Structural effects of LacI variants
|
|
TMD
Change[1] |
Variant |
Assembly |
Y282D
Reversion[2] |
Protein
Stability |
Chemical
Modification |
Solvent
Exposure Compared
to WT |
Monoclonal
Exposure |
UV
Difference |
|
Y7 |
|
W/Wless[3] |
|
|
|
|
|
|
|
|
M42 |
|
I |
|
X |
|
|
|
|
|
|
L62 |
|
W/Wless[3]
|
|
|
|
|
|
|
|
|
I64 |
1 |
|
|
|
|
|
|
|
|
|
V66 |
1 |
|
|
|
|
|
|
|
|
|
L71 |
2 |
|
|
|
|
|
|
|
|
|
L73 |
3 |
|
|
|
|
|
|
|
|
|
H74 |
2 |
R |
|
X |
|
|
|
|
|
|
S77 |
2 |
L[4] |
|
|
|
|
ANS
more apolar |
|
Bigger
>300 nm |
|
Q78 |
1 |
|
|
|
|
|
|
|
|
|
V80 |
1 |
|
|
|
|
|
|
|
|
|
A81 |
|
V[5] |
|
|
|
C107
IPTG sensitivity lost |
|
|
Very
small diff |
|
I83 |
1 |
|
|
|
|
|
|
|
|
|
K84 |
1,2 |
E |
|
X[6] |
High[7] |
|
|
WT6 |
All
bigger[8]
peaks All
bigger peaks |
|
D88 |
1 |
|
|
|
|
|
|
|
|
|
L90 |
1 |
|
|
|
|
|
|
|
|
|
S93 |
1 |
|
|
|
|
|
|
|
|
|
V94 |
1 |
|
|
|
|
|
|
|
|
|
V95 |
|
|
|
|
|
|
|
|
|
|
V96 |
1 |
|
|
|
|
|
|
|
|
|
S97 |
1 |
|
|
|
|
|
|
|
|
|
M98 |
1 |
I |
|
X |
|
|
|
|
|
|
E100 |
1 |
W/Wless[3]
|
|
|
|
|
|
|
|
|
N113 |
1 |
|
|
|
|
|
|
|
|
|
Q117 |
1 |
W/Wless[3]
|
|
|
|
|
|
|
|
|
R118 |
|
|
|
|
|
|
|
|
|
|
Y126 |
1 |
|
|
|
|
|
|
|
|
|
L128 |
1 |
|
|
|
|
|
|
|
|
|
A133 |
|
T |
|
X |
|
|
|
|
|
|
L146 |
1 |
|
|
|
|
|
|
|
|
|
L148 |
|
F[9] |
|
|
|
|
|
|
|
|
D149 |
1 |
N
|
|
X |
|
|
|
|
|
|
V150 |
|
I |
|
X |
|
|
|
|
|
|
S151 |
|
P[8]
|
|
X |
|
|
|
|
|
|
F161 |
3 |
|
|
|
|
|
|
|
|
|
S162 |
3 |
|
|
|
|
|
|
|
|
|
H163 |
3 |
|
|
|
|
|
|
|
|
|
E164 |
3 |
|
|
|
|
|
|
|
|
|
S191 |
|
F |
|
X |
|
|
|
|
|
|
S193 |
1 |
|
|
|
|
|
|
|
|
|
R197 |
1 |
G[10] |
|
|
|
|
|
|
|
|
W201[11] |
|
|
|
|
|
|
|
|
|
|
W22011
|
|
|
|
|
|
|
|
|
|
|
F226 |
|
W/Wless[3]
|
|
|
|
|
|
|
|
|
M223 |
|
I |
|
X |
|
|
|
|
|
|
M232 |
|
I |
|
X |
|
|
|
|
|
|
N246 |
3 |
S |
|
X |
|
|
|
|
|
|
Q248 |
3 |
R |
|
X |
|
|
|
|
|
|
L251 |
|
A[12] |
|
|
|
|
|
|
|
|
Y273 |
|
W/Wless[3]
|
|
|
|
|
|
|
|
|
D274 |
3 |
|
X |
Easily
proteolyzed |
|
|
More
exposed |
|
|
|
T276 |
2 |
A |
|
X |
|
|
|
|
|
|
D278 |
|
L[15] |
|
|
|
|
|
|
|
|
C281[16] |
|
S |
|
|
|
|
|
|
|
|
Y282[17] |
|
D |
Monomer |
|
|
|
|
|
|
|
P284 |
|
S |
|
X |
|
|
|
|
|
|
K290 |
2 |
|
|
|
|
|
|
|
|
|
Q291 |
2 |
|
|
|
|
|
|
|
|
|
D292 |
2 |
|
|
|
|
|
|
|
|
|
F293 |
2 |
W/Wless[3]
|
|
|
|
|
|
|
|
|
L295 |
2 |
|
|
|
|
|
|
|
|
|
L296 |
2 |
M |
|
X |
|
|
|
|
|
|
V301 |
1 |
|
|
|
|
|
|
|
|
|
L304 |
1 |
|
|
|
|
|
|
|
|
|
L305 |
1 |
|
|
|
|
|
|
|
|
|
L318 |
3 |
|
|
|
|
|
|
|
|
|
L319 |
3 |
|
|
|
|
|
|
|
|
|
P320 |
3 |
A[8]
|
|
|
|
|
|
|
|
|
V321 |
3 |
I |
|
X |
|
|
|
|
|
|
S322 |
3 |
|
|
|
|
|
|
|
|
|
K325 |
|
W/Wless[3]
|
|
|
|
|
|
|
|
|
R326[18] |
|
K |
|
|
|
|
|
|
|
|
S354 |
|
F |
|
X |
|
|
|
|
|
References
Bandyopadhyay,
P. K. and C.-W. Wu (1979). "Heterogeneity of the Two Tryptophanyl Residues
on the lac Repressor of Escherichia coli." Arch.Biochem.Biophys. 195,
No. 2: 558-564.
Barry,
J. K. and K. S. Matthews (1997). "Ligand-induced conformational changes in
lactose repressor: a fluorescence study of single tryptophan mutants." Biochemistry
36(50): 15632-42.
Burns,
L. E., A. H. Maki, et al. (1992). "Characterization of the two tryptophan
residues of the lactose repressor from Escherichia coliby phosphorescence
and optical detection of magnetic resonance." Biochemistry 32:
12821-12829.
Chakerian,
A. E. and K. S. Matthews (1991). "Characterization of mutations in
oligomerization domain of Lac repressor protein." J Biol Chem 266(33):
22206-14.
Chakerian,
A. E., M. Pfahl, et al. (1985). "A mutant lactose repressor with altered
inducer and operator binding parameters." J Mol Biol 183(1): 43-51.
Chang,
W.-I., P. Barrera, et al. (1994).
"Identification and characterization of aspartate residues that play key
roles in the allosteric regulation of a transcription factor: Aspartate 274 is
essential for inducer binding in lac repressor." Biochemistry
33: 3607-3616.
Chang,
W. I. and K. S. Matthews (1995). "Role of Asp274 in lac repressor:
Diminished sugar binding and altered conformational effects in mutants." Biochemistry
34(28): 9227-9234.
Chang,
W. I., J. S. Olson, et al. (1993). "Lysine 84 is at the subunit interface
of lac repressor protein." J Biol Chem 268(23): 17613-22.
Chen,
J. and K. S. Matthews (1992). "T41 mutation in lac repressor is
Tyr282----Asp." Gene 111(1): 145-6.
Chou,
W. Y. and K. S. Matthews (1989). "Mutation in hinge region of lactose
repressor protein alters physical and functional properties." J Biol
Chem 264(11): 6171-6.
Daly,
T. J. and K. S. Matthews (1986). "Characterization and modification of a
monomeric mutant of the lactose repressor protein." Biochemistry 25(19):
5474-8.
Dong,
F., S. Spott, et al. (1999). "Dimerisation mutants of Lac repressor. I. A
monomeric mutant, L251A, that binds Lac operator DNA as a dimer." J Mol
Biol 290(3): 653-66.
Flynn,
T. C., L. Swint-Kruse, et al. (2003). "Allosteric transition pathways in
the lactose repressor protein core domains: asymmetric motions in a homodimer."
Protein Sci 12(11): 2523-41.
Gardner,
J. A. and K. S. Matthews (1990). "Characterization of two mutant lactose
repressor proteins containing single tryptophans." J Biol Chem 265(34):
21061-7.
Li,
L. and K. S. Matthews (1995). "Characterization of Mutants Affecting the
KRK Sequence in the Carboxyl-terminal Domain of lac Repressor." J.Biol.Chem.
270,no.18: 10640-10649.
Nichols,
J. C. and K. S. Matthews (1997). "Combinatorial mutations of lac repressor.
Stability of monomer-monomer interface is increased by apolar substitution at
position 84." J Biol Chem 272(30): 18550-7.
Ozarowski,
A., J. K. Barry, et al. (1999). "Ligand-induced conformational changes in
lactose repressor: a phosphorescence and ODMR study of single-tryptophan
mutants." Biochemistry 38(21): 6715-22.
Royer,
C. A., J. A. Gardner, et al. (1990). "Resolution of the fluorescence decay
of the two tryptophan residues of lac repressor
using single tryptophan mutants." Biophys J 58: 363-378.
Schmitz,
A., U. Schmeissner, et al. (1976). "Mutations affecting the quaternary
structure of the lac repressor." J Biol Chem 251(11):
3359-66.
Spott,
S., F. Dong, et al. (2000). "Dimerisation mutants of Lac repressor. II. A
single amino acid substitution, D278L, changes the specificity of dimerisation."
J Mol Biol 296(2): 673-84.
Spotts,
R. O., A. E. Chakerian, et al. (1991). "Arginine 197 of lac repressor
contributes significant energy to inducer binding. Confirmation of homology to
periplasmic sugar binding proteins." J Biol Chem 266(34):
22998-3002.
Swint-Kruse,
L., C. R. Elam, et al. (2001).
"Plasticity of quaternary structure: twenty-two ways to form a LacI dimer."
Protein Sci 10(2): 262-76.
Swint-Kruse,
L., H. Zhan, et al. (2003). "Perturbation from a distance: mutations that
alter LacI function through long-range effects." Biochemistry 42(47):
14004-16.
Swint-Kruse,
L., H. Zhan, et al. (2005). "Integrated insights from simulation,
experiment, and mutational analysis yield new details of LacI function." Biochemistry
44(33): 11201-13.
Footnotes
[1] Number indicates whether
residue participates in pathways 1, 2, or 3.
(Flynn, Swint-Kruse et al. 2003)
[2] (Swint-Kruse, Elam et al. 2001)
[3] (Barry and Matthews 1997)
[4] All data: (Chou and Matthews 1989)
[5] All data: (Chakerian, Pfahl et al. 1985)
[6]
A, E, R, L : (Chang, Olson et al. 1993)
[7] A, L: (Nichols and Matthews 1997)
[8] A, L: (Swint-Kruse, Zhan et al. 2005)
[9] (Swint-Kruse, Zhan et al. 2003)
[10] (Spotts, Chakerian et al. 1991)
[11] (Bandyopadhyay and Wu 1979; Gardner and Matthews 1990; Royer, Gardner et al. 1990; Burns, Maki et al. 1992; Barry and Matthews 1997; Ozarowski, Barry et al. 1999)
[12] (Dong, Spott et al. 1999)
[13] (Chang and Matthews 1995)
[14] (Chang, Barrera et al. 1994)
[15] LOTS OF OTHER MUTATIONS IN THIS PAPER (Spott, Dong et al. 2000)
[16] (Chakerian and Matthews 1991)
[17] (Schmitz, Schmeissner et al. 1976; Daly and Matthews 1986; Chakerian and Matthews 1991; Chen and Matthews 1992)
[18] (Li and Matthews 1995)