Related Articles15N NMR relaxation studies of free and inhibitor-bound 4-oxalocrotonate tautomerase: backbone dynamics and entropy changes of an enzyme upon inhibitor binding.
Biochemistry. 1996 Dec 17;35(50):16036-47
Authors: Stivers JT, Abeygunawardana C, Mildvan AS
The solution secondary structure of 4-oxalocrotonate tautomerase (4-OT), a 41 kDa homohexamer with 62 residues per subunit, consists of an alpha-helix, two beta-strands, a beta-hairpin, two loops, two turns, and a C-terminal coil [Stivers et al. (1996) Protein Sci. 5, 729-741]. The general base, proline-1, as well as the two loops and the beta-hairpin have been shown to comprise the active site [Stivers et al. (1996) Biochemistry 35, 814-823]. The backbone dynamics of both the free enzyme and its complex with a substrate analog have been studied by 1H-detected 15N relaxation rates and NOE determinations at 500 and 600 MHz. Analysis of the data using the model-free formalism showed that the nanosecond to picosecond motion of 53 of the 60 backbone 15N-H vectors was highly restricted with a mean order parameter mean value of S2 = 0.87 +/- 0.03. The lowest backbone mobility (S2 > 0.90) is found in the beta 1-strand, loop 2, and turn 2. Greater backbone mobility is found in the active site (0.5 < or = S2 < or = 0.83) and at C-terminal residues 58-62 (0.03 < or = S2 < or = 0.70). A tau m value for the free hexamer of 13.7 ns at 42 degrees C was determined, consistent with a compact globular molecule of 41 kDa. Saturation of 4-OT with the analog of the dienolic intermediate and linear competitive inhibitor cis, cis-muconate (4) (KD = 0.59 mM) increased the backbone S2 of seven residues and decreased the backbone S2 of another eight residues, both at the active site and at the antiparallel beta 1-beta 1 interface. The S2 values of the other 44 detectable NH vectors were not altered by the binding of 4. The increases in S2, resulting from the "freezing" of the backbone NH vectors of seven residues upon the binding of 4, correspond to an unfavorable entropic contribution to delta Gbinding of 3.2 +/- 1.1 kcal/mol. This freezing is partially compensated for by the mobilization of the other eight residues, since the decreases in S2 for these residues correspond to an entropic contribution to binding of -1.9 +/- 0.1 kcal/mol. These entropy changes, resulting solely from alterations in high-frequency motion, are significant compared to the overall delta Gbinding = -4.6 kcal/mol for 4. Other effects of the binding of 4 include (1) changes in 15N and NH chemical shifts localized to the active site and (2) increases in the exchange contributions (R(ex)) to 1/T2 of backbone 15N resonances at the active site and at the subunit interface, reflecting microsecond to millisecond motions which may play a role in substrate binding (k(on) > or = 4 x 10(6) M-1 s-1) and/or catalysis (kcat = 10(3) s-1).
[NMR paper] Structure of an allosteric inhibitor of LFA-1 bound to the I-domain studied by crysta
Structure of an allosteric inhibitor of LFA-1 bound to the I-domain studied by crystallography, NMR, and calorimetry.
Related Articles Structure of an allosteric inhibitor of LFA-1 bound to the I-domain studied by crystallography, NMR, and calorimetry.
Biochemistry. 2004 Mar 9;43(9):2394-404
Authors: Crump MP, Ceska TA, Spyracopoulos L, Henry A, Archibald SC, Alexander R, Taylor RJ, Findlow SC, O'Connell J, Robinson MK, Shock A
LFA-1 (lymphocyte function-associated antigen-1) plays a role in intercellular adhesion and lymphocyte trafficking...
nmrlearner
Journal club
0
11-24-2010 09:25 PM
[NMR paper] NMR structure of alpha-bungarotoxin free and bound to a mimotope of the nicotinic ace
NMR structure of alpha-bungarotoxin free and bound to a mimotope of the nicotinic acetylcholine receptor.
Related Articles NMR structure of alpha-bungarotoxin free and bound to a mimotope of the nicotinic acetylcholine receptor.
Biochemistry. 2002 Feb 5;41(5):1457-63
Authors: Scarselli M, Spiga O, Ciutti A, Bernini A, Bracci L, Lelli B, Lozzi L, Calamandrei D, Di Maro D, Klein S, Niccolai N
A combinatorial library approach was used to produce synthetic peptides mimicking the snake neurotoxin binding site of nicotinic receptors. Among the...
nmrlearner
Journal club
0
11-24-2010 08:49 PM
[NMR paper] 15N NMR relaxation studies of free and ligand-bound human acidic fibroblast growth fa
15N NMR relaxation studies of free and ligand-bound human acidic fibroblast growth factor.
Related Articles 15N NMR relaxation studies of free and ligand-bound human acidic fibroblast growth factor.
J Biol Chem. 2000 Dec 15;275(50):39444-50
Authors: Chi Y, Kumar TK, Chiu IM, Yu C
15N NMR relaxation data have been used to characterize the backbone dynamics of the human acidic fibroblast growth factor (hFGF-1) in its free and sucrose octasulfate (SOS)-bound states. (15)N longitudinal (R(1)), transverse (R(2)) relaxation rates and (1H)-(15)N...
nmrlearner
Journal club
0
11-19-2010 08:29 PM
[NMR paper] NMR studies of the pbx1 TALE homeodomain protein free in solution and bound to DNA: p
NMR studies of the pbx1 TALE homeodomain protein free in solution and bound to DNA: proposal for a mechanism of HoxB1-Pbx1-DNA complex assembly.
Related Articles NMR studies of the pbx1 TALE homeodomain protein free in solution and bound to DNA: proposal for a mechanism of HoxB1-Pbx1-DNA complex assembly.
J Mol Biol. 1999 Aug 20;291(3):521-30
Authors: Jabet C, Gitti R, Summers MF, Wolberger C
The Hox homeodomain proteins are transcription factors involved in developmental regulation. Many of the vertebrate Hox proteins bind DNA cooperatively...
nmrlearner
Journal club
0
11-18-2010 08:31 PM
[NMR paper] High-resolution solution structure of the inhibitor-free catalytic fragment of human
High-resolution solution structure of the inhibitor-free catalytic fragment of human fibroblast collagenase determined by multidimensional NMR.
Related Articles High-resolution solution structure of the inhibitor-free catalytic fragment of human fibroblast collagenase determined by multidimensional NMR.
Biochemistry. 1998 Feb 10;37(6):1495-504
Authors: Moy FJ, Chanda PK, Cosmi S, Pisano MR, Urbano C, Wilhelm J, Powers R
The high-resolution solution structure of the inhibitor-free catalytic fragment of human fibroblast collagenase (MMP-1), a...
nmrlearner
Journal club
0
11-17-2010 11:06 PM
[NMR paper] 31P-NMR of free and protein-bound molybdopterin guanine dinucleotide.
31P-NMR of free and protein-bound molybdopterin guanine dinucleotide.
Related Articles 31P-NMR of free and protein-bound molybdopterin guanine dinucleotide.
Biofactors. 1992 Jan;3(3):197-200
Authors: Bastian NR, Johnson JL, Rajagopalan KV
Molybdopterin guanine dinucleotide was studied by 31P-NMR in the free, iodoacetamide derivatized form and in the native state in the dimethyl sulfoxide reductase from Rhodobacter sphaeroides. The spectra confirm the presence of a pyrophosphate moiety in the cofactor molecule. Comparison of the spectrum of...
nmrlearner
Journal club
0
08-21-2010 11:41 PM
[NMR paper] NMR studies of [U-13C]cyclosporin A bound to cyclophilin: bound conformation and port
NMR studies of cyclosporin A bound to cyclophilin: bound conformation and portions of cyclosporin involved in binding.
Related Articles NMR studies of cyclosporin A bound to cyclophilin: bound conformation and portions of cyclosporin involved in binding.
Biochemistry. 1991 Jul 2;30(26):6574-83
Authors: Fesik SW, Gampe RT, Eaton HL, Gemmecker G, Olejniczak ET, Neri P, Holzman TF, Egan DA, Edalji R, Simmer R
Cyclosporin A (CsA), a potent immunosuppressant, is known to bind with high specificity to cyclophilin (CyP), a 17.7 kDa protein with...
nmrlearner
Journal club
0
08-21-2010 11:12 PM
[NMR paper] NMR studies of [U-13C]cyclosporin A bound to cyclophilin: bound conformation and port
NMR studies of cyclosporin A bound to cyclophilin: bound conformation and portions of cyclosporin involved in binding.
Related Articles NMR studies of cyclosporin A bound to cyclophilin: bound conformation and portions of cyclosporin involved in binding.
Biochemistry. 1991 Jul 2;30(26):6574-83
Authors: Fesik SW, Gampe RT, Eaton HL, Gemmecker G, Olejniczak ET, Neri P, Holzman TF, Egan DA, Edalji R, Simmer R
Cyclosporin A (CsA), a potent immunosuppressant, is known to bind with high specificity to cyclophilin (CyP), a 17.7 kDa protein with...