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165 results on '"Henry van den Bedem"'

151. Crystal structure of a tandem cystathionine-beta-synthase (CBS) domain protein (TM0935) from Thermotoga maritima at 1.87 A resolution

Author

Jaume M. Canaves, Timothy M. McPhillips, Kevin Quijano, Linda S. Brinen, Mitchell D. Miller, Peter Kuhn, Polat Abdubek, Ross Floyd, Mike DiDonato, John Wooley, Guenter Wolf, Jamison Cambell, Eric Koesema, Marc-André Elsliger, Raymond C. Stevens, Carina Grittini, Daniel McMullan, Inna Levin, Xiaoping Dai, Henry van den Bedem, Said Eshagi, Cathy Karlak, Alyssa Robb, Andrew T. Morse, Juli Vincent, Kin Moy, Jie Ouyang, Slawomir K. Grzechnik, Andreas Kreusch, Rebecca Page, Bill West, Frank von Delft, Keith O. Hodgson, Heath E. Klock, Hsiu-Ju Chiu, Robert Schwarzenbacher, Xianhong Wang, Scott A. Lesley, John S. Kovarik, Jeff Velasquez, Lukasz Jaroszewski, Qingping Xu, Eric Hampton, Tanya Biorac, Adam Godzik, Ashley M. Deacon, Ian A. Wilson, Eileen Ambing, and Glen Spraggon

Subjects
Models, Molecular, Crystallography, biology, Tandem, Resolution (electron density), Molecular Sequence Data, CBS domain, Cystathionine beta-Synthase, Crystal structure, biology.organism_classification, Biochemistry, Cystathionine beta synthase, Protein Structure, Secondary, Protein Structure, Tertiary, Bacterial Proteins, Structural Biology, Thermotoga maritima, biology.protein, Transferase, Amino Acid Sequence, Molecular Biology
Published
2004

152. Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 A resolution

Author

Lukasz Jaroszewski, Alyssa Robb, Glen Spraggon, John Wooley, Andrew T. Morse, Jie Ouyang, Juli Vincent, Qingping Xu, Jaume M. Canaves, John S. Kovarik, Slawomir K. Grzechnik, Jamison Cambell, Eric Koesema, Mitchell D. Miller, Guenter Wolf, Linda S. Brinen, Daniel McMullan, Bill West, Xianhong Wang, Scott A. Lesley, Eric Hampton, Fred Rezezadeh, Raymond C. Stevens, Inna Levin, Timothy M. McPhillips, Heath E. Klock, Ian A. Wilson, Eric Sims, Mike DiDonato, Jeff Velasquez, Carina Grittini, Peter Kuhn, Eileen Ambing, Henry van den Bedem, Andreas Kreusch, Rebecca Page, Cathy Karlak, Ross Floyd, Robert Schwarzenbacher, Keith O. Hodgson, Ashley M. Deacon, Xiaoping Dai, Kevin Quijano, Kin Moy, Polat Abdubek, Ron Reyes, Tanya Biorac, Adam Godzik, Marc-André Elsliger, Frank von Delft, and Hsiu-Ju Chiu

Subjects
Models, Molecular, biology, Chemistry, Molecular Sequence Data, Resolution (electron density), Saccharomyces cerevisiae, Crystal structure, Crystallography, X-Ray, biology.organism_classification, Biochemistry, Protein Structure, Secondary, Ureohydrolases, Protein Structure, Tertiary, Multienzyme Complexes, Structural Homology, Protein, Structural Biology, Hydrolase, Allantoicase, Amino Acid Sequence, Molecular Biology, Conserved Sequence
Published
2004

153. Crystal structure of an orphan protein (TM0875) from Thermotoga maritima at 2.00-A resolution reveals a new fold

Author

Lukasz Jaroszewski, Ian A. Wilson, Alyssa Robb, Bill West, Carina Grittini, Glen Spraggon, Andrew T. Morse, Juli Vincent, Said Eshagi, Marc-André Elsliger, Timothy M. McPhillips, Raymond C. Stevens, Kevin Quijano, Keith O. Hodgson, Ashley M. Deacon, Frank von Delft, Guenter Wolf, Jaume M. Canaves, Mitchell D. Miller, Kin Moy, Adam Godzik, Xianhong Wang, Scott A. Lesley, Jie Ouyang, Eric Koesema, Henry van den Bedem, Linda S. Brinen, Robert Schwarzenbacher, Xiaoping Dai, Constantina Bakolitsa, Daniel McMullan, Andreas Kreusch, Rebecca Page, Peter Kuhn, H. Klock, Ross Floyd, Cathy Karlak, Slawomir K. Grzechnik, John Wooley, Jeff Velasquez, and John S. Kovarik

Subjects
Models, Molecular, Molecular Sequence Data, Sequence Homology, Fold (geology), Crystal structure, Biology, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Crystallography, Bacterial Proteins, Structural Biology, Structural Homology, Protein, Thermotoga maritima, Multiprotein Complexes, Amino Acid Sequence, Molecular Biology
Published
2004

154. Crystal structure of a putative NADPH-dependent oxidoreductase (GI: 18204011) from mouse at 2.10 A resolution

Author

Andreas Kreusch, Rebecca Page, Qingping Xu, Henry van den Bedem, Carina Grittini, Xiaoping Dai, Raymond C. Stevens, Slawomir K. Grzechnik, Hsiu-Ju Chiu, Jie Ouyang, Guenter Wolf, Bill West, Kevin Quijano, Heath E. Klock, Xianhong Wang, Scott A. Lesley, Michael Didonato, Jamison Cambell, Polat Abdubek, Marc-André Elsliger, Jaume M. Canaves, Eric Koesema, Kin Moy, Lukasz Jaroszewski, Frank von Delft, Alyssa Robb, Keith O. Hodgson, Andrew T. Morse, Juli Vincent, Inna Levin, Jeff Velasquez, John Wooley, Cathy Karlak, Mitchell D. Miller, Glen Spraggon, Peter Kuhn, Eric Hampton, Robert Schwarzenbacher, Tanya Biorac, Adam Godzik, Daniel McMullan, Ron Reyes, Timothy M. McPhillips, Eric Sims, Ian A. Wilson, Eileen Ambing, and Ashley M. Deacon

Subjects
chemistry.chemical_classification, Models, Molecular, Binding Sites, Chemistry, Stereochemistry, Resolution (electron density), Molecular Sequence Data, Crystal structure, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Protein Structure, Tertiary, Crystallography, Mice, Structural Biology, Oxidoreductase, Structural Homology, Protein, Animals, Amino Acid Sequence, Quinone Reductases, Oxidoreductases, Molecular Biology, NADP
Published
2004

155. Crystal structure of a ribose-5-phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 A resolution

Author

Xianhong Wang, Scott A. Lesley, Jie Ouyang, Timothy M. McPhillips, Marc-André Elsliger, Kevin Quijano, John S. Kovarik, Linda S. Brinen, Guenter Wolf, Ashley M. Deacon, Robert Schwarzenbacher, Kin Moy, Henry van den Bedem, Frank von Delft, John Wooley, Raymond C. Stevens, Glen Spraggon, Peter Kuhn, Alyssa Robb, Jeff Velasquez, Ross Floyd, Andrew T. Morse, Mitchell D. Miller, Juli Vincent, Jaume M. Canaves, Andreas Kreusch, Keith O. Hodgson, Rebecca Page, Xiaoping Dai, Slawomir K. Grzechnik, Bill West, Said Eshagi, Cathy Karlak, Ian A. Wilson, Carina Grittini, Eric Koesema, Adam Godzik, Daniel McMullan, Inna Levin, Lukasz Jaroszewski, Qingping Xu, and Heath E. Klock

Subjects
Models, Molecular, biology, Chemistry, Stereochemistry, Resolution (electron density), Reproducibility of Results, Isomerase, Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Ribose-5-phosphate isomerase, Structural Biology, Thermotoga maritima, Crystallization, Molecular Biology, Aldose-Ketose Isomerases
Published
2004

156. Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution

Author

Jie Ouyang, Andreas Kreusch, Rebecca Page, John Wooley, Heath E. Klock, Ashley M. Deacon, Mitchell D. Miller, Hsiu-Ju Chiu, Jaume M. Canaves, Glen Spraggon, Mike DiDonato, Jamison Campbell, Henry van den Bedem, Linda S. Brinen, Guenter Wolf, Kin Moy, Eric Hampton, Marc-André Elsliger, Keith O. Hodgson, Tanya Biorac, Adam Godzik, Ian A. Wilson, Peter Kuhn, Jeff Velasquez, Fred Rezezadeh, Ross Floyd, Bill West, Eileen Ambing, Ron Reyes, Raymond C. Stevens, Timothy M. McPhillips, Frank von Delft, Xiaoping Dai, Eric Sims, John S. Kovarik, Eric Koesema, Robert Schwarzenbacher, Alyssa Robb, Andrew T. Morse, Juli Vincent, Xianhong Wang, Scott A. Lesley, Kevin Quijano, Carina Grittini, Slawomir K. Grzechnik, Polat Abdubek, Daniel McMullan, Inna Levin, Cathy Karlak, Qingping Xu, and Lukasz Jaroszewski

Subjects
Exonucleases, Models, Molecular, Protein Folding, Protein Conformation, Archaeal Proteins, Molecular Sequence Data, Crystal structure, Siphoviridae, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Viral Proteins, Protein structure, Structural Biology, Amino Acid Sequence, Molecular Biology, Peptide sequence, Binding Sites, Sequence Homology, Amino Acid, Resolution (electron density), Archaeoglobus fulgidus, Protein Structure, Tertiary, N-terminus, Crystallography, Protein folding, PIN domain
Published
2004

157. Crystal structure of an aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 A resolution

Author

Glen Spraggon, Slawomir K. Grzechnik, Andreas Kreusch, Rebecca Page, Kevin Quijano, Polat Abdubek, Jie Ouyang, Marc-André Elsliger, H.-J. Chiu, Cathy Karlak, Adam Godzik, Raymond C. Stevens, Alyssa Robb, Said Eshagi, Frank von Delft, Kin Moy, Tanja Biorac, Guenter Wolf, Andrew T. Morse, Juli Vincent, Linda S. Brinen, Heath E. Klock, Jaume M. Canaves, Carina Grittini, Robert Schwarzenbacher, John Wooley, Ashley M. Deacon, Daniel McMullan, Inna Levin, Peter Kuhn, Xiaoping Dai, Jamison Cambell, Ian A. Wilson, Ross Floyd, Eric Koesema, Mitchell D. Miller, Jeff Velasquez, Eileen Ambing, Xianhong Wang, Scott A. Lesley, Keith O. Hodgson, John S. Kovarik, Lukasz Jaroszewski, Mike DiDonato, Henry van den Bedem, Qingping Xu, Eric Hampton, Bill West, and Timothy M. McPhillips

Subjects
Models, Molecular, biology, Chemistry, Resolution (electron density), Molecular Sequence Data, Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Crystallography, Bacterial Proteins, Structural Biology, Thermotoga maritima, Transferase, Amino Acid Sequence, Aspartate Aminotransferases, Molecular Biology, Peptide sequence
Published
2004

158. Crystal structure of an HEPN domain protein (TM0613) from Thermotoga maritima at 1.75 A resolution

Author

Heidi, Erlandsen, Jaume M, Canaves, Marc-André, Elsliger, Frank, von Delft, Linda S, Brinen, Xiaoping, Dai, Ashley M, Deacon, Ross, Floyd, Adam, Godzik, Carina, Grittini, Slawomir K, Grzechnik, Lukasz, Jaroszewski, Heath E, Klock, Eric, Koesema, John S, Kovarik, Andreas, Kreusch, Peter, Kuhn, Scott A, Lesley, Daniel, McMullan, Timothy M, McPhillips, Mitchell D, Miller, Andrew, Morse, Kin, Moy, Jie, Ouyang, Rebecca, Page, Alyssa, Robb, Kevin, Quijano, Robert, Schwarzenbacher, Glen, Spraggon, Raymond C, Stevens, Henry, van den Bedem, Jeff, Velasquez, Juli, Vincent, Xianhong, Wang, Bill, West, Guenter, Wolf, Keith O, Hodgson, John, Wooley, and Ian A, Wilson

Subjects
Models, Molecular, Bacterial Proteins, Genes, Bacterial, Molecular Sequence Data, Reproducibility of Results, Thermotoga maritima, Amino Acid Sequence, Crystallography, X-Ray, Protein Structure, Tertiary
Published
2004

159. Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 A resolution

Author

John Wooley, Xiaoping Dai, Glen Spraggon, Said Eshaghi, Keith O. Hodgson, Slawomir K. Grzechnik, Jaume M. Canaves, Mitchell D. Miller, Lukasz Jaroszewski, John S. Kovarik, Jie Ouyang, Eric Koesema, Timothy M. McPhillips, Adam Godzik, Frank von Delft, Kin Moy, Alyssa Robb, Andrew T. Morse, Juli Vincent, Jeff Velasquez, Raymond C. Stevens, Guenter Wolf, Ian A. Wilson, Andreas Kreusch, Peter Kuhn, Rebecca Page, Ross Floyd, Robert Schwarzenbacher, Marc A. Elsliger, Xianhong Wang, Scott A. Lesley, Ashley M. Deacon, Linda S. Brinen, Henry van den Bedem, Kevin Rodrigues, Bill West, Thomas L. Selby, Daniel McMullan, Carina Grittini, Mark A. Miller, Cathy Karlak, Chittibabu Guda, and Heath E. Klock

Subjects
Models, Molecular, Stereochemistry, Molecular Sequence Data, Alcohol oxidoreductase, Dehydrogenase, Crystal structure, Crystallography, X-Ray, Biochemistry, chemistry.chemical_compound, Bacterial Proteins, Structural Biology, Oxidoreductase, Iron-Binding Proteins, Thermotoga maritima, 1,3-Propanediol, Amino Acid Sequence, Molecular Biology, Alcohol dehydrogenase, chemistry.chemical_classification, biology, Resolution (electron density), Alcohol Dehydrogenase, biology.organism_classification, Alcohol Oxidoreductases, chemistry, biology.protein
Published
2004

160. Automation of High-Throughput Crystal Screening and Data Collection at SSRL

Author

Timothy M. McPhillips, Henry van den Bedem, Ashley M. Deacon, Günter Wolf, S.E. McPhillips, Paul J. Ellis, Aina E. Cohen, R. Paul Phizackerley, Linda S. Brinen, Zepu Zhang, S. Michael Soltis, Qingping Xu, and Mitchell D. Miller

Subjects
Engineering, Data collection, Beamline, business.industry, Interface (computing), Electrical engineering, business, Distributed control system, Automation, Throughput (business), Sample (graphics), Computer hardware, Graphical user interface
Abstract

A robotic system for auto‐mounting crystals from liquid nitrogen is now operational on SSRL beamlines (Cohen et al., J. Appl. Cryst. (2002). 35, 720–726). The system uses a small industrial 4‐axis robot with a custom built actuator. Once mounted, automated alignment of the sample loop to the X‐ray beam readies the crystal for data collection. After data collection, samples are returned to the cassette. The beamline Dewar accommodates three compact sample cassettes (holding up to 96 samples each). During the past 4 months, the system on beamline 11‐1 has been used to screen over 1000 crystals. The system has reduced both screening time and manpower. Integration of the hardware components is accomplished in the Distributed Control System architecture developed at SSRL (McPhillips et al., J. Synchrotron Rad. (2002) 9, 401–406). A crystal‐screening interface has been implemented in Blu‐Ice. Sample details can be uploaded from an Excel spreadsheet. The JCSG generates these spreadsheets automatically from their tracking database using standard database tools (http://www.jcsg.org). New diffraction image analysis tools are being employed to aid in extracting results. Automation also permits tele‐presence. For example, samples have been changed during the night without leaving home and scientists have screened crystals 1600 miles from the beamline. The system developed on beamline 11‐1 has been replicated onto 1‐5, 9‐1, 9‐2, and 11‐3 and is used by both general users and the JCSG.

Published
2004
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161. Crystal structure of uronate isomerase (TM0064) from Thermotoga maritima at 2.85 A resolution

Author

Robert, Schwarzenbacher, Jaume M, Canaves, Linda S, Brinen, Xiaoping, Dai, Ashley M, Deacon, Marc A, Elsliger, Said, Eshaghi, Ross, Floyd, Adam, Godzik, Carina, Grittini, Slawomir K, Grzechnik, Chittibabu, Guda, Lukasz, Jaroszewski, Cathy, Karlak, Heath E, Klock, Eric, Koesema, John S, Kovarik, Andreas, Kreusch, Peter, Kuhn, Scott A, Lesley, Daniel, McMullan, Timothy M, McPhillips, Mark A, Miller, Mitchell D, Miller, Andrew, Morse, Kin, Moy, Jie, Ouyang, Alyssa, Robb, Kevin, Rodrigues, Thomas L, Selby, Glen, Spraggon, Raymond C, Stevens, Henry, van den Bedem, Jeff, Velasquez, Juli, Vincent, Xianhong, Wang, Bill, West, Guenter, Wolf, Keith O, Hodgson, John, Wooley, and Ian A, Wilson

Subjects
Models, Molecular, Molecular Structure, Thermotoga maritima, Crystallography, X-Ray, Aldose-Ketose Isomerases, Protein Structure, Tertiary
Published
2003

162. Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 A resolution

Author

Peter, Kuhn, Scott A, Lesley, Irimpan I, Mathews, Jaume M, Canaves, Linda S, Brinen, Xiaoping, Dai, Ashley M, Deacon, Marc A, Elsliger, Said, Eshaghi, Ross, Floyd, Adam, Godzik, Carina, Grittini, Slawomir K, Grzechnik, Chittibabu, Guda, Keith O, Hodgson, Lukasz, Jaroszewski, Cathy, Karlak, Heath E, Klock, Eric, Koesema, John M, Kovarik, Andreas T, Kreusch, Daniel, McMullan, Timothy M, McPhillips, Mark A, Miller, Mitchell, Miller, Andrew, Morse, Kin, Moy, Jie, Ouyang, Alyssa, Robb, Kevin, Rodrigues, Thomas L, Selby, Glen, Spraggon, Raymond C, Stevens, Susan S, Taylor, Henry, van den Bedem, Jeff, Velasquez, Juli, Vincent, Xianhong, Wang, Bill, West, Guenter, Wolf, John, Wooley, and Ian A, Wilson

Subjects
Models, Molecular, Thermotoga maritima, Thymidylate Synthase, Crystallography, X-Ray, Sensitivity and Specificity
Published
2002

163. Radiation damage effects on protein conformation at room temperature and 100K

Author

Shawn Kann, Silvia Russi, Henry van den Bedem, and Ana Gonzalez

Subjects
Inorganic Chemistry, Protein structure, Structural Biology, Chemistry, Biophysics, Radiation damage, General Materials Science, Physical and Theoretical Chemistry, Condensed Matter Physics, Biochemistry
Abstract

Protein crystallography data collection at synchrotrons today is routinely carried out at cryogenic temperatures to mitigate radiation damage to the crystal. Although damage still takes place, at 100 K and below, the immobilization of free radicals increases the lifetime of the crystals by orders of magnitude. Increasingly, experiments are carried out at room temperature. The lack of adequate cryo-protectants, the induced lattice changes or internal disorders during the cooling process, and the convenience of collecting data directly from the crystallization plates, are some of the reasons. Moreover, recent studies have shown that flash-freezing affects the conformational ensemble of crystal structures [1], and can hide important functional mechanisms from observation [2]. While there has been a considerable amount of effort in studying radiation damage at cryo-temperatures, its effects at room temperature are still not well understood. We investigated the effects of data collection temperature on secondary local damage to the side chain and main chain from different proteins. Data were collected from crystals of thaumatin and lysozyme at 100 K and room temperature. To carefully control the total absorbed dose, full data sets at room temperature were assembled from a few diffraction images per crystal. Several data sets were collected at increasing levels of absorbed dose. Our analysis shows that while at cryogenic temperatures, radiation damage increases the conformational variability, _x0004_at room temperature it has the opposite effect_x0005_. We also observed that disulfide bonds appear to break up at a different relative rate at room temperature, perhaps because of a more active repair mechanism. Our analysis suggests that elevated conformational heterogeneity in crystal structures at room temperature is observed despite radiation damage, and not as a result thereof.

Published
2014
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164. Bacterial Pleckstrin Homology Domains: A Prokaryotic Origin for the PH Domain

Author

Lukasz Jaroszewski, Dustin C. Ernst, Keith O. Hodgson, Lian Duan, Tamara Astakhova, Abhinav Kumar, Tiffany Wooten, Michelle Chiu, Julie Feuerhelm, Edward Nigoghossian, Daniel McMullan, Gye Won Han, Qingping Xu, Christine B Trame, Linda Okach, Debanu Das, Herbert L. Axelrod, Polat Abdubek, Heath E. Klock, Carol L. Farr, Mitchell D. Miller, Sanjay Krishna, Alex Bateman, Henry van den Bedem, Anna Grzechnik, David Marciano, Thomas Clayton, Marc C. Deller, Connie Chen, Christopher L. Rife, Natasha Sefcovic, John Wooley, Constantina Bakolitsa, Kevin K. Jin, Hsiu-Ju Chiu, Amanda Nopakun, Marc André Elsliger, Andrew T. Morse, Dennis Carlton, Ian A. Wilson, Christina Puckett, Adam Godzik, Ashley M. Deacon, Kyle Ellrott, Joanna C Grant, Robert D. Finn, Dana Weekes, Piotr Kozbial, Henry J Tien, Mark W. Knuth, Ron Reyes, and Scott A. Lesley

Subjects
Models, Molecular, asu, asymmetric unit, Protein Data Bank (RCSB PDB), SSRL, Stanford Synchrotron Radiation Lightsource, Crystallography, X-Ray, Protein Structure, Secondary, chemistry.chemical_compound, PH, Pleckstrin homology, Structural Biology, Pleckstrin homology (PH) domain, Conserved Sequence, 0303 health sciences, 030302 biochemistry & molecular biology, bacterial PH domain (PHb), Pleckstrin homology domain, Eukaryotic Cells, Biochemistry, Domain (ring theory), TCEP, higher-order symmetry, DUF1696, domain of unknown function family 1696, lipids (amino acids, peptides, and proteins), VPS36, vacuolar protein sorting protein 36, Protein Binding, Protein family, Surface Properties, Stereochemistry, Molecular Sequence Data, PTB, phosphotyrosine binding, protein assembly, Biology, Ring (chemistry), Article, TEV, tobacco etch virus, Structural genomics, Evolution, Molecular, 03 medical and health sciences, TCEP, tris(2-carboxyethyl)phosphine–HCl, Bacterial Proteins, PDB, Protein Data Bank, MAD, multiwavelength anomalous diffraction, ALS, Advanced Light Source, Amino Acid Sequence, Protein Structure, Quaternary, PIPE, Polymerase Incomplete Primer Extension, protein evolution, Molecular Biology, PEG, polyethylene glycol, 030304 developmental biology, Binding Sites, Bacteria, Sequence Homology, Amino Acid, biology.organism_classification, Protein Structure, Tertiary, JCSG, Joint Center for Structural Genomics, Prokaryotic Cells, chemistry, PHb, bacterial PH domain, Sequence Alignment
Abstract

Pleckstrin homology (PH) domains have been identified only in eukaryotic proteins to date. We have determined crystal structures for three members of an uncharacterized protein family (Pfam PF08000), which provide compelling evidence for the existence of PH-like domains in bacteria (PHb). The first two structures contain a single PHb domain that forms a dome-shaped, oligomeric ring with C5 symmetry. The third structure has an additional helical hairpin attached at the C-terminus and forms a similar but much larger ring with C12 symmetry. Thus, both molecular assemblies exhibit rare, higher-order, cyclic symmetry but preserve a similar arrangement of their PHb domains, which gives rise to a conserved hydrophilic surface at the intersection of the β-strands of adjacent protomers that likely mediates protein–protein interactions. As a result of these structures, additional families of PHb domains were identified, suggesting that PH domains are much more widespread than originally anticipated. Thus, rather than being a eukaryotic innovation, the PH domain superfamily appears to have existed before prokaryotes and eukaryotes diverged.

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165. Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR

Author

James S. Fraser, Gregory A. Petsko, Mark A. Wilson, Daniel A. Keedy, David A. Sivak, Dagmar Ringe, and Henry van den Bedem

Subjects
Models, Molecular, Protein Structure, Protein Conformation, Physics::Instrumentation and Detectors, Static Electricity, Biophysics, Molecular Dynamics Simulation, Crystallography, X-Ray, Article, Crystal, Molecular dynamics, Protein structure, Models, Structural Biology, Information and Computing Sciences, Dihydrofolate reductase, Static electricity, Escherichia coli, Molecular Biology, Quantitative Biology::Biomolecules, Crystallography, Quenching (fluorescence), biology, Chemistry, Escherichia coli Proteins, Molecular, Energy landscape, Biological Sciences, Protein Structure, Tertiary, Cold Temperature, Tetrahydrofolate Dehydrogenase, Chemical Sciences, X-Ray, biology.protein, Generic health relevance, Crystallization, Tertiary, Macromolecule
Abstract

SummaryMost macromolecular X-ray structures are determined from cryocooled crystals, but it is unclear whether cryocooling distorts functionally relevant flexibility. Here we compare independently acquired pairs of high-resolution data sets of a model Michaelis complex of dihydrofolate reductase (DHFR), collected by separate groups at both room and cryogenic temperatures. These data sets allow us to isolate the differences between experimental procedures and between temperatures. Our analyses of multiconformer models and time-averaged ensembles suggest that cryocooling suppresses and otherwise modifies side-chain and main-chain conformational heterogeneity, quenching dynamic contact networks. Despite some idiosyncratic differences, most changes from room temperature to cryogenic temperature are conserved and likely reflect temperature-dependent solvent remodeling. Both cryogenic data sets point to additional conformations not evident in the corresponding room temperature data sets, suggesting that cryocooling does not merely trap preexisting conformational heterogeneity. Our results demonstrate that crystal cryocooling consistently distorts the energy landscape of DHFR, a paragon for understanding functional protein dynamics.

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