X28C Publications

1. J Bohon, J Smedley, E Muller, J Keister, Development of Diamond-Based X-ray Detection for High Flux Beamline Diagnostics, in Diamond Electronics and Bioelectronics — Fundamentals to Applications III, Materials Research Society Fall 2009 Meeting, Vol 1203, p. J19-03, sponsored by MRS (2010).
2. T Orban, S Gupta, K Palczewski, M Chance, Visualizing Water Molecules in Transmembrane Proteins Using Radiolytic Labeling Methods, Biochemistry, Jan4, Web (2010).
3. T Orban, G Bereta, M Miyagi, B Wang, M Chance, M Sousa, K Palczewski, Conformational Changes in Guanylate Cyclase-Activating Protein 1 Induced by Ca2+ and N-Terminal Fatty Acid Acylation, Structure, 18(1), 116-126 (2010).
4. T Angel, S Gupta, B Jastrzebska, K Palczewski, M Chance, Structural Waters Define a Functional Channel Mediating Activation of the GPCR, rhodopsin, Proc Natl Acad Sci USA, 106(34), 14367-72 (2009).[ premier ]
5. T Angel, M Chance, K Palczewski, Conserved waters mediate structural and functional activation of family A (rhodopsin-like) G protein-coupled receptors, Proc Natl Acad Sci USA, 106(21), 8555-60 (2009).[ premier ]
6. P Kaur, J Kiselar, M Chance, Integrated Algorithms for High-Throughput Examination of Covalently Labeled Biomolecules by Structural Mass Spectrometry, Anal. Chem., 81(19), 8141-9 (2009).
7. R D'Mello, S Gupta, J Bohen, D Abel, J Toomey, M Sullivan, M Chance, X-ray Footprinting at Beamline X28C: A National Resource for Studying Macromolecular Structure and Dynamics, Biophys. J., 96(3), 66a-67a (2009).
8. T Adilakshmi, D Bellur, S Woodson, Concurrent Nucleation of 16S Folding and Induced Fit in 30S Ribosome Assembly, Nature, 455, 1268-1272 (2008).[ premier ]
9. J Amisha Kamal, Computational Approaches to Examining Protein-Protein Interactions: Combining Experimental and Computational Data in the Era of Structural Genomics, Mass Spectrometry Analysis for Protein-Protein Interactions and Dynamics, p. 189-215, Wiley, Hoboken (2008).
10. X Zheng, P Wintrode, Transferrin: Receptor Complex formation Examined by Hydroxyl Radical Footprinting, Mass Spectrometry Analysis for Protein-Protein Interactions and Dynamics, p. 69-90, Wiley, Hoboken (2008).
11. J Kiselar, K Takamoto, Covalent labeling Methods for Examining Protein Structure and Protein Interactions, Mass Spectrometry Analysis for Protein-Protein Interactions and Dynamics, p. 45-68, Wiley, Hoboken (2008).
12. S Swiatkowski, M Chance, Overview of Mass Spectrometry Technologies for Examining Protein Structure: Current and Future Directions, Mass Spectrometry Analysis for Protein-Protein Interactions and Dynamics, p. 1-9, Wiley, Hoboken (2008).
13. L Jennings, Translocation and Proteolysis by the Energy-Dependent Protease ClpAP: Coordination of Conformational Changes and Active Site Chemistry, Ph.D. Thesis. Massachusetts Institute of Technology, Cambridge (2008).
14. L Jennings, J Bohon, M Chance, S Licht, The ClpP N-Terminus Coordinates Substrate Access with Protease Active Site Reactivity, Biochemistry, 47, 11031-11040 (2008).
15. J Amisha Kamal, M Chance, Modeling of Protein Binary Complexes Using Structural Mass Spectrometry Data, Protein Sci., 17(1), 79-94 (2008).
16. X Zheng, P Wintrode, M Chance, Complementary Structural Mass Spectrometry Techniques Reveal Local Dynamics in Functionally Important Regions of a Metastable Serpin, Structure, 16(1), 38-51 (2008).
17. M Sullivan, S Rekhi, J Bohon, S Gupta, D Abel, J Toomey, M Chance, Installation and Testing of a Focusing Mirror at Beamline X28C for High Flux X-ray Radiolysis of Biological Macromolecules, Rev. Sci. Instrum., 79, 025101 (2008).
18. J Bohon, L Jennings, C Phillips, S Licht, M Chance, Synchrotron Protein Footprinting Supports Substrate Translocation by ClpA via ATP-Induced Movements of the D2 Loop, Structure, 16, 1157-1165 (2008).
19. I Shcherbakova, S Mitra, R Beer, M Brenowitz, Following Molecular Transitions with Single Residue Spatial and Millisecond Time Resolution, Methods Cell Biol., 84, 589-615 (2008).
20. K Takamoto, J Amisha Kamal, M Chance, Biological and Chemical Implications of a Three Dimensional Model of Monomeric Actin Bound to Magnesium Chelated ATP, Structure, 15(1), 39-51 (2007).
21. G Xu, M Chance, Hydroxyl Radical-Mediated Modification of Proteins as Probes for Structural Proteomics, Chem. Rev., 107, 3514-3543 (2007).[ premier ]
22. R Lease, T Adilakshmi, S Heilman-Miller, S Woodson, Communication Between RNA Folding Domains Revealed by Folding of Circularly Permuted Ribozymes, J. Mol. Biol., 373, 197-210 (2007).
23. S Gupta, M Sullivan, J Toomey, J Kiselar, M Chance, The Beamline X28C of the Center for Synchrotron Biosciences: a National Resource for Biomolecular Structure and Dynamics Experiments Using Synchrotron Footprinting, J. Synch. Rad., 14(3), 233-43 (2007).
24. R Russell, P Tijerina, A Chadee, H Bhaskaran, Deletion of the P5abc Peripheral Element Accelerates Early and Late Folding Steps of the Tetrahymena Group I Ribozyme, Biochemistry, 46, 4951-4961 (2007).
25. S Gupta, H Cheng, A Mollah, E Jamison, S Morris, M Chance, S Khrapunov, M Brenowitz, DNA and Protein Footprinting Analysis of the Modulation of DNA Binding by the N-Terminal Domain of the Saccharomyces cervisiae TATA Binding Protein, Biochemistry, 46, 9886-9898 (2007).
26. E Johnson, A Lyndaker, A Deyhim, M Sullivan, M Chance, D Abel, J Toomey, S Hulbert, White Light Focusing Mirror, Ninth International Conference on Synchrotron Radiation Instrumentation, Vol 879, p. 675, sponsored by AIP (2007). [77823]
27. J Kiselar, R Mahaffy, T Pollard, S Almo, M Chance, Visualizing Arp2/3 Complex Activation Mediated by Binding of ATP and WASp using Structural Mass Spectrometry, Proc Natl Acad Sci USA, 104(5), 1552-1557 (2007).[ premier ]
28. J Amisha Kamal, S Benchaar, K Takamoto, E Reisler, M Chance, Three-Dimensional Structure of Cofilin Bound to Monomeric Actin Derived by Structural Mass Spectrometry Data, Proc Natl Acad Sci USA, 104(19), 7910-7915 (2007).[ premier ]
29. A Laederach, I Shcherbakova, M Jonikas, R Altman, M Brenowitz, Distinct Contribution of Electrostatics, Initial Conformational Ensemble, and Macromolecular Stability in RNA Folding, Proc Natl Acad Sci USA, 104, 7045-7050 (2007).[ premier ]
30. T Nguyenle, M Laurberg, M Brenowitz, H Noller, Following the Dynamics of Changes in Solvent Accessiblity of 16 S and 23 S RRNA During Ribsomal Subunit Assocaition Using Synchrotron-Generated Hydroxyl Radicals, J. Mol. Biol., 359(5), 1235-1248 (2006).
31. A Laederach, I Shcherbakova, M Liang, M Brenowitz, R Altman, Local Kinetic Measures of Macromolecular Structure Reveal Partitioning Among Multiple Parallel Pathways from the Earliest Steps in the Folding of a Large RNA Molecule, J. Mol. Biol., 358, 1179-1190 (2006).
32. L Kwok, I Scherbakova, J Lamb, H Park, K Andresen, H Smith, M Brenowitz, L Pollack, Concordant Exploration of the Kinetics of RNA Folding from Global and Local Perspectives, J. Mol. Biol., 355, 282-293 (2006).
33. I Shcherbakova, S Mitra, R Beer, M Brenowitz, Fast Fenton Footprinting: A Laboratory-Based Method for the Time-Resolved Analysis of DNA, RNA and Proteins, Nucleic Acids Res., 34, e48 (2006).[ premier ]
34. T Adilakshmi, R Lease, S Woodson, Hydroxyl Radical Footprinting in vivo: Mapping Macromolecular Structures with Synchrotron Radiation, Nucleic Acids Res., 34(8), 1-7 (2006).[ premier ]
35. T Adilakshmi, R Lease, S Woodson, Hydroxyl Radical Footprinting in vivo: Mapping Macromolecular Structures with Synchrotron Radiation, Nucleic Acids Res., 34(8), e64 (2006).[ premier ]
36. K Takamoto, M Chance, Protein-protein Interactions using Radiolytic Footprinting, Annu. Rev. Bioph. Biom., 35, 251-275 (2006).[ premier ]
37. G Xu, R Liu, O Zak, P Aisen, M Chance, Structural Allostery and Binding of the Transferring Receptor Complex, Mol. Cell. Proteomics, 4, 1959-1967 (2005).[ premier ]
38. J Guan, M Chance, Structural Proteomics of Macromolecular Assemblies using Oxidative Footprinting and Mass Spectroscopy, Trends Biochem. Sci., 30, 583-592 (2005).[ premier ]
39. I Shcherbakova, M Brenowitz, Perturbation of the Hierarchical Folding of a Large RNA by the Destabilization of its Scaffold's Tertiary Structure, J. Mol. Biol., 354, 483-496 (2005).
40. S Gupta, W Mangel, M Sullivan, K Takamoto, M Chance, Synchrotron Footprinting Provides Insight into Adenovirus Protease-DNA Interactions, Synch. Rad. News, 18, 25-33 (2005).
41. T Adilakshmi, P Ramaswamy, S Woodson, Protein-Independent Folding Pathway of the 16 S rRNA 5' Domain, J. Mol. Biol., 351(3), 508-519 (2005).
42. J Guan, K Takamoto, S Almo, E Reisler, M Chance, Structure and Dynamics of the Actin Filament, Biochemistry, 44, 3166-3175 (2005).
43. S Woodson, Metal Ions and RNA Folding: A Highly Charged Topic with a Dynamic Future, Curr Opin Chem Biol, 9, 104-109 (2005).[ premier ]
44. M Brenowitz, D Erie, M Chance, Catching RNA Polymerase in the act of Binding: Intermediates in Transcription Illuminated by Synchrotron Footprinting, Proc Natl Acad Sci USA, 102, 4659-4660 (2005).[ premier ]
45. K Takamoto, M Chance, A New Approach for Nucleic Acid Footprinting Data Analysis, BioTech. J., 5, 194-197 (2005).
46. G Xu, M Chance, Radiolytic Modification of Sulfur Containing Acidic Amino Residues in Model Peptides: Fundamental Studies for Protein Footprinting, Anal. Chem., 77, 2437-2449 (2005).
47. G Xu, J Kiselar, Q He, M Chance, Secondary Reactions and Strategies to Improve Quantitative Protein Footprinting, Anal. Chem., 77, 3029-3037 (2005).
48. G Xu, M Chance, Radiolytic Modification and Reactivity of Amino Acid Residues Serving as Structural Probes for Protein Footprinting, Anal. Chem., 77, 4549-55 (2005).
49. P Rangan, Folding of the Azoarcus Intron, Ph.D. Thesis. John Hopkins University, Baltimore (2005).
50. K Takamoto, M Chance, Footprinting Methods to Examine the Structure and Dynamics of Nucleic Acids, Encyclopedia of Molecular Cell Biology and Molecular Medicine, p. 521-548, Wiley, Inc., Weinheim (2004).
51. J Guan, M Chance, Footprinting Methods to Examine the Structure and Dynamics of Proteins, Encyclopedia of Molecular Cell Biology and Molecular Medicine, p. 549-568, Wiley, Inc., Weinheim (2004).
52. G Xu, M Chance, Radiolytic Modification of Acidic Amino Acids: New Probes of Protein Footprinting, Anal. Chem., 76, 1213-1221 (2004).
53. I Shcherbakova, S Gupta, M Chance , M Brenowitz, Monovalent Ion-Mediated Folding of the Tetrahymena thermophila Ribozyme, J. Mol. Biol., 342, 1431-1442 (2004).
54. U Perez-Salas, P Rangan, S Krueger, R Briber, D Thirumalai, S Woodson, Compaction of a Bacterial Group I Ribozyme Coincides with the Assembly of Core Helices, Biochemistry, 43, 1746-1753 (2004).
55. E Koculi, N Lee, D Thirumalai, S Woodson, Folding of the Tetrahymena Ribozyme by Polyamines: Importance of Counterion Valence and Size, J. Mol. Biol., 341, 27-36 (2004).
56. K Takamoto, M Chance, M Brenowitz, Semi-Automated, Single-Band Peak-Fitting Analysis of Hydroxyl Radical Nucleic Acid Footprint Auto-Radiograms for the Quantitative Analysis of Transitions, Nucleic Acids Res., 32, E119 (2004).[ premier ]
57. P Rangan, B Masquida, E Westhof, S Woodson, Architecture and Folding Mechanism of the Azoarcus Group I Pre-tRNA, J. Mol. Biol., 339, 41-51 (2004).
58. K Takamoto, R Das, M Brenowitz, D Herschlag, M Chance, Principles of RNA Compaction: Insights from the Equilibrium Folding Pathway of the P4-P6 RNA Domain in Monovalent Cations, J. Mol. Biol., 343, 1195-206 (2004).
59. S Koduvayur, S Woodson, Intracellular Folding of the Tetrahymena Group I Intron Depends on Exon Sequence and Promoter Choice, RNA, 10, 1526-1532 (2004).[ premier ]
60. J Guan, S Almo, M Chance, Synchrotron Radiolysis and Mass Spectrometry: A New Approach to Research on the Actin Cytoskeleton, Acct. Chem. Res., 37, 221-229 (2004).[ premier ]
61. S Gupta, W Mangel, W McGrath, J Perek, D Lee, K Takamoto, M Chance, DNA Binding Provides a Molecular Strap Activating the Adenovirus Proteinase, Mol. Cell. Proteomics, 3, 950-959 (2004).[ premier ]
62. J Kiselar, P Janmey, S Almo, M Chance, Structural Analysis of Gelsolin Using Synchrotron Protein Footprinting, Mol. Cell. Proteomics, 2, 1120-1132 (2003).[ premier ]
63. J Guan, S Almo, E Reisler, M Chance, Structural Reorganization of Proteins Revealed by Radiolysis and Mass Spectrometry: G-Actin Solution Structure is Divalent Cation Dependent, Biochemistry, 42, 11992-12000 (2003).
64. R Liu, J Guan, O Zak, P Aisen, M Chance, Structural Reorganization of the Transferrin C-Lobe and Transferrin Receptor upon Complex Formation: The C-Lobe Binds to the Receptor Helical Domain, Biochemistry, 42, 12447-12454 (2003).
65. L Su, M Brenowitz, A Pyle, An Alternative Route for the Folding of Large RNAs: Apparent Two-State Folding by a Group II Intron Ribozyme, J. Mol. Biol., 334, 639-652 (2003).
66. T Ucida, K Takamoto, Q He, M Chance, M Brenowitz, Multiple Monovalent Ion-Dependent Pathways for the Folding of the L-21 Tetrahymena Thermophila Ribozyme, J. Mol. Biol., 328, 463-478 (2003).
67. H Rashidzadeh, S Khrapunov, M Chance, M Brenowitz, Solution Structure and Interdomain Interactions of the Saccharomyces cerevisiae "TATA Binding Protein" (TBP) Probed by Radiolytic Protein Footprinting, Biochemistry, 42, 3655-3665 (2003). [ ]
68. G Xu, K Takamoto, M Chance, Radiiolytic Modification of Basic Amino Acids: New Probes for Protein Footprinting, Anal. Chem., 75, 6995-7007 (2003).
69. G Dhavan, M Chance, M Brenowitz, Kinetics Analysis of DNA-Protein Interactions by Time-Resolved Synchrotron X-Ray Footprinting , Analysis of Macromolecules: A Practical Approach, p. 75-86, IRL Press at Oxford University Press, Oxford (2003). [ ]
70. J Kiselar, P Janmey, S Almo, M Chance, Visualizing the Ca2+-dependent activation of gelsolin by using synchrotron footprinting, Proc Natl Acad Sci USA, 100(7), 3942-3947 (2003). [ ][ premier ]
71. P Rangan, B Masquida, E Westhof, S Woodson, Assembly of Core Helices and Rapid Tertiary Folding of a Small Bacterial Group I Ribozyme, Proc Natl Acad Sci USA, 100(4), 1574-1579 (2003).[ premier ]
72. S Woodson, Folding Mechanisms of Group I Ribozymes: Role of Stability and Contact Order, Biochem Soc Trans, 30, 1166-1169 (2002).
73. M Brenowitz, M Chance, G Dhavan, K Takamoto, Probing the Structural Dynamics of Nucleic Acid Structure by Quantitive Time-Resolved and Equilibrium Hydroxyl Radical "Footprinting", Curr. Opin. Struct. Biol., 12, 648-653 (2002).[ premier ]
74. T Uchida, Q He, C Ralston, M Brenowitz, M Chance, Linkage of Monovalent and Divalent Ion Binding in the Folding of the P4-P6 Domain of the Tetrahymena Thermophila Ribozyme, Biochemistry, 41, 5799-5806 (2002).
75. J Guan, S Vorobiev, S Almo, M Chance, Mapping the G-Actin Binding Surface of Cofilin Using Synchrotron Protein Footprinting, Biochemistry, 41(18), 5765-5775 (2002).
76. G Dhavan, D Crothers, M Chance, M Brenowitz, Concerted Binding and Bending of DNA by Eschericia Coli Integration Host Factor , J. Mol. Biol., 315, 1027-1037 (2002).
77. K Takamoto, Q He, S Morris, M Chance, M Brenowitz, Monovalent Cations Mediate Formation of Native Tertiary Structure of the Tetrahymena Thermophila Ribozyme: Implications for the Kinetics of Folding, Nat. Struct. Mol. Biol., 9, 928-933 (2002).[ premier ]
78. J Kiselar, S Maleknia, M Sullivan, K Downard, M Chance, Hydroxyl Radical Probe of Protein Surfaces Using Synchrotron X-Ray Radiolysis and Mass Spectrometry, Int. J. Radiat. Biol., 78, 101-114 (2002).
79. S Maleknia, C Ralston, M Brenowitz, K Downard, M Chance, Determination of Macromolecular Folding and Structure by Synchrotron X-Ray Radiolysis Techniques, Anal. Biochem., 289, 103-115 (2001).
80. S Maleknia, K Downard, Unfolding of Apomyoglobin Helices by Synchrotron Radiolysis and Mass Spectrometry , Eur. J. Biochem., 268, 5578-5588 (2001).
81. M Chance, Unfolding of Apomyoglobin Examined by Synchrotron Footprinting, Biochem. Biophys. Res. Commun., 287, 614-621 (2001).
82. D Thirumalai, N Lee, S Woodson, D Klimov, Early Events in RNA Folding, Annu. Rev. Phys. Chem., 52, 751-762 (2001).[ premier ]
83. S Goldsmith, J Guan, S Almo, M Chance, Synchrotron Protein Footprinting: A Technique to Investigate Protein-Protein Interactions, J. Biomol. Struct. Dyn., 19, 405-419 (2001).
84. S Heilman-Miller, J Pan, D Thirumalai, S Woodson, Role of Counterion Condensation in Folding of the Tetrahymena Ribozyme II Counterion-Dependence of Folding Kinetics, J. Mol. Biol., 309, 57-68 (2001).
85. S Woodson, M Deras, M Brenowitz, Time-Resolved Hydroxyl Radical Footprinting of RNA with X-Rays, Current Protocols in Nucleic Acid Chemistry , p. 11.6.1-11.6.23, John Wiley Sons, New York (2001).
86. J Pan, M Deras, S Woodson, Fast Folding of a Ribozyme by Stabilizing Core Interactions: Evidence for Multiple Folding Pathways in RNA, J. Mol. Biol., 1(133-144) (2000).
87. N Pastor, H Weinstein, E Jamison, M Brenowitz, A Detailed Interpretation of OH Radical Footprints in a TBP-DNA Complex Reveals the Role of Dynamics in the Mechanism of Sequence-Specific Binding, J. Mol. Biol., 304, 55-68 (2000).
88. C Ralston, B Sclavi, M Sullivan, M Deras, S Woodson, M Chance, M Brenowitz, Time-Resolved Synchrotron X-Ray Footprinting and its Application to RNA Folding, Meth. Enzymol., 317, 353-368 (2000).
89. C Ralston, Q He, M Brenowitz, M Chance, Stability and Cooperativity of Individual Tertiary Contacts in RNA Revealed through Chemical Denaturation, Nat. Struct. Mol. Biol., 7, 371-374 (2000).[ premier ]
90. C Ralston, B Sclavi, M Brenowitz, M Sullivan, M Chance, The Early Folding Intermediates of the Tetrahymena Ribozyme are Kinetically Trapped, J. Biomol. Struct. Dyn., 11, 195-200 (2000).
91. S Silverman, M Deras, S Woodson, S Scaringe, T Cech, Multiple folding pathways for the P4-P6 RNA domain, Biochemistry, 39, 12465-12475 (2000).
92. S Maleknia, M Chance, K Downard, Electrospray-Assisted Modification of Proteins by Radicals, Rapid Commun. Mass Spectrom., 13, 2352-2358 (1999).
93. S Maleknia, M Brenowitz, M Chance, Millisecond Radiolytic Modification of Peptides by Synchrotron X-Rays Identified by Mass Spectrometry, Anal. Chem., 71, 3965-3973 (1999).

[ premier ] - A publication is considered premier if the journal has an impact factor of 6 or greater (from Journal Citation Report 2003, Thomson Institute for Scientific Information). These journals represent approximately the top 3% of all journals. Two additional journals are included in the NSLS premier list, Applied Physics Letters (impact factor 4.0) and Environmental Sciences and Technology (impact factor 3.6), because these journals represent the "best in class" for the NSLS industrial and environmental science users, even though their impact factors are less than 6.