-
1
-
-
33748559498
-
Nucleobase catalysis in ribozyme mechanism
-
Bevilacqua, P. C. and Yajima, R. (2006) Nucleobase catalysis in ribozyme mechanism Curr. Opin. Chem. Biol. 10, 455-464
-
(2006)
Curr. Opin. Chem. Biol.
, vol.10
, pp. 455-464
-
-
Bevilacqua, P.C.1
Yajima, R.2
-
3
-
-
84899550322
-
Nucleic acid catalysis: Metals, nucleobases, and other cofactors
-
Ward, W. L., Plakos, K., and DeRose, V. J. (2014) Nucleic acid catalysis: Metals, nucleobases, and other cofactors Chem. Rev. 114, 4318-4342
-
(2014)
Chem. Rev.
, vol.114
, pp. 4318-4342
-
-
Ward, W.L.1
Plakos, K.2
Derose, V.J.3
-
4
-
-
70349279881
-
Identification of catalytic metal ion ligands in ribozymes
-
Frederiksen, J. K. and Piccirilli, J. A. (2009) Identification of catalytic metal ion ligands in ribozymes Methods 49, 148-166
-
(2009)
Methods
, vol.49
, pp. 148-166
-
-
Frederiksen, J.K.1
Piccirilli, J.A.2
-
5
-
-
0032192761
-
The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone
-
Murray, J. B., Seyhan, A. A., Walter, N. G., Burke, J. M., and Scott, W. G. (1998) The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone Chem. Biol. 5, 587-595
-
(1998)
Chem. Biol.
, vol.5
, pp. 587-595
-
-
Murray, J.B.1
Seyhan, A.A.2
Walter, N.G.3
Burke, J.M.4
Scott, W.G.5
-
6
-
-
0034712097
-
General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme
-
Nakano, S., Chadalavada, D. M., and Bevilacqua, P. C. (2000) General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme Science 287, 1493-1497
-
(2000)
Science
, vol.287
, pp. 1493-1497
-
-
Nakano, S.1
Chadalavada, D.M.2
Bevilacqua, P.C.3
-
7
-
-
33749016245
-
HDV ribozyme activity in monovalent cations
-
Perrotta, A. T. and Been, M. D. (2006) HDV ribozyme activity in monovalent cations Biochemistry 45, 11357-11365
-
(2006)
Biochemistry
, vol.45
, pp. 11357-11365
-
-
Perrotta, A.T.1
Been, M.D.2
-
8
-
-
33645462033
-
Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions
-
Roth, A., Nahvi, A. L. I., Lee, M., Jona, I., and Breaker, R. R. (2006) Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions RNA 12, 607-619
-
(2006)
RNA
, vol.12
, pp. 607-619
-
-
Roth, A.1
Nahvi, A.L.I.2
Lee, M.3
Jona, I.4
Breaker, R.R.5
-
9
-
-
84891008536
-
A widespread self-cleaving ribozyme class is revealed by bioinformatics
-
Roth, A., Weinberg, Z., Chen, A. G. Y., Kim, P. B., Ames, T. D., and Breaker, R. R. (2014) A widespread self-cleaving ribozyme class is revealed by bioinformatics Nat. Chem. Biol. 10, 56-60
-
(2014)
Nat. Chem. Biol.
, vol.10
, pp. 56-60
-
-
Roth, A.1
Weinberg, Z.2
Chen, A.G.Y.3
Kim, P.B.4
Ames, T.D.5
Breaker, R.R.6
-
10
-
-
0031215134
-
An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis
-
Nesbitt, S., Hegg, L. A., and Fedor, M. J. (1997) An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis Chem. Biol. 4, 619-630
-
(1997)
Chem. Biol.
, vol.4
, pp. 619-630
-
-
Nesbitt, S.1
Hegg, L.A.2
Fedor, M.J.3
-
11
-
-
0031194873
-
A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage
-
Hampel, A. and Cowan, J. A. (1997) A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage Chem. Biol. 4, 513-517
-
(1997)
Chem. Biol.
, vol.4
, pp. 513-517
-
-
Hampel, A.1
Cowan, J.A.2
-
14
-
-
34249059298
-
Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme
-
Roychowdhury-Saha, M. and Burke, D. H. (2007) Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme RNA 13, 841-848
-
(2007)
RNA
, vol.13
, pp. 841-848
-
-
Roychowdhury-Saha, M.1
Burke, D.H.2
-
15
-
-
0034687167
-
Cobalt hexammine inhibition of the hammerhead ribozyme
-
Horton, T. E. and DeRose, V. J. (2000) Cobalt hexammine inhibition of the hammerhead ribozyme Biochemistry 39, 11408-11416
-
(2000)
Biochemistry
, vol.39
, pp. 11408-11416
-
-
Horton, T.E.1
Derose, V.J.2
-
16
-
-
0035833978
-
Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism
-
Nakano, S., Proctor, D. J., and Bevilacqua, P. C. (2001) Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism Biochemistry 40, 12022-12038
-
(2001)
Biochemistry
, vol.40
, pp. 12022-12038
-
-
Nakano, S.1
Proctor, D.J.2
Bevilacqua, P.C.3
-
17
-
-
0035020626
-
The hammerhead cleavage reaction in monovalent cations
-
Curtis, E. A. and Bartel, D. P. (2001) The hammerhead cleavage reaction in monovalent cations RNA 7, 546-552
-
(2001)
RNA
, vol.7
, pp. 546-552
-
-
Curtis, E.A.1
Bartel, D.P.2
-
18
-
-
0035001461
-
Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations
-
O'Rear, J. L., Wang, S., Feig, A. L., Beigelman, L., Uhlenbeck, O. C., and Herschlag, D. (2001) Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations RNA 7, 537-545
-
(2001)
RNA
, vol.7
, pp. 537-545
-
-
O'rear, J.L.1
Wang, S.2
Feig, A.L.3
Beigelman, L.4
Uhlenbeck, O.C.5
Herschlag, D.6
-
19
-
-
84884235787
-
Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme
-
Thaplyal, P., Ganguly, A., Golden, B. L., Hammes-Schiffer, S., and Bevilacqua, P. C. (2013) Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme Biochemistry 52, 6499-6514
-
(2013)
Biochemistry
, vol.52
, pp. 6499-6514
-
-
Thaplyal, P.1
Ganguly, A.2
Golden, B.L.3
Hammes-Schiffer, S.4
Bevilacqua, P.C.5
-
20
-
-
33749034196
-
A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene
-
Salehi-Ashtiani, K., Lupták, A., Litovchick, A., and Szostak, J. W. (2006) A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene Science 313, 1788-1792
-
(2006)
Science
, vol.313
, pp. 1788-1792
-
-
Salehi-Ashtiani, K.1
Lupták, A.2
Litovchick, A.3
Szostak, J.W.4
-
21
-
-
72449145407
-
Widespread occurrence of self-cleaving ribozymes
-
Webb, C.-H. T., Riccitelli, N. J., Ruminski, D. J., and Lupták, A. (2009) Widespread occurrence of self-cleaving ribozymes Science 326, 953
-
(2009)
Science
, vol.326
, pp. 953
-
-
Webb, C.-H.T.1
Riccitelli, N.J.2
Ruminski, D.J.3
Lupták, A.4
-
23
-
-
85027554708
-
An integrated picture of HDV ribozyme catalysis
-
in (Russell, R. Ed.) Springer, New York.
-
Golden, B. L., Hammes-Schiffer, S., Carey, P. R., and Bevilacqua, P. C. (2013) An integrated picture of HDV ribozyme catalysis, in Biophysics of RNA Folding (Russell, R., Ed.) pp 135-168. Springer, New York.
-
(2013)
Biophysics of RNA Folding
, pp. 135-168
-
-
Golden, B.L.1
Hammes-Schiffer, S.2
Carey, P.R.3
Bevilacqua, P.C.4
-
24
-
-
24644454458
-
General acid catalysis by the hepatitis delta virus ribozyme
-
Das, S. R. and Piccirilli, J. A. (2005) General acid catalysis by the hepatitis delta virus ribozyme Nat. Chem. Biol. 1, 45-52
-
(2005)
Nat. Chem. Biol.
, vol.1
, pp. 45-52
-
-
Das, S.R.1
Piccirilli, J.A.2
-
25
-
-
80054929125
-
Characterization of the structure and dynamics of the hdv ribozyme in different stages along the reaction path
-
Lee, T. S., Giambaşu, G. M., Harris, M. E., and York, D. M. (2011) Characterization of the structure and dynamics of the hdv ribozyme in different stages along the reaction path J. Phys. Chem. Lett. 2, 2538-2543
-
(2011)
J. Phys. Chem. Lett.
, vol.2
, pp. 2538-2543
-
-
Lee, T.S.1
Giambaşu, G.M.2
Harris, M.E.3
York, D.M.4
-
26
-
-
84925253393
-
New tools provide a second look at HDV ribozyme structure, dynamics and cleavage
-
Kapral, G. J., Jain, S., Noeske, J., Doudna, J. A., Richardson, D. C., and Richardson, J. S. (2014) New tools provide a second look at HDV ribozyme structure, dynamics and cleavage Nucleic Acids Res. 42, 12833-12846
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 12833-12846
-
-
Kapral, G.J.1
Jain, S.2
Noeske, J.3
Doudna, J.A.4
Richardson, D.C.5
Richardson, J.S.6
-
27
-
-
84902654651
-
Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape
-
Sripathi, K. N., Tay, W. W., Banas, P., Otyepka, M., Sponer, J., and Walter, N. G. (2014) Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape RNA 20, 1112-1118
-
(2014)
RNA
, vol.20
, pp. 1112-1118
-
-
Sripathi, K.N.1
Tay, W.W.2
Banas, P.3
Otyepka, M.4
Sponer, J.5
Walter, N.G.6
-
28
-
-
35848964370
-
Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography
-
Gong, B., Chen, J.-H., Chase, E., Chadalavada, D. M., Yajima, R., Golden, B. L., Bevilacqua, P. C., and Carey, P. R. (2007) Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography J. Am. Chem. Soc. 129, 13335-13342
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 13335-13342
-
-
Gong, B.1
Chen, J.-H.2
Chase, E.3
Chadalavada, D.M.4
Yajima, R.5
Golden, B.L.6
Bevilacqua, P.C.7
Carey, P.R.8
-
29
-
-
70349095576
-
Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation
-
Guo, M., Spitale, R. C., Volpini, R., Krucinska, J., Cristalli, G., Carey, P. R., and Wedekind, J. E. (2009) Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation J. Am. Chem. Soc. 131, 12908-12909
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 12908-12909
-
-
Guo, M.1
Spitale, R.C.2
Volpini, R.3
Krucinska, J.4
Cristalli, G.5
Carey, P.R.6
Wedekind, J.E.7
-
30
-
-
80052557910
-
The glmS ribozyme tunes the catalytically critical pK(a) of its coenzyme glucosamine-6-phosphate
-
Gong, B., Klein, D. J., Ferré-D'Amaré, A. R., and Carey, P. R. (2011) The glmS ribozyme tunes the catalytically critical pK(a) of its coenzyme glucosamine-6-phosphate J. Am. Chem. Soc. 133, 14188-14191
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 14188-14191
-
-
Gong, B.1
Klein, D.J.2
Ferré-D'amaré, A.R.3
Carey, P.R.4
-
31
-
-
81755171288
-
Quantum mechanical/molecular mechanical study of the HDV ribozyme: impact of the catalytic metal ion on the mechanism
-
Ganguly, A., Bevilacqua, P. C., and Hammes-Schiffer, S. (2011) Quantum mechanical/molecular mechanical study of the HDV ribozyme: impact of the catalytic metal ion on the mechanism J. Phys. Chem. Lett. 2, 2906-2911
-
(2011)
J. Phys. Chem. Lett.
, vol.2
, pp. 2906-2911
-
-
Ganguly, A.1
Bevilacqua, P.C.2
Hammes-Schiffer, S.3
-
32
-
-
84901921779
-
Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path
-
Heldenbrand, H., Janowski, P. A., Giambaşu, G., Giese, T. J., Wedekind, J. E., and York, D. M. (2014) Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path J. Am. Chem. Soc. 136, 7789-7792
-
(2014)
J. Am. Chem. Soc.
, vol.136
, pp. 7789-7792
-
-
Heldenbrand, H.1
Janowski, P.A.2
Giambaşu, G.3
Giese, T.J.4
Wedekind, J.E.5
York, D.M.6
-
34
-
-
55549085243
-
Mechanistic characterization of the HDV genomic ribozyme: solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid
-
Cerrone-Szakal, A. L., Siegfried, N. A., and Bevilacqua, P. C. (2008) Mechanistic characterization of the HDV genomic ribozyme: solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid J. Am. Chem. Soc. 130, 14504-14520
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 14504-14520
-
-
Cerrone-Szakal, A.L.1
Siegfried, N.A.2
Bevilacqua, P.C.3
-
36
-
-
84893445982
-
Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme
-
Ganguly, A., Thaplyal, P., Rosta, E., Bevilacqua, P. C., and Hammes-Schiffer, S. (2014) Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme J. Am. Chem. Soc. 136, 1483-1496
-
(2014)
J. Am. Chem. Soc.
, vol.136
, pp. 1483-1496
-
-
Ganguly, A.1
Thaplyal, P.2
Rosta, E.3
Bevilacqua, P.C.4
Hammes-Schiffer, S.5
-
37
-
-
77955258795
-
A 1.9 Å crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage
-
Chen, J.-H., Yajima, R., Chadalavada, D. M., Chase, E., Bevilacqua, P. C., and Golden, B. L. (2010) A 1.9 Å crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage Biochemistry 49, 6508-6518
-
(2010)
Biochemistry
, vol.49
, pp. 6508-6518
-
-
Chen, J.-H.1
Yajima, R.2
Chadalavada, D.M.3
Chase, E.4
Bevilacqua, P.C.5
Golden, B.L.6
-
38
-
-
84858236151
-
Mechanistic analysis of the hepatitis delta virus ribozyme
-
Chadalavada, D. M., Cerrone-Szakal, A. L., Wilcox, J. L., Siegfried, N. A., and Bevilacqua, P. C. (2012) Mechanistic analysis of the hepatitis delta virus ribozyme Methods Mol. Biol. 848, 21-40
-
(2012)
Methods Mol. Biol.
, vol.848
, pp. 21-40
-
-
Chadalavada, D.M.1
Cerrone-Szakal, A.L.2
Wilcox, J.L.3
Siegfried, N.A.4
Bevilacqua, P.C.5
-
39
-
-
0020346954
-
Solvent isotope effects on enzyme systems
-
Schowen, B. K. and Schowen, R. L. (1982) Solvent isotope effects on enzyme systems Methods Enzymol. 87, 551-606
-
(1982)
Methods Enzymol.
, vol.87
, pp. 551-606
-
-
Schowen, B.K.1
Schowen, R.L.2
-
40
-
-
0024792371
-
Proton inventory of a bifunctional ribonuclease model
-
Anslyn, E. and Breslow, R. (1989) Proton inventory of a bifunctional ribonuclease model J. Am. Chem. Soc. 111, 8931-8932
-
(1989)
J. Am. Chem. Soc.
, vol.111
, pp. 8931-8932
-
-
Anslyn, E.1
Breslow, R.2
-
41
-
-
77954057644
-
-
v. 2.2 () D. E. Shaw Research, New York.
-
Desmond Molecular Dynamics System, v. 2.2 (2009) D. E. Shaw Research, New York.
-
(2009)
Desmond Molecular Dynamics System
-
-
-
42
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules J. Am. Chem. Soc. 117, 5179-5197
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
43
-
-
79959537078
-
Mechanistic strategies in the HDV ribozyme: chelated and diffuse metal ion interactions and active site protonation
-
Veeraraghavan, N., Ganguly, A., Golden, B. L., Bevilacqua, P. C., and Hammes-Schiffer, S. (2011) Mechanistic strategies in the HDV ribozyme: chelated and diffuse metal ion interactions and active site protonation J. Phys. Chem. B 115, 8346-8357
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 8346-8357
-
-
Veeraraghavan, N.1
Ganguly, A.2
Golden, B.L.3
Bevilacqua, P.C.4
Hammes-Schiffer, S.5
-
44
-
-
33746228126
-
Tertiary contacts distant from the active site prime a ribozyme for catalysis
-
Martick, M. and Scott, W. G. (2006) Tertiary contacts distant from the active site prime a ribozyme for catalysis Cell 126, 309-320
-
(2006)
Cell
, vol.126
, pp. 309-320
-
-
Martick, M.1
Scott, W.G.2
-
45
-
-
77956170803
-
Long-distance communication in the HDV ribozyme: insights from molecular dynamics and experiments
-
Veeraraghavan, N., Bevilacqua, P. C., and Hammes-Schiffer, S. (2010) Long-distance communication in the HDV ribozyme: insights from molecular dynamics and experiments J. Mol. Biol. 402, 278-291
-
(2010)
J. Mol. Biol.
, vol.402
, pp. 278-291
-
-
Veeraraghavan, N.1
Bevilacqua, P.C.2
Hammes-Schiffer, S.3
-
46
-
-
79953205188
-
Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions
-
Veeraraghavan, N., Ganguly, A., Chen, J.-H., Bevilacqua, P. C., Hammes-Schiffer, S., and Golden, B. L. (2011) Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions Biochemistry 50, 2672-2682
-
(2011)
Biochemistry
, vol.50
, pp. 2672-2682
-
-
Veeraraghavan, N.1
Ganguly, A.2
Chen, J.-H.3
Bevilacqua, P.C.4
Hammes-Schiffer, S.5
Golden, B.L.6
-
47
-
-
33947356675
-
Mechanistic characterization of the HDV genomic ribozyme: a mutant of the C41 motif provides insight into the positioning and thermodynamic linkage of metal ions and protons
-
Nakano, S. and Bevilacqua, P. C. (2007) Mechanistic characterization of the HDV genomic ribozyme: a mutant of the C41 motif provides insight into the positioning and thermodynamic linkage of metal ions and protons Biochemistry 46, 3001-3012
-
(2007)
Biochemistry
, vol.46
, pp. 3001-3012
-
-
Nakano, S.1
Bevilacqua, P.C.2
-
48
-
-
33746563448
-
Advances in methods and algorithms in a modern quantum chemistry program package
-
Shao, Y., Molnar, F., Jung, Y., Brown, S. T., Gilbert, A. T. B., Slipchenko, L. V., Levchenko, S. V., Neill, D. P. O., Jr, A. D., Rohini, C., Wang, T., Beran, G. J. O., Besley, N. A., John, M., Lin, Y., Voorhis, T. Van, Chien, H., Sodt, A., Steele, P., Rassolov, V. A., Maslen, P. E., Korambath, P. P., Adamson, D., Austin, B., Baker, J., Byrd, E. F. C., Dachsel, H., Doerksen, R. J., Dreuw, A., Dunietz, B. D., Dutoi, A. D., Furlani, T. R., Gwaltney, S. R., Heyden, A., Hirata, S., Hsu, P., Kedziora, G., Khalliulin, R. Z., Klunzinger, P., Aaron, M., Lee, M. S., Liang, W., Lotan, I., Nair, N., Peters, B., Proynov, E. I., Pieniazek, P. A., Rhee, M., Ritchie, J., Sherrill, C. D., Simmonett, A. C., Subotnik, J. E., Lee, H., Iii, W., Zhang, W., Bell, A. T., Chakraborty, A. K., Daniel, M., Keil, F. J., Warshel, A., Hehre, W. J., Schaefer, H. F., Kong, J., Krylov, A. I., Gill, M. W., and Head-Gordon, M. (2006) Advances in methods and algorithms in a modern quantum chemistry program package Phys. Chem. Chem. Phys. 8, 3172-3191
-
(2006)
Phys. Chem. Chem. Phys.
, vol.8
, pp. 3172-3191
-
-
Shao, Y.1
Molnar, F.2
Jung, Y.3
Brown, S.T.4
Gilbert, A.T.B.5
Slipchenko, L.V.6
Levchenko, S.V.7
Neill, D.P.O.8
Jr, A.D.9
Rohini, C.10
Wang, T.11
Beran, G.J.O.12
Besley, N.A.13
John, M.14
Lin, Y.15
Voorhis, T.V.16
Chien, H.17
Sodt, A.18
Steele, P.19
Rassolov, V.A.20
Maslen, P.E.21
Korambath, P.P.22
Adamson, D.23
Austin, B.24
Baker, J.25
Byrd, E.F.C.26
Dachsel, H.27
Doerksen, R.J.28
Dreuw, A.29
Dunietz, B.D.30
Dutoi, A.D.31
Furlani, T.R.32
Gwaltney, S.R.33
Heyden, A.34
Hirata, S.35
Hsu, P.36
Kedziora, G.37
Khalliulin, R.Z.38
Klunzinger, P.39
Aaron, M.40
Lee, M.S.41
Liang, W.42
Lotan, I.43
Nair, N.44
Peters, B.45
Proynov, E.I.46
Pieniazek, P.A.47
Rhee, M.48
Ritchie, J.49
Sherrill, C.D.50
Simmonett, A.C.51
Subotnik, J.E.52
Lee, H.53
Iii, W.54
Zhang, W.55
Bell, A.T.56
Chakraborty, A.K.57
Daniel, M.58
Keil, F.J.59
Warshel, A.60
Hehre, W.J.61
Schaefer, H.F.62
Kong, J.63
Krylov, A.I.64
Gill, M.W.65
Head-Gordon, M.66
more..
-
49
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4, 187-217
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
50
-
-
34250817103
-
A new mixing of Hartree-Fock and local density-functional theories
-
Becke, A. D. (1993) A new mixing of Hartree-Fock and local density-functional theories J. Chem. Phys. 98, 1372-1377
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 1372-1377
-
-
Becke, A.D.1
-
51
-
-
79958776843
-
Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations
-
Rosta, E., Nowotny, M., Yang, W., and Hummer, G. (2011) Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations J. Am. Chem. Soc. 133, 8934-8941
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 8934-8941
-
-
Rosta, E.1
Nowotny, M.2
Yang, W.3
Hummer, G.4
-
52
-
-
84921519751
-
Role of the active site guanine in the glms ribozyme self-cleavage mechanism: Quantum mechanical/molecular mechanical free energy simulations
-
Zhang, S., Ganguly, A., Goyal, P., Bingaman, J., Bevilacqua, P. C., and Hammes-Schiffer, S. (2015) Role of the active site guanine in the glms ribozyme self-cleavage mechanism: Quantum mechanical/molecular mechanical free energy simulations J. Am. Chem. Soc. 137, 784-798
-
(2015)
J. Am. Chem. Soc.
, vol.137
, pp. 784-798
-
-
Zhang, S.1
Ganguly, A.2
Goyal, P.3
Bingaman, J.4
Bevilacqua, P.C.5
Hammes-Schiffer, S.6
-
53
-
-
0015138001
-
Sites and thermodynamic quantitities associated with proton and metal ion interaction with ribonucleic acid, deoxyribonucleic acid, and their constituent bases, nucleosides, and nucleotides
-
Izatt, R. M., Christensen, J. J., and Rytting, J. H. (1971) Sites and thermodynamic quantitities associated with proton and metal ion interaction with ribonucleic acid, deoxyribonucleic acid, and their constituent bases, nucleosides, and nucleotides Chem. Rev. 71, 439-481
-
(1971)
Chem. Rev.
, vol.71
, pp. 439-481
-
-
Izatt, R.M.1
Christensen, J.J.2
Rytting, J.H.3
-
54
-
-
0035085466
-
Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions
-
Juneau, K., Podell, E., Harrington, D. J., and Cech, T. R. (2001) Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions Structure 9, 221-231
-
(2001)
Structure
, vol.9
, pp. 221-231
-
-
Juneau, K.1
Podell, E.2
Harrington, D.J.3
Cech, T.R.4
-
55
-
-
0030929889
-
A magnesium ion core at the heart of a ribozyme domain
-
Cate, J. H., Hanna, R. L., and Doudna, J. A. (1997) A magnesium ion core at the heart of a ribozyme domain Nat. Struct. Biol. 4, 553-558
-
(1997)
Nat. Struct. Biol.
, vol.4
, pp. 553-558
-
-
Cate, J.H.1
Hanna, R.L.2
Doudna, J.A.3
-
56
-
-
0037452909
-
Mechanistic characterization of the HDV genomic ribozyme: classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism
-
Nakano, S., Cerrone, A. L., and Bevilacqua, P. C. (2003) Mechanistic characterization of the HDV genomic ribozyme: classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism Biochemistry 42, 2982-2994
-
(2003)
Biochemistry
, vol.42
, pp. 2982-2994
-
-
Nakano, S.1
Cerrone, A.L.2
Bevilacqua, P.C.3
-
57
-
-
77952575505
-
Phosphate residues of antigenomic HDV ribozyme important for catalysis that are revealed by phosphorothioate modification
-
Wrzesinski, J., Wichłacz, A., Nijakowska, D., Rebowska, B., Nawrot, B., and Ciesiołka, J. (2010) Phosphate residues of antigenomic HDV ribozyme important for catalysis that are revealed by phosphorothioate modification New J. Chem. 34, 1018-1026
-
(2010)
New J. Chem.
, vol.34
, pp. 1018-1026
-
-
Wrzesinski, J.1
Wichłacz, A.2
Nijakowska, D.3
Rebowska, B.4
Nawrot, B.5
Ciesiołka, J.6
-
58
-
-
0026095948
-
Evidence that genomic and antigenomic RNA self-cleaving elements from hepatitis delta virus have similar secondary structures
-
Rosenstein, S. P. and Been, M. D. (1991) Evidence that genomic and antigenomic RNA self-cleaving elements from hepatitis delta virus have similar secondary structures Nucleic Acids Res. 19, 5409-5416
-
(1991)
Nucleic Acids Res.
, vol.19
, pp. 5409-5416
-
-
Rosenstein, S.P.1
Been, M.D.2
-
59
-
-
84863107506
-
Characterization of the trans Watson-Crick GU base pair located in the catalytic core of the antigenomic HDV ribozyme
-
Lévesque, D., Reymond, C., and Perreault, J. P. (2012) Characterization of the trans Watson-Crick GU base pair located in the catalytic core of the antigenomic HDV ribozyme PLoS One 7, e40309
-
(2012)
PLoS One
, vol.7
, pp. 40309
-
-
Lévesque, D.1
Reymond, C.2
Perreault, J.P.3
-
60
-
-
0033215448
-
Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme
-
Perrotta, A. T., Shih, I., and Been, M. D. (1999) Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme Science 286, 123-126
-
(1999)
Science
, vol.286
, pp. 123-126
-
-
Perrotta, A.T.1
Shih, I.2
Been, M.D.3
-
61
-
-
0037425552
-
A novel calcium-dependent bacterial phosphatidylinositol-specific phospholipase C displaying unprecedented magnitudes of thio effect, inverse thio effect, and stereoselectivity
-
Zhao, L., Liu, Y., Bruzik, K. S., and Tsai, M. D. (2003) A novel calcium-dependent bacterial phosphatidylinositol-specific phospholipase C displaying unprecedented magnitudes of thio effect, inverse thio effect, and stereoselectivity J. Am. Chem. Soc. 125, 22-23
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 22-23
-
-
Zhao, L.1
Liu, Y.2
Bruzik, K.S.3
Tsai, M.D.4
-
62
-
-
4143088173
-
Simple method for determining nucleobase pKa values by indirect labeling and demonstration of a pKa of neutrality in dsDNA
-
Moody, E. M., Brown, T. S., and Bevilacqua, P. C. (2004) Simple method for determining nucleobase pKa values by indirect labeling and demonstration of a pKa of neutrality in dsDNA J. Am. Chem. Soc. 126, 10200-10201
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 10200-10201
-
-
Moody, E.M.1
Brown, T.S.2
Bevilacqua, P.C.3
-
63
-
-
0037532732
-
Comparisons of phosphorothioate with phosphate transfer reactions for a monoester, diester, and triester: isotope effect studies
-
Catrina, I. E. and Hengge, A. C. (2003) Comparisons of phosphorothioate with phosphate transfer reactions for a monoester, diester, and triester: isotope effect studies J. Am. Chem. Soc. 125, 7546-7552
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 7546-7552
-
-
Catrina, I.E.1
Hengge, A.C.2
-
64
-
-
26844447061
-
The thermodynamics of phosphate versus phosphorothioate ester hydrolysis
-
Purcell, J. and Hengge, A. C. (2005) The thermodynamics of phosphate versus phosphorothioate ester hydrolysis J. Org. Chem. 70, 8437-8442
-
(2005)
J. Org. Chem.
, vol.70
, pp. 8437-8442
-
-
Purcell, J.1
Hengge, A.C.2
-
65
-
-
0037418547
-
Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme
-
Bevilacqua, P. C. (2003) Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme Biochemistry 42, 2259-2265
-
(2003)
Biochemistry
, vol.42
, pp. 2259-2265
-
-
Bevilacqua, P.C.1
-
66
-
-
0003604405
-
-
2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
-
Feig, A. L. and Uhlenbeck, O. C. (1999) The RNA World, 2nd ed., pp 290-291, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
-
(1999)
The RNA World
, pp. 290-291
-
-
Feig, A.L.1
Uhlenbeck, O.C.2
-
67
-
-
33845279880
-
Absolute electronegativity and hardness: application to inorganic chemistry
-
Pearson, R. G. (1988) Absolute electronegativity and hardness: application to inorganic chemistry Inorg. Chem. 27, 734-740
-
(1988)
Inorg. Chem.
, vol.27
, pp. 734-740
-
-
Pearson, R.G.1
-
70
-
-
0000847775
-
Ionic Radii from scaled particle theory of the salt effect
-
Masterton, W. L., Bolocofsky, D., and Lee, T. P. (1971) Ionic Radii from scaled particle theory of the salt effect J. Phys. Chem. 76, 2809-2815
-
(1971)
J. Phys. Chem.
, vol.76
, pp. 2809-2815
-
-
Masterton, W.L.1
Bolocofsky, D.2
Lee, T.P.3
|