PubAg

Main content area

You searched for: Publication Year 2011 Remove constraint Publication Year: 2011 Subject crystal structure Remove constraint Subject: crystal structure Text Availability Full Text Remove constraint Text Availability: Full Text
Start Over

Search

335  Search Results

« Previous | 1 - 20 of 335 |
Number of results to display per page

Search Results

1. SlyA Is a Transcriptional Regulator Involved in the Virulence of Enterococcus faecalis

Author:
Michaux, Charlotte; Sanguinetti, Maurizio; Reffuveille, Fany; Auffray, Yanick; Posteraro, Brunella; Gilmore, Michael S.; Hartke, Axel; Giard, Jean-Christophe
Source:
Infection and immunity 2011 v.79 no.7 pp. 2638-2645
ISSN:
0019-9567
Subject:
transcription factors; Enterococcus faecalis; liver; loci; gene overexpression; crystal structure; microarray technology; stress response; macrophages; models; phylogeny; Galleria mellonella; transcription (genetics); mice; virulence; mutants; kidneys; insects; regulon
Abstract:
... Phylogenetic analysis of the crystal structure of the Enterococcus faecalis SlyA (EF_3002) transcriptional factor places it between the SlyA and MarR regulator subfamilies. Proteins of these families are often involved in the regulation of genes important for bacterial virulence and stress response. To gather evidence for the role of this putative regulator in E. faecalis biology, we dissected the ...
DOI:
10.1128/IAI.01132-10
PubMed:
21536798
PubMed Central:
PMC3191995

2. A SOS3 homologue maps to HvNax4, a barley locus controlling an environmentally sensitive Na⁺ exclusion trait

Author:
Rivandi, J.; Miyazaki, J.; Hrmova, M.; Pallotta, M.; Tester, M.; Collins, N.C.
Source:
Journal of experimental botany 2011 v.62 no.3 pp. 1201-1216
ISSN:
0022-0957
Subject:
rice; alleles; shoots; barley; molecular models; crystal structure; parents; hydroponics; gene expression; messenger RNA; Arabidopsis; complementary DNA; barley protein; hydrogen bonding; salt tolerance; loci; amino acid substitution; soil types; Brachypodium; nucleotide sequences; post-translational modification; crops
Abstract:
... Genes that enable crops to limit Na⁺ accumulation in shoot tissues represent potential sources of salinity tolerance for breeding. In barley, the HvNax4 locus lowered shoot Na⁺ content by between 12% and 59% (g⁻¹ DW), or not at all, depending on the growth conditions in hydroponics and a range of soil types, indicating a strong influence of environment on expression. HvNax4 was fine-mapped on the ...
DOI:
10.1093/jxb/erq346
PubMed:
21047983
PubMed Central:
PMC3022402

3. A structural basis for Staphylococcal complement subversion: X-ray structure of the complement-binding domain of Staphylococcus aureus protein Sbi in complex with ligand C3d

Author:
Clark, Elizabeth A.; Crennell, Susan; Upadhyay, Abhishek; Zozulya, Alexey V.; Mackay, Julia D.; Svergun, Dmitri I.; Bagby, Stefan; van den Elsen, Jean M.H.
Source:
Molecular immunology 2011 v.48 no.4 pp. 452-462
ISSN:
0161-5890
Subject:
Staphylococcus aureus; X-radiation; bacterial proteins; binding sites; chemical interactions; complement; crystal structure; structure-activity relationships
Abstract:
... The structure of the complement-binding domain of Staphylococcus aureus protein Sbi (Sbi-IV) in complex with ligand C3d is presented. The 1.7Å resolution structure reveals the molecular details of the recognition of thioester-containing fragment C3d of the central complement component C3, involving interactions between residues of Sbi-IV helix α2 and the acidic concave surface of C3d. The complex ...
DOI:
10.1016/j.molimm.2010.09.017
PubMed:
21055811
PubMed Central:
PMC3025320

4. A Three-Dimensional RNA Motif in Potato spindle tuber viroid Mediates Trafficking from Palisade Mesophyll to Spongy Mesophyll in Nicotiana benthamiana

Author:
Takeda, Ryuta; Petrov, Anton I.; Leontis, Neocles B.; Ding, Biao
Source:
The plant cell 2011 v.23 no.1 pp. 258-272
ISSN:
1040-4651
Subject:
Nicotiana benthamiana; Potato spindle tuber viroid; RNA; X-radiation; crystal structure; databases; genes; leaves; mesophyll; models; mutants; sequence analysis; structure-activity relationships
Abstract:
... Cell-to-cell trafficking of RNA is an emerging biological principle that integrates systemic gene regulation, viral infection, antiviral response, and cell-to-cell communication. A key mechanistic question is how an RNA is specifically selected for trafficking from one type of cell into another type. Here, we report the identification of an RNA motif in Potato spindle tuber viroid (PSTVd) required ...
DOI:
10.1105/tpc.110.081414
PubMed:
21258006
PubMed Central:
PMC3051236

5. Structural insights into cis element recognition of non-polyadenylated RNAs by the Nab3-RRM

Author:
Lunde, Bradley M.; Hörner, Maximilian; Meinhart, Anton
Source:
Nucleic acids research 2011 v.39 no.1 pp. 337-346
ISSN:
0305-1048
Subject:
RNA; Saccharomyces cerevisiae; binding sites; chemical elements; crystal structure; cytidine; cytosine; hydrogen bonding; serine; uracil
Abstract:
... Transcription termination of non-polyadenylated RNAs in Saccharomyces cerevisiae occurs through the action of the Nrd1-Nab3-Sen1 complex. Part of the decision to terminate via this pathway occurs via direct recognition of sequences within the nascent transcript by RNA recognition motifs (RRMs) within Nrd1 and Nab3. Here we present the 1.6 Å structure of Nab3-RRM bound to its UCUU recognition seque ...
DOI:
10.1093/nar/gkq751
PubMed:
20805243
PubMed Central:
PMC3017603

6. Structure and function of the Rad9-binding region of the DNA-damage checkpoint adaptor TopBP1

Author:
Rappas, Mathieu; Oliver, Antony W.; Pearl, Laurence H.
Source:
Nucleic acids research 2011 v.39 no.1 pp. 313-324
ISSN:
0305-1048
Subject:
DNA damage; crystal structure; humans; phosphopeptides; scaffolding proteins; single-stranded DNA
Abstract:
... TopBP1 is a scaffold protein that coordinates activation of the DNA-damage-checkpoint response by coupling binding of the 9-1-1 checkpoint clamp at sites of ssDNA, to activation of the ATR-ATRIP checkpoint kinase complex. We have now determined the crystal structure of the N-terminal region of human TopBP1, revealing an unexpected triple-BRCT domain structure. The arrangement of the BRCT domains d ...
DOI:
10.1093/nar/gkq743
PubMed:
20724438
PubMed Central:
PMC3017600

7. Systematic mutation and thermodynamic analysis of central tyrosine pairs in polyspecific NKG2D receptor interactions

Author:
Culpepper, David J.; Maddox, Michael K.; Caldwell, Andrew B.; McFarland, Benjamin J.
Source:
Molecular immunology 2011 v.48 no.4 pp. 516-523
ISSN:
0161-5890
Subject:
amino acid substitution; antigen-antibody reactions; binding capacity; binding sites; crystal structure; enthalpy; histocompatibility antigens; hydrophobicity; immunologic receptors; mutants; natural killer cells; protein-protein interactions; structure-activity relationships; tyrosine
Abstract:
... The homodimeric, activating natural killer cell receptor NKG2D interacts with multiple monomeric ligands polyspecifically, yet without central conformational flexibility. Crystal structures of multiple NKG2D–ligand interactions have identified the NKG2D tyrosine pair Tyr 152 and Tyr 199 as forming multiple specific but diverse interactions with MICA and related proteins. Here we systematically alt ...
DOI:
10.1016/j.molimm.2010.10.007
PubMed:
21074271
PubMed Central:
PMC3014408

8. The phosphate clamp: a small and independent motif for nucleic acid backbone recognition

Author:
Komeda, Seiji; Moulaei, Tinoush; Chikuma, Masahiko; Odani, Akira; Kipping, Ralph; Farrell, Nicholas P.; Williams, Loren Dean
Source:
Nucleic acids research 2011 v.39 no.1 pp. 325-336
ISSN:
0305-1048
Subject:
B-DNA; ammonia; antineoplastic activity; cations; crystal structure; crystallization; geometry; phosphates; platinum; sugars
Abstract:
... The 1.7 Å X-ray crystal structure of the B-DNA dodecamer, [d(CGCGAATTCGCG)]₂ (DDD)-bound non-covalently to a platinum(II) complex, [{Pt(NH₃)₃}₂-μ-{trans-Pt(NH₃)₂(NH₂(CH₂)₆NH₂)₂}](NO₃)₆ (1, TriplatinNC-A,) shows the trinuclear cation extended along the phosphate backbone and bridging the minor groove. The square planar tetra-am(m)ine Pt(II) units form bidentate N-O-N complexes with OP atoms, in a P ...
DOI:
10.1093/nar/gkq723
PubMed:
20736180
PubMed Central:
PMC3017591

9. A model of the C14-EPIC complex indicates hotspots for a protease-inhibitor arms race in the oomycete-potato interaction

Author:
Kaschani, Farnusch; Van der Hoorn, Renier A. L.
Source:
Plant signaling & behavior 2011 v.6 no.1 pp. 109-112
ISSN:
1559-2324
Subject:
Phytophthora infestans; coevolution; crystal structure; models; plant pathogens; potatoes; proteinase inhibitors; proteinases; proteins
Abstract:
... The oomycete pathogen Phytophthora infestans secretes cystatin-like effector proteins (EPICs) that inhibit secreted host proteases during infection. We recently found that the C14 protease is a relevant target of EPICs and that this protease is under diversifying selection in wild potato species with which P. infestans has coevolved. Here we generated a model of the EPIC-C14 complex based on cysta ...
DOI:
10.4161/psb.6.1.14190
PubMed:
21301220
PubMed Central:
PMC3122019

10. Evolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization

Author:
Romão, Célia V.; Ladakis, Dimitrios; Lobo, Susana A.L.; Carrondo, Maria A.; Brindley, Amanda A.; Deery, Evelyne; Matias, Pedro M.; Pickersgill, Richard W.; Saraiva, Lígia M.; Warren, Martin J.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2011 v.108 no.1 pp. 97-102
ISSN:
0027-8424
Subject:
Archaeoglobus; Desulfovibrio vulgaris; Salmonella enterica; active sites; biosynthesis; chelation; cobalt; crystal structure; enzymes; evolution; heme; iron; oligomerization; protein subunits; protoporphyrin; vitamin B12
Abstract:
... The class II chelatases associated with heme, siroheme, and cobalamin biosynthesis are structurally related enzymes that insert a specific metal ion (Fe²⁺ or Co²⁺) into the center of a modified tetrapyrrole (protoporphyrin or sirohydrochlorin). The structures of two related class II enzymes, CbiXS from Archaeoglobus fulgidus and CbiK from Salmonella enterica, that are responsible for the insertion ...
DOI:
10.1073/pnas.1014298108
PubMed:
21173279
PubMed Central:
PMC3017170

11. Pressure-induced superconductivity in topological parent compound Bi₂Te₃

Author:
Zhang, J.L.; Zhang, S.J.; Weng, H.M.; Zhang, W.; Yang, L.X.; Liu, Q.Q.; Feng, S.M.; Wang, X.C.; Yu, R.C.; Cao, L.Z.; Wang, L.; Yang, W.G.; Liu, H.Z.; Zhao, W.Y.; Zhang, S.C.; Dai, X.; Fang, Z.; Jin, C.Q.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2011 v.108 no.1 pp. 24-28
ISSN:
0027-8424
Subject:
X-ray diffraction; crystal structure; phase transition; topology
Abstract:
... We report a successful observation of pressure-induced superconductivity in a topological compound Bi₂Te₃ with Tc of ~3 K between 3 to 6 GPa. The combined high-pressure structure investigations with synchrotron radiation indicated that the superconductivity occurred at the ambient phase without crystal structure phase transition. The Hall effects measurements indicated the hole-type carrier in the ...
DOI:
10.1073/pnas.1014085108
PubMed:
21173267
PubMed Central:
PMC3017179

12. Visualizing key hinges and a potential major source of compliance in the lever arm of myosin

Author:
Brown, Jerry H.; Senthil Kumar, V.S.; O'Neall-Hennessey, Elizabeth; Reshetnikova, Ludmila; Robinson, Howard; Nguyen-McCarty, Michelle; Szent-Györgyi, Andrew G.; Cohen, Carolyn
Source:
Proceedings of the National Academy of Sciences of the United States of America 2011 v.108 no.1 pp. 114-119
ISSN:
0027-8424
Subject:
Placopecten magellanicus; crystal structure; muscles; myosin light chains; phosphorylation
Abstract:
... We have determined the 2.3-Å-resolution crystal structure of a myosin light chain domain, corresponding to one type found in sea scallop catch ("smooth") muscle. This structure reveals hinges that may function in the "on" and "off" states of myosin. The molecule adopts two different conformations about the heavy chain "hook" and regulatory light chain (RLC) helix D. This conformational change resu ...
DOI:
10.1073/pnas.1016288107
PubMed:
21149681
PubMed Central:
PMC3017161

13. Crystal Structure and Allosteric Activation of Protein Kinase C βII

Author:
Leonard, Thomas A.; Różycki, Bartosz; Saidi, Layla F.; Hummer, Gerhard; Hurley, James H.
Source:
Cell 2011 v.144 no.1 pp. 55-66
ISSN:
0092-8674
Subject:
X-radiation; cell membranes; crystal structure; isozymes; protein conformation; protein kinase C
Abstract:
... Protein kinase C (PKC) isozymes are the paradigmatic effectors of lipid signaling. PKCs translocate to cell membranes and are allosterically activated upon binding of the lipid diacylglycerol to their C1A and C1B domains. The crystal structure of full-length protein kinase C βII was determined at 4.0 Å, revealing the conformation of an unexpected intermediate in the activation pathway. Here, the k ...
DOI:
10.1016/j.cell.2010.12.013
PubMed:
21215369
PubMed Central:
PMC3104240

14. Crystal Structure of the Phage T4 Recombinase UvsX and Its Functional Interaction with the T4 SF2 Helicase UvsW

Author:
Gajewski, Stefan; Webb, Michael R.; Galkin, Vitold; Egelman, Edward H.; Kreuzer, Kenneth N.; White, Stephen W.
Source:
Journal of molecular biology 2011 v.405 no.1 pp. 65-76
ISSN:
0022-2836
Subject:
DNA helicases; DNA nucleotidyltransferases; adenosine diphosphate; adenosine triphosphate; bacteriophages; binding sites; crystal structure; electron microscopy; homologous recombination; protein subunits
Abstract:
... Bacteriophage T4 provides an important model system for studying the mechanism of homologous recombination. We have determined the crystal structure of the T4 UvsX recombinase, and the overall architecture and fold closely resemble those of RecA, including a highly conserved ATP binding site. Based on this new structure, we reanalyzed electron microscopy reconstructions of UvsX–DNA filaments and d ...
DOI:
10.1016/j.jmb.2010.10.004
PubMed:
21035462
PubMed Central:
PMC3006652

15. Crystal structure of the receptor binding domain of the botulinum C–D mosaic neurotoxin reveals potential roles of lysines 1118 and 1136 in membrane interactions

Author:
Zhang, Yanfeng; Buchko, Garry W.; Qin, Ling; Robinson, Howard; Varnum, Susan M.
Source:
Biochemical and biophysical research communications 2011 v.404 no.1 pp. 407-412
ISSN:
0006-291X
Subject:
Clostridium botulinum C; Clostridium botulinum D; amino acid sequences; bacteria; binding properties; binding sites; botulinum toxin; crystal structure; hybrids; lysine; phosphatidylethanolamines; serotypes
Abstract:
... The botulinum neurotoxins (BoNTs) produced by different strains of the bacterium Clostridium botulinum are responsible for the disease botulism and include a group of immunologically distinct serotypes (A, B, E, and F) that are considered to be the most lethal natural proteins known for humans. Two BoNT serotypes, C and D, while rarely associated with human infection, are responsible for deadly bo ...
DOI:
10.1016/j.bbrc.2010.11.134
PubMed:
21130733
PubMed Central:
PMC3019264

16. Crystal Structures of Penicillin-Binding Protein 3 from Pseudomonas aeruginosa: Comparison of Native and Antibiotic-Bound Forms

Author:
Sainsbury, Sarah; Bird, Louise; Rao, Vincenzo; Shepherd, Sharon M.; Stuart, David I.; Hunter, William N.; Owens, Raymond J.; Ren, Jingshan
Source:
Journal of molecular biology 2011 v.405 no.1 pp. 173-184
ISSN:
0022-2836
Subject:
Escherichia coli; Gram-negative bacteria; Pseudomonas aeruginosa; binding sites; carbenicillin; crystal structure; humans; mechanism of action; pathogens; thermal stability
Abstract:
... We report the first crystal structures of a penicillin-binding protein (PBP), PBP3, from Pseudomonas aeruginosa in native form and covalently linked to two important β-lactam antibiotics, carbenicillin and ceftazidime. Overall, the structures of apo and acyl complexes are very similar; however, variations in the orientation of the amino-terminal membrane-proximal domain relative to that of the car ...
DOI:
10.1016/j.jmb.2010.10.024
PubMed:
20974151
PubMed Central:
PMC3025346

17. Structure-Guided Identification of a Laminin Binding Site on the Laminin Receptor Precursor

Author:
Jamieson, Kelly V.; Hubbard, Stevan R.; Meruelo, Daniel
Source:
Journal of molecular biology 2011 v.405 no.1 pp. 24-32
ISSN:
0022-2836
Subject:
Archaeoglobus; RNA; antibodies; binding sites; cell movement; crystal structure; gene overexpression; humans; laminin; metastasis; mutation; phenotype; prions; therapeutics; viruses
Abstract:
... The 37/ 67-kDa human laminin receptor (LamR) is a cell surface receptor for laminin, prion protein, and a variety of viruses. Because of its wide range of ligands, LamR plays a role in numerous pathologies. LamR overexpression correlates with a highly invasive cell phenotype and increased metastatic ability, mediated by interactions between LamR and laminin. In addition, the specific targeting of ...
DOI:
10.1016/j.jmb.2010.10.028
PubMed:
21040730
PubMed Central:
PMC3008175

18. RNA polymerase and transcription elongation factor Spt4/5 complex structure

Author:
Klein, Brianna J.; Bose, Daniel; Baker, Kevin J.; Yusoff, Zahirah M.; Zhang, Xiaodong; Murakami, Katsuhiko S.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2011 v.108 no.2 pp. 546-550
ISSN:
0027-8424
Subject:
DNA; DNA-directed DNA polymerase; DNA-directed RNA polymerase; RNA; claws; cryo-electron microscopy; crystal structure; eukaryotic cells; models; transcription (genetics)
Abstract:
... Spt4/5 in archaea and eukaryote and its bacterial homolog NusG is the only elongation factor conserved in all three domains of life and plays many key roles in cotranscriptional regulation and in recruiting other factors to the elongating RNA polymerase. Here, we present the crystal structure of Spt4/5 as well as the structure of RNA polymerase-Spt4/5 complex using cryoelectron microscopy reconstr ...
DOI:
10.1073/pnas.1013828108
PubMed:
21187417
PubMed Central:
PMC3021056

19. Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping

Author:
Tyka, Michael D.; Keedy, Daniel A.; André, Ingemar; DiMaio, Frank; Song, Yifan; Richardson, David C.; Richardson, Jane S.; Baker, David
Source:
Journal of molecular biology 2011 v.405 no.2 pp. 607-618
ISSN:
0022-2836
Subject:
binding proteins; crystal structure; crystallography; energy; landscapes; models; nuclear magnetic resonance spectroscopy; prediction; protein structure
Abstract:
... What conformations do protein molecules populate in solution? Crystallography provides a high-resolution description of protein structure in the crystal environment, while NMR describes structure in solution but using less data. NMR structures display more variability, but is this because crystal contacts are absent or because of fewer data constraints? Here we report unexpected insight into this ...
DOI:
10.1016/j.jmb.2010.11.008
PubMed:
21073878
PubMed Central:
PMC3046547

20. Arginine Kinase: Joint Crystallographic and NMR RDC Analyses Link Substrate-Associated Motions to Intrinsic Flexibility

Author:
Niu, Xiaogang; Bruschweiler-Li, Lei; Davulcu, Omar; Skalicky, Jack J.; Brüschweiler, Rafael; Chapman, Michael S.
Source:
Journal of molecular biology 2011 v.405 no.2 pp. 479-496
ISSN:
0022-2836
Subject:
Limulus; adenosine triphosphate; arginine kinase; creatine kinase; crystal structure; deformation; enzyme substrates; models; nuclear magnetic resonance spectroscopy; protein conformation; proteins
Abstract:
... The phosphagen kinase family, including creatine and arginine kinases (AKs), catalyzes the reversible transfer of a “high-energy” phosphate between ATP and a phosphoguanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differen ...
DOI:
10.1016/j.jmb.2010.11.007
PubMed:
21075117
PubMed Central:
PMC3017626