W Yang

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis
    Marcin Nowotny
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Cell 121:1005-16. 2005
  2. doi request reprint Protein-nucleic acid complexes: large, small, old, and new
    Gregory D Van Duyne
    Curr Opin Struct Biol 18:67-9. 2008
  3. doi request reprint Nucleases: diversity of structure, function and mechanism
    Wei Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bldg 5, Rm B1 03, Bethesda, MD 20892, USA
    Q Rev Biophys 44:1-93. 2011
  4. pmc Structure and mechanism of human DNA polymerase eta
    Christian Biertümpfel
    Laboratory of Molecular Biology, NIDDK, NIH, 9000 Rockville Pike, Building 5, Room B103, Bethesda, Maryland 20892, USA
    Nature 465:1044-8. 2010
  5. pmc Watching DNA polymerase η make a phosphodiester bond
    Teruya Nakamura
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Nature 487:196-201. 2012
  6. pmc Mechanism of mismatch recognition revealed by human MutSβ bound to unpaired DNA loops
    Shikha Gupta
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, USA
    Nat Struct Mol Biol 19:72-8. 2012
  7. ncbi request reprint Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation
    Mikalai Lapkouski
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
    Nat Struct Mol Biol 20:230-6. 2013
  8. doi request reprint Topoisomerases and site-specific recombinases: similarities in structure and mechanism
    Wei Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Crit Rev Biochem Mol Biol 45:520-34. 2010
  9. pmc Surviving the sun: repair and bypass of DNA UV lesions
    Wei Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Rm B1 03, Bethesda, Maryland 20892, USA
    Protein Sci 20:1781-9. 2011
  10. ncbi request reprint Damage repair DNA polymerases Y
    Wei Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Curr Opin Struct Biol 13:23-30. 2003

Detail Information

Publications92

  1. ncbi request reprint Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis
    Marcin Nowotny
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Cell 121:1005-16. 2005
    ..In transposases, they are symmetrically coordinated and exchange roles to alternately activate a water and a 3'-OH for successive strand cleavage and transfer by a ping-pong mechanism...
  2. doi request reprint Protein-nucleic acid complexes: large, small, old, and new
    Gregory D Van Duyne
    Curr Opin Struct Biol 18:67-9. 2008
  3. doi request reprint Nucleases: diversity of structure, function and mechanism
    Wei Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bldg 5, Rm B1 03, Bethesda, MD 20892, USA
    Q Rev Biophys 44:1-93. 2011
    ..I also find several previously unnoted relationships between different nucleases and shared catalytic configurations...
  4. pmc Structure and mechanism of human DNA polymerase eta
    Christian Biertümpfel
    Laboratory of Molecular Biology, NIDDK, NIH, 9000 Rockville Pike, Building 5, Room B103, Bethesda, Maryland 20892, USA
    Nature 465:1044-8. 2010
    ..The structures also provide an insight into the role of Poleta in replicating through D loop and DNA fragile sites...
  5. pmc Watching DNA polymerase η make a phosphodiester bond
    Teruya Nakamura
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Nature 487:196-201. 2012
    ..A third Mg(2+) ion, which arrives with the new bond and stabilizes the intermediate state, may be an unappreciated feature of the two-metal-ion mechanism...
  6. pmc Mechanism of mismatch recognition revealed by human MutSβ bound to unpaired DNA loops
    Shikha Gupta
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, USA
    Nat Struct Mol Biol 19:72-8. 2012
    ..The C-terminal dimerization domains form an integral part of the MutS structure and coordinate asymmetrical ATP hydrolysis by Msh2 and Msh3 with mismatch binding to signal for repair...
  7. ncbi request reprint Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation
    Mikalai Lapkouski
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
    Nat Struct Mol Biol 20:230-6. 2013
    ..RT mutations that confer drug resistance but are distant from the inhibitor-binding sites often map to the unique RT-hybrid interface that undergoes conformational changes between two catalytic states...
  8. doi request reprint Topoisomerases and site-specific recombinases: similarities in structure and mechanism
    Wei Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Crit Rev Biochem Mol Biol 45:520-34. 2010
    ..This mechanism is reminiscent of DNA topoisomerization and does not require subunit rotation...
  9. pmc Surviving the sun: repair and bypass of DNA UV lesions
    Wei Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Rm B1 03, Bethesda, Maryland 20892, USA
    Protein Sci 20:1781-9. 2011
    ..Similar stress tests are likely conducted in eukaryotic nucleotide excision repair...
  10. ncbi request reprint Damage repair DNA polymerases Y
    Wei Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Curr Opin Struct Biol 13:23-30. 2003
    ....
  11. pmc What a difference a decade makes: insights into translesion DNA synthesis
    Wei Yang
    National Institute of Diabetes and Digestive and Kidney Diseases and Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 104:15591-8. 2007
    ..Our perspective focuses on the mechanistic insights into TLS by the Y-family polymerases, how they are regulated, and their effects on genomic (in)stability that have been described in the past decade...
  12. pmc An equivalent metal ion in one- and two-metal-ion catalysis
    Wei Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Building 5, Room B1 03 Bethesda, Maryland 20892, USA
    Nat Struct Mol Biol 15:1228-31. 2008
    ..Structural and mechanistic comparisons show that these seemingly unrelated nucleotidyl-transferases share a functionally equivalent metal ion...
  13. pmc Lessons learned from UvrD helicase: mechanism for directional movement
    Wei Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Annu Rev Biophys 39:367-85. 2010
    ..Motors powered by ATPases likely deliver each power stroke in two parts, before and after ATP hydrolysis. Implications of these findings for analyzing hexameric helicase, F(1)F(0) ATPase, and kinesin are discussed...
  14. ncbi request reprint Structure and function of mismatch repair proteins
    W Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Mutat Res 460:245-56. 2000
    ..These crystal structures also shed light on the general mechanism of mismatch repair and the roles of Mut proteins in preventing mutagenesis...
  15. ncbi request reprint Poor base stacking at DNA lesions may initiate recognition by many repair proteins
    Wei Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    DNA Repair (Amst) 5:654-66. 2006
    ..It also raises the possibility that sampling of a lesion by one protein could facilitate loading of another by direct protein-protein or DNA mediated interactions...
  16. pmc Human MutLalpha: the jack of all trades in MMR is also an endonuclease
    Wei Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    DNA Repair (Amst) 6:135-9. 2007
    ..Here, the implications of this exciting new finding are discussed in the context of mismatch repair in Escherichia coli and humans...
  17. ncbi request reprint Site-specific recombination in plane view
    W Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, 9000 Rockville Pike, Building 5, Rm B1 03, Bethesda, MD 20892, USA
    Structure 5:1401-6. 1997
    ..The structures of several lambda integrase family members published recently have answered many of the questions about this process...
  18. ncbi request reprint Portraits of a Y-family DNA polymerase
    Wei Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    FEBS Lett 579:868-72. 2005
    ..In this short review, I will summarize the biochemical properties and structural features of Y-family DNA polymerases...
  19. ncbi request reprint Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity
    Wei Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Mol Cell 22:5-13. 2006
    ..Based on the exquisite sensitivity of Mg2+ ions to the ligand geometry and electrostatic environment, we propose that two-metal-ion catalysis greatly enhances substrate recognition and catalytic specificity...
  20. ncbi request reprint Structure and mechanism for DNA lesion recognition
    Wei Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Cell Res 18:184-97. 2008
    ..After initial recognition of this shared structural feature of lesions, different DNA repair pathways use unique verification mechanisms to ensure correct lesion identification and removal...
  21. ncbi request reprint Composite active site of an ABC ATPase: MutS uses ATP to verify mismatch recognition and authorize DNA repair
    M S Junop
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Cell 7:1-12. 2001
    ..We propose that the MutS ATPase activity plays a proofreading role in DNA mismatch repair, verification of mismatch recognition, and authorization of repair...
  22. pmc Homologous segments in three subunits of the guanine nucleotide exchange factor eIF2B mediate translational regulation by phosphorylation of eIF2
    G D Pavitt
    Laboratory of Eukaryotic Gene Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
    Mol Cell Biol 17:1298-313. 1997
    ..Most of the eIF2 is phosphorylated in certain mutants, suggesting that these substitutions allow eIF2B to accept phosphorylated eIF2 as a substrate for nucleotide exchange...
  23. ncbi request reprint Crystal structure and ATPase activity of MutL: implications for DNA repair and mutagenesis
    C Ban
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Cell 95:541-52. 1998
    ..We provide evidence that the flexible, yet conserved, loops surrounding this ATP-binding site undergo conformational changes upon ATP hydrolysis thereby modulating interactions between MutL and other components of the repair machinery...
  24. ncbi request reprint Transformation of MutL by ATP binding and hydrolysis: a switch in DNA mismatch repair
    C Ban
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Cell 97:85-97. 1999
    ..Dimerization of the LN40 region is required for and is the rate-limiting step in ATP hydrolysis by MutL. The ATPase activity of MutL is stimulated by DNA and likely acts as a switch to coordinate DNA mismatch repair...
  25. pmc Structure and function of the N-terminal 40 kDa fragment of human PMS2: a monomeric GHL ATPase
    A Guarné
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    EMBO J 20:5521-31. 2001
    ..The potential heterodimer interface revealed by crystallography provides a mutagenesis target for functional studies of MutLalpha...
  26. pmc Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases
    C Ban
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    EMBO J 17:1526-34. 1998
    ..With sequence homology to Sau3AI and structural similarity to PvuII endonuclease, MutH is clearly related to these enzymes by divergent evolution, and this suggests that type II restriction endonucleases evolved from a common ancestor...
  27. ncbi request reprint Disruption of the helix-u-turn-helix motif of MutS protein: loss of subunit dimerization, mismatch binding and ATP hydrolysis
    I Biswas
    Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    J Mol Biol 305:805-16. 2001
    ..These findings indicate that dimerization is critical for both the ATPase and DNA mismatch binding activities of MutS, and corroborate several key features of the MutS structure recently deduced from X-ray crystallographic studies...
  28. ncbi request reprint Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication
    H Ling
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Cell 107:91-102. 2001
    ..Dpo4 is also captured in the crystal translocating two template bases to the active site at once, suggesting a possible mechanism for bypassing thymine dimers...
  29. ncbi request reprint Asymmetric recognition of DNA local distortion. Structure-based functional studies of eukaryotic Msh2-Msh6
    K Drotschmann
    Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    J Biol Chem 276:46225-9. 2001
    ..The importance of these contacts decreases with increasing distance from the mismatch, implying that interactions at and near the mismatch are important for binding in a kinked DNA conformation...
  30. pmc Structure of the MutL C-terminal domain: a model of intact MutL and its roles in mismatch repair
    Alba Guarné
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
    EMBO J 23:4134-45. 2004
    ..A model of how MutL utilizes its ATPase and DNA-binding activities to mediate mismatch-dependent activation of MutH endonuclease and UvrD helicase is proposed...
  31. ncbi request reprint Investigating the role of the little finger domain of Y-family DNA polymerases in low fidelity synthesis and translesion replication
    Francois Boudsocq
    Section on DNA Replication, Repair, and Mutagenesis, Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 2725, USA
    J Biol Chem 279:32932-40. 2004
    ..Our studies indicate that the unique but variable LF domain of Y-family polymerases plays a major role in determining the enzymatic and biological properties of each individual Y-family member...
  32. pmc UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke
    Jae Young Lee
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Cell 127:1349-60. 2006
    ..Finally, a gateway for ssDNA translocation and an alternative strand-displacement mode may explain the varying step sizes reported previously...
  33. ncbi request reprint Insights into negative modulation of E. coli replication initiation from the structure of SeqA-hemimethylated DNA complex
    Alba Guarné
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Nat Struct Biol 9:839-43. 2002
    ..The tetrameric protein-DNA complex found in the crystal suggests that SeqA binds multiple GATC sites on separate DNA duplexes, altering the overall DNA topology and sequestering oriC from replication initiation...
  34. ncbi request reprint Replication of a cis-syn thymine dimer at atomic resolution
    Hong Ling
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Nature 424:1083-7. 2003
    ..A model of the pol eta-CPD complex built from the crystal structures of Saccharomyces cerevisiae apo-pol eta and the Dpo4-CPD complex suggests unique features that allow pol eta to efficiently bypass CPDs...
  35. ncbi request reprint MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage
    Jae Young Lee
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Cell 20:155-66. 2005
    ..We propose that this Lys, which is conserved in many restriction endonucleases and is replaced by Glu or Gln in BamHI and BglII, is a sensor for DNA binding and the linchpin that couples base recognition and DNA cleavage...
  36. ncbi request reprint Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription
    Marcin Nowotny
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Cell 28:264-76. 2007
    ..The region that accommodates this conformational change offers a target to develop HIV-specific inhibitors...
  37. ncbi request reprint In vitro and in vivo studies of MutS, MutL and MutH mutants: correlation of mismatch repair and DNA recombination
    Murray S Junop
    Laboratory of Molecular Biology, NIDDK, National Institutes of Health, 9000 Rockville Pike, Bldg 5, Room B1 03, Bethesda, MD 20892, USA
    DNA Repair (Amst) 2:387-405. 2003
    ..coli...
  38. ncbi request reprint Structure-based interpretation of missense mutations in Y-family DNA polymerases and their implications for polymerase function and lesion bypass
    Francois Boudsocq
    Section on DNA Replication, Repair and Mutagenesis, Building 6, Room 1A13, National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bethesda MD 20892 2725, USA
    DNA Repair (Amst) 1:343-58. 2002
    ....
  39. ncbi request reprint Proliferating cell nuclear antigen-dependent coordination of the biological functions of human DNA polymerase iota
    Antonio E Vidal
    Laboratory of Genomic Integrity, NICHD, National Institutes of Health, Bethesda, Maryland 20892 2725, USA
    J Biol Chem 279:48360-8. 2004
    ..Thus, PCNA, acting as both a scaffold and a modulator of the different activities involved in replication, appears to recruit and coordinate replicative and translesion DNA synthesis polymerases to ensure genome integrity...
  40. ncbi request reprint Monovalent cation dependence and preference of GHKL ATPases and kinases
    Xiaojian Hu
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    FEBS Lett 544:268-73. 2003
    ..Dependence on different monovalent cations for catalysis may be exploited for future drug design specifically targeting each individual member of the GHKL superfamily...
  41. pmc Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis
    Alexandra Vaisman
    Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    EMBO J 24:2957-67. 2005
    ..The correct incoming nucleotide allows DNA synthesis to overcome pyrophosphorolysis, but an incorrect incoming nucleotide does not...
  42. ncbi request reprint Homeostatic regulation of copper uptake in yeast via direct binding of MAC1 protein to upstream regulatory sequences of FRE1 and CTR1
    Y Yamaguchi-Iwai
    Cell Biology and Metabolism Branch, NICHHD, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 272:17711-8. 1997
    ..This model defines the homeostatic mechanism by which yeast regulates the cell acquisition of copper in response to copper scarcity or excess...
  43. pmc Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD
    Marcin Nowotny
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    EMBO J 27:1172-81. 2008
    ..Similar activity enhancement by small substrate-binding domains linked to the catalytic domain likely occurs in other nucleic acid enzymes...
  44. pmc Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase
    Hong Ling
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 101:2265-9. 2004
    ..These structures also suggest a mechanism by which mutations are generated during replication of DNA containing BPDE adducts...
  45. pmc The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2
    Santiago Ramon-Maiques
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 104:18993-8. 2007
    ....
  46. pmc Crystal structure of a SeqA-N filament: implications for DNA replication and chromosome organization
    Alba Guarné
    Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
    EMBO J 24:1502-11. 2005
    ..We propose a model of a SeqA filament interacting with multiple GATC sites that accounts for both origin sequestration and chromosome organization...
  47. pmc Structure of a two-domain fragment of HIV-1 integrase: implications for domain organization in the intact protein
    J Y Wang
    Laboratory of Molecular Biology, NIDDK, National Institutes of Health, 5 Center Drive MSC 0560, Bethesda, MD 20892, USA
    EMBO J 20:7333-43. 2001
    ..Furthermore, an integrase tetramer formed by crystal lattice contacts bears structural resemblance to a related bacterial transposase, Tn5, and exhibits positively charged channels suitable for DNA binding...
  48. ncbi request reprint A Ku bridge over broken DNA
    J M Jones
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Building 5, Room B1-03, Bethesda, MD 20892, USA
    Structure 9:881-4. 2001
    ..The recently determined structure of Ku provides insights into how it can both bind to the DNA ends and allow access by the other proteins required to rejoin them...
  49. ncbi request reprint Crystal structure of T4 endonuclease VII resolving a Holliday junction
    Christian Biertümpfel
    National Institute of Diabetes and Digestive and Kidney Diseases, Laboratory of Molecular Biology, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
    Nature 449:616-20. 2007
    ....
  50. ncbi request reprint Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts
    Hong Ling
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Cell 13:751-62. 2004
    ..In addition, the structure of an unproductive Dpo4 ternary complex suggests that the flexible little finger domain facilitates DNA orientation and translocation during translesion synthesis...
  51. pmc Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release
    Marcin Nowotny
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    EMBO J 25:1924-33. 2006
    ..Lastly, product release probably requires dissociation of metal ion A, which is inhibited by either high concentrations of divalent cations or mutation of an assisting protein residue...
  52. ncbi request reprint Repression of transcription of the p27(Kip1) cyclin-dependent kinase inhibitor gene by c-Myc
    W Yang
    Department of Biochemistry, Boston University Medical School, Boston, Maryland, MA 02118, USA
    Oncogene 20:1688-702. 2001
    ..Overall, these studies identify the p27 CKI gene as a new target whereby c-Myc can control cell proliferation, survival and neoplastic transformation...
  53. pmc Structural insight into translesion synthesis by DNA Pol II
    Feng Wang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Building 5, Room B1 03, Bethesda, MD 20892, USA
    Cell 139:1279-89. 2009
    ..Compared to the replicative B family polymerases, DNA Pol II has subtle amino acid changes remote from the active site that allow it to replicate normal DNA with high efficiency yet conduct translesion synthesis when needed...
  54. pmc CHARMM: the biomolecular simulation program
    B R Brooks
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Comput Chem 30:1545-614. 2009
    ..This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983...
  55. pmc Initial stages of V(D)J recombination: the organization of RAG1/2 and RSS DNA in the postcleavage complex
    Gabrielle J Grundy
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Cell 35:217-27. 2009
    ..These first images of the V(D)J recombinase in its postcleavage state provide a framework for modeling RAG domains and their interactions with DNA...
  56. ncbi request reprint A novel phosphotyrosine motif with a critical amino acid at position -2 for the SH2 domain-mediated activation of the tyrosine phosphatase SHP-1
    D N Burshtyn
    Laboratory of Immunogenetics, NIAID, National Institutes of Health, Rockville, Maryland 20852, USA
    J Biol Chem 272:13066-72. 1997
    ..The contribution of a hydrophobic amino acid two residues upstream of the tyrosine in the SHP-1-binding motif may be an important feature that distinguishes inhibitory receptors from those that provide activation signals...
  57. pmc Identification of a regulatory subcomplex in the guanine nucleotide exchange factor eIF2B that mediates inhibition by phosphorylated eIF2
    W Yang
    Laboratory of Eukaryotic Gene Regulation, National Institute of Child Health and Human Development, Bethesda, Maryland 20892 2785, USA
    Mol Cell Biol 16:6603-16. 1996
    ..Together, our results provide strong evidence that GCN3, GCD7, and the C-terminal half of GCD2 comprise the regulatory domain in eIF2B...
  58. pmc Modulation of tRNA(iMet), eIF-2, and eIF-2B expression shows that GCN4 translation is inversely coupled to the level of eIF-2.GTP.Met-tRNA(iMet) ternary complexes
    T E Dever
    Section on Molecular Genetics of Lower Eukaryotes, National Institute of Child Health and Human Development, Bethesda, Maryland 20892 2785, USA
    Mol Cell Biol 15:6351-63. 1995
    ..Met-tRNA(iMet) ternary complexes is the cardinal parameter determining the site of reinitiation on GCN4 mRNA and support the idea that reinitiation at GCN4 is inversely related to the concentration of ternary complexes in the cell...
  59. ncbi request reprint Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA
    Anirban Banerjee
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    Nature 434:612-8. 2005
    ..The structure reveals a remarkably effective gate-keeping strategy for lesion discrimination and suggests a mechanism for oxoG insertion into the hOGG1 active site...
  60. ncbi request reprint Probing site-specific calmodulin calcium and lanthanide affinity by grafting
    Yiming Ye
    Department of Chemistry, Center for Drug Design and Advanced Biotechnology, Georgia State University, Atlanta, Georgia 30303, USA
    J Am Chem Soc 127:3743-50. 2005
    ..Our grafting method provides a new strategy to obtain site-specific Ca2+ binding properties and a better estimation of the cooperativity and conformational change contributions of coupled EF-hand proteins...
  61. pmc RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination
    Adam G W Matthews
    Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
    Nature 450:1106-10. 2007
    ..Furthermore, our results provide the first evidence indicating that disrupting the read-out of histone modifications can cause an inherited human disease...
  62. pmc Activation of integrin beta-subunit I-like domains by one-turn C-terminal alpha-helix deletions
    Wei Yang
    CBR Institute for Biomedical Research and Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 101:2333-8. 2004
    ....
  63. ncbi request reprint Tetramerization and DNA ligase IV interaction of the DNA double-strand break repair protein XRCC4 are mutually exclusive
    Mauro Modesti
    Department of Cell Biology and Genetics, Erasmus Medical Center, P O Box 1738, 3000 DR, Rotterdam, The Netherlands
    J Mol Biol 334:215-28. 2003
    ..We propose that the putative function of the XRCC4 tetramer is distinct from its DNA ligase IV-associated function...
  64. ncbi request reprint Yeast POL5 is an evolutionarily conserved regulator of rDNA transcription unrelated to any known DNA polymerases
    Wei Yang
    National Center for Biotechnology Inforamtion, National Library of Medicine, National Institutes of Health Bethesda, Maryland 20894, USA
    Cell Cycle 2:120-2. 2003
    ..These proteins are confidently predicted to have an entirely a-helical structure and are unrelated to the B class DNA polymerases, as claimed for yeast POL5, or any other known polymerases...
  65. ncbi request reprint Pruning DNA: structure-specific endonucleases (XPF/Rad1/Mus81)
    Wei Yang
    Structure 11:365-6. 2003
  66. ncbi request reprint Product-assisted catalysis in base-excision DNA repair
    J Christopher Fromme
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Nat Struct Biol 10:204-11. 2003
    ..To our knowledge, the present example represents the first documented case of product-assisted catalysis in an enzyme-catalyzed reaction...
  67. ncbi request reprint Crystal structure and biochemical analysis of the MutS.ADP.beryllium fluoride complex suggests a conserved mechanism for ATP interactions in mismatch repair
    Eric Alani
    Department of Molecular Biology and Genetics, 459 Biotechnology Building, Cornell University, Ithaca, NY 14853 2703, USA
    J Biol Chem 278:16088-94. 2003
    ....
  68. ncbi request reprint Evidence for sequential action of two ATPase active sites in yeast Msh2-Msh6
    Karin Drotschmann
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
    DNA Repair (Amst) 1:743-53. 2002
    ..This suggests sequential action of the two ATPase active sites, in which ATP binds to Msh6 first to trigger downstream events in mismatch repair...
  69. ncbi request reprint Amyloid fibril formation by a domain of rat cell adhesion molecule
    Amy Carroll
    Department of Chemistry, Center of Drug Design, Georgia State University, Atlanta, GA, USA
    Cell Biochem Biophys 44:241-9. 2006
    ..Our studies indicate that partial formation of a non-native conformation and the exposure of the hydrophobic interior could be the origins of oligomerization and fibril formation of CD2-1...
  70. ncbi request reprint Alternative conformations of the archaeal Nop56/58-fibrillarin complex imply flexibility in box C/D RNPs
    Sri Oruganti
    Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
    J Mol Biol 371:1141-50. 2007
    ..We propose that hinge motion within Nop56/58 has important implications for the possibility of simultaneously positioning two catalytic sites at the two target sites of a bipartite box C/D guide RNA...
  71. pmc Regulation of outside-in signaling and affinity by the beta2 I domain of integrin alphaLbeta2
    JianFeng Chen
    CBR Institute for Biomedical Research and Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 103:13062-7. 2006
    ..Furthermore, ADMIDAS mutation abolished spreading on ligand-bearing substrates. Thus, beta(2) I domain metal ion-binding sites regulate alpha(L) I domain affinity, and the ADMIDAS is required for outside-in signaling...
  72. pmc AL-57, a ligand-mimetic antibody to integrin LFA-1, reveals chemokine-induced affinity up-regulation in lymphocytes
    Motomu Shimaoka
    CBR Institute for Biomedical Research and Department of Anesthesia, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 103:13991-6. 2006
    ..Affinity up-regulation correlates with global conformational changes of LFA-1 to the extended form. Affinity increase stimulated by CXCL-12 is transient and peaks 2 to 5 min after stimulation...
  73. ncbi request reprint A quantum mechanics/molecular mechanics study of the reaction mechanism of the hepatitis C virus NS3 protease with the NS5A/5B substrate
    Carolina Oliva
    Departament de Química Física i Centre de Recerca en Química Teòrica, Universitat de Barcelona i Parc Cientific de Barcelona, c Marti i Franques 1, 08028 Barcelona, Spain
    Proteins 66:444-55. 2007
    ..The residues of the oxyanion hole were confirmed as the most important for the electrostatic stabilization of the tetracoordinate intermediate. Moreover, the role of other residues, e.g., Arg-155 and Asp-79, was also explained...
  74. pmc Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase
    Kevin A Fiala
    Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
    J Mol Biol 365:590-602. 2007
    ..This unprecedented base-stacking pattern can be applied to subsequent blunt-end additions only if all incorporated dAMPs are extrahelical, leading to predominantly single non-templated dATP incorporation...
  75. ncbi request reprint A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase
    Yi Qin Gao
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Cell 123:195-205. 2005
    ..The model shows that the pathway for ATP hydrolysis is not simply the pathway for ATP synthesis in reverse. The findings of the model also explain why the cellular concentration of ATP does not inhibit ATP synthesis...
  76. ncbi request reprint Structural analysis, identification, and design of calcium-binding sites in proteins
    Wei Yang
    Department of Biology Drug Design, Georgia State University, Atlanta, Georgia, USA
    Proteins 47:344-56. 2002
    ..Our results suggest that it is possible to identify calcium- and magnesium-binding sites in proteins and design de novo metal-binding sites...
  77. ncbi request reprint The effects of Ca2+ binding on the dynamic properties of a designed Ca2+-binding protein
    Wei Yang
    Department of Chemistry, Center for Drug Design, Georgia State University, Atlanta, Georgia 30303, USA
    Biochemistry 44:8267-73. 2005
    ..Our study suggests that Ca(2+) binding has a differential effect on the rigidity of the residues depending on their flexibility and location within the secondary structure...
  78. pmc 'In-line attack' conformational effect plays a modest role in an enzyme-catalyzed RNA cleavage: a free energy simulation study
    Donghong Min
    School of Computational Science, Florida State University, Tallahassee, FL 32306, USA
    Nucleic Acids Res 35:4001-6. 2007
    ....
  79. pmc The primacy of affinity over clustering in regulation of adhesiveness of the integrin {alpha}L{beta}2
    Minsoo Kim
    The CBR Institute for Biomedical Research and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
    J Cell Biol 167:1241-53. 2004
    ..Thus, LFA-1 clustering does not precede ligand binding, and instead functions in adhesion strengthening after binding to multivalent ligands...
  80. ncbi request reprint Metal-binding studies for a de novo designed calcium-binding protein
    Anna L Wilkins
    Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
    Protein Eng 15:571-4. 2002
    ..Our designed protein exhibits a stronger affinity for Tb(III), with a K(d) of 21 microM, than natural calcium-binding proteins with a similar Greek key scaffold...
  81. ncbi request reprint Using protein design to dissect the effect of charged residues on metal binding and protein stability
    Anna Wilkins Maniccia
    Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, Georgia 30303, USA
    Biochemistry 45:5848-56. 2006
    ....
  82. ncbi request reprint Identification of the calmodulin binding domain of connexin 43
    Yubin Zhou
    Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
    J Biol Chem 282:35005-17. 2007
    ....
  83. ncbi request reprint Mapping electron paramagnetic resonance spin label conformations by the simulated scaling method
    Mikolai I Fajer
    Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
    J Am Chem Soc 129:13840-6. 2007
    ....
  84. ncbi request reprint Protein structural transitions and their functional role
    Martin Karplus
    Laboratoire de Chimie Biophysique, ISIS, Universite Louis Pasteur, Strasbourg, France
    Philos Trans A Math Phys Eng Sci 363:331-55; discussion 355-6. 2005
    ..In this paper we outline our studies of two such protein machines. One is GroEL, the chaperone from Escherichia coli, which aids in protein folding; the other is F(1)-ATPase, a motor protein which synthesizes and hydrolyses ATP...
  85. ncbi request reprint Rational design of a calcium-binding protein
    Wei Yang
    Department of Chemistry, Center of Drug Design, Georgia State University, Atlanta 30303, USA
    J Am Chem Soc 125:6165-71. 2003
    ....
  86. ncbi request reprint Differential protein expression induced by transient transfection of metallothionein-3 gene in SH-SY5Y neuroblastoma cell line
    Bo Zhou
    Proteome Group, National Laboratory of Protein Engineering, College of Life Sciences, Peking University, Beijing 100871, China
    Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 35:522-8. 2003
    ..which were involved in several important pathways regulating the functions of central nervous system. The results showed that MT-3 might exert its unique functions by regulating the expression of these proteins...
  87. ncbi request reprint 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
    Motomu Shimaoka
    The CBR Institute for Biomedical Research, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Immunity 19:391-402. 2003
    ....
  88. pmc Identification and dissection of Ca(2+)-binding sites in the extracellular domain of Ca(2+)-sensing receptor
    Yun Huang
    Department of Chemistry, Center for Biotechnology and Drug Design Georgia State University, Atlanta, Georgia 30303, USA
    J Biol Chem 282:19000-10. 2007
    ....
  89. ncbi request reprint Numerical calculation of the combinatorial entropy of partially ordered ice
    Bernd A Berg
    School of Computational Science, Florida State University, Tallahassee, Florida 32306 4120, USA
    J Chem Phys 127:224502. 2007
    ..For the considered case, corrections to an (approximate) analytical formula are found to be small, never exceeding 0.5%. The method allows one as well to calculate combinatorial entropies for other systems...
  90. ncbi request reprint DNA-remethylation around a STAT5-binding enhancer in the alphaS1-casein promoter is associated with abrupt shutdown of alphaS1-casein synthesis during acute mastitis
    Jens Vanselow
    Research Institute for the Biology of Farm Animals FBN, Wilhelm Stahl Allee 2, 18196 Dummerstorf, Germany
    J Mol Endocrinol 37:463-77. 2006
    ..This provides a rare example for an acute regulatory significance of CpG methylation...
  91. pmc Rational design of a novel calcium-binding site adjacent to the ligand-binding site on CD2 increases its CD48 affinity
    Lisa M Jones
    Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, Georgia 30303, USA
    Protein Sci 17:439-49. 2008
    ..The study provides site-specific information for regulating cell adhesion within CD2 and gives insight into the structural factors required for Ca2+-modulated biological processes...
  92. ncbi request reprint Calcium and lanthanide affinity of the EF-loops from the C-terminal domain of calmodulin
    Yiming Ye
    Department of Chemistry, Center of Drug Design, Georgia State University, University Plaza, Atlanta, GA 30303, USA
    J Inorg Biochem 99:1376-83. 2005
    ..The CaM-CD2-III-5G-52 has stronger affinities to Ca(2+), Tb(3+) and La(3+) than CaM-CD2-IV-5G-52, indicating differential intrinsic metal-binding affinities of the EF-loops...