-
1
-
-
0002903441
-
Analog approaches to the structure of the transition state in enzyme reactions
-
Wolfenden, R. (1972) Analog approaches to the structure of the transition state in enzyme reactions Acc. Chem. Res. 5, 10-18
-
(1972)
Acc. Chem. Res.
, vol.5
, pp. 10-18
-
-
Wolfenden, R.1
-
2
-
-
0015924871
-
Enzymatic catalysis and transition-state theory
-
Lienhard, G. E. (1973) Enzymatic catalysis and transition-state theory Science 180, 149-154
-
(1973)
Science
, vol.180
, pp. 149-154
-
-
Lienhard, G.E.1
-
3
-
-
0035543093
-
The depth of chemical time and the power of enzymes as catalysts
-
Wolfenden, R. and Snider, M. J. (2001) The depth of chemical time and the power of enzymes as catalysts Acc. Chem. Res. 34, 938-945
-
(2001)
Acc. Chem. Res.
, vol.34
, pp. 938-945
-
-
Wolfenden, R.1
Snider, M.J.2
-
4
-
-
0035949442
-
Site-bound water and the shortcomings of a less than perfect transition state analogue
-
DOI 10.1021/bi011189+
-
Snider, M. J. and Wolfenden, R. (2001) Site-bound water and the shortcomings of a less than perfect transition state analogue Biochemistry 40, 11364-11371 (Pubitemid 32911279)
-
(2001)
Biochemistry
, vol.40
, Issue.38
, pp. 11364-11371
-
-
Snider, M.J.1
Wolfenden, R.2
-
5
-
-
13144259628
-
Escherichia coli cytidine deaminase provides a molecular model for ApoB RNA editing and a mechanism for RNA substrate recognition
-
DOI 10.1006/jmbi.1997.1506
-
Navaratnam, N., Fujino, T., Bayliss, J., Jarmuz, A., How, A., Richardson, N., Somasekaram, A., Bhattacharya, S., Carter, C., and Scott, J. (1998) Escherichia coli cytidine deaminase provides a molecular model for ApoB RNA editing and a mechanism for RNA substrate recognition J. Mol. Biol. 275, 695-714 (Pubitemid 28064211)
-
(1998)
Journal of Molecular Biology
, vol.275
, Issue.4
, pp. 695-714
-
-
Navaratnam, N.1
Fujino, T.2
Bayliss, J.3
Jarmuz, A.4
How, A.5
Richardson, N.6
Somasekaram, A.7
Bhattacharya, S.8
Carter, C.9
Scott, J.10
-
6
-
-
0037039154
-
15N kinetic isotope effects on uncatalyzed and enzymatic deamination of cytidine
-
DOI 10.1021/bi011410i
-
15N kinetic isotope effects on uncatalyzed and enzymatic deamination of cytidine Biochemistry 41, 415-421 (Pubitemid 34049417)
-
(2002)
Biochemistry
, vol.41
, Issue.1
, pp. 415-421
-
-
Snider, M.J.1
Reinhardt, L.2
Wolfenden, R.3
Cleland, W.W.4
-
7
-
-
0028958685
-
Transition-state selectivity for a single hydroxyl group during catalysis by cytidine deaminase
-
Xiang, S., Short, S. A., Wolfenden, R., and Carter, C. W., Jr. (1995) Transition-state selectivity for a single hydroxyl group during catalysis by cytidine deaminase Biochemistry 34, 4516-4523
-
(1995)
Biochemistry
, vol.34
, pp. 4516-4523
-
-
Xiang, S.1
Short, S.A.2
Wolfenden, R.3
Carter Jr., C.W.4
-
8
-
-
0028057520
-
Cytidine deaminase. The 2.3 Å crystal structure of an enzyme:transition-state analog complex
-
Betts, L., Xiang, S., Short, S. A., Wolfenden, R., and Carter, C. W., Jr. (1994) Cytidine deaminase. The 2.3 Å crystal structure of an enzyme:transition-state analog complex J. Mol. Biol. 235, 635-656
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 635-656
-
-
Betts, L.1
Xiang, S.2
Short, S.A.3
Wolfenden, R.4
Carter, C.W.5
-
9
-
-
0030887895
-
The structure of the cytidine deaminase-product complex provides evidence for efficient proton transfer and ground-state destabilization
-
DOI 10.1021/bi963091e
-
Xiang, S., Short, S. A., Wolfenden, R., and Carter, C. W., Jr. (1997) The structure of the cytidine deaminase-product complex provides evidence for efficient proton transfer and ground-state destabilization Biochemistry 36, 4768-4774 (Pubitemid 27180957)
-
(1997)
Biochemistry
, vol.36
, Issue.16
, pp. 4768-4774
-
-
Xiang, S.1
Short, S.A.2
Wolfenden, R.3
Carter Jr., C.W.4
-
11
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
DOI 10.1073/pnas.181342398
-
Baker, N. A., Sept, D., Joseph, S., Holst, M. J., and McCammon, J. A. (2001) Electrostatics of nanosystems: Application to microtubules and the ribosome Proc. Natl. Acad. Sci. U.S.A. 98, 10037-10041 (Pubitemid 32802969)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.18
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
12
-
-
3242886771
-
PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
-
Dolinsky, T. J., Nielsen, J. E., McCammon, J. A., and Baker, N. A. (2004) PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations Nucleic Acids Res. 32, W665-W667
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Dolinsky, T.J.1
Nielsen, J.E.2
McCammon, J.A.3
Baker, N.A.4
-
13
-
-
34547559704
-
PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations
-
Dolinsky Todd, J., Czodrowski, P., Li, H., Nielsen Jens, E., Jensen Jan, H., Klebe, G., and Baker Nathan, A. (2007) PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations Nucleic Acids Res. 35, W522-W525
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Dolinsky Todd, J.1
Czodrowski, P.2
Li, H.3
Nielsen Jens, E.4
Jensen Jan, H.5
Klebe, G.6
Baker Nathan, A.7
-
14
-
-
7444221098
-
Fourier transform ion cyclotron resonance MS reveals the presence of a water molecule in an enzyme transition-state analogue complex
-
DOI 10.1073/pnas.0406781101
-
Borchers, C. H., Marquez, V. E., Schroeder, G. K., Short, S. A., Snider, M. J., Speir, J. P., and Wolfenden, R. (2004) Fourier transform ion cyclotron resonance MS reveals the presence of a water molecule in an enzyme transition-state analogue complex Proc. Natl. Acad. Sci. U.S.A. 101, 15341-15345 (Pubitemid 39441543)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.43
, pp. 15341-15345
-
-
Borchers, C.H.1
Marquez, V.E.2
Schroeder, G.K.3
Short, S.A.4
Snider, M.J.5
Speir, J.P.6
Wolfenden, R.7
-
15
-
-
0015240571
-
Cytidine deaminase from Escherichia coli. Purification, properties, and inhibition by the potential transition state analog 3,4,5,6-tetrahydrouridine
-
Cohen, R. M. and Wolfenden, R. (1971) Cytidine deaminase from Escherichia coli. Purification, properties, and inhibition by the potential transition state analog 3,4,5,6-tetrahydrouridine J. Biol. Chem. 246, 7561-7565
-
(1971)
J. Biol. Chem.
, vol.246
, pp. 7561-7565
-
-
Cohen, R.M.1
Wolfenden, R.2
-
16
-
-
0030066275
-
Role of glutamate-104 in generating a transition state analogue inhibitor at the active site of cytidine deaminase
-
DOI 10.1021/bi951498y
-
Carlow, D. C., Short, S. A., and Wolfenden, R. (1996) Role of glutamate-104 in generating a transition state analog inhibitor at the active site of cytidine deaminase Biochemistry 35, 948-954 (Pubitemid 26034581)
-
(1996)
Biochemistry
, vol.35
, Issue.3
, pp. 948-954
-
-
Carlow, D.C.1
Short, S.A.2
Wolfenden, R.3
-
17
-
-
0024332902
-
Binding of pyrimidin-2-one ribonucleoside by cytidine deaminase as the transition-state analogue 3,4-dihydrouridine and the contribution of the 4-hydroxyl group to its binding affinity
-
DOI 10.1021/bi00450a027
-
Frick, L., Yang, C., Marquez, V. E., and Wolfenden, R. V. (1989) Binding of pyrimidin-2-one ribonucleoside by cytidine deaminase as the transition-state analog 3,4-dihydrouridine and contribution of the 4-hydroxyl group to its binding affinity Biochemistry 28, 9423-9430 (Pubitemid 20000718)
-
(1989)
Biochemistry
, vol.28
, Issue.24
, pp. 9423-9430
-
-
Frick, L.1
Yang, C.2
Marquez, V.E.3
Wolfenden, R.4
-
18
-
-
0028246560
-
Mutations affecting transition-state stabilization by residues coordinating zinc at the active site of cytidine deaminase
-
DOI 10.1021/bi00187a012
-
Smith, A. A., Carlow, D. C., Wolfenden, R., and Short, S. A. (1994) Mutations affecting transition-state stabilization by residues coordinating zinc at the active site of cytidine deaminase Biochemistry 33, 6468-6474 (Pubitemid 24189357)
-
(1994)
Biochemistry
, vol.33
, Issue.21
, pp. 6468-6474
-
-
Smith, A.A.1
Carlow, D.C.2
Wolfenden, R.3
Short, S.A.4
-
19
-
-
0026708581
-
Cloning and nucleotide sequence of the Escherichia coli cytidine deaminase (ccd) gene
-
Yang, C., Carlow, D., Wolfenden, R., and Short, S. A. (1992) Cloning and nucleotide sequence of the Escherichia coli cytidine deaminase (ccd) gene Biochemistry 31, 4168-4174
-
(1992)
Biochemistry
, vol.31
, pp. 4168-4174
-
-
Yang, C.1
Carlow, D.2
Wolfenden, R.3
Short, S.A.4
-
20
-
-
60549105802
-
Global Kinetic Explorer: A new computer program for dynamic simulation and fitting of kinetic data
-
Johnson, K. A., Simpson, Z. B., and Blom, T. (2009) Global Kinetic Explorer: A new computer program for dynamic simulation and fitting of kinetic data Anal. Biochem. 387, 20-29
-
(2009)
Anal. Biochem.
, vol.387
, pp. 20-29
-
-
Johnson, K.A.1
Simpson, Z.B.2
Blom, T.3
-
21
-
-
0021900271
-
Halogenated nucleic acids: Base properties and conformation of fluorinated derivatives
-
Alderfer, J. L., Loomis, R. E., Sharma, M., and Hazel, G. (1985) Halogenated nucleic acids: Base properties and conformation of fluorinated derivatives Prog. Clin. Biol. Res. 172, 249-261
-
(1985)
Prog. Clin. Biol. Res.
, vol.172
, pp. 249-261
-
-
Alderfer, J.L.1
Loomis, R.E.2
Sharma, M.3
Hazel, G.4
-
22
-
-
0000958578
-
Methylation of nucleic acid-bases with trimethyl phosphate
-
Yamauchi, K., Tanabe, T., and Kinoshita, M. (1976) Methylation of nucleic acid-bases with trimethyl phosphate J. Org. Chem. 41, 3691-3696
-
(1976)
J. Org. Chem.
, vol.41
, pp. 3691-3696
-
-
Yamauchi, K.1
Tanabe, T.2
Kinoshita, M.3
-
23
-
-
33947488759
-
Some 5-fluoropyrimidines
-
Durr, G. J. (1965) Some 5-fluoropyrimidines J. Med. Chem. 8, 253-254
-
(1965)
J. Med. Chem.
, vol.8
, pp. 253-254
-
-
Durr, G.J.1
-
24
-
-
37049109540
-
Stereochemistry of the formation of 4-alkoxyimino-5,6-dihydro-6- alkoxyaminopyrimidin-2(1H)-ones from cytosines and hydroxylamines
-
Atkins, P. J. and Hall, C. D. (1983) Stereochemistry of the formation of 4-alkoxyimino-5,6-dihydro-6-alkoxyaminopyrimidin-2(1H)-ones from cytosines and hydroxylamines J. Chem. Soc., Perkin Trans. 2, 155-160
-
(1983)
J. Chem. Soc., Perkin Trans. 2
, pp. 155-160
-
-
Atkins, P.J.1
Hall, C.D.2
-
25
-
-
0031441544
-
Stability indicating high performance liquid chromatography methods for 5-fluorouridine in aqueous solution
-
Dorta, M. J., Munguia, O., Farina, J. B., Martin, V. S., and Llabres, M. (1997) Stability indicating high performance liquid chromatography methods for 5-fluorouridine in aqueous solution Arzneim. Forsch., 1388-1392 (Pubitemid 28015507)
-
(1997)
Arzneimittel-Forschung/Drug Research
, vol.47
, Issue.12
, pp. 1388-1392
-
-
Dorta, M.J.1
Munguia, O.2
Farina, J.B.3
Martin, V.S.4
Llabres, M.5
-
26
-
-
0032566330
-
Substrate connectivity effects in the transition state for cytidine deaminase
-
DOI 10.1021/bi980959n
-
Carlow, D. and Wolfenden, R. (1998) Substrate connectivity effects in the transition state for cytidine deaminase Biochemistry 37, 11873-11878 (Pubitemid 28400059)
-
(1998)
Biochemistry
, vol.37
, Issue.34
, pp. 11873-11878
-
-
Carlow, D.1
Wolfenden, R.2
-
27
-
-
0040597031
-
Solvent effects on equilibria of addition of nucleophiles to acetaldehyde and the hydrophilic character of diols
-
Bone, R., Cullis, P., and Wolfenden, R. (1983) Solvent effects on equilibria of addition of nucleophiles to acetaldehyde and the hydrophilic character of diols J. Am. Chem. Soc. 105, 1339-1343
-
(1983)
J. Am. Chem. Soc.
, vol.105
, pp. 1339-1343
-
-
Bone, R.1
Cullis, P.2
Wolfenden, R.3
-
28
-
-
0032541103
-
Hydrophobicities of the nucleic acid bases: Distribution coefficients from water to cyclohexane
-
DOI 10.1006/jmbi.1998.1880
-
Shih, P., Pedersen, L. G., Gibbs, P. R., and Wolfenden, R. (1998) Hydrophobicities of the nucleic acid bases: Distribution coefficients from water to cyclohexane J. Mol. Biol. 280, 421-430 (Pubitemid 28327280)
-
(1998)
Journal of Molecular Biology
, vol.280
, Issue.3
, pp. 421-430
-
-
Shih, P.1
Pedersen, L.G.2
Gibbs, P.R.3
Wolfenden, R.4
-
29
-
-
0024849506
-
Fluoromalonaldehyde bis(dialkyl acetals): Synthesis by carbene condensation and transformation to dialkyl flouoromalonates and fluorinated heterocyclic compounds
-
DOI 10.1021/jo00284a042
-
Molines, H. and Wakselman, C. (1989) Fluoromalonaldehyde bis(dialkyl acetals): Synthesis by carbene condensation and transformation to dialkyl fluoromalonates and fluorinated heterocyclic compounds J. Org. Chem. 54, 5618-5620 (Pubitemid 20016920)
-
(1989)
Journal of Organic Chemistry
, vol.54
, Issue.23
, pp. 5618-5620
-
-
Molines, H.1
Wakselman, C.2
-
30
-
-
13344252565
-
Nucleic acid components and their analogs. CXCI. 5-Fluoro-2-pyrimidinone and its N1-substituted derivatives
-
Cech, D., Beerbaum, H., and Holy, A. (1977) Nucleic acid components and their analogs. CXCI. 5-Fluoro-2-pyrimidinone and its N1-substituted derivatives Collect. Czech. Chem. Commun. 42, 2694-2700
-
(1977)
Collect. Czech. Chem. Commun.
, vol.42
, pp. 2694-2700
-
-
Cech, D.1
Beerbaum, H.2
Holy, A.3
-
32
-
-
0032319019
-
Theoretical aspects of isothermal titration calorimetry
-
DOI 10.1016/S0076-6879(98)95048-0
-
Indyk, L. and Fisher, H. F. (1998) Theoretical aspects of isothermal titration calorimetry Methods Enzymol. 295, 350-364 (Pubitemid 29349922)
-
(1998)
Methods in Enzymology
, vol.295
, pp. 350-364
-
-
Indyk, L.1
Fisher, H.F.2
-
33
-
-
0024356301
-
Rapid measurement of binding constants and heats of binding using a new titration calorimeter
-
DOI 10.1016/0003-2697(89)90213-3
-
Wiseman, T., Williston, S., Brandts, J. F., and Lin, L. N. (1989) Rapid measurement of binding constants and heats of binding using a new titration calorimeter Anal. Biochem. 179, 131-137 (Pubitemid 19149635)
-
(1989)
Analytical Biochemistry
, vol.179
, Issue.1
, pp. 131-137
-
-
Wiseman, T.1
Williston, S.2
Brandts, J.F.3
Lin, L.-N.4
-
34
-
-
60549112465
-
FitSpace Explorer: An algorithm to evaluate multidimensional parameter space in fitting kinetic data
-
Johnson, K. A., Simpson, Z. B., and Blom, T. (2009) FitSpace Explorer: An algorithm to evaluate multidimensional parameter space in fitting kinetic data Anal. Biochem. 387, 30-41
-
(2009)
Anal. Biochem.
, vol.387
, pp. 30-41
-
-
Johnson, K.A.1
Simpson, Z.B.2
Blom, T.3
-
35
-
-
0033002411
-
Probing the energetics of dissociation of carbonic anhydrase-ligand complexes in the gas phase
-
Gao, J., Wu, Q., Carbeck, J., Lei, Q. P., Smith, R. D., and Whitesides, G. M. (1999) Probing the energetics of dissociation of carbonic anhydrase-ligand complexes in the gas phase Biophys. J. 76, 3253-3260 (Pubitemid 29269472)
-
(1999)
Biophysical Journal
, vol.76
, Issue.6
, pp. 3253-3260
-
-
Gao, J.1
Wu, Q.2
Carbeck, J.3
Lei, Q.P.4
Smith, R.D.5
Whitesides, G.M.6
-
36
-
-
0042021429
-
A snapshot of enzyme catalysis using electrospray ionization mass spectrometry
-
DOI 10.1021/ja0354768
-
Li, Z., Sau, A. K., Shen, S., Whitehouse, C., Baasov, T., and Anderson, K. S. (2003) A snapshot of enzyme catalysis using electrospray ionization mass spectrometry J. Am. Chem. Soc. 125, 9938-9939 (Pubitemid 36994920)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.33
, pp. 9938-9939
-
-
Li, Z.1
Sau, A.K.2
Shen, S.3
Whitehouse, C.4
Baasov, T.5
Anderson, K.S.6
-
37
-
-
4744338745
-
Characterization of noncovalent protein-ligand complexes and associated enzyme intermediates of GlcNAc-6-O-Sulfotransferase by electrospray ionization FT-ICR mass spectrometry
-
DOI 10.1016/j.jasms.2004.06.002, PII S104403050400368X
-
Yu, Y., Kirkup, C. E., Pi, N., and Leary, J. A. (2004) Characterization of noncovalent protein-ligand complexes and associated enzyme intermediates of GlcNAc-6-O-sulfotransferase by electrospray ionization FT-ICR mass spectrometry J. Am. Soc. Mass Spectrom. 15, 1400-1407 (Pubitemid 39311690)
-
(2004)
Journal of the American Society for Mass Spectrometry
, vol.15
, Issue.10
, pp. 1400-1407
-
-
Yu, Y.1
Kirkup, C.E.2
Pi, N.3
Leary, J.A.4
-
38
-
-
0021742143
-
Inhibition of Escherichia coli cytidine deaminase by a phosphapyrimidine nucleoside
-
Ashley, G. W. and Bartlett, P. A. (1984) Inhibition of Escherichia coli cytidine deaminase by a phosphapyrimidine nucleoside J. Biol. Chem. 259, 13621-13627 (Pubitemid 15221844)
-
(1984)
Journal of Biological Chemistry
, vol.259
, Issue.21
, pp. 13621-13627
-
-
Ashley, G.W.1
Bartlett, P.A.2
-
39
-
-
0037177245
-
Catalysis by entropic effects: The action of cytidine deaminase on 5,6-dihydrocytidine
-
DOI 10.1021/bi011696r
-
Snider, M. J., Lazarevic, D., and Wolfenden, R. (2002) Catalysis by entropic effects: The action of cytidine deaminase on 5,6-dihydrocytidine Biochemistry 41, 3925-3930 (Pubitemid 34251031)
-
(2002)
Biochemistry
, vol.41
, Issue.12
, pp. 3925-3930
-
-
Snider, M.J.1
Lazarevic, D.2
Wolfenden, R.3
-
40
-
-
84863030115
-
A complex of methylthioadenosine/S-adenosylhomocysteine nucleosidase, transition state analogue, and nucleophilic water identified by mass spectrometry
-
Wang, S., Lim, J., Thomas, K., Yan, F., Angeletti, R. H., and Schramm, V. L. (2012) A complex of methylthioadenosine/S-adenosylhomocysteine nucleosidase, transition state analogue, and nucleophilic water identified by mass spectrometry J. Am. Chem. Soc. 134, 1468-1470
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 1468-1470
-
-
Wang, S.1
Lim, J.2
Thomas, K.3
Yan, F.4
Angeletti, R.H.5
Schramm, V.L.6
-
41
-
-
0034663824
-
Temperature effects on the catalytic efficiency, rate enhancement, and transition state affinity of cytidine deaminase, and the thermodynamic consequences for catalysis of removing a substrate 'anchor'
-
DOI 10.1021/bi000914y
-
Snider, M. J., Gaunitz, S., Ridgway, C., Short, S. A., and Wolfenden, R. (2000) Temperature effects on the catalytic efficiency, rate enhancement, and transition state affinity of cytidine deaminase, and the thermodynamic consequences for catalysis of removing a substrate "anchor" Biochemistry 39, 9746-9753 (Pubitemid 30627552)
-
(2000)
Biochemistry
, vol.39
, Issue.32
, pp. 9746-9753
-
-
Snider, M.J.1
Gaunitz, S.2
Ridgway, C.3
Short, S.A.4
Wolfenden, R.5
|