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WEI YANG

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Mikalai Lapkouski; Stuart F J Le Grice; Jennifer T Miller; Lan Tian; WEI YANG
Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation.
Zhiqi Yin; Mikalai Lapkouski; WEI YANG; Robert Craigie
Assembly of prototype foamy virus strand transfer complexes on product DNA bypassing catalysis of integration.
Wojciech Kuban; John P McDonald; Alexandra Vaisman; Myron F Goodman; Kiyonobu Karata; WEI YANG; Roger Woodgate
Escherichia coli UmuC active site mutants: effects on translesion DNA synthesis, mutagenesis and cell survival.

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All Publications

2013: Mikalai Lapkouski; Stuart F J Le Grice; Jennifer T Miller; Lan Tian; WEI YANG
Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation.
Nature structural & molecular biology 2013;20(2):230-6.
2012: Zhiqi Yin; Mikalai Lapkouski; WEI YANG; Robert Craigie
Assembly of prototype foamy virus strand transfer complexes on product DNA bypassing catalysis of integration.
Protein science : a publication of the Protein Society 2012;21(12):1849-57.
2012: Wojciech Kuban; John P McDonald; Alexandra Vaisman; Myron F Goodman; Kiyonobu Karata; WEI YANG; Roger Woodgate
Escherichia coli UmuC active site mutants: effects on translesion DNA synthesis, mutagenesis and cell survival.
DNA repair 2012;11(9):726-32.
2012: Teruya Nakamura; Yuriko Yamagata; Yue-jin Hua; Ye Zhao; WEI YANG
Watching DNA polymerase η make a phosphodiester bond.
Nature 2012;487(7406):196-201.
2012: Alexandra Vaisman; WEI YANG; Myron F Goodman; Kiyonobu Karata; Wojciech Kuban; John P McDonald; Roger Woodgate
Critical amino acids in Escherichia coli UmuC responsible for sugar discrimination and base-substitution fidelity.
Nucleic acids research 2012;40(13):6144-57.
2012: Shikha Gupta; Martin Gellert; WEI YANG
Mechanism of mismatch recognition revealed by human MutSβ bound to unpaired DNA loops.
Nature structural & molecular biology 2012;19(1):72-8.
2011: WEI YANG
Surviving the sun: repair and bypass of DNA UV lesions.
Protein science : a publication of the Protein Society 2011;20(11):1781-9.
2011: Edina Rosta; WEI YANG; Marcin Nowotny; Gerhard Hummer
Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations.
Journal of the American Chemical Society 2011;133(23):8934-41.
2011: WEI YANG
Nucleases: diversity of structure, function and mechanism.
Quarterly reviews of biophysics 2011;44(1):1-93.
2010: Gabrielle J Grundy; WEI YANG; Martin Gellert
Autoinhibition of DNA cleavage mediated by RAG1 and RAG2 is overcome by an epigenetic signal in V(D)J recombination.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(52):22487-92.
2010: WEI YANG
Topoisomerases and site-specific recombinases: similarities in structure and mechanism.
Critical reviews in biochemistry and molecular biology 2010;45(6):520-34.
2010: Christian Biertümpfel; Ye Zhao; Yuji Kondo; Santiago Ramón-Maiques; Mark Gregory; Jae Young Lee; Chikahide Masutani; Alan R Lehmann; Fumio Hanaoka; WEI YANG
Structure and mechanism of human DNA polymerase eta.
Nature 2010;465(7301):1044-8.
2010: Hongzhou Gu; WEI YANG; Nadrian C Seeman
DNA scissors device used to measure MutS binding to DNA mis-pairs.
Journal of the American Chemical Society 2010;132(12):4352-7.
2010: WEI YANG
Lessons learned from UvrD helicase: mechanism for directional movement.
Annual review of biophysics 2010;39():367-85.
2009: Feng Wang; WEI YANG
Structural insight into translesion synthesis by DNA Pol II.
Cell 2009;139(7):1279-89.
2009: Hongmin Zhang; Jin-Huan Liu; WEI YANG; Timothy Springer; Motomu Shimaoka; Jia-huai Wang
Structural basis of activation-dependent binding of ligand-mimetic antibody AL-57 to integrin LFA-1.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(43):18345-50.
2009: Gabrielle J Grundy; Santiago Ramón-Maiques; Emilios K Dimitriadis; Svetlana Kotova; Christian Biertümpfel; J Bernard Heymann; Alasdair C Steven; Martin Gellert; WEI YANG
Initial stages of V(D)J recombination: the organization of RAG1/2 and RSS DNA in the postcleavage complex.
Molecular cell 2009;35(2):217-27.
2009: Marcin Nowotny; WEI YANG
Structural and functional modules in RNA interference.
Current opinion in structural biology 2009;19(3):286-93.
2009: Víctor M Castillo-Acosta; Luis M Ruiz-Pérez; WEI YANG; Dolores González-Pacanowska; Antonio E Vidal
Identification of a residue critical for the excision of 3'-blocking ends in apurinic/apyrimidinic endonucleases of the Xth family.
Nucleic acids research 2009;37(6):1829-42.
2008: Gilbert Chu; WEI YANG
Here comes the sun: recognition of UV-damaged DNA.
Cell 2008;135(7):1172-4.
2008: WEI YANG
An equivalent metal ion in one- and two-metal-ion catalysis.
Nature structural & molecular biology 2008;15(11):1228-31.
2008: Marcin Nowotny; Susana M Cerritelli; Rodolfo Ghirlando; Sergei A Gaidamakov; Robert J Crouch; WEI YANG
Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD.
The EMBO journal 2008;27(7):1172-81.
2008: WEI YANG
Structure and mechanism for DNA lesion recognition.
Cell research 2008;18(1):184-97.
2007: Adam G W Matthews; Alex J Kuo; Santiago Ramón-Maiques; Sunmi Han; Karen S Champagne; Dmitri N. Ivanov; Mercedes Gallardo; Dylan Carney; Peggie Cheung; David N Ciccone; Kay L Walter; Paul J Utz; Yang Shi; Tatiana G Kutateladze; WEI YANG; Or Gozani; Marjorie A Oettinger
RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination.
Nature 2007;450(7172):1106-10.
2007: Santiago Ramón-Maiques; Alex J Kuo; Dylan Carney; Adam G W Matthews; Marjorie A Oettinger; Or Gozani; WEI YANG
The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(48):18993-8.
2007: Marcin Nowotny; Sergei A Gaidamakov; Rodolfo Ghirlando; Susana M Cerritelli; Robert J Crouch; WEI YANG
Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription.
Molecular cell 2007;28(2):264-76.
2007: Christian Biertümpfel; WEI YANG; Dietrich Suck
Crystal structure of T4 endonuclease VII resolving a Holliday junction.
Nature 2007;449(7162):616-20.
2007: WEI YANG; Roger Woodgate
What a difference a decade makes: insights into translesion DNA synthesis.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(40):15591-8.
2007: Kevin A. Fiala; Jessica A Brown; Hong Ling; Ajay K Kshetry; Jun Zhang; John-Stephen Taylor; WEI YANG; Zucai Suo
Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase.
Journal of molecular biology 2007;365(3):590-602.
2007: WEI YANG
Human MutLalpha: the jack of all trades in MMR is also an endonuclease.
DNA repair 2007;6(1):135-9.
2006: Jae Young Lee; WEI YANG
UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke.
Cell 2006;127(7):1349-60.
2006: WEI YANG; Christopher V Carman; Minsoo Kim; Azucena Salas; Motomu Shimaoka; Timothy A Springer
A small molecule agonist of an integrin, alphaLbeta2.
The Journal of biological chemistry 2006;281(49):37904-12.
2006: Motomu Shimaoka; Minsoo Kim; Edward H Cohen; WEI YANG; Nathan S Astrof; Dan Peer; Azucena Salas; Audrey Ferrand; Timothy A Springer
AL-57, a ligand-mimetic antibody to integrin LFA-1, reveals chemokine-induced affinity up-regulation in lymphocytes.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(38):13991-6.
2006: JianFeng Chen; WEI YANG; Minsoo Kim; Christopher V Carman; Timothy A Springer
Regulation of outside-in signaling and affinity by the beta2 I domain of integrin alphaLbeta2.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(35):13062-7.
2006: WEI YANG
Poor base stacking at DNA lesions may initiate recognition by many repair proteins.
DNA repair 2006;5(6):654-66.
2006: Ryan Bitetti-Putzer; Aaron R Dinner; WEI YANG; Martin Karplus
Conformational sampling via a self-regulating effective energy surface.
The Journal of chemical physics 2006;124(17):174901.
2006: Marcin Nowotny; WEI YANG
Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release.
The EMBO journal 2006;25(9):1924-33.
2006: WEI YANG; Jae Young Lee; Marcin Nowotny
Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity.
Molecular cell 2006;22(1):5-13.
2005: Yi Qin Gao; WEI YANG; Martin Karplus
A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase.
Cell 2005;123(2):195-205.
2005: Jae Young Lee; Judy Chang; Nimesh Joseph; Rodolfo Ghirlando; Desirazu N Rao; WEI YANG
MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage.
Molecular cell 2005;20(1):155-66.
2005: Alexandra Vaisman; Hong Ling; Roger Woodgate; WEI YANG
Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis.
The EMBO journal 2005;24(17):2957-67.
2005: Marcin Nowotny; Sergei A Gaidamakov; Robert J Crouch; WEI YANG
Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis.
Cell 2005;121(7):1005-16.
2005: Alba Guarné; Therese Brendler; Qinghai Zhao; Rodolfo Ghirlando; Stuart Austin; WEI YANG
Crystal structure of a SeqA-N filament: implications for DNA replication and chromosome organization.
The EMBO journal 2005;24(8):1502-11.
2005: Anirban Banerjee; WEI YANG; Martin Karplus; Gregory L Verdine
Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA.
Nature 2005;434(7033):612-8.
2005: Martin Karplus; Yi Qin Gao; Jianpeng Ma; Arjan van der Vaart; WEI YANG
Protein structural transitions and their functional role.
Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 2005;363(1827):331-55; discussion 355-6.
2005: WEI YANG
Portraits of a Y-family DNA polymerase.
FEBS letters 2005;579(4):868-72.
2004: Minsoo Kim; Christopher V Carman; WEI YANG; Azucena Salas; Timothy A Springer
The primacy of affinity over clustering in regulation of adhesiveness of the integrin {alpha}L{beta}2.
The Journal of cell biology 2004;167(6):1241-53.
2004: Antonio E Vidal; Patricia Kannouche; Vladimir N Podust; WEI YANG; Alan Lehmann; Roger Woodgate
Proliferating cell nuclear antigen-dependent coordination of the biological functions of human DNA polymerase iota.
The Journal of biological chemistry 2004;279(46):48360-8.
2004: Alba Guarné; Santiago Ramon-Maiques; Erika M Wolff; Rodolfo Ghirlando; Xiaojian Hu; Jeffrey H Miller; WEI YANG
Structure of the MutL C-terminal domain: a model of intact MutL and its roles in mismatch repair.
The EMBO journal 2004;23(21):4134-45.
2004: François Boudsocq; Robert J Kokoska; Brian S Plosky; Alexandra Vaisman; Hong Ling; Thomas A Kunkel; WEI YANG; Roger Woodgate
Investigating the role of the little finger domain of Y-family DNA polymerases in low fidelity synthesis and translesion replication.
The Journal of biological chemistry 2004;279(31):32932-40.
2004: WEI YANG; Ryan Bitetti-Putzer; Martin Karplus
Chaperoned alchemical free energy simulations: a general method for QM, MM, and QM/MM potentials.
The Journal of chemical physics 2004;120(20):9450-3.
2004: Hong Ling; François Boudsocq; Roger Woodgate; WEI YANG
Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts.
Molecular cell 2004;13(5):751-62.
2004: WEI YANG; Motomu Shimaoka; Azucena Salas; Junichi Takagi; Timothy A Springer
Intersubunit signal transmission in integrins by a receptor-like interaction with a pull spring.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(9):2906-11.
2004: WEI YANG; Motomu Shimaoka; JianFeng Chen; Timothy A Springer
Activation of integrin beta-subunit I-like domains by one-turn C-terminal alpha-helix deletions.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(8):2333-8.
2004: Hong Ling; Jane M Sayer; Brian S Plosky; Haruhiko Yagi; François Boudsocq; Roger Woodgate; Donald M Jerina; WEI YANG
Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(8):2265-9.
2004: WEI YANG; Ryan Bitetti-Putzer; Martin Karplus
Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence.
The Journal of chemical physics 2004;120(6):2618-28.
2003: Mauro Modesti; Murray S Junop; Rodolfo Ghirlando; Mandy W M M van de Rakt; Martin Gellert; WEI YANG; Roland Kanaar
Tetramerization and DNA ligase IV interaction of the DNA double-strand break repair protein XRCC4 are mutually exclusive.
Journal of molecular biology 2003;334(2):215-28.
2003: Yi Qin Gao; WEI YANG; Rudolph A Marcus; Martin Karplus
A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F1-ATPase.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(20):11339-44.
2003: Motomu Shimaoka; Azucena Salas; WEI YANG; Gabriele Weitz-Schmidt; Timothy A Springer
Small molecule integrin antagonists that bind to the beta2 subunit I-like domain and activate signals in one direction and block them in the other.
Immunity 2003;19(3):391-402.
2003: Hong Ling; François Boudsocq; Brian S Plosky; Roger Woodgate; WEI YANG
Replication of a cis-syn thymine dimer at atomic resolution.
Nature 2003;424(6952):1083-7.
2003: Xiaojian Hu; Mischa Machius; WEI YANG
Monovalent cation dependence and preference of GHKL ATPases and kinases.
FEBS letters 2003;544(1-3):268-73.
2003: Eric Alani; Jae Young Lee; Mark J Schofield; Amanda Wraith Kijas; Peggy Hsieh; WEI YANG
Crystal structure and biochemical analysis of the MutS.ADP.beryllium fluoride complex suggests a conserved mechanism for ATP interactions in mismatch repair.
The Journal of biological chemistry 2003;278(18):16088-94.
2003: Murray S Junop; WEI YANG; Pauline Funchain; Wendy Clendenin; Jeffrey H Miller
In vitro and in vivo studies of MutS, MutL and MutH mutants: correlation of mismatch repair and DNA recombination.
DNA repair 2003;2(4):387-405.
2003: J Christopher Fromme; Steven D Bruner; WEI YANG; Martin Karplus; Gregory L Verdine
Product-assisted catalysis in base-excision DNA repair.
Nature structural biology 2003;10(3):204-11.
2003: WEI YANG; Yi Qin Gao; Qiang Cui; Jianpeng Ma; Martin Karplus
The missing link between thermodynamics and structure in F1-ATPase.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(3):874-9.
2003: WEI YANG
Damage repair DNA polymerases Y.
Current opinion in structural biology 2003;13(1):23-30.
2002: Alba Guarné; Qinghai Zhao; Rodolfo Ghirlando; WEI YANG
Insights into negative modulation of E. coli replication initiation from the structure of SeqA-hemimethylated DNA complex.
Nature structural biology 2002;9(11):839-43.
2002: Karin Drotschmann; WEI YANG; Thomas A Kunkel
Evidence for sequential action of two ATPase active sites in yeast Msh2-Msh6.
DNA repair 2002;1(9):743-53.
2002: François Boudsocq; Hong Ling; WEI YANG; Roger Woodgate
Structure-based interpretation of missense mutations in Y-family DNA polymerases and their implications for polymerase function and lesion bypass.
DNA repair 2002;1(5):343-58.
2001: J Y Wang; Hong Ling; WEI YANG; Robert Craigie
Structure of a two-domain fragment of HIV-1 integrase: implications for domain organization in the intact protein.
The EMBO journal 2001;20(24):7333-43.
2001: Karin Drotschmann; WEI YANG; Floyd E Brownewell; Eric T Kool; Thomas A Kunkel
Asymmetric recognition of DNA local distortion. Structure-based functional studies of eukaryotic Msh2-Msh6.
The Journal of biological chemistry 2001;276(49):46225-9.
2001: Hong Ling; François Boudsocq; Roger Woodgate; WEI YANG
Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication.
Cell 2001;107(1):91-102.
2001: Jessica M Jones; Martin Gellert; WEI YANG
A Ku bridge over broken DNA.
Structure (London, England : 1993) 2001;9(10):881-4.
2001: Alba Guarné; Murray S Junop; WEI YANG
Structure and function of the N-terminal 40 kDa fragment of human PMS2: a monomeric GHL ATPase.
The EMBO journal 2001;20(19):5521-31.
2001: Indranil Biswas; Galina Obmolova; M Takahashi; A Herr; M A Newman; WEI YANG; Peggy Hsieh
Disruption of the helix-u-turn-helix motif of MutS protein: loss of subunit dimerization, mismatch binding and ATP hydrolysis.
Journal of molecular biology 2001;305(4):805-16.
2001: Murray S Junop; Galina Obmolova; K Rausch; Peggy Hsieh; WEI YANG
Composite active site of an ABC ATPase: MutS uses ATP to verify mismatch recognition and authorize DNA repair.
Molecular cell 2001;7(1):1-12.
2000: Murray S Junop; Mauro Modesti; Alba Guarné; Rodolfo Ghirlando; Martin Gellert; WEI YANG
Crystal structure of the Xrcc4 DNA repair protein and implications for end joining.
The EMBO journal 2000;19(22):5962-70.
2000: Galina Obmolova; C Ban; Peggy Hsieh; WEI YANG
Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA.
Nature 2000;407(6805):703-10.
2000: WEI YANG
Structure and function of mismatch repair proteins.
Mutation research 2000;460(3-4):245-56.
2000: WEI YANG; Murray S Junop; C Ban; Galina Obmolova; Peggy Hsieh
DNA mismatch repair: from structure to mechanism.
Cold Spring Harbor symposia on quantitative biology 2000;65():225-32.
1999: DR Kim; Y Dai; Cynthia L Mundy; WEI YANG; Marjorie A Oettinger
Mutations of acidic residues in RAG1 define the active site of the V(D)J recombinase.
Genes & development 1999;13(23):3070-80.
1999: Indranil Biswas; C Ban; Karen Fleming; J Qin; J W Lary; D A Yphantis; WEI YANG; Peggy Hsieh
Oligomerization of a MutS mismatch repair protein from Thermus aquaticus.
The Journal of biological chemistry 1999;274(33):23673-8.
1999: C Ban; Murray S Junop; WEI YANG
Transformation of MutL by ATP binding and hydrolysis: a switch in DNA mismatch repair.
Cell 1999;97(1):85-97.
1998: C Ban; WEI YANG
Crystal structure and ATPase activity of MutL: implications for DNA repair and mutagenesis.
Cell 1998;95(4):541-52.
1998: C Ban; WEI YANG
Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases.
The EMBO journal 1998;17(5):1526-34.
1997: WEI YANG; Kiyoshi Mizuuchi
Site-specific recombination in plane view.
Structure (London, England : 1993) 1997;5(11):1401-6.
1997: Sergey Leikin; V Adrian Parsegian; WEI YANG; G E Walrafen
Raman spectral evidence for hydration forces between collagen triple helices.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(21):11312-7.
1997: Y Yamaguchi-Iwai; M Serpe; David Haile; WEI YANG; Daniel J Kosman; Richard D Klausner; Andrew Dancis
Homeostatic regulation of copper uptake in yeast via direct binding of MAC1 protein to upstream regulatory sequences of FRE1 and CTR1.
The Journal of biological chemistry 1997;272(28):17711-8.
1996: M E Handlogten; E E Dudenhausen; WEI YANG; Michael S Kilberg
Association of hepatic system A amino acid transporter with the membrane-cytoskeletal proteins ankyrin and fodrin.
Biochimica et biophysica acta 1996;1282(1):107-14.
1995: WEI YANG; Thomas A Steitz
Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site.
Cell 1995;82(2):193-207.
1995: WEI YANG; Thomas A Steitz
Recombining the structures of HIV integrase, RuvC and RNase H.
Structure (London, England : 1993) 1995;3(2):131-4.