SALVAGE METHODS APPLIED TO FAILED PFAM FAMILIES Anna Grzechnik 1, Dennis Carlton 1, Heath Klock 2 Mark W. Knuth 2 and Scott A. Lesley 1,2* 1 The Joint Center for Structural Genomics (JCSG), The Scripps Research Institute 2 JCSG, The Genomics Institute of the Novartis Research Institute NIH Bottlenecks Meeting 4/15/08

Protein families come in all shapes and sizes Common traits which allow us to recognize them but individual characteristics can vary greatly

Protein families are collections of related sequences. Draft 1 and 2 Pfam families are large with many potential targets.

With 100 or more potential family members, we have the pick of the litter We want these targets. Not these targets.

Target Selection Within Pfam Assignments PG1132I A resolution Practical Filters: genomic DNA, #met, #cys 8 targets with crystals to beamline 87 targets pursued from PF

Just doing more targets is not enough. Select 82 families from 400 Draft 1 and 2 targets which failed using multiple targets. Find the best possible targets from all genomes and process through a full panel of salvage strategies.

Low Temperature Expression 37C 25C 188 Targets from failed 82 families Microscreen expression and purification with total yield solubility cutoff

Low Temperature Expression Micro-ANSEC analysis. Highly parallel, quick (12 min) run times, minimal resolution for aggregation testing

Low Temperature Expression

Making Truncations Klock HE, Koesema EJ, Knuth MW, Lesley SA (2008) Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts. Proteins 7: PIPE cloning facilitates making truncations and point mutations What truncations to make? nested N- and C-terminal bioinformatic predictions experimentally determined

1 MRGMMLGMLAETHIHSGAGRSEGFVDLPVA REAVTSYPVIAGSSLKGALRDAARERGMDE SIFGDQDRAGDVLVSDARLLLLPVRSLTGS YRWVTCPHILERLSRDMRLCGISDGFEGAS VERGKACCTDDLNQIFLEEREFQRSNGIDG ALIDALKKMVPHKQTASRLERQLVIISDDD FGWFASYGLPVIARNKLDDNKKSKNLWYEE ALAPDTLMYAMVFERKDGALGKVQSMFETK PYLQLGGNETVGMGWFAVKILEQGEGR 267 Uncleaved Cleaved 1 MRGMMLGMLAETHIHSGAGRSEGFVDLPVA REAVTSYPVIAGSSLKGALRDAARERGMDE SIFGDQDRAGDVLVSDARLLLLPVRSLTGS YRWVTCPHILERLSRDMRLCGISDGFEGAS VERGKACCTDDLNQIFLEEREFQRSNGIDG ALIDALKKMVPHKQTASRLERQLVIISDDD FGWFASYGLPVIARNKLDDNKKSKNLWYEE ALAPDTLMYAMVFERKDGALGKVQSMFETK PYLQLGGNETVGMGWFAVKILEQGEGR 267 Overlapping fragment not pursued further PT03787B-mth Partial Proteolysis PT03787B-mth Fragment was reconstructed, re-expressed and is currently in crystal trials.

Deuterium Exchange Mass Spectrometry (DXMS) DXMS identifies regions of disorder and flexibility by mapping the location of rapid hydrogen/deuterium exchange to peptides derived from targets of interest. The information can be used to design expression constructs with improved crystallization properties (Spraggon et al., 2004). PFAM 6249: Ethanolamine utilization protein eutQ from Salmonella typhimurium LT2 FL-protein: poor crystallization Truncation: 1.9 Å structure

I II III IV V

Surface Mutagenesis

Ligand Screening Target: PG1132F Target PG1132F binds Blue resin suggesting nucleotide binding. Target is screened against nucleotide ligand library by thermofluor. Binding to ADP and GDP is observed. 185 Targets 74 Non binding targets Targets that do not bind to the resin are screened against a 300 ligand library 111 Targets bind Affi-Gel Blue Method courtesy of Chang Yub-Kim Methods of ligand screening used: Thermofluor: fluorescent detection of melting temperature DSC: detection of differences in protein heat capacity Stargazer: light scattering detection of aggregation Nucleotide-Like Ligand Library: ADP GDP ADP Ribose GTP AMP NAD ATP NADP CDP NADPH CMP Tryptophan CTP cAMP

Target PS04248 RM Target PS03963 No mountable crystals were available from native protein. After reductive methylation, two conditions produced harvestable crystals which are currently in finescreening. Structure of PS04248 was solved with Reductive Methylation RM Reductive Methylation

UCSD & Burnham Bioinformatics Core John Wooley Adam Godzik Lukasz Jaroszewski Sri Krishna Subramanian Andrew Morse Tamara Astakhova Lian Duan Piotr Kozbial Dana Weekes Natasha Sefcovic Prasad Burra Josie Alaoen Cindy Cook GNF & TSRI Crystallomics Core Scott Lesley Mark Knuth Heath Klock Dennis Carlton Thomas Clayton Christina Trout Marc Deller Daniel McMullan Polat Abdubek Julie Feuerhelm Joanna Hale Jessica Paulsen Thamara Janaratne Hope Johnson Edward Nigoghossian Linda Okach Sebastian Sudek Glen Spraggon Sanjay Agarwalla Anna Grzechnik Regina Gorski Connie Chen Dustin Ernst TSRI NMR Core Kurt Wüthrich Reto Horst Maggie Johnson Amaranth Chatterjee Michael Geralt Wojtek Augustyniak Pedro Serrano Bill Pedrini William Placzek TSRI Administrative Core Ian Wilson Marc Elsliger Gye Won Han David Marciano Henry Tien Lisa van Veen Stanford /SSRL Structure Determination Core Keith Hodgson Ashley Deacon Mitchell Miller Herbert Axelrod Hsiu-Ju (Jessica) Chiu Kevin Jin Christopher Rife Qingping Xu Silvya Oommachen Henry van den Bedem Scott Talafuse Ronald Reyes Abhinav Kumar Christine Trame The JCSG is supported by the NIH Protein Structure Initiative (PSI) Grant U54 GM from NIGMS (