-
1
-
-
55249084867
-
Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly
-
Adilakshmi, T., Bellur, D. L., and Woodson, S. A. (2008) Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly. Nature 455, 1268-1272
-
(2008)
Nature
, vol.455
, pp. 1268-1272
-
-
Adilakshmi, T.1
Bellur, D.L.2
Woodson, S.A.3
-
2
-
-
0036816641
-
Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical "footprinting."
-
Brenowitz, M., Chance, M. R., Dhavan, G., and Takamoto, K. (2002) Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical "footprinting." Curr. Opin. Struct. Biol. 12, 648-653
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 648-653
-
-
Brenowitz, M.1
Chance, M.R.2
Dhavan, G.3
Takamoto, K.4
-
3
-
-
0032549780
-
RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting
-
Sclavi, B., Sullivan, M., Chance, M. R., Brenowitz, M., and Woodson, S. A. (1998) RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science 279, 1940-1943
-
(1998)
Science
, vol.279
, pp. 1940-1943
-
-
Sclavi, B.1
Sullivan, M.2
Chance, M.R.3
Brenowitz, M.4
Woodson, S.A.5
-
4
-
-
0036894697
-
Monovalent cations mediate formation of native tertiary structure of the Tetrahymena thermophila ribozyme
-
Takamoto, K., He, Q., Morris, S., Chance, M. R., and Brenowitz, M. (2002) Monovalent cations mediate formation of native tertiary structure of the Tetrahymena thermophila ribozyme. Nat. Struct. Biol. 9, 928-933
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 928-933
-
-
Takamoto, K.1
He, Q.2
Morris, S.3
Chance, M.R.4
Brenowitz, M.5
-
5
-
-
4444370899
-
Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme
-
Shcherbakova, I., Gupta, S., Chance, M. R., and Brenowitz, M. (2004) Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme. J. Mol. Biol. 342, 1431-1442
-
(2004)
J. Mol. Biol.
, vol.342
, pp. 1431-1442
-
-
Shcherbakova, I.1
Gupta, S.2
Chance, M.R.3
Brenowitz, M.4
-
6
-
-
69849100869
-
Probing protein structure by amino acid-specific covalent labeling and mass spectrometry
-
Mendoza, V. L., and Vachet, R. W. (2009) Probing protein structure by amino acid-specific covalent labeling and mass spectrometry. Mass Spectrom. Rev. 28, 785-815
-
(2009)
Mass Spectrom. Rev.
, vol.28
, pp. 785-815
-
-
Mendoza, V.L.1
Vachet, R.W.2
-
7
-
-
84869451240
-
Fast photochemical oxidation of proteins and mass spectrometry follow submillisecond protein folding at the amino-acid level
-
Chen, J., Rempel, D. L., Gau, B. C., and Gross, M. L. (2012) Fast photochemical oxidation of proteins and mass spectrometry follow submillisecond protein folding at the amino-acid level. J. Am. Chem. Soc. 134, 18724-18731
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 18724-18731
-
-
Chen, J.1
Rempel, D.L.2
Gau, B.C.3
Gross, M.L.4
-
8
-
-
33745742438
-
Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions
-
Sinz, A. (2006) Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. Mass Spectrom. Rev. 25, 663-682
-
(2006)
Mass Spectrom. Rev.
, vol.25
, pp. 663-682
-
-
Sinz, A.1
-
9
-
-
77953480345
-
Hydrogen exchange mass spectrometry: What is it and what can it tell us?
-
Marcsisin, S. R., and Engen, J. R. (2010) Hydrogen exchange mass spectrometry: what is it and what can it tell us? Anal. Bioanal. Chem. 397, 967-972
-
(2010)
Anal. Bioanal. Chem.
, vol.397
, pp. 967-972
-
-
Marcsisin, S.R.1
Engen, J.R.2
-
10
-
-
34548337296
-
Hydroxyl radical-mediated modification of proteins as probes for structural proteomics
-
Xu, G., and Chance, M. R. (2007) Hydroxyl radical-mediated modification of proteins as probes for structural proteomics. Chem. Rev. 107, 3514-3543
-
(2007)
Chem. Rev.
, vol.107
, pp. 3514-3543
-
-
Xu, G.1
Chance, M.R.2
-
11
-
-
49549086897
-
Protein structure and dynamics studied by mass spectrometry: H/D exchange, hydroxyl radical labeling, and related approaches
-
Konermann, L., Tong, X., and Pan, Y. (2008) Protein structure and dynamics studied by mass spectrometry: H/D exchange, hydroxyl radical labeling, and related approaches. J. Mass Spectrom. 43, 1021-1036
-
(2008)
J. Mass Spectrom.
, vol.43
, pp. 1021-1036
-
-
Konermann, L.1
Tong, X.2
Pan, Y.3
-
12
-
-
0035964867
-
Unfolding of apomyoglobin examined by synchrotron footprinting
-
Chance, M. R. (2001) Unfolding of apomyoglobin examined by synchrotron footprinting. Biochem. Biophys. Res. Commun. 287, 614-621
-
(2001)
Biochem. Biophys. Res. Commun.
, vol.287
, pp. 614-621
-
-
Chance, M.R.1
-
13
-
-
14644435764
-
Structure and dynamics of the actin filament
-
Guan, J. Q., Takamoto, K., Almo, S. C., Reisler, E., and Chance, M. R. (2005) Structure and dynamics of the actin filament. Biochemistry 44, 3166-3175
-
(2005)
Biochemistry
, vol.44
, pp. 3166-3175
-
-
Guan, J.Q.1
Takamoto, K.2
Almo, S.C.3
Reisler, E.4
Chance, M.R.5
-
14
-
-
3042662113
-
In silico proteome analysis to facilitate proteomics experiments using mass spectrometry
-
Cagney, G., Amiri, S., Premawaradena, T., Lindo, M., and Emili, A. (2003) In silico proteome analysis to facilitate proteomics experiments using mass spectrometry. Proteome Sci. 1, 5
-
(2003)
Proteome Sci.
, vol.1
, pp. 5
-
-
Cagney, G.1
Amiri, S.2
Premawaradena, T.3
Lindo, M.4
Emili, A.5
-
15
-
-
51549112221
-
A simple test to detect hydrogen/deuterium scrambling during gas-phase peptide fragmentation
-
Hamuro, Y., Tomasso, J. C., and Coales, S. J. (2008) A simple test to detect hydrogen/deuterium scrambling during gas-phase peptide fragmentation. Anal. Chem. 80, 6785-6790
-
(2008)
Anal. Chem.
, vol.80
, pp. 6785-6790
-
-
Hamuro, Y.1
Tomasso, J.C.2
Coales, S.J.3
-
16
-
-
33846233476
-
Hydrogen/deuterium scrambling during quadrupole time-of-flight MS/MS analysis of a zinc-binding protein domain
-
Ferguson, P. L., Pan, J., Wilson, D. J., Dempsey, B., Lajoie, G., Shilton, B., and Konermann, L. (2007) Hydrogen/deuterium scrambling during quadrupole time-of-flight MS/MS analysis of a zinc-binding protein domain. Anal. Chem. 79, 153-160
-
(2007)
Anal. Chem.
, vol.79
, pp. 153-160
-
-
Ferguson, P.L.1
Pan, J.2
Wilson, D.J.3
Dempsey, B.4
Lajoie, G.5
Shilton, B.6
Konermann, L.7
-
17
-
-
67650756766
-
Protein hydrogen exchange measured at single-residue resolution by electron transfer dissociation mass spectrometry
-
Rand, K. D., Zehl, M., Jensen, O. N., and Jorgensen, T. J. (2009) Protein hydrogen exchange measured at single-residue resolution by electron transfer dissociation mass spectrometry. Anal. Chem. 81, 5577-5584
-
(2009)
Anal. Chem.
, vol.81
, pp. 5577-5584
-
-
Rand, K.D.1
Zehl, M.2
Jensen, O.N.3
Jorgensen, T.J.4
-
18
-
-
84856276827
-
Automated hydrogen/deuterium exchange electron transfer dissociation high resolution mass spectrometry measured at single-amide resolution
-
Landgraf, R. R., Chalmers, M. J., and Griffin, P. R. (2012) Automated hydrogen/deuterium exchange electron transfer dissociation high resolution mass spectrometry measured at single-amide resolution. J. Am. Soc. Mass Spectrom. 23, 301-309
-
(2012)
J. Am. Soc. Mass Spectrom.
, vol.23
, pp. 301-309
-
-
Landgraf, R.R.1
Chalmers, M.J.2
Griffin, P.R.3
-
19
-
-
78650717220
-
Future directions of structural mass spectrometry using hydroxyl radical footprinting
-
Kiselar, J. G., and Chance, M. R. (2010) Future directions of structural mass spectrometry using hydroxyl radical footprinting. J. Mass Spectrom. 45, 1373-1382
-
(2010)
J. Mass Spectrom.
, vol.45
, pp. 1373-1382
-
-
Kiselar, J.G.1
Chance, M.R.2
-
20
-
-
80054704826
-
Fast photochemical oxidation of proteins for epitope mapping
-
Jones, L. M., Sperry, J. B., Carroll, J. A., Gross, M. L. (2011) Fast photochemical oxidation of proteins for epitope mapping. Anal. Chem. 83, 7657-7661
-
(2011)
Anal. Chem.
, vol.83
, pp. 7657-7661
-
-
Jones, L.M.1
Sperry, J.B.2
Carroll, J.A.3
Gross, M.L.4
-
21
-
-
78650772189
-
Fast photochemical oxidation of proteins for comparing structures of protein-ligand complexes: The calmodulin-peptide model system
-
Zhang, H., Gau, B. C., Jones, L. M., Vidavsky, I., and Gross, M. L. (2011) Fast photochemical oxidation of proteins for comparing structures of protein-ligand complexes: the calmodulin-peptide model system. Anal. Chem. 83, 311-318
-
(2011)
Anal. Chem.
, vol.83
, pp. 311-318
-
-
Zhang, H.1
Gau, B.C.2
Jones, L.M.3
Vidavsky, I.4
Gross, M.L.5
-
22
-
-
84885350132
-
Protein hydrogen exchange at residue resolution by proteolytic fragmentation mass spectrometry analysis
-
Kan, Z. Y., Walters, B. T., Mayne, L., and Englander, S. W. (2013) Protein hydrogen exchange at residue resolution by proteolytic fragmentation mass spectrometry analysis. Proc. Natl. Acad. Sci. U.S.A. 110, 16438-16443
-
(2013)
Proc. Natl. Acad. Sci. U.S.A.
, vol.110
, pp. 16438-16443
-
-
Kan, Z.Y.1
Walters, B.T.2
Mayne, L.3
Englander, S.W.4
-
23
-
-
55149093649
-
Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: Application to galectin-1
-
Charvatova, O., Foley, B. L., Bern, M. W., Sharp, J. S., Orlando, R., and Woods, R. J. (2008) Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: application to galectin-1. J. Am. Soc. Mass Spectrom. 19, 1692-1705
-
(2008)
J. Am. Soc. Mass Spectrom.
, vol.19
, pp. 1692-1705
-
-
Charvatova, O.1
Foley, B.L.2
Bern, M.W.3
Sharp, J.S.4
Orlando, R.5
Woods, R.J.6
-
24
-
-
84878112619
-
Fast photochemical oxidation of proteins for comparing solvent-accessibility changes accompanying protein folding: Data processing and application to barstar
-
Gau, B. C., Chen, J., and Gross, M. L. (2013) Fast photochemical oxidation of proteins for comparing solvent-accessibility changes accompanying protein folding: data processing and application to barstar. Biochim. Biophys. Acta 1834, 1230-1238
-
(2013)
Biochim. Biophys. Acta
, vol.1834
, pp. 1230-1238
-
-
Gau, B.C.1
Chen, J.2
Gross, M.L.3
-
25
-
-
83755181357
-
Structural analysis of proinsulin hexamer assembly by hydroxyl radical footprinting and computational modeling
-
Kiselar, J. G., Datt, M., Chance, M. R., and Weiss, M. A. (2011) Structural analysis of proinsulin hexamer assembly by hydroxyl radical footprinting and computational modeling. J. Biol. Chem. 286, 43710-43716
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 43710-43716
-
-
Kiselar, J.G.1
Datt, M.2
Chance, M.R.3
Weiss, M.A.4
-
26
-
-
84866280220
-
Structure and dynamics of protein waters revealed by radiolysis and mass spectrometry
-
Gupta, S., D'Mello, R., and Chance, M. R. (2012) Structure and dynamics of protein waters revealed by radiolysis and mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 109, 14882-14887
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 14882-14887
-
-
Gupta, S.1
D'Mello, R.2
Chance, M.R.3
-
27
-
-
77954635392
-
Conformational changes during the gating of a potassium channel revealed by structural mass spectrometry
-
Gupta, S., Bavro, V. N., D'Mello, R., Tucker, S. J., Venien-Bryan, C., and Chance, M. R. (2010) Conformational changes during the gating of a potassium channel revealed by structural mass spectrometry. Structure 18, 839-846
-
(2010)
Structure
, vol.18
, pp. 839-846
-
-
Gupta, S.1
Bavro, V.N.2
D'Mello, R.3
Tucker, S.J.4
Venien-Bryan, C.5
Chance, M.R.6
-
28
-
-
77956221747
-
A bridging interaction allows calmodulin to activate NO synthase through a bimodal mechanism
-
Tejero, J., Haque, M. M., Durra, D., and Stuehr, D. J. (2010) A bridging interaction allows calmodulin to activate NO synthase through a bimodal mechanism. J. Biol. Chem. 285, 25941-25949
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 25941-25949
-
-
Tejero, J.1
Haque, M.M.2
Durra, D.3
Stuehr, D.J.4
-
29
-
-
33745041235
-
Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes
-
Takamoto, K., and Chance, M. R. (2006) Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes. Annu. Rev. Biophys. Biomol. Struct. 35, 251-276
-
(2006)
Annu. Rev. Biophys. Biomol. Struct.
, vol.35
, pp. 251-276
-
-
Takamoto, K.1
Chance, M.R.2
-
30
-
-
25144465204
-
Radiolytic modification and reactivity of amino acid residues serving as structural probes for protein footprinting
-
Xu, G., and Chance, M. R. (2005) Radiolytic modification and reactivity of amino acid residues serving as structural probes for protein footprinting. Anal. Chem. 77, 4549-4555
-
(2005)
Anal. Chem.
, vol.77
, pp. 4549-4555
-
-
Xu, G.1
Chance, M.R.2
-
31
-
-
34247159926
-
The Beamline X28C of the Center for Synchrotron Biosciences: A national resource for biomolecular structure and dynamics experiments using synchrotron footprinting
-
Gupta, S., Sullivan, M., Toomey, J., Kiselar, J., and Chance, M. R. (2007) The Beamline X28C of the Center for Synchrotron Biosciences: a national resource for biomolecular structure and dynamics experiments using synchrotron footprinting. J. Synchrotron Rad. 14, 233-243
-
(2007)
J. Synchrotron Rad.
, vol.14
, pp. 233-243
-
-
Gupta, S.1
Sullivan, M.2
Toomey, J.3
Kiselar, J.4
Chance, M.R.5
-
32
-
-
70349614659
-
Integrated algorithms for high-throughput examination of covalently labeled biomolecules by structural mass spectrometry
-
Kaur, P., Kiselar, J. G., and Chance, M. R. (2009) Integrated algorithms for high-throughput examination of covalently labeled biomolecules by structural mass spectrometry. Anal. Chem. 81, 8141-8149
-
(2009)
Anal. Chem.
, vol.81
, pp. 8141-8149
-
-
Kaur, P.1
Kiselar, J.G.2
Chance, M.R.3
-
33
-
-
79955595074
-
mProphet: Automated data processing and statistical validation for large-scale SRM experiments
-
Reiter, L., Rinner, O., Picotti, P., Huttenhain, R., Beck, M., Brusniak, M. Y., Hengartner, M. O., and Aebersold, R. (2011) mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat. Methods 8, 430-435
-
(2011)
Nat. Methods
, vol.8
, pp. 430-435
-
-
Reiter, L.1
Rinner, O.2
Picotti, P.3
Huttenhain, R.4
Beck, M.5
Brusniak, M.Y.6
Hengartner, M.O.7
Aebersold, R.8
-
34
-
-
54049090766
-
Selected reaction monitoring for quantitative proteomics: A tutorial
-
Lange, V., Picotti, P., Domon, B., and Aebersold, R. (2008) Selected reaction monitoring for quantitative proteomics: A tutorial. Mol. Syst. Biol. 4, 1-14
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 1-14
-
-
Lange, V.1
Picotti, P.2
Domon, B.3
Aebersold, R.4
-
35
-
-
34447642869
-
Improved sequencing of oxidized cysteine and methionine containing peptides using electron transfer dissociation
-
Srikanth, R., Wilson, J., Bridgewater, J. D., Numbers, J. R., Lim, J., Olbris, M. R., Kettani, A., and Vachet, R. W. (2007) Improved sequencing of oxidized cysteine and methionine containing peptides using electron transfer dissociation. J. Am. Soc. Mass Spectrom. 18, 1499-1506
-
(2007)
J. Am. Soc. Mass Spectrom.
, vol.18
, pp. 1499-1506
-
-
Srikanth, R.1
Wilson, J.2
Bridgewater, J.D.3
Numbers, J.R.4
Lim, J.5
Olbris, M.R.6
Kettani, A.7
Vachet, R.W.8
-
36
-
-
84885615235
-
Improved identification and relative quantification of sites of Peptide and protein oxidation for hydroxyl radical footprinting
-
Li, X., Li, Z., Xie, B., and Sharp, J. S. (2013) Improved identification and relative quantification of sites of Peptide and protein oxidation for hydroxyl radical footprinting. J. Am. Soc. Mass Spectrom. 24, 1767-1776
-
(2013)
J. Am. Soc. Mass Spectrom.
, vol.24
, pp. 1767-1776
-
-
Li, X.1
Li, Z.2
Xie, B.3
Sharp, J.S.4
-
37
-
-
0345548657
-
Random forest: A classification and regression tool for compound classification and QSAR modeling
-
Svetnik, V., Liaw, A., Tong, C., Culberson, J. C., Sheridan, R. P., and Feuston, B. P. (2003) Random forest: a classification and regression tool for compound classification and QSAR modeling. J. Chem. Inf. Comput. Sci. 43, 1947-1958
-
(2003)
J. Chem. Inf. Comput. Sci.
, vol.43
, pp. 1947-1958
-
-
Svetnik, V.1
Liaw, A.2
Tong, C.3
Culberson, J.C.4
Sheridan, R.P.5
Feuston, B.P.6
-
38
-
-
54049090766
-
Selected reaction monitoring for quantitative proteomics: A tutorial
-
Lange, V., Picotti, P., Domon, B., and Aebersold, R. (2008) Selected reaction monitoring for quantitative proteomics: a tutorial. Mol. Syst. Biol. 4, 222
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 222
-
-
Lange, V.1
Picotti, P.2
Domon, B.3
Aebersold, R.4
-
39
-
-
84861990380
-
Selected reaction monitoring-based proteomics: Workflows, potential, pitfalls, and future directions
-
Picotti, P., and Aebersold, R. (2012) Selected reaction monitoring-based proteomics: workflows, potential, pitfalls, and future directions. Nat. Methods 9, 555-566
-
(2012)
Nat. Methods
, vol.9
, pp. 555-566
-
-
Picotti, P.1
Aebersold, R.2
-
40
-
-
0347882733
-
Structural analysis of gelsolin using synchrotron protein footprinting
-
Kiselar, J. G., Janmey, P. A., Almo, S. C., and Chance, M. R. (2003) Structural analysis of gelsolin using synchrotron protein footprinting. Mol. Cell. Proteomics 2, 1120-1132
-
(2003)
Mol. Cell. Proteomics
, vol.2
, pp. 1120-1132
-
-
Kiselar, J.G.1
Janmey, P.A.2
Almo, S.C.3
Chance, M.R.4
-
41
-
-
0037388073
-
Visualizing the Ca2+-dependent activation of gelsolin by using synchrotron footprinting
-
Kiselar, J. G., Janmey, P. A., Almo, S. C., and Chance, M. R. (2003) Visualizing the Ca2+-dependent activation of gelsolin by using synchrotron footprinting. Proc. Natl. Acad. Sci. U.S.A. 100, 3942-3947
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 3942-3947
-
-
Kiselar, J.G.1
Janmey, P.A.2
Almo, S.C.3
Chance, M.R.4
-
42
-
-
0023645203
-
Interior and surface of monomeric proteins
-
Miller, S., Janin, J., Lesk, A. M., and Chothia, C. (1987) Interior and surface of monomeric proteins. J. Mol. Biol. 196, 641-656
-
(1987)
J. Mol. Biol.
, vol.196
, pp. 641-656
-
-
Miller, S.1
Janin, J.2
Lesk, A.M.3
Chothia, C.4
-
43
-
-
66249099205
-
Correct identification of oxidized histidine residues using electron-transfer dissociation
-
Srikanth, R., Wilson, J., and Vachet, R. W. (2009) Correct identification of oxidized histidine residues using electron-transfer dissociation. J. Mass Spectrom. 44, 755-762
-
(2009)
J. Mass Spectrom.
, vol.44
, pp. 755-762
-
-
Srikanth, R.1
Wilson, J.2
Vachet, R.W.3
-
44
-
-
55849104839
-
Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications
-
Wiesner, J., Premsler, T., and Sickmann, A. (2008) Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications. Proteomics 8, 4466-4483
-
(2008)
Proteomics
, vol.8
, pp. 4466-4483
-
-
Wiesner, J.1
Premsler, T.2
Sickmann, A.3
-
45
-
-
84905577487
-
Visualizing the kinetic power stroke that drives proton-coupled Zn(II) transport
-
Gupta, S. F., D., and Chance, M. R. (2014) Visualizing the kinetic power stroke that drives proton-coupled Zn(II) transport Nature 512, 101-104
-
(2014)
Nature
, vol.512
, pp. 101-104
-
-
Gupta, S.F.D.1
Chance, M.R.2
-
46
-
-
84920946226
-
Quantitative topological mapping of protein structure by hydroxyl radical footprinting mediated structural mass spectrometry
-
Huang, W., Ravikumar, K.M., Chance, M. R., and Yang, S. (2015) Quantitative topological mapping of protein structure by hydroxyl radical footprinting mediated structural mass spectrometry. Biophys. J. 108, 107-115
-
(2015)
Biophys. J.
, vol.108
, pp. 107-115
-
-
Huang, W.1
Ravikumar, K.M.2
Chance, M.R.3
Yang, S.4
|