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The collection includes articles from PSI research groups and the broader community
April 2010
Structural mechanism of host Rab1 activation by the bifunctional Legionella type IV effector SidM/DrrA
Zhua Y., Hua L., Zhou Y., Yaoa Q., Liua L. et al.
Proceedings of the National Academy of Sciences 107, 4699 (2010)
Visualization of macromolecular structures
O'Donoghue S., Goodsell D., Frangakis A., Jossinet F., Laskowski R. et al.
Nature Methods 7, S42 (2010)
Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4
Rechkoblit O., Kolbanovskiy A., Malinina L., Geacintov N., Broyde S. et al.
Nat Struct Mol Biol 17, 379 - 388 (2010)
The structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase
Lee L., Stewart A., Donohoe M., Bernal R. and Stock D.
Nat Struct Mol Biol 17, 373 - 378 (2010)
Two-step adhesive binding by classical cadherins
Harrison O., Bahna F., Katsamba P., Jin X., Brasch J. et al.
Nat Struct Mol Biol 17, 348 - 357 (2010)
T-cadherin structures reveal a novel adhesive binding mechanism
Ciatto C., Bahna F., Zampieri N., Vansteenhouse H., Katsamba P. et al.
Nat Struct Mol Biol 17, 339 - 347 (2010)
Molecular mechanism of the synaptotagmin-SNARE interaction in Ca2+-triggered vesicle fusion
Vrljic M., Strop P., Ernst J., Sutton R., Chu S. et al.
Nat Struct Mol Biol 17, 325 - 331 (2010)
The structure of the catalytic subunit FANCL of the Fanconi anemia core complex
Cole A., Lewis L. and Walden H.
Nat Struct Mol Biol 17, 294 - 298 (2010)
The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome
Stanley R., Blaha G., Grodzicki R., Strickler M. and Steitz T.
Nat Struct Mol Biol 17, 289 - 293 (2010)
Munc13 C2B domain is an activity-dependent Ca2+ regulator of synaptic exocytosis
Shin O., Lu J., Rhee J., Tomchick D., Pang Z. et al.
Nat Struct Mol Biol 17, 280 - 288 (2010)
Intersubunit capture of regulatory segments is a component of cooperative CaMKII activation
Chao L., Pellicena P., Deindl S., Barclay L., Schulman H. et al.
Nat Struct Mol Biol 17, 264 - 272 (2010)
Active site remodelling accompanies thioester bond formation in the SUMO E1
Olsen S., Capili A., Lu X., Tan D. and Lima C.
Nature 463, 906 - 912 (2010)
Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium
Tripp H.J., Bench S., Turk K., Foster R., Desany B. et al.
Nature 464, 90 - 94 (2010)
A human gut microbial gene catalogue established by metagenomic sequencing
Qin J., Li R., Raes J., Arumugam M., Burgdorf K. et al.
Nature 464, 59 - 65 (2010)
iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis
Stocker G., Fischer M., Rieder D., Bindea G., Kainz S. et al.
BMC Bioinformatics 10, 390 (2009)
'Hot' macromolecular crystals
Koclega K., Chruszcz M., Zimmerman M., Bujacz G. and Minor W.
Cryst Growth Des 10, 580 (2009)
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
Capra J., Laskowski R., Thornton J., Singh M. and Funkhouser T.
PLoS Comput Biology 5, e1000585 (2009)
Correlating protein function and stability through the analysis of single amino acid substitutions
Bromberg Y. and Rost B.
BMC Bioinformatics 10 Suppl 8, S8 (2009)
NMR structure and dynamics of the engineered fluorescein-binding lipocalin FluA reveal rigidification of beta-barrel and variable loops upon enthalpy-driven ligand binding
Mills J., Liu G., Skerra A. and Szyperski T.
Biochemistry 48, 7411 - 7419 (2009)
Clean absorption mode NMR data acquisition based on time-proportional phase incrementation
Wu Y., Ghosh A. and Szyperski T.
J Struct Funct Genomics 10, 227 - 232 (2009)
A primer on metagenomics
Wooley J., Godzik A. and Friedberg I.
PLoS Comput Biol 6, e1000667 (2010)
Metagenomics for the discovery of novel human viruses
Tang P. and Chiu C.
Future Microbiol 5, 177 - 189 (2010)
Identification and characterization of genes conferring salt tolerance to Escherichia coli from pond water metagenome
Kapardar R., Ranjan R., Grover A., Puri M. and Sharma R.
Bioresour Technol 101, 3917 - 3924 (2010)
From Galactic archeology to soil metagenomics - surfing on massive data streams
Martin N. and Martin F.
New Phytol 185, 343 - 347 (2010)
Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists
Katritch V., Jaakola V., Lane J., Lin J., Ijzerman A. et al.
J Med Chem 53, 1799 - 1809 (2010)
Simultaneous prediction of protein folding and docking at high resolution
Das R., André I., Shen Y., Wu Y., Lemak A. et al.
Proc Natl Acad Sci U S A 106, 18978 - 18983 (2009)
Rastering strategy for screening and centring of microcrystal samples of human membrane proteins with a sub-10 micron size X-ray synchrotron beam.
Cherezov V., Hanson M., Griffith M., Hilgart M., Sanishvili R. et al.
J R Soc Interface. 6 Suppl 5, S587 - 97 (2009)
Analysis of the varicella-zoster virus IE62 N-terminal acidic transactivating domain and its interaction with the human mediator complex
Yamamoto S., Eletsky A., Szyperski T., Hay J. and Ruyechan W.
J Virol 83, 6300 - 6305 (2009)
Discovery of new GPCR biology: one receptor structure at a time
Hanson M. and Stevens R.
Structure 17, 8 - 14 (2009)
Laterally mobile, functionalized self-assembled monolayers at the fluorous-aqueous interface in a plug-based microfluidic system: characterization and testing with membrane protein crystallization
Kreutz J., Li L., Roach L., Hatakeyama T. and Ismagilov R.
J Am Chem Soc 131, 6042 - 6043 (2009)
The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus At1g79260.1
Bianchetti C., Blouin G., Bitto E., Olson J. and Phillips J.G.
Proteins 78, 917 - 931 (2010)
Structures of RNA polymerase-antibiotic complexes
Ho M., Hudson B., Das K., Arnold E. and Ebright R.
Curr Opin Struct Biol 19, 715 - 723 (2009)
Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community
Cormier C., Mohr S., Zuo D., Hu Y., Rolfs A. et al.
Nucleic Acids Res 38, D743 - 9 (2010)
Accurate automated protein NMR structure determination using unassigned NOESY data
Raman S., Huang Y., Mao B., Rossi P., Aramini J. et al.
J Am Chem Soc. 132, 202 - 207 (2010)
User-loaded SlipChip for equipment-free multiplexed nanoliter-scale experiments
Li L., Du W. and Ismagilov R.
J Am Chem Soc 132, 106 - 111 (2010)
Multiparameter screening on SlipChip used for nanoliter protein crystallization combining free interface diffusion and microbatch methods
Li L., Du W. and Ismagilov R.
J Am Chem Soc. 132, 112 - 119 (2010)
Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety
Burgin A., Magnusson O., Singh J., Witte P., Staker B. et al.
Nat Biotech 28, 63 - 70 (2010)
NMR structure of F-actin-binding domain of Arg/Abl2 from Homo sapiens
Liu G., Huang Y., Xiao R., Wang D., Acton T. et al.
Proteins 78, 1326 - 1330 (2010)
NMR structure determination for larger proteins using backbone-only data
Raman S., Lange O., Rossi P., Tyka M., Wang X. et al.
Science 327, 1014 - 1018 (2010)
Capillarity theory for the fly-casting mechanism
Trizac E., Levy Y. and Wolynes P.
Proceedings of the National Academy of Sciences 107, 2746 - 2750 (2010)
Turning enzymes ON with small molecules
Zorn J. and Wells J.
Nat Chem Biol 6, 179 - 188 (2010)
The (un)targeted cancer kinome
Fedorov O., Muller S. and Knapp S.
Nat Chem Biol 6, 166 - 169 (2010)
DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility
Antes I.
Proteins Structure Function and Bioinformatics 78, 1084 - 1104 (2010)
Ultrafast solvation dynamics at binding and active sites of photolyases
Chang C., Guo L., Kao Y., Li J., Tan C. et al.
Proc. Natl Acad. Sci. USA 107, 2914 - 2919 (2010)
Mass spectrometry for biologists
Baker M.
Nat Meth 7, 157 - 161 (2010)
Practical cell-free protein synthesis system using purified wheat embryos
Takai K., Sawasaki T. and Endo Y.
Nat. Protocols 5, 227 - 238 (2010)
One-shot structure determination
Doerr A.
Nat Meth 7, 96 - 97 (2010)
Conformational Spread as a Mechanism for Cooperativity in the Bacterial Flagellar Switch
Branch R. and Pilizota T.
Science 327, 685 - 689 (2010)
Mechanism of folding chamber closure in a group II chaperonin
Zhang J., Baker M., Schroder G., Douglas N., Reissmann S. et al.
Nature 463, 379 - 383 (2010)
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains
Lee D., Rentzsch R. and Orengo C.
Nucleic Acids Res 38, 720 - 737 (2010)
Characterization of a Bacillus subtilis transporter for petrobactin, an anthrax stealth siderophore
Zawadzka A., Kim Y., Maltseva N., Nichiporuk R., Fan Y. et al.
Proc Natl Acad Sci U S A 106, 21854 - 21859 (2009)
Extra-cytoplasmic PAS-like Domains are Common In Signal Transduction Proteins
Chang C., Tesar C., Gu M., Babnigg G., Joachimiak A. et al.
J Bacteriol. 192, 1156 - 1159 (2010)
Structure and mechanism of a pentameric formate channel
Waight A., Love J. and Wang D.
Nat Struct Mol Biol 17, 31 - 37 (2010)
Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175
Singarapu K., Mills J., Xiao R., Acton T., Punta M. et al.
Proteins 78, 779 - 784 (2010)
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)
[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pubmed&term=18941213[uid]]
