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The collection includes articles from PSI research groups and the broader community
December 2008
Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering.
Marcaida M., Prieto J., Redondo P., Nadra A., Alibés A. et al.
Proc Natl Acad Sci 105, 16888 - 16893 (2008)
Crystal structure and activity of Bacillus subtilis YoaJ (EXLX1), a bacterial expansin that promotes root colonization.
Kerff F., Amoroso A., Herman R., Sauvage E., Petrella S. et al.
Proc Natl Acad Sci 105, 16876 - 16881 (2008)
The molecular basis of N-end rule recognition
Wang K., Roman-Hernandez G., Grant R., Sauer R. and Baker T.
Mol Cell 32, 406 - 414 (2008)
Structure and substrate recruitment of the human spindle checkpoint kinase Bub1
Kang J., Yang M., Li B., Qi W., Zhang C. et al.
Mol Cell 32, 394 - 405 (2008)
The RNA polymerase “switch region” is a target for inhibitors
Mukhopadhyay J., Das K., Ismail S., Koppstein D., Jang M. et al.
Cell 135, 295 - 307 (2008)
The structure of a transcribing T7 RNA polymerase in transition from initiation to elongation
Durniak K., Bailey S. and Steitz T.
Science 322, 553 - 557 (2008)
Structure and molecular mechanism of a Nucleobase-Cation-Symport-1 family transporter
Weyand S., Shimamura T., Yajima S., Suzuki S., Mirza O. et al.
Science 322, 709 - 713 (2008)
Structural insights into a circadian oscillator
Johnson C., Egli M. and Stewart P.
Science 322, 697 - 701 (2008)
Insights into translational termination from the structure of RF2 bound to the ribosome
Weixlbaumer A., Jin H., Neubauer C., Voorhees R., Petry S. et al.
Science 322, 953 - 956 (2008)
Structural basis for exon recognition by a group II intron
Toor N., Rajashankar K., Keating K. and Pyle A.
Nat Struct Mol Biol 15, 1221 - 1222 (2008)
Insights into interferon regulatory factor activation from the crystal structure of dimeric IRF5
Chen W., Lam S., Srinath H., Jiang Z., Correia J. et al.
Nat Struct Mol Biol 15, 1213 - 1220 (2008)
Localization of Prp8, Brr2, Snu114 and U4/U6 proteins in the yeast tri-snRNP by electron microscopy
Hacker I., Sander B., Golas M., Wolf E., Karagoz E. et al.
Nat Struct Mol Biol 15, 1206 - 1212 (2008)
Structural elucidation of a PRP8 core domain from the heart of the spliceosome
Ritchie D., Schellenberg M., Gesner E., Raithatha S., Stuart D. et al.
Nat Struct Mol Biol 15, 1199 - 1205 (2008)
Activation of Slo1 BK channels by Mg2+ coordinated between the voltage sensor and RCK1 domains
Yang H., Shi J., Zhang G., Yang J., Delaloye K. et al.
Nat Struct Mol Biol 15, 1152 - 1159 (2008)
Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications
Holden L., Prochnow C., Chang Y., Bransteitter R., Chelico L. et al.
Nature 456, 121 - 124 (2008)
Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases
Redondo P., Prieto J., Munoz I., Alibes A., Stricher F. et al.
Nature 456, 107 - 111 (2008)
Biochemistry: Enzymes under the nanoscope
Kirby A. and Hollfelder F.
Nature 456, 45 - 47 (2008)
Physical protein-protein interactions predicted from microarrays
Soong T., Wrzeszczynski K. and Rost B.
Bioinformatics 24, 2608 - 2614 (2008)
Wheat germ cell-free translation, purification, and assembly of a functional human stearoyl-CoA desaturase complex
Goren M. and Fox B.
Prot Express Purif 62, 171 - 178 (2008)
Optimal design of thermally stable proteins
Bannen R., Suresh V., Phillips G., Jr , Wright S. et al.
Bioinformatics 24, 2339 - 2343 (2008)
Biochemical and sructural insights of the early glycosylation steps in calicheamicin biosynthesis
Zhang C., Bitto E., Goff R., Singh S., Bingman C. et al.
Chem Biol 15, 842 - 853 (2008)
X-ray structure of a soluble Rieske-type ferredoxin from Mus musculus
Elsen N. and Phillips J.
Acta Crystallogr D Biol Crystallogr 64, 933 - 940 (2008)
Bioinformatic method for protein thermal stabilization by structural entropy optimization
Bae E., Bannen R. and Phillips G. N., Jr.
Proc Natl Acad Sci 105, 9594 - 9597 (2008)
Data mining of metal ion environments present in protein structures
Zhenga H., Chruszcza M., Lasotaa P., Lebiodab L. and Minor W.
J Inorgan Biochem 102, 1765 - 1776 (2008)
Crystal structures of the effector-binding domain of repressor central glycolytic gene regulator from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates
Rezácová P., Kožíšek M., Moy S., Sieglová I., Joachimiak A. et al.
Mol Microbiol 69, 895 - 910 (2008)
Functional and structural characterization of four glutaminases from Escherichia coli and Bacillus subtilis
Brown G., Singer A., Proudfoot M., Skarina T., Kim Y. et al.
Biochemistry 47, 5724 - 5735 (2008)
Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000
Aceti D., Bitto E., Yakunin A., Proudfoot M., Bingman C. et al.
Proteins 73, 241 - 253 (2008)
The solution structure of ZNF593 from Homo sapiens reveals a zinc finger in a predominately unstructured protein
Hayes P., Lytle B., Volkman B. and Peterson F.
Prot Sci 17, 571 - 576 (2008)
Structural basis for the catalytic mechanism of mammalian 25-kDa thiamine triphosphatase
Song J., Bettendorff L., Tonelli M. and Markley J.
J Biol Chem 283, 10939 - 10948 (2008)
A graphical approach to tracking and reporting target status in structural genomics
Pan X., Wesenberg G., Markley J., Fox B., Phillips J.G. et al.
J Struct Funct Genomics 8, 209 - 216 (2007)
Intrinsically disordered gamma-subunit of cGMP phosphodiesterase encodes functionally relevant transient secondary and tertiary structure
Song J., Guo L., Muradov H., Artemyev N., Ruoho A. et al.
Proc Natl Acad Sci 105, 1505 - 1510 (2008)
A Protein Structure Initiative approach to expression, purification, and in situ delivery of human cytochrome b5 to membrane vesicles
Sobradoa P., Gorena M., Jamesa D., Amundsona C. and Fox B.
Prot Express Purif 58, 229 - 241 (2008)
Solution structure of At3g28950 from Arabidopsis thaliana
de la Cruz N., Peterson F. and Volkman B.
Prot Struct Funct Bioinform 71, 546 - 551 (2008)
The 1.38 Å crystal structure of DmsD protein fromSalmonella typhimurium, a proofreading chaperone on the Tat pathway
Qiu A., Zhang R., Binkowski T., Tereshko V., Joachimiak A. et al.
Prot Struct Funct Bioinformatics 71, 525 - 533 (2008)
Predicting protein function from sequence and structure
Lee D., Redfern O. and Orengo C.
Nat Rev Mol Cell Biol 8, 995 - 1005 (2007)
Small-scale, semi-automated purification of eukaryotic proteins for structure determination
Frederick R., Bergeman L., Blommel P., Bailey L., McCoy J. et al.
J Struct Funct Genomics 8, 153 - 166 (2007)
Comparison of apo- and meme-bound crystal structures of a truncated human heme oxygenase-2
Bianchetti C., Yi L., Ragsdale S., Phillips G. N. Jr.
J Biol Chem 282, 37624 - 37631 (2007)
Soluble expression and purification of the oxidoreductase component of toluene 4-monooxygenase
Baileya L., Elsena N., Piercea B. and Fox B.
Protein Express Purif 57, 9 - 16 (2008)
Creating protein models from electron-density maps using particle-filtering methods
Dimaio F., Kondrashov D., Bitto E., Soni A., Bingman C. et al.
Bioinformatics 23, 2851 - 2858 (2007)
Crystal structure of Homo sapiens protein LOC79017
Bae E., Bingman C., Aceti D. and Phillips J.G.
Proteins 70, 588 - 591 (2008)
Bis-methionyl coordination in the crystal structure of the heme-binding domain of the streptococcal Cell Surface Protein Shp
Aranda I.R., Worley C., Liu M., Bitto E., Cates M. et al.
J Mol Biol 374, 374 - 383 (2007)
Nearest-neighbor effects on backbone alpha and beta carbon chemical shifts in proteins
Wang L., Eghbalnia H. and Markley J.
J Biomol NMR 39, 247 - 257 (2007)
The structure of flavin-dependent tryptophan 7-halogenase RebH
Bitto E., Huang Y., Bingman C., Singh S., Thorson J. et al.
Prot Struct Funct Bioinformatics 70, 289 - 293 (2008)
Ensemble refinement of protein crystal structures: validation and application
Kondrashov D. and Phillips J.
Structure 15, 1040 - 1052 (2007)
Structures of proteins of biomedical interest from the Center for Eukaryotic Structural Genomics
Phillips J.G., Fox B., Markley J., Volkman B., Bae E. et al.
J Struct Funct Genomics 8, 73 - 84 (2007)
Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase
Davis C., Bingman C., Landick R., Record J.M. and Saecker R.
Proc Natl Acad Sci 104, 7833 - 7838 (2007)
Simple host-guest chemistry to modulate the process of concentration and crystallization of membrane proteins by detergent capture in a microfluidic device
Li L., Nachtergaele S., Seddon A., Tereshko V., Ponomarenko N. et al.
J Am Chem Soc 130, 14324 - 14328 (2008)
Structural Characterization of the 1918 Influenza Virus H1N1 Neuraminidase
Xu X., Zhu X., Dwek R., Stevens J. and Wilson I.
J Virology 82, 10493 - 10501 (2008)
Structure of Human J-type Co-chaperone HscB Reveals a Tetracysteine Metal-binding Domain
Bitto E., Bingman R., Bittova L., Kondrashov D., Bannen R. et al.
J Biol Chem 283, 30184 - 30192 (2008)
Solution structure of the iron:sulfur cluster cochaperone HscB and its binding surface for the iron:sulfur assembly scaffold protein IscU
Füzéry A., Tonelli M., Ta D., Cornilescu G., Vickery L. et al.
Biochemistry 47, 9394 - 9404 (2008)
Microscale NMR screening of new detergents for membrane protein structural biology
Zhang Q., Horst R., Geralt M., Ma X., Hong W. et al.
J Am Chem Soc 130, 7357 - 7363 (2008)
High-resolution structure prediction and the crystallographic phase problem
Qian B., Raman S., Das R., Bradley P., McCoy A. et al.
Nature advanced online publication, 259 - 264 (2007)
BAX activation is initiated at a novel interaction site
Gavathiotis E., Suzuki M., Davis M., Pitter K., Bird G. et al.
Nature 455, 1076 - 1081 (2008)
Protein-folding location can regulate manganese-binding versus copper- or zinc-binding
Tottey S., Waldron K., Firbank S., Reale B., Bessant C. et al.
Nature 455, 1138 - 1142 (2008)
Apoptosis: Stabbed in the BAX
Green D. and Chipuk J.
Nature 455, 1047 - 1049 (2008)
The RNA polymerase “switch region” is a target for inhibitors
Mukhopadhyay J., Das K., Ismail S., Koppstein D., Jang M. et al.
Cell 135, 295 - 307 (2008)
Predicting the sizes of large RNA molecules.
Yoffe A., Prinsen P., Gopal A., Knobler C., Gelbart W. et al.
Proc Natl Acad Sci 105, 16153 - 16158 (2008)
Emergence of symmetry in homooligomeric biological assemblies.
André I., Strauss C., Kaplan D., Bradley P. and Baker D.
Proc Natl Acad Sci 105, 16148 - 16152 (2008)
Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism.
Zhou C. and Huang R.
Proc Natl Acad Sci 105, 16142 - 16147 (2008)
Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme.
Vey J., Yang J., Li M., Broderick W., Broderick J. et al.
Proc Natl Acad Sci 105, 16137 - 16141 (2008)
Remodeling of DNA replication structures by the branch point translocase FANCM.
Gari K., Décaillet C., Delannoy M., Wu L. and Constantinou A.
Proc Natl Acad Sci 105, 16107 - 16112 (2008)
Individual binding pockets of importin-{beta} for FG-nucleoporins have different binding properties and different sensitivities to RanGTP.
Otsuka S., Iwasaka S., Yoneda Y., Takeyasu K. and Yoshimura S.
Proc Natl Acad Sci 105, 16101 - 16106 (2008)
Cortisone dissociates the Shaker family K+ channels from their [beta] subunits
Pan Y., Weng J., Kabaleeswaran V., Li H., Cao Y. et al.
Nat Chem Biol 4, 708 - 714 (2008)
Targeted polypharmacology: discovery of dual inhibitors of tyrosine and phosphoinositide kinases
Apsel B., Blair J., Gonzalez B., Nazif T., Feldman M. et al.
Nat Chem Biol 4, 691 - 699 (2008)
Conformational transition of Sec machinery inferred from bacterial SecYE structures
Tsukazaki T., Mori H., Fukai S., Ishitani R., Mori T. et al.
Nature 455, 988 - 991 (2008)
A role for the two-helix finger of the SecA ATPase in protein translocation
Erlandson K., Miller S., Nam Y., Osborne A., Zimmer J. et al.
Nature 455, 984 - 987 (2008)
The mode of Hedgehog binding to Ihog homologues is not conserved across different phyla
McLellan J., Zheng X., Hauk G., Ghirlando R., Beachy P. et al.
Nature 455, 979 - 983 (2008)
Structure of a complex of the ATPase SecA and the protein-translocation channel
Zimmer J., Nam Y. and Rapoport T.
Nature 455, 936 - 943 (2008)
Structural biology: Clamour for a kiss
Economou A.
Nature 455, 879 - 880 (2008)
Structural and mechanistic insights into STIM1-mediated initiation of store-operated calcium entry
Cell 135, 110 - 122 (2008)
Small molecule-induced allosteric activation of the Vibrio cholerae RTX cysteine protease domain
Lupardus P., Shen A., Bogyo M. and Garcia K.
Science 322, 265 - 268 (2008)
The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix
Hashimoto H., Horton J., Zhang X., Bostick M., Jacobsen S. et al.
Nature 455, 826 - 829 (2008)
Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1
Avvakumov G., Walker J., Xue S., Li Y., Duan S. et al.
Nature 455, 822 - 825 (2008)
Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism
Arita K., Ariyoshi M., Tochio H., Nakamura Y. and Shirakawa M.
Nature 455, 818 - 821 (2008)
Large-scale evaluation of protein reductive methylation for improving protein crystallization
Kim Y., Quartey P., Li H., Volkart L., Hatzos C. et al.
Nature Methods 5, 853 - 854 (2008)
Data management in structural genomics: an overview
Haquin S., Oeuillet E., Pajon A., Harris M., Jones A. et al.
Methods Mol Biol 426, 49 - 79 (2008)
Structures of open (R) and close (T) states of prephenate dehydratase (PDT)--implication of allosteric regulation by L-phenylalanine
Tan K., Li H., Zhang R., Gu M., Clancy S. et al.
J Struct Biol 162, 94 - 107 (2008)
Physical protein-protein interactions predicted from microarrays
Soong T., Wrzeszczynski K. and Rost B.
Bioinformatics 24, 2608 - 2614 (2008)
Automated identification of complementarity determining regions (CDRs) reveals peculiar characteristics of CDRs and B cell epitopes
Ofran Y., Schlessinger A. and Rost B.
J Immunol 181, 6230 - 6235 (2008)
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