 1 Tf
1 TL
-0.004 Tc
0 0 Td
(/2)Tj
1.0261 0 Td
(with)Tj
/F14 1 Tf
0 Tc
1.9956 0 Td
(h)Tj
/F13 1 Tf
()Tj
ET
Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 352.4031 555.8173 cm
BT
/F6 1 Tf
1 TL
-0.0053 Tc
0 0 Td
(ns)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 359.2062 551.3952 cm
BT
/F14 1 Tf
1 TL
0 0 Td
(i)Tj
/F6 1 Tf
-0.004 Tc
(,)Tj
/F11 1 Tf
0.8333 0 Td
[()]TJ
/F6 1 Tf
0.686 0 Td
(the)Tj
1.4683 0 Td
(mean)Tj
2.4435 0 Td
(and)Tj
1.7348 0 Td
(standard)Tj
3.719 0 Td
(deviation,)Tj
4.1726 0 Td
(respectively,)Tj
5.1137 0 Td
(of)Tj
-36.0904 -1.2982 Td
(the)Tj
1.4683 0 Td
(distribution)Tj
4.9663 0 Td
(of)Tj
1.0148 0 Td
(binding)Tj
3.3505 0 Td
(energies)Tj
3.5036 0 Td
(to)Tj
1.0261 0 Td
(non-specific)Tj
5.1476 0 Td
(sites)Tj
1.9276 0 Td
(and)Tj
/F21 1 Tf
1.7348 0 Td
()Tj
/F6 1 Tf
0.703 0 Td
(=)Tj
0.7993 0 Td
(\()Tj
/F11 1 Tf
[()]TJ
ET
Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 464.485 536.7118 cm
BT
/F6 1 Tf
1 TL
-0.0053 Tc
0 0 Td
(B)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 468.8503 538.4125 cm
BT
/F11 1 Tf
1 TL
-0.004 Tc
0 0 Td
[()]TJ
/F6 1 Tf
(\))Tj
ET
Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 478.148 542.8346 cm
BT
/F20 1 Tf
1 TL
-0.0053 Tc
0 0 Td
[()]TJ
/F6 1 Tf
(1)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 488.1826 538.4125 cm
BT
/F6 1 Tf
1 TL
-0.004 Tc
0 0 Td
([)Tj
0.83 0.64 0.02 0 k
(46)Tj
0 g
(].)Tj
2.0749 0 Td
(All)Tj
1.3946 0 Td
(energies)Tj
3.5036 0 Td
(in)Tj
-35.7899 -1.3039 Td
(this)Tj
1.6725 0 Td
(work)Tj
2.279 0 Td
(are)Tj
1.4513 0 Td
(given)Tj
2.3754 0 Td
(relative)Tj
3.1408 0 Td
(to)Tj
1.0261 0 Td
(this)Tj
1.6725 0 Td
(reference)Tj
3.9174 0 Td
(energy.)Tj
-16.3388 -1.2982 Td
(We)Tj
1.6101 0 Td
(start)Tj
1.9842 0 Td
(with)Tj
1.9956 0 Td
(the)Tj
1.474 0 Td
(simplest)Tj
3.5093 0 Td
(nontrivial)Tj
4.1669 0 Td
(regulatory)Tj
4.32 0 Td
(architecture)Tj
5.0059 0 Td
(referred)Tj
3.4243 0 Td
(to)Tj
1.0203 0 Td
(as)Tj
1.0148 0 Td
(`simple)Tj
3.0841 0 Td
(repres-)Tj
-33.8057 -1.2983 Td
(sion,')Tj
2.3414 0 Td
(as)Tj
1.0148 0 Td
(illustrated)Tj
4.2236 0 Td
(in)Tj
1.0375 0 Td
(the)Tj
1.4683 0 Td
(first)Tj
1.8029 0 Td
(column)Tj
3.2938 0 Td
(in)Tj
0.83 0.64 0.02 0 k
1.0375 0 Td
(Fig)Tj
1.4796 0 Td
(1)Tj
0 g
(.)Tj
0.9185 0 Td
(This)Tj
1.9899 0 Td
(architecture)Tj
5.0059 0 Td
(consists)Tj
3.3505 0 Td
(of)Tj
1.0147 0 Td
(a)Tj
0.652 0 Td
(promoter)Tj
4.0365 0 Td
(and)Tj
1.7291 0 Td
(an)Tj
-36.3965 -1.2983 Td
(operator)Tj
3.651 0 Td
(site)Tj
1.5647 0 Td
(for)Tj
1.389 0 Td
(a)Tj
0.652 0 Td
(repressor)Tj
3.9288 0 Td
(molecule.)Tj
4.0648 0 Td
(An)Tj
1.4514 0 Td
(RNAP)Tj
2.8176 0 Td
(can)Tj
1.627 0 Td
(bind)Tj
2.0693 0 Td
(to)Tj
1.0262 0 Td
(the)Tj
1.474 0 Td
(promoter)Tj
4.0307 0 Td
(with)Tj
2.0013 0 Td
(binding)Tj
-31.7478 -1.3039 Td
(energy)Tj
/F13 1 Tf
0 Tc
2.9084 0 Td
()Tj
ET
Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 233.0078 471.7417 cm
BT
/F6 1 Tf
1 TL
-0.0053 Tc
0 0 Td
(P)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 237.2031 473.3858 cm
BT
/F6 1 Tf
1 TL
-0.004 Tc
0 0 Td
(,)Tj
0.4478 0 Td
(and)Tj
1.7291 0 Td
(a)Tj
0.652 0 Td
(repressor)Tj
3.9288 0 Td
(can)Tj
1.6271 0 Td
(bind)Tj
2.0693 0 Td
(to)Tj
1.0261 0 Td
(the)Tj
1.4683 0 Td
(operator)Tj
3.651 0 Td
(site)Tj
1.5704 0 Td
(with)Tj
1.9956 0 Td
(energy)Tj
/F13 1 Tf
0 Tc
2.9083 0 Td
()Tj
ET
Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 471.9118 471.7417 cm
BT
/F6 1 Tf
1 TL
-0.0053 Tc
0 0 Td
(R)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 476.5606 473.3858 cm
BT
/F6 1 Tf
1 TL
-0.004 Tc
0 0 Td
(,)Tj
0.4422 0 Td
(while)Tj
2.3697 0 Td
(the)Tj
1.4683 0 Td
(simultaneous)Tj
-31.9348 -1.2982 Td
(binding)Tj
3.3506 0 Td
(of)Tj
1.0147 0 Td
(both,)Tj
2.2848 0 Td
(RNAP)Tj
2.8232 0 Td
(and)Tj
1.7292 0 Td
(repressor)Tj
3.9288 0 Td
(is)Tj
0.8447 0 Td
(prohibited)Tj
4.4333 0 Td
(by)Tj
1.1849 0 Td
(excluded-volume)Tj
7.1148 0 Td
(interactions.)Tj
-27.5128 -1.2983 Td
(The)Tj
1.7858 0 Td
(grand)Tj
2.5682 0 Td
(canonical)Tj
4.0479 0 Td
(partition)Tj
3.7303 0 Td
(function)Tj
3.6284 0 Td
([)Tj
0.83 0.64 0.02 0 k
(38)Tj
0 g
(])Tj
1.8538 0 Td
(of)Tj
1.0148 0 Td
(a)Tj
0.652 0 Td
(single)Tj
2.5341 0 Td
(gene)Tj
2.0806 0 Td
(with)Tj
1.9956 0 Td
(this)Tj
1.6724 0 Td
(regulatory)Tj
4.3199 0 Td
(architec-)Tj
-33.08 -1.3039 Td
(ture)Tj
1.8425 0 Td
(unit)Tj
1.8595 0 Td
(is)Tj
0.8448 0 Td
(given)Tj
2.3811 0 Td
(by)Tj
/F19 1 Tf
0 Tc
2.5001 -4.2973 Td
(X)Tj
/F14 1 Tf
0.9411 0 Td
()Tj
/F16 1 Tf
1.0488 0.9468 Td
(X)Tj
ET
Q
q
1 j
1 J
0 w
5.9998 0 0 5.9998 319.8614 402.8598 cm
BT
/F15 1 Tf
1 TL
0 0 Td
(1)Tj
/F11 1 Tf
-0.6236 -3.6568 Td
[()]TJ
/F14 1 Tf
()Tj
/F15 1 Tf
(0)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 328.5921 400.8755 cm
BT
/F16 1 Tf
1 TL
0 0 Td
(X)Tj
ET
Q
q
1 j
1 J
0 w
5.9998 0 0 5.9998 330.4629 403.4834 cm
BT
/F15 1 Tf
1 TL
0 0 Td
(1)Tj
/F14 1 Tf
( )Tj
/F11 1 Tf
1.2756 0 Td
[()]TJ
-1.2284 -3.7607 Td
[( )]TJ
/F14 1 Tf
0.3969 0 Td
()Tj
/F15 1 Tf
(0)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 342.9354 391.4078 cm
BT
/F12 1 Tf
1 TL
0 0 Td
(l)Tj
ET
Q
q
1 j
1 J
0 w
5.9998 0 0 5.9998 347.9244 396.17 cm
BT
/F11 1 Tf
1 TL
0 0 Td
[()]TJ
/F20 1 Tf
0 -1.2567 Td
[()]TJ
ET
Q
q
1 j
1 J
0 w
10 0 0 10 351.7795 391.4078 cm
BT
/F12 1 Tf
1 TL
0 0 Td
(l)Tj
ET
Q
q
1 j
1 J
0 w
5.9998 0 0 5.9998 356.8251 396.17 cm
BT
/F11 1 Tf
1 TL
0 0 Td
[( )]TJ
/F20 1 Tf
0 -1.2567 Td
[()]TJ
ET
Q
q
1 j
1 J
0 w
10 0 0 10 361.1338 391.4078 cm
BT
/F11 1 Tf
1 TL
0 0 Td
[(\n)]TJ
/F14 1 Tf
0.6236 0 Td
()Tj
/F11 1 Tf
[()]TJ
/F13 1 Tf
(;)Tj
/F11 1 Tf
1.3039 0 Td
[( )]TJ
/F14 1 Tf
0.3912 0 Td
()Tj
0.6633 0 Td
()Tj
/F15 1 Tf
1.0488 0 Td
(1)Tj
/F14 1 Tf
0.72 0 Td
()Tj
/F12 1 Tf
0.9978 0 Td
(l)Tj
ET
Q
q
1 j
1 J
0 w
5.9998 0 0 5.9998 423.6094 388.9133 cm
BT
/F20 1 Tf
1 TL
0 0 Td
[()]TJ
ET
Q
q
1 j
1 J
0 w
10 0 0 10 427.4645 391.4078 cm
BT
/F11 1 Tf
1 TL
0 0 Td
[()]TJ
ET
Q
q
1 j
1 J
0 w
5.9998 0 0 5.9998 432.17 388.9133 cm
BT
/F20 1 Tf
1 TL
0 0 Td
[()]TJ
ET
Q
q
1 j
1 J
0 w
10 0 0 10 438.2929 391.4078 cm
BT
/F14 1 Tf
1 TL
0 0 Td
()Tj
/F12 1 Tf
0.9921 0 Td
(l)Tj
ET
Q
q
1 j
1 J
0 w
5.9998 0 0 5.9998 453.2031 388.9133 cm
BT
/F20 1 Tf
1 TL
0 0 Td
[()]TJ
ET
Q
q
1 j
1 J
0 w
10 0 0 10 457.5118 391.4078 cm
BT
/F11 1 Tf
1 TL
0 0 Td
[()]TJ
ET
Q
q
1 j
1 J
0 w
5.9998 0 0 5.9998 462.2173 388.9133 cm
BT
/F20 1 Tf
1 TL
0 0 Td
[()]TJ
ET
Q
q
1 j
1 J
0 w
10 0 0 10 466.5259 391.4078 cm
BT
/F13 1 Tf
1 TL
0 0 Td
(;)Tj
/F14 1 Tf
9.6944 -0.0453 Td
()Tj
/F6 1 Tf
(1)Tj
/F14 1 Tf
()Tj
/F6 1 Tf
-0.004 Tc
-36.3455 -4.6828 Td
(where)Tj
2.6475 0 Td
(the)Tj
1.4684 0 Td
(fugacity)Tj
3.3788 0 Td
(of)Tj
1.0148 0 Td
(a)Tj
0.6577 0 Td
(repressor)Tj
3.9231 0 Td
(molecule)Tj
3.8381 0 Td
(is)Tj
0.8504 0 Td
(given)Tj
2.3811 0 Td
(by)Tj
/F12 1 Tf
0 Tc
1.1792 0 Td
(l)Tj
ET
Q
q
1 j
1 J
0 w
5.9998 0 0 5.9998 418.3937 341.6314 cm
BT
/F20 1 Tf
1 TL
0 0 Td
[()]TJ
ET
Q
q
1 j
1 J
0 w
10 0 0 10 425.4803 344.1259 cm
BT
/F14 1 Tf
1 TL
0 0 Td
()Tj
/F11 1 Tf
1.0488 0 Td
[()]TJ
ET
Q
q
1 j
1 J
0 w
5.9998 0 0 5.9998 439.937 347.7543 cm
BT
/F12 1 Tf
1 TL
0 0 Td
(bm)Tj
ET
Q
q
1 j
1 J
0 w
5 0 0 5 446.57 346.2236 cm
BT
/F20 1 Tf
1 TL
0 0 Td
[()]TJ
ET
Q
q
1 j
1 J
0 w
10 0 0 10 450.7653 344.1259 cm
BT
/F6 1 Tf
1 TL
-0.004 Tc
0 0 Td
(,)Tj
0.4422 0 Td
(where)Tj
/F11 1 Tf
2.6532 0 Td
[(\r)]TJ
ET
Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 486.7653 342.4818 cm
BT
/F6 1 Tf
1 TL
-0.0053 Tc
0 0 Td
(R)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 493.6251 344.1259 cm
BT
/F6 1 Tf
1 TL
-0.004 Tc
0 0 Td
(is)Tj
0.8503 0 Td
(the)Tj
1.4684 0 Td
(chemical)Tj
-31.6797 -1.3379 Td
(potential)Tj
3.7587 0 Td
(of)Tj
1.0148 0 Td
(a)Tj
0.652 0 Td
(repressor)Tj
3.9287 0 Td
(molecule.)Tj
4.0649 0 Td
(Similarly)Tj
/F12 1 Tf
0 Tc
3.7984 0 Td
(l)Tj
ET
Q
q
1 j
1 J
0 w
5.9998 0 0 5.9998 377.2346 328.2519 cm
BT
/F20 1 Tf
1 TL
0 0 Td
[()]TJ
ET
Q
q
1 j
1 J
0 w
10 0 0 10 383.8677 330.7464 cm
BT
/F14 1 Tf
1 TL
0 0 Td
()Tj
/F11 1 Tf
1.0488 0 Td
[()]TJ
ET
Q
q
1 j
1 J
0 w
5.9998 0 0 5.9998 398.3244 334.3748 cm
BT
/F12 1 Tf
1 TL
0 0 Td
(bm)Tj
ET
Q
q
1 j
1 J
0 w
5 0 0 5 404.9574 332.9007 cm
BT
/F20 1 Tf
1 TL
0 0 Td
[()]TJ
ET
Q
q
1 j
1 J
0 w
10 0 0 10 410.9669 330.7464 cm
BT
/F6 1 Tf
1 TL
-0.004 Tc
0 0 Td
(where)Tj
/F11 1 Tf
2.6475 0 Td
[(\r)]TJ
ET
Q
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