PubRank

John A Tainer

Author PubWeight™ 251.70‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys 2007 9.07
2 Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat Methods 2009 6.77
3 Type IV pilus structure and bacterial pathogenicity. Nat Rev Microbiol 2004 4.29
4 Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair. Cell 2008 4.26
5 The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair. Nature 2002 3.48
6 Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions. Mol Cell 2006 3.36
7 Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell 2004 3.33
8 Accurate assessment of mass, models and resolution by small-angle scattering. Nature 2013 3.18
9 XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations. Cell 2008 3.14
10 Mre11-Rad50-Nbs1 is a keystone complex connecting DNA repair machinery, double-strand break signaling, and the chromatin template. Biochem Cell Biol 2007 3.13
11 Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2. EMBO J 2003 2.95
12 Nbs1 flexibly tethers Ctp1 and Mre11-Rad50 to coordinate DNA double-strand break processing and repair. Cell 2009 2.90
13 Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law. Biopolymers 2011 2.87
14 DNA binding and nucleotide flipping by the human DNA repair protein AGT. Nat Struct Mol Biol 2004 2.86
15 Type IV pilin structure and assembly: X-ray and EM analyses of Vibrio cholerae toxin-coregulated pilus and Pseudomonas aeruginosa PAK pilin. Mol Cell 2003 2.78
16 SUMO-targeted ubiquitin ligases in genome stability. EMBO J 2007 2.77
17 Microbial metalloproteomes are largely uncharacterized. Nature 2010 2.62
18 Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering. Curr Opin Struct Biol 2010 2.45
19 Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily. Cell 2011 2.44
20 ATM regulates Mre11-dependent DNA end-degradation and microhomology-mediated end joining. Cell Cycle 2010 2.32
21 Structural basis for isozyme-specific regulation of electron transfer in nitric-oxide synthase. J Biol Chem 2004 2.28
22 Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage. EMBO J 2006 2.27
23 The intricate structural chemistry of base excision repair machinery: implications for DNA damage recognition, removal, and repair. DNA Repair (Amst) 2007 2.26
24 A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol Cell 2006 2.23
25 DNA base damage recognition and removal: new twists and grooves. Mutat Res 2005 2.21
26 The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome. Cell Cycle 2011 2.15
27 Conserved XPB core structure and motifs for DNA unwinding: implications for pathway selection of transcription or excision repair. Mol Cell 2006 2.13
28 Identification of a new cryptochrome class. Structure, function, and evolution. Mol Cell 2003 2.11
29 A SIM-ultaneous role for SUMO and ubiquitin. Trends Biochem Sci 2008 2.05
30 Mre11-Rad50-Nbs1 conformations and the control of sensing, signaling, and effector responses at DNA double-strand breaks. DNA Repair (Amst) 2010 1.96
31 Rad50/SMC proteins and ABC transporters: unifying concepts from high-resolution structures. Curr Opin Struct Biol 2003 1.93
32 Ku and DNA-dependent protein kinase dynamic conformations and assembly regulate DNA binding and the initial non-homologous end joining complex. J Biol Chem 2009 1.91
33 MDB: the Metalloprotein Database and Browser at The Scripps Research Institute. Nucleic Acids Res 2002 1.89
34 Recognition of RNA polymerase II and transcription bubbles by XPG, CSB, and TFIIH: insights for transcription-coupled repair and Cockayne Syndrome. Mol Cell 2005 1.89
35 Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys J 2013 1.83
36 ALS mutants of human superoxide dismutase form fibrous aggregates via framework destabilization. J Mol Biol 2003 1.82
37 Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism. EMBO J 2007 1.77
38 DNA charge transport as a first step in coordinating the detection of lesions by repair proteins. Proc Natl Acad Sci U S A 2012 1.71
39 A structural model for regulation of NHEJ by DNA-PKcs autophosphorylation. DNA Repair (Amst) 2010 1.71
40 Flipping of alkylated DNA damage bridges base and nucleotide excision repair. Nature 2009 1.70
41 Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source. J Appl Crystallogr 2013 1.69
42 DNA double-strand break repair from head to tail. Curr Opin Struct Biol 2002 1.67
43 ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair. Nat Struct Mol Biol 2011 1.66
44 Nickel superoxide dismutase structure and mechanism. Biochemistry 2004 1.66
45 Improving small-angle X-ray scattering data for structural analyses of the RNA world. RNA 2010 1.60
46 WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing. Nat Struct Mol Biol 2006 1.55
47 XRCC4 protein interactions with XRCC4-like factor (XLF) create an extended grooved scaffold for DNA ligation and double strand break repair. J Biol Chem 2011 1.48
48 Protein mimicry of DNA and pathway regulation. DNA Repair (Amst) 2005 1.46
49 DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Nat Struct Mol Biol 2008 1.46
50 XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase. DNA Repair (Amst) 2011 1.45
51 Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures. Proc Natl Acad Sci U S A 2003 1.41
52 Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB. Structure 2013 1.39
53 Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications. Nucleic Acids Res 2006 1.37
54 Structural basis for endothelial nitric oxide synthase binding to calmodulin. EMBO J 2003 1.37
55 Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes. Proc Natl Acad Sci U S A 2009 1.36
56 Super-resolution in solution X-ray scattering and its applications to structural systems biology. Annu Rev Biophys 2013 1.36
57 DNA binding, nucleotide flipping, and the helix-turn-helix motif in base repair by O6-alkylguanine-DNA alkyltransferase and its implications for cancer chemotherapy. DNA Repair (Amst) 2007 1.36
58 XLF regulates filament architecture of the XRCC4·ligase IV complex. Structure 2010 1.33
59 Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis. J Mol Biol 2008 1.32
60 Human DNA ligase III recognizes DNA ends by dynamic switching between two DNA-bound states. Biochemistry 2010 1.32
61 Structural dynamics in DNA damage signaling and repair. Curr Opin Struct Biol 2010 1.31
62 Cloning, expression, and characterization of a nitric oxide synthase protein from Deinococcus radiodurans. Proc Natl Acad Sci U S A 2001 1.30
63 Comprehensive macromolecular conformations mapped by quantitative SAXS analyses. Nat Methods 2013 1.29
64 gammaH2A binds Brc1 to maintain genome integrity during S-phase. EMBO J 2010 1.28
65 Structural characterization of zinc-deficient human superoxide dismutase and implications for ALS. J Mol Biol 2007 1.26
66 Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair. Nat Struct Mol Biol 2009 1.26
67 Anchored plasticity opens doors for selective inhibitor design in nitric oxide synthase. Nat Chem Biol 2008 1.25
68 A novel processive mechanism for DNA synthesis revealed by structure, modeling and mutagenesis of the accessory subunit of human mitochondrial DNA polymerase. J Mol Biol 2006 1.25
69 High-throughput SAXS for the characterization of biomolecules in solution: a practical approach. Methods Mol Biol 2014 1.22
70 Structural analysis of flexible proteins in solution by small angle X-ray scattering combined with crystallography. J Struct Biol 2006 1.21
71 The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase. Nucleic Acids Res 2007 1.21
72 Insights into Lou Gehrig's disease from the structure and instability of the A4V mutant of human Cu,Zn superoxide dismutase. J Mol Biol 2002 1.20
73 Structural tuning of the fluorescent protein iLOV for improved photostability. J Biol Chem 2012 1.19
74 The rad50 signature motif: essential to ATP binding and biological function. J Mol Biol 2004 1.19
75 Three metal ions participate in the reaction catalyzed by T5 flap endonuclease. J Biol Chem 2008 1.16
76 The structure of the CRISPR-associated protein Csa3 provides insight into the regulation of the CRISPR/Cas system. J Mol Biol 2010 1.16
77 Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element. Nat Struct Mol Biol 2012 1.16
78 Molecular mimicry of SUMO promotes DNA repair. Nat Struct Mol Biol 2009 1.14
79 Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV. Proc Natl Acad Sci U S A 2007 1.14
80 ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling. EMBO J 2014 1.14
81 Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2. Nat Struct Mol Biol 2012 1.12
82 ModBase, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 2013 1.12
83 A new structural framework for integrating replication protein A into DNA processing machinery. Nucleic Acids Res 2013 1.12
84 The ARTT motif and a unified structural understanding of substrate recognition in ADP-ribosylating bacterial toxins and eukaryotic ADP-ribosyltransferases. Int J Med Microbiol 2002 1.12
85 Cancer, cadmium and genome integrity. Nat Genet 2003 1.11
86 Substrate recognition and catalysis by flap endonucleases and related enzymes. Biochem Soc Trans 2010 1.10
87 Structure and activity of a thermostable thymine-DNA glycosylase: evidence for base twisting to remove mismatched normal DNA bases. J Mol Biol 2002 1.09
88 XRCC4 and XLF form long helical protein filaments suitable for DNA end protection and alignment to facilitate DNA double strand break repair. Biochem Cell Biol 2013 1.09
89 Insights into FlaI functions in archaeal motor assembly and motility from structures, conformations, and genetics. Mol Cell 2013 1.09
90 Differential arrangements of conserved building blocks among homologs of the Rad50/Mre11 DNA repair protein complex. J Mol Biol 2004 1.09
91 Structural insights into the interaction of IL-33 with its receptors. Proc Natl Acad Sci U S A 2013 1.09
92 Crystallographic structures of Discosoma red fluorescent protein with immature and mature chromophores: linking peptide bond trans-cis isomerization and acylimine formation in chromophore maturation. Biochemistry 2005 1.08
93 Structural chemistry of a green fluorescent protein Zn biosensor. J Am Chem Soc 2002 1.07
94 Flap endonucleases pass 5'-flaps through a flexible arch using a disorder-thread-order mechanism to confer specificity for free 5'-ends. Nucleic Acids Res 2012 1.06
95 Understanding GFP posttranslational chemistry: structures of designed variants that achieve backbone fragmentation, hydrolysis, and decarboxylation. J Am Chem Soc 2006 1.06
96 ATP-stimulated, DNA-mediated redox signaling by XPD, a DNA repair and transcription helicase. J Am Chem Soc 2011 1.05
97 Nse1 RING-like domain supports functions of the Smc5-Smc6 holocomplex in genome stability. Mol Biol Cell 2008 1.05
98 Structural basis of guanine nucleotide exchange mediated by the T-cell essential Vav1. J Mol Biol 2008 1.05
99 Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA. Proc Natl Acad Sci U S A 2011 1.04
100 Structural dynamics and single-stranded DNA binding activity of the three N-terminal domains of the large subunit of replication protein A from small angle X-ray scattering. Biochemistry 2010 1.04
101 Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice/DCS control system. J Synchrotron Radiat 2010 1.03
102 SUMO-targeted ubiquitin ligase, Rad60, and Nse2 SUMO ligase suppress spontaneous Top1-mediated DNA damage and genome instability. PLoS Genet 2011 1.02
103 Unpairing and gating: sequence-independent substrate recognition by FEN superfamily nucleases. Trends Biochem Sci 2011 1.02
104 Understanding GFP chromophore biosynthesis: controlling backbone cyclization and modifying post-translational chemistry. Biochemistry 2005 1.01
105 Ultrahigh resolution and full-length pilin structures with insights for filament assembly, pathogenic functions, and vaccine potential. J Biol Chem 2011 1.01
106 Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair. J Mol Biol 2010 1.01
107 Catalytic and structural effects of amino acid substitution at histidine 30 in human manganese superoxide dismutase: insertion of valine C gamma into the substrate access channel. Biochemistry 2003 1.01
108 p38alpha MAP kinase C-terminal domain binding pocket characterized by crystallographic and computational analyses. J Mol Biol 2009 1.00
109 Retracted The ATPase activity of BfpD is greatly enhanced by zinc and allosteric interactions with other Bfp proteins. J Biol Chem 2005 1.00
110 Defining the role of arginine 96 in green fluorescent protein fluorophore biosynthesis. Biochemistry 2005 0.99
111 Solution structure of RNase P RNA. RNA 2011 0.99
112 The case of the missing ring: radical cleavage of a carbon-carbon bond and implications for GFP chromophore biosynthesis. J Am Chem Soc 2007 0.99
113 DNA repair and global sumoylation are regulated by distinct Ubc9 noncovalent complexes. Mol Cell Biol 2011 0.98
114 Comparison of the catalytic parameters and reaction specificities of a phage and an archaeal flap endonuclease. J Mol Biol 2007 0.97
115 The structure of the MAP2K MEK6 reveals an autoinhibitory dimer. Structure 2009 0.97
116 Structure and function of the double-strand break repair machinery. DNA Repair (Amst) 2004 0.97
117 Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability. Proc Natl Acad Sci U S A 2012 0.96
118 Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes. J Biol Chem 2013 0.96
119 Archaeal flagellar ATPase motor shows ATP-dependent hexameric assembly and activity stimulation by specific lipid binding. Biochem J 2011 0.96
120 Amyotrophic lateral sclerosis. Adv Exp Med Biol 2010 0.96
121 Kinetic mechanism of activation of the Cdk2/cyclin A complex. Key role of the C-lobe of the Cdk. J Biol Chem 2002 0.95
122 DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals. Proc Natl Acad Sci U S A 2013 0.95
123 Characterization of the electrophile binding site and substrate binding mode of the 26-kDa glutathione S-transferase from Schistosoma japonicum. Proteins 2003 0.94
124 Reaction intermediates in the catalytic mechanism of Escherichia coli MutY DNA glycosylase. J Biol Chem 2004 0.93
125 Vibrio cholerae El Tor TcpA crystal structure and mechanism for pilus-mediated microcolony formation. Mol Microbiol 2010 0.93
126 Contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis. Biochemistry 2009 0.93
127 The disordered C-terminal domain of human DNA glycosylase NEIL1 contributes to its stability via intramolecular interactions. J Mol Biol 2013 0.93
128 Structure of an essential type IV pilus biogenesis protein provides insights into pilus and type II secretion systems. J Mol Biol 2012 0.92
129 Alkyltransferase-like proteins: molecular switches between DNA repair pathways. Cell Mol Life Sci 2010 0.92
130 Structural basis of O6-alkylguanine recognition by a bacterial alkyltransferase-like DNA repair protein. J Biol Chem 2010 0.92
131 Identification of a coiled coil in werner syndrome protein that facilitates multimerization and promotes exonuclease processivity. J Biol Chem 2010 0.92
132 Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase. Nucleic Acids Res 2012 0.90
133 Structural evidence for an enolate intermediate in GFP fluorophore biosynthesis. J Am Chem Soc 2006 0.90
134 Repair of O6-G-alkyl-O6-G interstrand cross-links by human O6-alkylguanine-DNA alkyltransferase. Biochemistry 2008 0.90
135 A nanomachine for making ends meet: MRN is a flexing scaffold for the repair of DNA double-strand breaks. Mol Cell 2005 0.90
136 Double strand binding-single strand incision mechanism for human flap endonuclease: implications for the superfamily. Mech Ageing Dev 2012 0.90
137 Atl1 regulates choice between global genome and transcription-coupled repair of O(6)-alkylguanines. Mol Cell 2012 0.90
138 Synthesis and characterization of oligonucleotides containing 2'-fluorinated thymidine glycol as inhibitors of the endonuclease III reaction. Nucleic Acids Res 2006 0.89
139 Neutralizing mutations of carboxylates that bind metal 2 in T5 flap endonuclease result in an enzyme that still requires two metal ions. J Biol Chem 2011 0.89
140 Mechanistic insights into the role of Hop2-Mnd1 in meiotic homologous DNA pairing. Nucleic Acids Res 2013 0.89
141 The BARD1 C-terminal domain structure and interactions with polyadenylation factor CstF-50. Biochemistry 2008 0.89
142 Alkyltransferase-like protein (Atl1) distinguishes alkylated guanines for DNA repair using cation-π interactions. Proc Natl Acad Sci U S A 2012 0.89
143 Metals in biology: defining metalloproteomes. Curr Opin Biotechnol 2011 0.89
144 Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii. J Mol Biol 2003 0.89
145 Crystal and solution structures of a prokaryotic M16B peptidase: an open and shut case. Structure 2009 0.88
146 The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures. FEBS J 2014 0.88
147 Coprinus cinereus rad50 mutants reveal an essential structural role for Rad50 in axial element and synaptonemal complex formation, homolog pairing and meiotic recombination. Genetics 2008 0.88
148 MRE11 facilitates the removal of human topoisomerase II complexes from genomic DNA. Biol Open 2012 0.88
149 Developing advanced X-ray scattering methods combined with crystallography and computation. Methods 2013 0.88
150 RNF4 interacts with both SUMO and nucleosomes to promote the DNA damage response. EMBO Rep 2014 0.87
151 Hydrogen bonding in human manganese superoxide dismutase containing 3-fluorotyrosine. Biophys J 2005 0.87
152 Mapping interactions between the RNA chaperone FinO and its RNA targets. Nucleic Acids Res 2011 0.87
153 All stressed out without ATM kinase. Sci Signal 2011 0.87
154 Repair of O4-alkylthymine by O6-alkylguanine-DNA alkyltransferases. J Biol Chem 2009 0.86
155 Role of hydrogen bonding in the active site of human manganese superoxide dismutase. Biochemistry 2004 0.86
156 Anacardic acid inhibits the catalytic activity of matrix metalloproteinase-2 and matrix metalloproteinase-9. Mol Pharmacol 2012 0.86
157 Interaction interface of human flap endonuclease-1 with its DNA substrates. J Biol Chem 2004 0.85
158 Amino acid substitution at the dimeric interface of human manganese superoxide dismutase. J Biol Chem 2003 0.85
159 The pilus and porin of Neisseria gonorrhoeae cooperatively induce Ca(2+) transients in infected epithelial cells. Cell Microbiol 2005 0.85
160 Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic Thermophile Alvinella pompejana. J Nucleic Acids 2010 0.85
161 Nitric-oxide synthase forms N-NO-pterin and S-NO-cys: implications for activity, allostery, and regulation. J Biol Chem 2010 0.85
162 A computational framework for proteome-wide pursuit and prediction of metalloproteins using ICP-MS and MS/MS data. BMC Bioinformatics 2011 0.84
163 Conformational changes in nitric oxide synthases induced by chlorzoxazone and nitroindazoles: crystallographic and computational analyses of inhibitor potency. Biochemistry 2002 0.84
164 Design of a monomeric human glutathione transferase GSTP1, a structurally stable but catalytically inactive protein. Protein Eng 2002 0.84
165 The Rad50 hook domain regulates DNA damage signaling and tumorigenesis. Genes Dev 2014 0.83
166 Interfacial residues promote an optimal alignment of the catalytic center in human soluble guanylate cyclase: heterodimerization is required but not sufficient for activity. Biochemistry 2014 0.83
167 Mre11 ATLD17/18 mutation retains Tel1/ATM activity but blocks DNA double-strand break repair. Nucleic Acids Res 2012 0.81
168 Eukaryotic class II cyclobutane pyrimidine dimer photolyase structure reveals basis for improved ultraviolet tolerance in plants. J Biol Chem 2011 0.80
169 Sculpting of DNA at abasic sites by DNA glycosylase homolog mag2. Structure 2012 0.80
170 A mutation in the FHA domain of Coprinus cinereus Nbs1 Leads to Spo11-independent meiotic recombination and chromosome segregation. G3 (Bethesda) 2013 0.79
171 Kinetic and stoichiometric characterisation of streptavidin-binding aptamers. Chembiochem 2012 0.78
172 Manganese superoxide dismutase induction during measles virus infection. J Med Virol 2003 0.78
173 Learning our ABCs: Rad50 directs MRN repair functions via adenylate kinase activity from the conserved ATP binding cassette. Mol Cell 2007 0.76
174 P53 conformational switching for selectivity may reveal a general solution for specific DNA binding. EMBO J 2011 0.75
175 Flexibility promotes fidelity. Structure 2009 0.75
176 Achieving fidelity in homologous recombination despite extreme complexity: informed decisions by molecular profiling. Mol Cell 2010 0.75
177 A charged performance by gp17 in viral packaging. Cell 2008 0.75
178 112 Structurally distinct ubiquitin- and SUMO-modified PCNA: implications for their distinct roles in the DNA damage response. J Biomol Struct Dyn 2015 0.75
179 ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling. EMBO J 2016 0.75
180 Synthesis of oligonucleotides containing 2'-fluorinated thymidine glycol as mechanism-based inhibitors of endonuclease III. Nucleic Acids Symp Ser (Oxf) 2005 0.75
181 204 Structural insights into the RAD51 paralog complexes reveal molecular details of disease causing mutations. J Biomol Struct Dyn 2015 0.75