Research Topics
Genomes and Genes | W YangSummaryAffiliation: National Institutes of Health Country: USA Publications
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Publications
Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysisMarcin 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...- Protein-nucleic acid complexes: large, small, old, and newGregory D Van Duyne
Curr Opin Struct Biol 18:67-9. 2008 - Damage repair DNA polymerases YWei 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.... - Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificityWei 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... 
Nucleases: diversity of structure, function and mechanismWei 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...- Poor base stacking at DNA lesions may initiate recognition by many repair proteinsWei 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... 
Surviving the sun: repair and bypass of DNA UV lesionsWei 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...- An equivalent metal ion in one- and two-metal-ion catalysisWei 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... - Structure and mechanism for DNA lesion recognitionWei 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... - Structure and function of mismatch repair proteinsW 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... - Topoisomerases and site-specific recombinases: similarities in structure and mechanismWei 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... - Human MutLalpha: the jack of all trades in MMR is also an endonucleaseWei 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... - What a difference a decade makes: insights into translesion DNA synthesisWei 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... - Portraits of a Y-family DNA polymeraseWei 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... - Site-specific recombination in plane viewW 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... - Lessons learned from UvrD helicase: mechanism for directional movementWei 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... - Composite active site of an ABC ATPase: MutS uses ATP to verify mismatch recognition and authorize DNA repairM 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... - Homologous segments in three subunits of the guanine nucleotide exchange factor eIF2B mediate translational regulation by phosphorylation of eIF2G 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... - Crystal structure and ATPase activity of MutL: implications for DNA repair and mutagenesisC 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... - Transformation of MutL by ATP binding and hydrolysis: a switch in DNA mismatch repairC 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... - Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleasesC 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... - Structure and function of the N-terminal 40 kDa fragment of human PMS2: a monomeric GHL ATPaseA 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... - Disruption of the helix-u-turn-helix motif of MutS protein: loss of subunit dimerization, mismatch binding and ATP hydrolysisI 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... - Asymmetric recognition of DNA local distortion. Structure-based functional studies of eukaryotic Msh2-Msh6K 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... - Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replicationH 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... - Structure of the MutL C-terminal domain: a model of intact MutL and its roles in mismatch repairAlba 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... - Investigating the role of the little finger domain of Y-family DNA polymerases in low fidelity synthesis and translesion replicationFrancois 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... - UvrD helicase unwinds DNA one base pair at a time by a two-part power strokeJae 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... - MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavageJae 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... - Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcriptionMarcin 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... - Replication of a cis-syn thymine dimer at atomic resolutionHong 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... - Insights into negative modulation of E. coli replication initiation from the structure of SeqA-hemimethylated DNA complexAlba 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... - Structure and mechanism of human DNA polymerase etaChristian 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... - Structure-based interpretation of missense mutations in Y-family DNA polymerases and their implications for polymerase function and lesion bypassFrancois 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.... - In vitro and in vivo studies of MutS, MutL and MutH mutants: correlation of mismatch repair and DNA recombinationMurray 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... - Monovalent cation dependence and preference of GHKL ATPases and kinasesXiaojian 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... - Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysisAlexandra 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... - Proliferating cell nuclear antigen-dependent coordination of the biological functions of human DNA polymerase iotaAntonio 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... - Crystal structure of a SeqA-N filament: implications for DNA replication and chromosome organizationAlba 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... - The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2Santiago 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.... - Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymeraseHong 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... - Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBDMarcin 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... - Homeostatic regulation of copper uptake in yeast via direct binding of MAC1 protein to upstream regulatory sequences of FRE1 and CTR1Y 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... - Structure of a two-domain fragment of HIV-1 integrase: implications for domain organization in the intact proteinJ 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... - A Ku bridge over broken DNAJ 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... - Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product releaseMarcin 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... - Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshiftsHong 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... - Crystal structure of T4 endonuclease VII resolving a Holliday junctionChristian 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.... - Structural insight into translesion synthesis by DNA Pol IIFeng 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... - CHARMM: the biomolecular simulation programB 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... - Initial stages of V(D)J recombination: the organization of RAG1/2 and RSS DNA in the postcleavage complexGabrielle 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... - Identification of a regulatory subcomplex in the guanine nucleotide exchange factor eIF2B that mediates inhibition by phosphorylated eIF2W 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... - A novel phosphotyrosine motif with a critical amino acid at position -2 for the SH2 domain-mediated activation of the tyrosine phosphatase SHP-1D 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... - 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 complexesT 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... - Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymeraseKevin 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... - 'In-line attack' conformational effect plays a modest role in an enzyme-catalyzed RNA cleavage: a free energy simulation studyDonghong Min
School of Computational Science, Florida State University, Tallahassee, FL 32306, USA
Nucleic Acids Res 35:4001-6. 2007.... - RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombinationAdam 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... - Alternative conformations of the archaeal Nop56/58-fibrillarin complex imply flexibility in box C/D RNPsSri 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... - A quantum mechanics/molecular mechanics study of the reaction mechanism of the hepatitis C virus NS3 protease with the NS5A/5B substrateCarolina 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... - AL-57, a ligand-mimetic antibody to integrin LFA-1, reveals chemokine-induced affinity up-regulation in lymphocytesMotomu 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... - Probing site-specific calmodulin calcium and lanthanide affinity by graftingYiming 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... - Structural analysis, identification, and design of calcium-binding sites in proteinsWei 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... - Activation of integrin beta-subunit I-like domains by one-turn C-terminal alpha-helix deletionsWei 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.... - Yeast POL5 is an evolutionarily conserved regulator of rDNA transcription unrelated to any known DNA polymerasesWei 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... - Pruning DNA: structure-specific endonucleases (XPF/Rad1/Mus81)Wei Yang
Structure 11:365-6. 2003 - Product-assisted catalysis in base-excision DNA repairJ 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... - Crystal structure and biochemical analysis of the MutS.ADP.beryllium fluoride complex suggests a conserved mechanism for ATP interactions in mismatch repairEric Alani
Department of Molecular Biology and Genetics, 459 Biotechnology Building, Cornell University, Ithaca, NY 14853 2703, USA
J Biol Chem 278:16088-94. 2003.... - Evidence for sequential action of two ATPase active sites in yeast Msh2-Msh6Karin 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... - Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNAAnirban 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... - Regulation of outside-in signaling and affinity by the beta2 I domain of integrin alphaLbeta2JianFeng 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... - The effects of Ca2+ binding on the dynamic properties of a designed Ca2+-binding proteinWei 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... - A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPaseYi 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... - Tetramerization and DNA ligase IV interaction of the DNA double-strand break repair protein XRCC4 are mutually exclusiveMauro 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... - Amyloid fibril formation by a domain of rat cell adhesion moleculeAmy 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... - Identification of the calmodulin binding domain of connexin 43Yubin Zhou
Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
J Biol Chem 282:35005-17. 2007.... - Identification and dissection of Ca(2+)-binding sites in the extracellular domain of Ca(2+)-sensing receptorYun Huang
Department of Chemistry, Center for Biotechnology and Drug Design Georgia State University, Atlanta, Georgia 30303, USA
J Biol Chem 282:19000-10. 2007.... - DNA-remethylation around a STAT5-binding enhancer in the alphaS1-casein promoter is associated with abrupt shutdown of alphaS1-casein synthesis during acute mastitisJens 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... - Using protein design to dissect the effect of charged residues on metal binding and protein stabilityAnna Wilkins Maniccia
Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, Georgia 30303, USA
Biochemistry 45:5848-56. 2006.... - Metal-binding studies for a de novo designed calcium-binding proteinAnna 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... - Rational design of a calcium-binding proteinWei Yang
Department of Chemistry, Center of Drug Design, Georgia State University, Atlanta 30303, USA
J Am Chem Soc 125:6165-71. 2003.... - Differential protein expression induced by transient transfection of metallothionein-3 gene in SH-SY5Y neuroblastoma cell lineBo 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... - Small molecule integrin antagonists that bind to the beta2 subunit I-like domain and activate signals in one direction and block them in the otherMotomu Shimaoka
The CBR Institute for Biomedical Research, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
Immunity 19:391-402. 2003.... - Rational design of a novel calcium-binding site adjacent to the ligand-binding site on CD2 increases its CD48 affinityLisa 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... - The primacy of affinity over clustering in regulation of adhesiveness of the integrin {alpha}L{beta}2Minsoo 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... - Numerical calculation of the combinatorial entropy of partially ordered iceBernd 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... - Calcium and lanthanide affinity of the EF-loops from the C-terminal domain of calmodulinYiming 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... - Mapping electron paramagnetic resonance spin label conformations by the simulated scaling methodMikolai I Fajer
Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
J Am Chem Soc 129:13840-6. 2007.... - Protein structural transitions and their functional roleMartin 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...