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2013

June 2013
Resolution of structural heterogeneity in dynamic crystallography

Zhong Ren, Peter W. Y. Chan, Keith Moffat, Emil F. Pai, William E. Royer, Jr., Vukica Srajer and Xiaojing Yang
Acta Cryst. D69 (2013).
DOI: 10.1107/S0907444913003454

Dynamic behavior of proteins is critical to their function. X-ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic `structural changes' are often indirectly inferred from `structural differences' by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods.

March 2013
Structure of human enterovirus 71 in complex with a capsid-binding inhibitor

Pavel Plevka, Rushika Perera, Moh Lan Yap, Jane Cardosa, Richard J. Kuhn, and Michael G. Rossman
PNAS Early Edition (February 2013).
DOI: 10.1073/pnas.1222379110

Human enterovirus 71 is a picornavirus causing hand, foot, and mouth disease that may progress to fatal encephalitis in infants and small children. As of now, no cure is available for enterovirus 71 infections. Small molecule inhibitors binding into a hydrophobic pocket within capsid viral protein 1 were previously shown to effectively limit infectivity of many picornaviruses. Here we report a 3.2-Å-resolution X-ray structure of the enterovirus 71 virion complexed with the capsid-binding inhibitor WIN 51711. The inhibitor replaced the natural pocket factor within the viral protein 1 pocket without inducing any detectable rearrangements in the structure of the capsid. Furthermore, we show that the compound stabilizes enterovirus 71 virions and limits its infectivity, probably through restricting dynamics of the capsid necessary for genome release. Thus, our results provide a structural basis for development of antienterovirus 71 capsid-binding drugs.

February 2013
Volume-conserving trans-cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography

Yang Ouk Jung, Jae Hyuk Lee, Joonghan Kim, Marius Schmidt, Keith Moffat, Vukica Srajer, and Hyotcherl Ihee
Nat. Chem. 5, 212 (March 2013).
DOI: 10.1038/NCHEM.1565

Trans-to-cis isomerization, the key reaction in photoactive proteins, usually cannot occur through the standard one-bond-flip mechanism. Owing to spatial constraints imposed by a protein environment, isomerization probably proceeds through a volume-conserving mechanism in which highly choreographed atomic motions are expected, the details of which have not yet been observed directly. Here we employ time-resolved X-ray crystallography to visualize structurally the isomerization of the p-coumaric acid chromophore in photoactive yellow protein with a time resolution of 100 ps and a spatial resolution of 1.6 Å. The structure of the earliest intermediate (IT) resembles a highly strained transition state in which the torsion angle is located halfway between the trans- and cis-isomers. The reaction trajectory of IT bifurcates into two structurally distinct cis intermediates via hula-twist and bicycle-pedal pathways. The bifurcating reaction pathways can be controlled by weakening the hydrogen bond between the chromophore and an adjacent residue through E46Q mutation, which switches off the bicycle-pedal pathway.

See also Shedding Light on Chemistry with a Biological Twist


2012

November 2012
Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography

Friedrich Schotte, Hyun Sun Cho, Ville R.I. Kaila, Hironari Kamikubo, Naranbaatar Dashdorj, Eric R. Henry, Timothy J. Graber, Robert Henning, Michael Wulff, Gerhard Hummer, Mikio Kataoka, and Philip A. Anfinrud
Proc. Natl. Acad. Sci. USA 109(47), 19256 (November 2012)
DOI: 10.1073/pnas1210938109

To understand how signaling proteins function, it is crucial to know the time-ordered sequence of events that lead to the signaling state. We recently developed on the BioCARS 14-IDB beamline at the Advanced Photon Source the infrastructure required to characterize structural changes in protein crystals with near-atomic spatial resolution and 150-ps time resolution, and have used this capability to track the reversible photocycle of photoactive yellow protein (PYP) following trans-to-cis photoisomerization of its p-coumaric acid (pCA) chromophore over 10 decades of time. The first of four major intermediates characterized in this study is highly contorted, with the pCA carbonyl rotated nearly 90° out of the plane of the phenolate. A hydrogen bond between the pCA carbonyl and the Cys69 backbone constrains the chromophore in this unusual twisted conformation. Density functional theory calculations confirm that this structure is chemically plausible and corresponds to a strained cis intermediate. This unique structure is short-lived (∼600 ps), has not been observed in prior cryocrystallography experiments, and is the progenitor of intermediates characterized in previous nanosecond time-resolved Laue crystallography studies. The structural transitions unveiled during the PYP photocycle include trans/cis isomerization, the breaking and making of hydrogen bonds, formation/relaxation of strain, and gated water penetration into the interior of the protein. This mechanistically detailed, near-atomic resolution description of the complete PYP photocycle provides a framework for understanding signal transduction in proteins, and for assessing and validating theoretical/computational approaches in protein biophysics.

See also Watching a Protein as it Functions

October 2012
Time-resolved structural studies at synchrotrons and X-ray free electron lasers: opportunities and challenges

Richard Neutze, Keith Moffat,Current Opinion in Structural Biology. (2012). 22 (5), 651-659, doi: 10.1016/j.sbi.2012.08.006.

X-ray free electron lasers (XFELs) are potentially revolutionary X-ray sources because of their very short pulse duration, extreme peak brilliance and high spatial coherence, features that distinguish them from today's synchrotron sources. We review recent time-resolved Laue diffraction and time-resolved wide angle X-ray scattering (WAXS) studies at synchrotron sources, and initial static studies at XFELs. XFELs have the potential to transform the field of time-resolved structural biology, yet many challenges arise in devising and adapting hardware, experimental design and data analysis strategies to exploit their unusual properties. Despite these challenges, we are confident that XFEL sources are poised to shed new light on ultrafast protein reaction dynamics.

June 2012
Crystal Structure of Human Enterovirus 71

Pavel Plevka, Rushika Perera, Jane Cardosa, Richard J. Kuhn, Michael G. Rossmann, Science. (2012). 336 (6086), 1274, doi: 10.11263/science.1218713.

Enterovirus 71 is a picornavirus associated with fatal neurological illness in infants and young children. Here, we report the crystal structure of enterovirus 71 and show that, unlike in other enteroviruses, the “pocket factor,” a small molecule that stabilizes the virus, is partly exposed on the floor of the “canyon.” Thus, the structure of antiviral compounds may require a hydrophilic head group designed to interact with residues at the entrance of the pocket.

April 2012
Direct Observation of Cooperative Protein Structural Dynamics of Homodimeric Hemoglobin from 100 ps to 10 ms with Pump-Probe X-ray Solution Scattering

Kyung Hwan Kim, Srinivasan Muniyappan, Key Young Oang, Jong Goo Kim, Shunsuke Nozawa, Tokushi Sato, Shin-ya Koshihara, Robert Henning, Irina Kosheleva, Hosung Ki, Youngmin Kim, Tae Wu Kim, Jeongho Kim, Shin-ichi Adachi, and Hyotcherl Ihee, Journal of the American Chemical Society. (2012). 134 (16), 7001-7008, doi: 10.1021/ja210856v.

Proteins serve as molecular machines in performing their biological functions, but the detailed structural transitions are difficult to observe in their native aqueous environments in real time. For example, despite extensive studies, the solution-phase structures of the intermediates along the allosteric pathways for the transitions between the relaxed (R) and tense (T) forms have been elusive. In this work, we employed picosecond X-ray solution scattering and novel structural analysis to track the details of the structural dynamics of wild-type homodimeric hemoglobin (HbI) from the clam Scapharca inaequivalvis and its F97Y mutant over a wide time range from 100 ps to 56.2 ms. From kinetic analysis of the measured time-resolved X-ray solution scattering data, we identified three structurally distinct intermediates (I1, I2, and I3) and their kinetic pathways common for both the wild type and the mutant. The data revealed that the singly liganded and unliganded forms of each intermediate share the same structure, providing direct evidence that the ligand photolysis of only a single subunit induces the same structural change as the complete photolysis of both subunits does. In addition, by applying novel structural analysis to the scattering data, we elucidated the detailed structural changes in the protein, including changes in the heme–heme distance, the quaternary rotation angle of subunits, and interfacial water gain/loss. The earliest, R-like I1 intermediate is generated within 100 ps and transforms to the R-like I2 intermediate with a time constant of 3.2 ± 0.2 ns. Subsequently, the late, T-like I3 intermediate is formed via subunit rotation, a decrease in the heme–heme distance, and substantial gain of interfacial water and exhibits ligation-dependent formation kinetics with time constants of 730 ± 120 ns for the fully photolyzed form and 5.6 ± 0.8 μs for the partially photolyzed form. For the mutant, the overall kinetics are accelerated, and the formation of the T-like I3 intermediate involves interfacial water loss (instead of water entry) and lacks the contraction of the heme–heme distance, thus underscoring the dramatic effect of the F97Y mutation. The ability to keep track of the detailed movements of the protein in aqueous solution in real time provides new insights into the protein structural dynamics.

March 2012
The kinetic dose limit in room-temperature time-resolved macromolecular crystallography

M. Schmidt, V. Srajer, N. Purwar, and S. Tripathi,Journal of Synchrotron Radiation . (2012). 19, 264-273, doi: 10.1107/S090904951105549X.

Protein X-ray structures are determined with ionizing radiation that damages the protein at high X-ray doses. As a result, diffraction patterns deteriorate with the increased absorbed dose. Several strategies such as sample freezing or scavenging of X-ray-generated free radicals are currently employed to minimize this damage. However, little is known about how the absorbed X-ray dose affects time-resolved Laue data collected at physiological temperatures where the protein is fully functional in the crystal, and how the kinetic analysis of such data depends on the absorbed dose. Here, direct evidence for the impact of radiation damage on the function of a protein is presented using time-resolved macromolecular crystallography. The effect of radiation damage on the kinetic analysis of time-resolved X-ray data is also explored.

2011

December 2011
Cooperative macromolecular device revealed by meta-analysis of static and time-resolved structures

Zhong Ren, Vukica Srajer, James E. Knapp, and William E. Royer, Jr., PNAS. 2011 Dec 14. doi: 10.1073/pnas.1109213108. [Epub ahead of print].

Here we present a meta-analysis of a large collection of static structures of a protein in the Protein Data Bank in order to extract the progression of structural events during protein function. We apply this strategy to the homodimeric hemoglobin HbI from Scapharca inaequivalvis. We derive a simple dynamic model describing how binding of the first ligand in one of the two chemically identical subunits facilitates a second binding event in the other partner subunit. The results of our ultrafast time-resolved crystallographic studies support this model. We demonstrate that HbI functions like a homodimeric mechanical device, such as pliers or scissors. Ligand-induced motion originating in one subunit is transmitted to the other via conserved pivot points, where the E and F′ helices from two partner subunits are “bolted” together to form a stable dimer interface permitting slight relative rotation but preventing sliding.

October 2011
Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome

Yang X, Ren Z, Kuk J, Moffat K, Nature. 2011 Oct 16. doi: 10.1038/nature10506. [Epub ahead of print].

Light is a fundamental signal that regulates important physiological processes such as development and circadian rhythm in living organisms. Phytochromes form a major family of photoreceptors responsible for red light perception in plants, fungi and bacteria. They undergo reversible photoconversion between red-absorbing (Pr) and far-red-absorbing (Pfr) states, thereby ultimately converting a light signal into a distinct biological signal that mediates subsequent cellular responses. Several structures of microbial phytochromes have been determined in their dark-adapted Pr or Pfr states. However, the structural nature of initial photochemical events has not been characterized by crystallography. Here we report the crystal structures of three intermediates in the photoreaction of Pseudomonas aeruginosa bacteriophytochrome (PaBphP). We used cryotrapping crystallography to capture intermediates, and followed structural changes by scanning the temperature at which the photoreaction proceeded. Light-induced conformational changes in PaBphP originate in ring D of the biliverdin (BV) chromophore, and E-to-Z isomerization about the C15 = C16 double bond between rings C and D is the initial photochemical event. As the chromophore relaxes, the twist of the C15 methine bridge about its two dihedral angles is reversed. Structural changes extend further to rings B and A, and to the surrounding protein regions. These data indicate that absorption of a photon by the Pfr state of PaBphP converts a light signal into a structural signal via twisting and untwisting of the methine bridges in the linear tetrapyrrole within the confined protein cavity.

July 2011
Molecular Mechanisms of Viral and Host Cell Substrate Recognition by Hepatitis C Virus NS3/4A Protease

Romano, Keith P., Jennifer M. Laine, Laura M Deveau, Hong Cao, Francesca Massi, Celia A. Schiffer, J. Viro. 85 (13), 6106-6116 (2011).

Hepatitis C NS3/4A protease is a prime therapeutic target that is responsible for cleaving the viral polyprotein at junctions 3-4A, 4A4B , 4B5A, and 5A5B and two host cell adaptor proteins of the innate immune response, TRIF and MAVS. In this study, NS3/4A crystal structures of both host cell cleavage sites were determined and compared to the crystal structures of viral substrates. Two distinct protease conformations were observed and correlated with substrate specificity: (i) 3-4A, 4A4B, 5A5B, and MAVS, which are processed more efficiently by the protease, form extensive electrostatic networks when in complex with the protease, and (ii) TRIF and 4B5A, which contain polyproline motifs in their full-length sequences, do not form electrostatic networks in their crystal complexes. These findings provide mechanistic insights into NS3/4A substrate recognition, which may assist in a more rational approach to inhibitor design in the face of the rapid acquisition of resistance.

April 2011
Mapping the Reaction Coordinates of Enzymatic Defluorination

Chan, P.W.Y., Yakunin, A.F., Edwards, E.A. & Pai, E.F., J. Am. Chem. Soc. 133, 7461-7468 (2011).

The carbon−fluorine bond is the strongest covalent bond in organic chemistry, yet fluoroacetate dehalogenases can readily hydrolyze this bond under mild physiological conditions. Elucidating the molecular basis of this rare biocatalytic activity will provide the fundamental chemical insights into how this formidable feat is achieved. Here, we present a series of high-resolution (1.15−1.80 Å) crystal structures of a fluoroacetate dehalogenase, capturing snapshots along the defluorination reaction: the free enzyme, enzyme−fluoroacetate Michaelis complex, glycolyl−enzyme covalent intermediate, and enzyme−product complex. We demonstrate that enzymatic defluorination requires a halide pocket that not only supplies three hydrogen bonds to stabilize the fluoride ion but also is finely tailored for the smaller fluorine halogen atom to establish selectivity toward fluorinated substrates. We have further uncovered dynamics near the active site which may play pivotal roles in enzymatic defluorination. These findings may ultimately lead to the development of novel defluorinases that will enable the biotransformation of more complex fluorinated organic compounds, which in turn will assist the synthesis, detoxification, biodegradation, disposal, recycling, and regulatory strategies for the growing markets of organofluorines across major industrial sectors.

February 2011
Anisotropic Picosecond X-ray Solution Scattering from Photo-selectively Aligned Protein Molecules

Kim, J., K.H. Kim, J.G. Kim, T.W. Kim, Y. Kim, H. Ihee, J. Phys. Chem. Lett. 2 350-356 (2011).

Anisotropic X-ray scattering patterns of transiently aligned protein molecules in solution are measured by using pump−probe X-ray solution scattering. When a linearly polarized laser pulse interacts with an ensemble of molecules, the population of excited molecules is created with their transition dipoles preferentially aligned along the laser polarization direction. We measured the X-ray scattering from the myoglobin protein molecules excited by a linearly polarized, short laser pulse and obtained anisotropic scattering patterns on a 100 ps time scale. An anisotropic scattering pattern contains higher structural information content than a typical isotropic pattern available from randomly oriented molecules. In addition, multiple independent diffraction patterns measured by using various laser polarization orientations will give a substantially increased amount of structural information compared with that from a single isotropic pattern. By monitoring the temporal change of the anisotropic scattering pattern from 100 ps to 1 μs, we observed the orientational dynamics of photogenerated myoglobin with the rotational diffusion time of 15 ns.

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2010

December 2010
Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding

Keith P. Romano, Akbar Ali, William E. Royer, Celia A. Schiffer, PNAS 107 20986-20991 (2010)

Hepatitis C virus infects an estimated 180 million people worldwide, prompting enormous efforts to develop inhibitors targeting the essential NS3/4A protease. Resistance against the most promising protease inhibitors, telaprevir, boceprevir, and ITMN-191, has emerged in clinical trials. In this study, crystal structures of the NS3/4A protease domain reveal that viral substrates bind to the protease active site in a conserved manner defining a consensus volume, or substrate envelope. Mutations that confer the most severe resistance in the clinic occur where the inhibitors protrude from the substrate envelope, as these changes selectively weaken inhibitor binding without compromising the binding of substrates. These findings suggest a general model for predicting the susceptibility of protease inhibitors to resistance: drugs designed to fit within the substrate envelope will be less susceptible to resistance, as mutations affecting inhibitor binding would simultaneously interfere with the recognition of viral substrates.

June 2010
A self-assembly pathway to aligned monodomain gels

Shuming Zhang, Megan A. Greenfield, Alvaro Mata, Liam C. Palmer, Ronit Bitton, Jason R. Mantei, Conrado Aparicio, Monica Olvera de la Cruz, and Samuel I. Stupp, Nature Mater. 9 594–601 (2010) doi:10.1038/nmat2778

peptide amphiphile knotAggregates of charged amphiphilic molecules have been found to access a structure at elevated temperature that templates alignment of supramolecular fibrils over macroscopic scales. The thermal pathway leads to a lamellar plaque structure with fibrous texture that breaks on cooling into large arrays of aligned nanoscale fibres and forms a strongly birefringent liquid. By manually dragging this liquid crystal from a pipette onto salty media, it is possible to extend this alignment over centimetres in noodle-shaped viscoelastic strings. Using this approach, the solution of supramolecular filaments can be mixed with cells at physiological temperatures to form monodomain gels of aligned cells and filaments. The nature of the self-assembly process and its biocompatibility would allow formation of cellular wires in situ that have any length and customized peptide compositions for use in biological applications. (Wide-angle x-ray scattering data were taken at 14-BM-C as part of the fiber diffraction collaboration with BioCAT.) [Abstract and image reproduced by permission from Macmillan Publishers Ltd: Nature Mater. 9 594–601 (2010).]

April 2010
Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering

H. S. Cho, N. Dashdorj, F. Schotte, T. Graber, R. Henning, and P. Anfinrud, PNAS 107 7281-7286 (2010).

We have developed a time-resolved x-ray scattering diffractometer capable of probing structural dynamics of proteins in solution with 100-ps time resolution. This diffractometer, developed on the ID14B BioCARS (Consortium for Advanced Radiation Sources) beamline at the Advanced Photon Source, records x-ray scattering snapshots over a broad range of q spanning 0.02–2.5 Å-1, thereby providing simultaneous coverage of the small-angle x-ray scattering (SAXS) and wide-angle x-ray scattering (WAXS) regions. To demonstrate its capabilities, we have tracked structural changes in myoglobin as it undergoes a photolysis-induced transition from its carbon monoxy form (MbCO) to its deoxy form (Mb). Though the differences between the MbCO and Mb crystal structures are small (rmsd < 0.2 Å), time-resolved x-ray scattering differences recorded over 8 decades of time from 100 ps to 10 ms are rich in structure, illustrating the sensitivity of this technique. A strong, negative-going feature in the SAXS region appears promptly and corresponds to a sudden > 22 Å3 volume expansion of the protein. The ensuing conformational relaxation causes the protein to contract to a volume ∼2 Å3 larger than MbCO within ∼10 ns. On the timescale for CO escape from the primary docking site, another change in the SAXS/WAXS fingerprint appears, demonstrating sensitivity to the location of the dissociated CO. Global analysis of the SAXS/WAXS patterns recovered time-independent scattering fingerprints for four intermediate states of Mb. These SAXS/WAXS fingerprints provide stringent constraints for putative models of conformational states and structural transitions between them.

March 2010
Five-dimensional crystallography

M. Schmidt, T. Graber, R. Henning, V. Srajer, "Five-dimensional crystallography," Acta Cryst. A66 198-206 (2010)

A method for determining a comprehensive chemical kinetic mechanism in macromolecular reactions is presented. The method is based on five-dimensional crystallography, where, in addition to space and time, temperature is also taken into consideration and an analysis based on singular value decomposition is applied. First results of such a time-resolved crystallographic study are presented. Temperature-dependent time-resolved X-ray diffraction measurements were conducted on the newly upgraded BioCARS 14-ID-B beamline at the Advanced Photon Source and aimed at elucidating a comprehensive kinetic mechanism of the photoactive yellow protein photocycle. Extensive time series of crystallographic data were collected at two temperatures, 293 K and 303 K. Relaxation times of the reaction extracted from these time series exhibit measurable differences for the two temperatures, hence demonstrating that five-dimensional crystallography is feasible.

March 2010
Time-resolved synchrotron diffraction and theoretical studies of very short-lived photo-induced molecular species

Coppens, Philip, Jason Benedict, Marc Messerschmidt, Irina Novozhilova, Tim Graber, Yu-Sheng Chen, Ivan Vorontsov, Stephan Scheins, Shao-Liang Zheng, "Time-resolved synchrotron diffraction and theoretical studies of very short-lived photo-induced molecular species," Acta Cryst. A66 179-188 (2010)

Definitive experimental results on the geometry of fleeting species are at the time of writing still limited to monochromatic data collection, but methods for modifications of the polychromatic Laue data to increase their accuracy and their suitability for pump-probe experiments have been implemented and are reviewed. In the monochromatic experiments summarized, excited-state conversion percentages are small when neat crystals are used, but are higher when photoactive species are embedded in an inert framework in supramolecular crystals. With polychromatic techniques and increasing source brightness, smaller samples down to tenths of a micrometre or less can be used, increasing homogeneity of exposure and the fractional population of the excited species. Experiments described include a series of transition metal complexes and a fully organic example involving excimer formation. In the final section, experimental findings are compared with those from theoretical calculations on the isolated species. Qualitative agreement is generally obtained, but the theoretical results are strongly dependent on the details of the calculation, indicating the need for further systematic analysis.

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2009

October 7, 2009
2009 Nobel Winner Was Early User of BioCARS

One of the three winners of the 2009 Nobel Prize in Chemistry, Thomas Steitz, has conducted research at BioCARS. Steitz of Yale University, Ada Yonath of Israel's Weizmann Institute, and Venkatraman Ramakrishnan of Cambridge, England's Medical Research Center shared the award for their study of the structure and function of the ribosome. The following are publications by Steitz based on data taken at BioCARS.

October 6, 2009, Proceedings of the National Academy of Sciences
Natural and recombinant prion structure from X-ray fiber diffraction

Holger Wille, Wen Bian, Michele McDonald, Amy Kendall, David W. Colby, Lillian Bloch, Julian Ollesch, Alexander L. Borovinskiy, Fred E. Cohen, Stanley B. Prusiner, and Gerald Stubbs, "Natural and synthetic prion structure from X-ray fiber diffraction," PNAS 106, 16990-16995 (2009)

A collaboration between scientists at Vanderbilt University and the University of California, San Francisco has led to the first direct information about the molecular structure of prions. Prions are the infectious proteins responsible for human Creutzfeldt-Jakob disease, bovine spongiform encephalopathy, or "mad cow" disease, scrapie in sheep and several other related nervous system disorders in mammals.

In addition, the study has revealed surprisingly large structural differences between natural prions and the closest analogs that scientists have created in the lab. Artificial prions do not show the same degree of infectious behavior as their natural counterparts. "We expected to find subtle [structural] differences, but we found major differences instead," said Gerald Stubbs, professor of biological sciences at Vanderbilt University. "Although we cannot say for certain that the differences we've seen can explain why natural prions are so infectious, there is a good chance that they are closely related." The work was conducted at BioCARS biosafety level 2 (BSL-2) facilities under an agreement with BioCAT (APS sector 18). See full story ›

May 2009 - The Scientist
Article Traces Development of Research on Photoactive Proteins

An article entitled "LOV Story" in The Scientist features the work of the first researchers to study biological signaling based on the LOV domain--a segment of protein sensitive to light, oxygen, and voltage. The role of early BioCARS user Sean Crosson and sector PI Keith Moffat are highlighted.

May 2009 - The Scientist
BioCARS Principal Investigator Keith Moffat Profiled in The Scientist

In a companion "Careers" piece, The Scientist profiled Keith Moffat, whose interest in physics led to pioneering x-ray techniques for studying how protein molecules respond to light.  

February 8, 2009 - lightsources.org
Scientists Create First Crystal Structure of an Intermediate Particle in Virus Assembly

Ilya Gertsman, Lu Gan, Miklos Guttman, Kelly Lee, Jeffrey A. Speir, Robert L. Duda, Roger W. Hendrix, Elizabeth A. Komives, John E. Johnson, "An Unexpected Twist in Viral Capsid Maturation," Nature, advance online publication (8 February 2009)

A research team at the Scripps Research Institute has been able to produce the first crystal structure of a virus particle caught in the midst of assembling its impenetrable outer protein coat. The structure, described February 8 in an advance online publication of the journal Nature, provides fresh insights into the elegant dance that viral proteins perform to create the infectious structure that causes all manner of misery and disease. The work is based in part on data taken at BioCARS beamline 14-BM-C.

See also: Scripps Research Institute News & Views, February 23, 2009(image)

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2008

October 8, 2008 - lightsources.org
Scripps researchers seek to understand, and improve, virus that can
infect lung cancer cells

Sangita Venkataraman, Seshidhar P. Reddy, Jackie Loo, Neeraja Idamakanti, Paul L. Hallenbeck, and Vijay S. Reddy, "Structure of Seneca Valley Virus-001: An Oncolytic Picornavirus Representing a New Genus," Structure 16, 1555 (08 October 2008)

The structure of a virus that is harmless to normal human cells but an enemy of certain cancer cells has been determined by Scripps researchers. This new knowledge may help drug designers tweak the pathogen enough so that it can attack other tumor subtypes.

August 11, 2008 - lightsources.org
Australian scientists unravel Leukemia link

Guido Hansen, Timothy R. Hercus, Barbara J. McClure, Frank C. Stomski, Mara Dottore, Jason Powell, Hayley Ramshaw, Joanna M. Woodcock, Yibin Xu, Mark Guthridge, William J. McKinstry, Angel F. Lopez, and Michael W. Parke, "The Structure of the GM-CSF Receptor Complex Reveals a Distinct Mode of Cytokine Receptor Activation," Cell 134, 496-507 (2008)

In work done at 14-BM-C, scientists have unravelled the structure of a cell signalling receptor in the blood control system that, when damaged, is responsible for diseases such as leukemia. Their discovery helps to explain, for the first time, how this receptor is activated and will form the springboard for the development of new treatments.

May 4, 2008 (online)
Molecular clues to variable response of cancer patients to the common anti-cancer drug chlorambucil

L.J. Parker, S. Ciccone, L.C. Italiano, A. Primavera, A.J. Oakley, C.J. Morton, N.C. Hancock, M. Lo Bello, M.W. Parker, "The Anti-Cancer Drug Chlorambucil as a Substrate for the Human Polymorphic Enzyme Glutathione Transferase P1-1: Kinetic Properties and Crystallographic Characterisation of Allelic Variants," J. Mol. Biol. 380 (1), 131-144 (2008)

The commonly used anti-cancer drug chlorambucil is the primary treatment for patients with chronic lymphocytic leukaemia. Chlorambucil has been shown to be detoxified by human glutathione transferase Pi (GST P1-1), an enzyme that is often found over-expressed in cancer tissues. The allelic variants of GST P1-1 are associated with differing susceptibilities to leukaemia and differ markedly in their efficiency in catalysing glutathione (GSH) conjugation reactions. Here, we perform detailed kinetic studies of the allelic variants with the aid of three representative co-substrates. We show that the differing catalytic properties of the variants are highly substrate-dependent. We show also that all variants exhibit the same temperature stability in the range 10 °C to 45 °C. We have determined the crystal structures of GST P1-1 in complex with chlorambucil and its GSH conjugate for two of these allelic variants that have different residues at positions 104 and 113. Chlorambucil is found to bind in a non-productive mode to the substrate-binding site (H-site) in the absence of GSH. This result suggests that under certain stress conditions where GSH levels are low, GST P1-1 can inactivate the drug by sequestering it from the surrounding medium. However, in the presence of GSH, chlorambucil binds in the H-site in a productive mode and undergoes a conjugation reaction with GSH present in the crystal. The crystal structure of the GSH–chlorambucil complex bound to the *C variant is identical with the *A variant ruling out the hypothesis that primary structure differences between the variants cause structural changes at the active site. Finally, we show that chlorambucil is a very poor inhibitor of the enzyme in contrast to ethacrynic acid, which binds to the enzyme in a similar fashion but can act as both substrate and inhibitor.

April 23, 2008
Researchers reveal structure of protein that repairs damage to cancer cells

Cai-Guang Yang, Chengqi Yi, Erica M. Duguid, Christopher T. Sullivan, Xing Jian, Phoebe A. Rice, and Chuan He, "Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA," Nature 452, 961-965 (24 April 2008)

A team of University of Chicago scientists has shown how two proteins locate and repair damaged genetic material inside cells. One protein detects and repairs damage in malignant cells that may result from a certain type of cancer therapy. In a paper published in the April 24 issue of the journal Nature, the team raised the possibility of designing a molecule that could interfere with the repair process, making cancer treatment more effective. Full story (lightsources.org) ›

March 14, 2008
Study shows how new antibody recognizes and binds Alzheimer's peptide

L.A. Miles, S.W. Kwok, G.A.N. Crespi, M.T. Fodero-Tavoletti, D. Galatis, C.J. Bagley, K. Beyreuther, C.L. Masters, R. Cappai, W.J. McKinstry, K.J. Barnham, M.W. Parker, "Amyloid-β–Anti-Amyloid-β Complex Structure Reveals an Extended Conformation in the Immunodominant B-Cell Epitope," J. Mol. Biol. 377 (1), 181-192 (14 March 2008)

Alzheimer's disease (AD) is the most common form of dementia. Amyloid-β (Aβ) peptide, generated by proteolytic cleavage of the amyloid precursor protein, is central to AD pathogenesis. Most pharmaceutical activity in AD research has focused on Aβ, its generation and clearance from the brain. In particular, there is much interest in immunotherapy approaches with a number of anti-Aβ antibodies in clinical trials. We have developed a monoclonal antibody, called WO2, which recognises the Aβ peptide. To this end, we have determined the three-dimensional structure, to near atomic resolution, of both the antibody and the complex with its antigen, the Aβ peptide. The structures reveal the molecular basis for WO2 recognition and binding of Aβ. The Aβ peptide adopts an extended, coil-like conformation across its major immunodominant B-cell epitope between residues 2 and 8. We have also studied the antibody-bound Aβ peptide in the presence of metals known to affect its aggregation state and show that WO2 inhibits these interactions. Thus, antibodies that target the N-terminal region of Aβ, such as WO2, hold promise for therapeutic development.

March 2008 (online January 9, 2008)
Crystal structure of unliganded influenza B virus hemagglutinin

Q. Wang, F. Cheng, M. Lu, X. Tian, J. Ma, "Crystal structure of unliganded influenza B virus hemagglutinin," J. Virol. 82 (6), 3011-3020 (2008)

Here we report the crystal structure of hemagglutinin (HA) from influenza B/HK/8/73 virus determined to 2.8 Å. At a sequence identity of 25% to influenza A virus HAs, B/HK HA shares a similar overall structure and domain organization. More than two dozen of amino acid substitutions have been identified on influenza B virus HAs to cause antigenicity alteration in site-specific mutants, monoclonal antibody-escape mutants or field isolates. Mapping these substitutions on the structure of B/HK HA reveals four major epitopes, the 120-loop, 150-loop, 160-loop and 190-helix, that are located close in space to form a large, continuous antigenic site. Moreover, a systematic comparison of known HA structures across the entire influenza virus family reveals evolutionarily conserved ionizable residues at all regions along chain and subunit interface. These ionizable residues are likely the structural basis for the pH-dependence and sensitivity to ionic strength of influenza HA and HEF proteins.

February 26, 2008
CNK and HYP form a discrete dimer by their SAM domains to mediate RAF kinase signaling

T. Rajakulendran, M. Sahmi, I. Kurinov, M. Tyers, M. Therrien, F. Sicheri, "CNK and HYP form a discrete dimer by their SAM domains to mediate RAF kinase signaling," PNAS 105 (8), 2836-2841 (2008)

RAF kinase functions in the mitogen-activated protein kinase (MAPK) pathway to transmit growth signals to the downstream kinases MEK and ERK. Activation of RAF catalytic activity is facilitated by a regulatory complex comprising the proteins CNK (Connector enhancer of KSR), HYP (Hyphen), and KSR (Kinase Suppressor of Ras). The sterile α-motif (SAM) domain found in both CNK and HYP plays an essential role in complex formation. Here, we have determined the x-ray crystal structure of the SAM domain of CNK in complex with the SAM domain of HYP. The structure reveals a single-junction SAM domain dimer of 1:1 stoichiometry in which the binding mode is a variation of polymeric SAM domain interactions. Through in vitro and in vivo mutational analyses, we show that the specific mode of dimerization revealed by the crystal structure is essential for RAF signaling and facilitates the recruitment of KSR to form the CNK/HYP/KSR regulatory complex. We present two docking-site models to account for how SAM domain dimerization might influence the formation of a higher-order CNK/HYP/KSR complex.

February 2008
Impact of clonal competition for peptide-MHC complexes on the CD8+ T-cell repertoire selection in a persistent viral infection

K.K. Wynn, Z. Marland, L. Cooper, S.L. Silins, S. Gras, J.K. Archbold, F.E. Tynan, J.J. Miles, J. McCluskey, S.R. Burrows, J. Rossjohn, R. Khanna, "Impact of clonal competition for peptide-MHC complexes on the CD8+ T-cell repertoire selection in a persistent viral infection," Blood 111 (8), 4283-4292 (2008)

CD8+ T-cell responses to persistent viral infections are characterized by the accumulation of an oligoclonal T-cell repertoire and a reduction in the naive T-cell pool. However the precise mechanism for this phenomenon remains elusive. Here we show that human cytomegalovirus (HCMV)-specific CD8+ T-cells recognizing distinct epitopes from the pp65 protein and restricted through an identical HLA class I allele (HLA B*3508) exhibited either a highly conserved public T-cell repertoire or a private yet diverse T-cell response, which was uniquely altered in each donor following in vitro antigen exposure. Selection of a public TCR was coincident with an atypical MHC-peptide structure, in that the epitope adopted a helical conformation that bulged from the Ag-binding groove, whilst a diverse TCR profile was observed in response to the epitope that formed a flatter, more "featureless" landscape. Clonotypes with biased TCR usage demonstrated more efficient recognition of virus-infected cells, a greater CD8 dependency, and were more terminally differentiated in their phenotype when compared to the T-cells expressing diverse TCR. These findings provide new insights into our understanding on how the biology of antigen presentation in addition to the structural features of the pMHC-I might shape the T-cell repertoire and its phenotype.

January 2008
Structure–activity relationships of C6-uridine derivatives targeting Plasmodia orotidine monophosphate decarboxylase

A.M. Bello, E. Poduch, Y. Liu, L. Wei, I. Crandall, X. Wang, C. Dyanand, K.C. Kain, E.F. Pai, L.P. Kotra, "Structure–activity relationships of C6-uridine derivatives targeting Plasmodia orotidine monophosphate decarboxylase," J. Med. Chem. 51 (3), 439-448 (2008)

Malaria, caused by Plasmodia parasites, has re-emerged as a major problem, imposing its fatal effects on human health, especially due to multidrug resistance. In Plasmodia, orotidine 5′ monophosphate decarboxylase (ODCase) is an essential enzyme for the de novo synthesis of uridine 5′-monophosphate. Impairing ODCase in these pathogens is a promising strategy to develop novel classes of therapeutics. Encouraged by our recent discovery that 6-iodo uridine is a potent inhibitor of P. falciparum, we investigated the structure–activity relationships of various C6 derivatives of UMP. 6-Cyano, 6-azido, 6-amino, 6-methyl, 6-N-methylamino, and 6-N,N-dimethylamino derivatives of uridine were evaluated against P. falciparum. The mononucleotides of 6-cyano, 6-azido, 6-amino, and 6-methyl uridine derivatives were studied as inhibitors of plasmodial ODCase. 6-Azidouridine 5′-monophosphate is a potent covalent inhibitor of P. falciparum ODCase. 6-Methyluridine exhibited weak antimalarial activity against P. falciparum 3D7 isolate. 6-N-Methylamino and 6-N,N-dimethylamino uridine derivatives exhibited moderate antimalarial activities.

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2007

October 2007
Structural basis for the recruitment of profilin–actin complexes during filament elongation by Ena/VASP

François Ferron, Grzegorz Rebowski, Sung Haeng Lee, Roberto Dominguez, EMBO J. 26, 4597-4606 (2007)

Cells sustain high rates of actin filament elongation by maintaining a large pool of actin monomers above the critical concentration for polymerization. Profilin–actin complexes constitute the largest fraction of polymerization-competent actin monomers. Filament elongation factors such as Ena/VASP and formin catalyze the transition of profilin–actin from the cellular pool onto the barbed end of growing filaments. The molecular bases of this process are poorly understood. Here we present structural and energetic evidence for two consecutive steps of the elongation mechanism: the recruitment of profilin–actin by the last poly-Pro segment of vasodilator-stimulated phosphoprotein (VASP) and the binding of profilin–actin simultaneously to this poly-Pro and to the G-actin-binding (GAB) domain of VASP. The actin monomer bound at the GAB domain is proposed to be in position to join the barbed end of the growing filament concurrently with the release of profilin.

October 2007
Molecular basis for passive immunotherapy of Alzheimer's disease

Anna S. Gardberg, Lezlee T. Dice, Susan Ou, Rebecca L. Rich, Elizabeth Helmbrecht, Jan Ko, Ronald Wetzel, David G. Myszka, Paul H. Patterson, Chris Dealwis, PNAS 104, 15659-15664 (2007)

Amyloid aggregates of the amyloid-β (Aβ) peptide are implicated in the pathology of Alzheimer's disease. Anti-Aβ monoclonal antibodies (mAbs) have been shown to reduce amyloid plaques in vitro and in animal studies. Consequently, passive immunization is being considered for treating Alzheimer's, and anti-Aβ mAbs are now in phase II trials. We report the isolation of two mAbs (PFA1 and PFA2) that recognize Aβ monomers, protofibrils, and fibrils and the structures of their antigen binding fragments (Fabs) in complex with the Aβ(1–8) peptide DAEFRHDS. The immunodominant EFRHD sequence forms salt bridges, hydrogen bonds, and hydrophobic contacts, including interactions with a striking WWDDD motif of the antigen binding fragments. We also show that a similar sequence (AKFRHD) derived from the human protein GRIP1 is able to cross-react with both PFA1 and PFA2 and, when cocrystallized with PFA1, binds in an identical conformation to Aβ(1–8). Because such cross-reactivity has implications for potential side effects of immunotherapy, our structures provide a template for designing derivative mAbs that target Aβ with improved specificity and higher affinity.

June 2007
The N terminus of the serpin, tengpin, functions to trap the metastable native state

Qingwei Zhang, Ashley M. Buckle, Ruby H.P. Law, Mary C. Pearce, Lisa D. Cabrita, Gordon J. Lloyd, James A. Irving, A. Ian Smith, Katya Ruzyla, Jamie Rossjohn, Stephen P. Bottomley, James C. Whisstock, EMBO Reports 8, 658-663 (2007)

Serpins fold to a metastable native state and are susceptible to undergoing spontaneous conformational change to more stable conformers, such as the latent form. We investigated conformational change in tengpin, an unusual prokaryotic serpin from the extremophile Thermoanaerobacter tengcongensis. In addition to the serpin domain, tengpin contains a functionally uncharacterized 56-amino-acid amino-terminal region. Deletion of this domain creates a variant—tengpinΔ51—which folds past the native state and readily adopts the latent conformation. Analysis of crystal structures together with mutagenesis studies show that the N terminus of tengpin protects a hydrophobic patch in the serpin domain and functions to trap tengpin in its native metastable state. A 13-amino-acid peptide derived from the N terminus is able to mimick the role of the N terminus in stabilizing the native state of tengpinΔ51. Therefore, the function of the N terminus in tengpin resembles protein cofactors that prevent mammalian serpins from spontaneously adopting the latent conformation.

June 2007
An atomic model of the interferon-β enhanceosome

Daniel Panne, Tom Maniatis, Stephen C. Harrison, Cell 129 (6), 1111-1123 (2007)

Transcriptional activation of the interferon-β (IFN-β) gene requires assembly of an enhanceosome containing ATF-2/c-Jun, IRF-3/IRF-7, and NFκB. These factors bind cooperatively to the IFN-β enhancer and recruit coactivators and chromatin-remodeling proteins to the IFN-β promoter. We describe here a crystal structure of the DNA-binding domains of IRF-3, IRF-7, and NFκB, bound to one half of the enhancer, and use a previously described structure of the remaining half to assemble a complete picture of enhanceosome architecture in the vicinity of the DNA. Association of eight proteins with the enhancer creates a continuous surface for recognizing a composite DNA-binding element. Paucity of local protein-protein contacts suggests that cooperative occupancy of the enhancer comes from both binding-induced changes in DNA conformation and interactions with additional components such as CBP. Contacts with virtually every nucleotide pair account for the evolutionary invariance of the enhancer sequence.

July 2007
Crystal structure of the chromophore binding domain of an unusual bacteriophytochrome, RpBphP3, reveals residues that modulate photoconversion

Xiaojing Yang, Emina A. Stojkovic, Jane Kuk, Keith Moffat, PNAS 104 (30), 12571-12576 (2007)

Bacteriophytochromes RpBphP2 and RpBphP3 from the photosynthetic bacterium Rhodopseudomonas palustris work in tandem to modulate synthesis of the light-harvesting complex LH4 in response to light. Although RpBphP2 and RpBphP3 share the same domain structure with 52% sequence identity, they demonstrate distinct photoconversion behaviors. RpBphP2 exhibits the "classical" phytochrome behavior of reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states, whereas RpBphP3 exhibits novel photoconversion between Pr and a near-red (Pnr) light-absorbing states. We have determined the crystal structure at 2.2-Å resolution of the chromophore binding domains of RpBphP3, covalently bound with chromophore biliverdin IXα. By combining structural and sequence analyses with site-directed mutagenesis, we identify key residues that directly modulate the photochemical properties of RpBphP3 and RpBphP2. Remarkably, we identify a region spanning residues 207-212 in RpBphP3, in which a single mutation, L207Y, causes this unusual bacteriophytochrome to revert to the classical phenotype that undergoes reversible photoconversion between the Pr and Pfr states. The reverse mutation, Y193L, in the corresponding region in RpBphP2 significantly diminishes the formation of the Pfr state. We propose that residues 207-212 and the spatially adjacent conserved residues, Asp-216 and Tyr-272, interact with the chromophore and form part of the interface between the chromophore binding domains and the PHY domain that modulates photoconversion.

March 2007
Time-resolved crystallographic studies of the heme domain of the oxygen sensor FixL: Structural dynamics of ligand rebinding and their relation to signal transduction

The FixL protein of Bradyrhizobium japonicum is a dimeric oxygen sensor responsible for initiating regulation of transcription of genes encoding proteins involved in nitrogen fixation and oxidative stress. It consists of an N-terminal heme-bound PAS domain, denoted bjFixLH, and a C-terminal histidine kinase domain whose enzymatic activity depends on the ligation state of the heme. To investigate the molecular basis for this dependence and the dynamics associated with conversion between ligated and unligated states, we have conducted time-resolved Laue diffraction studies of CO recombination in bjFixLH. Time-dependent difference Fourier maps from 1 ms to 10 ms after photolysis of the heme-CO bond show movement of the side chain of Leu236 and the H and I β-strands into the ligand binding pocket formerly occupied by CO. Long-range conformational changes are evident in the protein, driven by relaxation of steric interactions between the bound ligand and amino acid side chains and/or changes in heme stereochemistry. These structural changes fully reverse as CO rebinds to the heme. Spectroscopic measurements of CO recombination kinetics in bjFixLH crystals relate the behavior of crystalline bjFixLH to solution and provide a framework for our time-resolved crystallographic experiments. Analysis of the time-dependent difference Fourier maps by singular value decomposition reveals that only one significant singular value accounts for the data. Thus only two structural states are present, the photolyzed and the CO-bound states. The first left singular vector represents the difference in density between these two states and shows features common to difference maps calculated from the static CO and deoxy states. The first right singular vector represents the time course of this difference density and agrees well with the CO recombination kinetics measured spectroscopically. We refine the structure of the photolyzed state present in the early-microsecond time range and find that it does not differ significantly in conformation from static, deoxy bjFixLH. Thus, structural relaxation from CO-bound to deoxy bjFixLH is complete in less than 1m s.

March 22, 2007 - lightsources.org
Biologists learn structure of enzyme needed to power "molecular motor"

Siyang Sun, Kiran Kondabagil, Petra M. Gentz, Michael G. Rossmann, and Venigalla B. Rao, "The Structure of the ATPase that Powers DNA Packaging into Bacteriophage T4 Procapsids," Molecular Cell 25, 943-949, 23 March 2007

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2006

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2005

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