M. Todd Washington,1† Irina G. Minko,2 Robert E. Johnson,1 William T. Wolfle,1 Thomas M. Harris,3 R. Stephen Lloyd,2 Satya Prakash,1 and Louise Prakash1 Efficient and Error-Free Replication Past a Minor-Groove DNA Adduct by the Sequential Action of Human DNA Polymerases and * pol13 Mol Cell Biol24,5287 2004
Robert E. Johnson, M. Todd Washington, atya Prakash, and Louise Prakash‡ Fidelity of Human DNA Polymerase h* pol15 JBC,275,7447,2000
Hans E. HuberS, Stanley Tabor, and Charles C. Richardson Escherichia coli Thioredoxin Stabilizes Complexes of Bacteriophage
T7 DNA Polymerase and Primed Templates pol16 JBC 262 16224 1987
Olga Potapova, Nigel D. F. Grindley, and Catherine M. Joyce The Mutational Specificity of the Dbh Lesion Bypass Polymerase
and Its Implications* pol17 JBC 277 28157 2002
Brigette Tippin, Sawami Kobayashi, Jeffrey G. Bertram, and Myron F. Goodman To Slip or Skip, Visualizing Frameshift Mutation Dynamics for Error-prone DNA Polymerases* pol18 JBC 279 45360 2004
Janina Cramer‡ and Tobias Restle Pre-steady-state Kinetic Characterization of the DinB
Homologue DNA Polymerase of Sulfolobus solfataricus pol19 JBC 280 40552 2005
Sylvie Doublie´ , Stanley Tabor, Alexander M. Long, Charles C. Richardson & Tom Ellenberger Crystal structureofabacteriophage
T7 DNA replication complex at 2.2A° resolution pol21 Nature 391 251 1998
Sylvie Doublié1, Michael R Sawaya2 and Tom Ellenberger2 An open and closed case for all polymerases pol22 structure 7 R31 1999 important pol22 structure 7 R31 1999 important
Ying Li, Sergey Korolev and Gabriel Waksman1 Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation pol23 EMBO J 17 7514 1998 impo
Indronil Chaudhuri, Johannes So¨ding, and Andrei N. Lupas* Evolution of the b-propeller fold propeller Proteins 71 795 2007 impo
Jacob Bauer†, Guangxin Xing†, Haruhiko Yagi‡, Jane M. Sayer‡, Donald M. Jerina‡, and Hong Ling†§ A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment pol24 PRONAS 104 14905 2007
Miguel Garcia-Diaz,1,2 Katarzyna Bebenek,1,2 Joseph M. Krahn,1 Lars C. Pedersen,1 and Thomas A. Kunkel1,2,* Structural Analysis of Strand Misalignment during DNA Synthesis by a Human DNA Polymerase pol 25 Cell 124 331 206 impo
Matthew C. Franklin,1 Jimin Wang,1 and Thomas A. Steitz1,2,3,4 Structure of the Replicating Complex of a Pol Family DNA Polymerase pol25 Cell 105 657 2001 impo Human DNA Polymerase k Encircles DNA: Implications for Mismatch Extension and Lesion Bypass pol27 Mol Cell 25 601 2007 impo
Angela M. DeLucia, Nigel D. F. Grindley, and Catherine M. Joyce* Conformational Changes during Normal and Error-Prone Incorporation of Nucleotides by a Y-Family DNA Polymerase Detected by 2-Aminopurine Fluorescence Biochemistry 2007, 46, 10790-10803
Michael R. Sawaya,*,§ Rajendra Prasad,| Samuel H. Wilson,| Joseph Kraut,§ and Huguette Pelletier Crystal Structures of Human DNA Polymerase â Complexed with Gapped and Nicked DNA: Evidence for an Induced Fit Mechanism†, Biochemistry 1997, 36, 11205-11215
Ying Li, Sergey Korolev and Gabriel Waksman1 Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation The EMBO Journal Vol.17 No.24 pp.7514–7525, 1998
Sylvie Doublie´ , Stanley Tabor, Alexander M. Long, Charles C. Richardson & Tom Ellenberger Crystal structureofabacteriophage
T7 DNA replication complex at 2.2A° resolution pol32 Nature 391 251 1998
Svend Kjær and Carlos F. Iba´n˜ ez‡ Identification of a Surface for Binding to the GDNF-GFR1 Complex in the First Cadherin-like Domain of RET* JBC 287 47898 2003
Svend Kjær and Carlos F. Iba´n˜ ez overall disulfide arrangement of GDNF conforms to the
structural cystine knot motif (3). Sequence and structural similarities have indicated that GDNF is a distant member of the
transforming JBC 287 47898 2003
Jonas Anders‡, Svend Kjær§, and Carlos F. Iba´n˜ ez Molecular Modeling of the Extracellular Domain of the RET
Receptor Tyrosine Kinase Reveals Multiple Cadherin-like Domains and a Calcium-binding Site JBC 276 35808 2001
Esther de Graaff, Shankar Srinivas, Carol Kilkenny, et al. Differential activities of the RET tyrosine kinase receptor isoforms during mammalian embryogenesis Genes dev 15 2433 2001
Mounou Hahn* and J. Michael Bishop Expression pattern of Drosophila ret suggests a common ancestral origin between the metamorphosis precursors in insect endoderm and the vertebrate enteric neurons PRONAS 98 1053 2001
Carl S. Kashuk*†, Eric A. Stone†‡§, Elizabeth A. Grice*, Matthew E. Portnoy¶, Eric D. Green¶, Arend Sidow§, Aravinda Chakravarti*,**, and Andrew S. McCallion*,**†† Phenotype–genotype correlation in Hirschsprung disease is illuminated by comparative analysis
of the RET protein sequence PRONAS 102 8949 2005
LAWRENCE SHAPIRO*, PETER D. KWONG*, ALLISON M. FANNONt, DAVID R. COLMANt, Considerations on the folding topology and evolutionary origin of cadherin domains cad6 PRONAS 92 6793 1995 Hum Mol Genet 12 2133 2003
Christian Hirsch1, Robert Gauss1, Sabine C. Horn1, Oliver Neuber1,2 & Thomas Sommer1 The ubiquitylation machinery of the
endoplasmic reticulum Nature 458 453 2009
Deepa Pednekar,1 Abhijit Tendulkar,2 and Susheel Durani2* Electrostatics-defying interaction between arginine termini as a thermodynamic driving force in protein–protein interaction structure1 74 155 2009
Alexander L. Simon*†, Eric A. Stone‡, and Arend Sidow§ Inference of functional regions in proteins by quantification of evolutionary constraints PRONAS 99 2912 2002
Mariann Bienz The PHD finger, a nuclear protein-interaction domain Trends Biochem Sci 31 35 2006
Christophe Dhalluin*, Justin E. Carlson*, Lei Zeng, Cheng He, Aneel K. Aggarwal & Ming-Ming Zhou Structure and ligand of a
histone acetyltransferase bromodomain Nature 399 491 1999
Haitao Li1, Serge Ilin1, Wooikoon Wang1, Elizabeth M. Duncan2, Joanna Wysocka2, C. David Allis2
& Dinshaw J. Patel1 Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF Nature 442 91 2006
Pedro V. Pen˜a1, Foteini Davrazou1, Xiaobing Shi3, Kay L. Walter3, Vladislav V. Verkhusha4, Or Gozani3, Rui Zhao2 & Tatiana G. Kutateladze1 Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2 Nature 442 100 2006
Adam G. W. Matthews1*, Alex J. Kuo2*, Santiago Ramo´n-Maiques3, Sunmi Han1, Karen S. Champagne4,
Dmitri Ivanov5, Mercedes Gallardo1, Dylan Carney2, Peggie Cheung2, David N. Ciccone1, Kay L. Walter2, Paul J. Utz6,
Yang Shi7, Tatiana G. Kutateladze4, Wei Yang3, Or Gozani2* & Marjorie A. Oettinger1* Paul J. Utz6, RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination Nature 450 1106 2007
Steen K. T. Ooi1*, Chen Qiu2*, Emily Bernstein3*, Keqin Li2*, Da Jia2, Zhe Yang2, Hediye Erdjument-Bromage4,
Paul Tempst4, Shau-Ping Lin5, C. David Allis3, Xiaodong Cheng2 & Timothy H. Bestor1 DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA Nature 448 714 2007
Wolfgang Fischle1, Boo Shan Tseng2, Holger L. Dormann1, Beatrix M. Ueberheide3, Benjamin A. Garcia3,
Jeffrey Shabanowitz3, Donald F. Hunt3,4, Hironori Funabiki2 & C. David Allis1 Regulation of HP1–chromatin binding
by histone H3 methylation and phosphorylation Nature 438 1116 2005
Wolfgang Fischle1, Boo Shan Tseng2, Holger L. Dormann1, Beatrix M. Ueberheide3, Benjamin A. Garcia3, Jeffrey Shabanowitz3, Donald F. Hunt3,4, Hironori Funabiki2 & C. David Allis1 Regulation of HP1–chromatin binding by histone H3 methylation and
phosphorylation Nature 442 86 2006 Nature 438 1181 2005
Pedro V. Pen˜a1, Foteini Davrazou1, Xiaobing Shi3, Kay L. Walter3, Vladislav V. Verkhusha4, Or Gozani3, Rui Zhao2 & Tatiana G. Kutateladze1 Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2 Nature 442 100 2006
Adam G. W. Matthews1*, Alex J. Kuo2*, Santiago Ramo´n-Maiques3, Sunmi Han1, Karen S. Champagne4,
Dmitri Ivanov5, Mercedes Gallardo1, Dylan Carney2, Peggie Cheung2, David N. Ciccone1, Kay L. Walter2, Paul J. Utz6,
Yang Shi7, Tatiana G. Kutateladze4, Wei Yang3, Or Gozani2* & Marjorie A. Oettinger1* RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination Nature 450 1106 2007
Steen K. T. Ooi1*, Chen Qiu2*, Emily Bernstein3*, Keqin Li2*, Da Jia2, Zhe Yang2, Hediye Erdjument-Bromage4,
Paul Tempst4, Shau-Ping Lin5, C. David Allis3, Xiaodong Cheng2 & Timothy H. Bestor1 DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA Nature 448 714 2007
Wolfgang Fischle1, Boo Shan Tseng2, Holger L. Dormann1, Beatrix M. Ueberheide3, Benjamin A. Garcia3,
Jeffrey Shabanowitz3, Donald F. Hunt3,4, Hironori Funabiki2 & C. David Allis1 Regulation of HP1–chromatin binding
by histone H3 methylation and phosphorylation DPF9 Nature 438 1116 2005
Wolfgang Fischle1, Boo Shan Tseng2, Holger L. Dormann1, Beatrix M. Ueberheide3, Benjamin A. Garcia3, Jeffrey Shabanowitz3, Donald F. Hunt3,4, Hironori Funabiki2 & C. David Allis1 Regulation of HP1–chromatin binding by histone H3 methylation and phosphorylation Nature 442 86 2006
John F. Flanagan1, Li-Zhi Mi2†, Maksymilian Chruszcz3, Marcin Cymborowski3, Katrina L. Clines1, Youngchang Kim4, Wladek Minor3, Fraydoon Rastinejad1,2 & Sepideh Khorasanizadeh1 Double chromodomains cooperate to recognize the methylated histone H3 tail Nature 438 1181 2005
Santiago Ramo´ n-Maiques*, Alex J. Kuo†, Dylan Carney†, Adam G. W. Matthews‡, Marjorie A. Oettinger‡, Or Gozani†, and Wei Yang*§ The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2 PRONAS 104 18993 2007
To˜nis Org1, Francesca Chignola2, Csaba Hete´nyi 3, Massimiliano Gaetani 2, Ana Rebane1, Ingrid Liiv1,
Uko Maran3, LucaMollica2, MatthewJ. Bottomley4, Giovanna Musco 2+& Pa¨rt Peterson1++ The autoimmune regulator PHD finger binds
to non-methylated histone H3K4 to activate gene expression EMBO rep 9 370 2008
Lei Zeng,1 Qiang Zhang,1 Guillermo Gerona-Navarro,1 Natalia Moshkina,1 and Ming-Ming Zhou1,* Structural Basis of Site-Specific Histone
Recognition by the Bromodomains of Human Coactivators PCAF and CBP/p300 Structure 16 643 2008
Suvobrata Chakravarty,1 Lei Zeng,1 and Ming-Ming Zhou1,* Structure and Site-Specific Recognition of Histone H3 by the PHD Finger of Human Autoimmune Regulator Structure 17 670 2009
Doug Phanstiel*, Justin Brumbaugh†, W. Travis Berggren‡§, Kevin Conard‡, Xuezhu Feng¶, Mark E. Levenstein‡, Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells PRONAS 105 4093 2008
Shiraz Mujtaba,1,4 Yan He,1,4 Lei Zeng,1 Sherry Yan,1 Olga Plotnikova,1 Sachchidanand,1 Roberto Sanchez,1 Nancy J. Zeleznik-Le,3
Ze’ev Ronai,2 and Ming-Ming Zhou1,* Structural Mechanism of the Bromodomain of the Coactivator CBP in p53 Transcriptional Activation Mol Cell 13 251 2004
Jacek Majewski*, Jurg Ott Jacek Majewski*, Jurg Ott Amino acid substitutions in the human genome: evolutionary implications
of single nucleotide polymorphisms Gene 305 167 2003
Pauline C. Ng and Steven Henikoff* SIFT: predicting amino acid changes that affect protein function Nucleic Acid Res 31 3812 2003
Saurabh D. Patel,1,5 Carlo Ciatto,1,5 Chien Peter Chen,1,5 Fabiana Bahna,1,5 Manisha Rajebhosale,3,5
Natalie Arkus,1 Ira Schieren,2 Thomas M. Jessell,1,2 Barry Honig,1,2 Stephen R. Price,3,* and Lawrence Shapiro1,4,* Type II Cadherin Ectodomain
Structures: Implications for Classical Cadherin Specificity Cell 124 1255 2006
Xiaodong Wang,1,6,7 John Venable,1,6 Paul LaPointe,1,6 Darren M. Hutt,1,6 Atanas V. Koulov,1 Judith Coppinger,1 Cemal Gurkan,1 Wendy Kellner,1 Jeanne Matteson,1 Helen Plutner, Hsp90 Cochaperone Aha1 Downregulation Rescues Misfolding of CFTR in Cystic Fibrosis Cell 127 803 2006
Friedel Nollet, Patrick Kools and Frans van Roy* Phylogenetic Analysis of the Cadherin Superfamily allows Identification of Six Major Subfamilies Besides
Several Solitary Members Mol Biol 299 551 2000
Arnold J. Levine p53, the Cellular Gatekeeper Review for Growth and Division Cell 88 323 1997
Andrew H. Huber and William I. Weis1 The Structure of the b-Catenin/E-Cadherin Complex and the Molecular Basis of Diverse Ligand Recognition by b-Catenin Cell 105 391 2001
Thomas A. Graham,*† Carole Weaver,‡§ Tcf is the critical step in the activation of Wnt target Cell 105 391 2001
Feng Mao,* David Kimelman and Wenqing Xu*k Crystal Structure of a b-Catenin/Tcf Complex Cell 103 885 2000
Traci M. Tanaka Hall,* Jeffery A. Porter, Keith E. Young,†‡ Eugene V. Koonin Philip A. Beachy,†‡ and Daniel J. Leahy*‡# Crystal Structure of a Hedgehog
Autoprocessing Domain: Homology between Hedgehog and Self-Splicing Proteins Cell 91 85 1997 impo
Daniel J. Moloney*†, Vladislav M. Panin†‡, Stuart H. Johnston†§k, Jihua Chen¶, Li Shao*, Richa Wilson‡, Yang Wang#, Pamela Stanley¶,
Kenneth D. Irvine‡, Robert S. Haltiwanger* & Thomas F. Vogt§k Fringe is a glycosyltransferase that modifies Notch Nature 406 369 2000
AREND SIDOW Diversification of the Wnt gene family on the ancestral lineage of vertebrates PRONAS 89 5098 1992
HIROSHI SAKURA*t, CHIE KANEI-ISHII*, TAKAHIRO NAGASE*t, HIDEKI NAKAGOSHI*§, THOMAS J. GONDA¶, AND SHUNSUKE ISHII*II Delineation of three functional domains of the transcriptional activator encoded by the c-myb protooncogene PRONAS 86 5758 1989
Carl S. Kashuk*†, Eric A. Stone†‡§, Elizabeth A. Grice*, Matthew E. Portnoy¶, Eric D. Green¶, Arend Sidow§, Aravinda Chakravarti*,**, and Andrew S. McCallion*,**†† Phenotype–genotype correlation in Hirschsprung disease is illuminated by comparative analysis of the RET protein sequence PRONAS 102 8949 2005
Kerrin S. Small*, Michael Brudno†, Matthew M. Hill*, and Arend Sidow*‡ Extreme genomic variation in a natural population PRONAS 104 5698 2007
The ENCODE Project Consortium* Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 447 799 2007
Rat Genome Sequencing Project Consortium* Genome sequence of the Brown Norway rat yields insights into mammalian evolution Nature 428 493 2004
Xiaoqun Duan,* Frederick S. Gimble and Florante A. Quiocho*† Crystal Structure of PI-SceI, a Homing Endonuclease with Protein Splicing Activity cell 89 555 1997
MICHAEL HAHN*, KIRILL PIOTUKHt, RAINER BORRiSSt, AND UDO HEINEMANN** rearranged to place residues 1-58 of the protein
behind a signal PRONAS 91 10417 1994
Richard L. Stevens,* Kym F. Faul1,S Kenneth A. Conklin,§ Brian N. Green,ll and Arvan L. Fluharty’JJ Porcine Cerebroside Sulfate Activator: Further Structural Characterization and Disulfide Identification Biochemistry 1993, 32, 405 1-4059
THOMAS KEITEL*, ORTWIN SIMONtt, RAINER BORRIsstl, AND UDO HEINEMANN*§ Molecular and active-site structure of a Bacillus 1,3-1,4-f8-glucanase Proc. Natl. Acad. Sci. USA Vol. 90, pp. 5287-5291, June 1993 Biochemistry
BRUCE A. CUNNINGHAM, JOHN J. HEMPERLY, THOMAS P. Hopp, AND GERALD M. EDELMAN Favin versus concanavalin A: Circularly permuted
amino acid sequences PRONAS 76 3218 1979