Daniel P. DePonte
SLAC National Accelerator Laboratory
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Featured researches published by Daniel P. DePonte.
Nature | 2011
Henry N. Chapman; Petra Fromme; Anton Barty; Thomas A. White; Richard A. Kirian; Andrew Aquila; Mark S. Hunter; Joachim Schulz; Daniel P. DePonte; Uwe Weierstall; R. Bruce Doak; Filipe R. N. C. Maia; Andrew V. Martin; Ilme Schlichting; Lukas Lomb; Nicola Coppola; Robert L. Shoeman; Sascha W. Epp; Robert Hartmann; Daniel Rolles; A. Rudenko; Lutz Foucar; Nils Kimmel; Georg Weidenspointner; Peter Holl; Mengning Liang; Miriam Barthelmess; Carl Caleman; Sébastien Boutet; Michael J. Bogan
X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction ‘snapshots’ are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.
Nature | 2011
M. Marvin Seibert; Tomas Ekeberg; Filipe R. N. C. Maia; Martin Svenda; Jakob Andreasson; O Jonsson; Duško Odić; Bianca Iwan; Andrea Rocker; Daniel Westphal; Max F. Hantke; Daniel P. DePonte; Anton Barty; Joachim Schulz; Lars Gumprecht; Nicola Coppola; Andrew Aquila; Mengning Liang; Thomas A. White; Andrew V. Martin; Carl Caleman; Stephan Stern; Chantal Abergel; Virginie Seltzer; Jean-Michel Claverie; Christoph Bostedt; John D. Bozek; Sébastien Boutet; A. Miahnahri; Marc Messerschmidt
X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions. Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma. The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval. Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a non-crystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source. Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.
Science | 2012
Sébastien Boutet; Lukas Lomb; Garth J. Williams; Thomas R. M. Barends; Andrew Aquila; R. Bruce Doak; Uwe Weierstall; Daniel P. DePonte; Jan Steinbrener; Robert L. Shoeman; Marc Messerschmidt; Anton Barty; Thomas A. White; Stephan Kassemeyer; Richard A. Kirian; M. Marvin Seibert; Paul A. Montanez; Chris Kenney; R. Herbst; P. Hart; J. Pines; G. Haller; Sol M. Gruner; Hugh T. Philipp; Mark W. Tate; Marianne Hromalik; Lucas J. Koerner; Niels van Bakel; John Morse; Wilfred Ghonsalves
Size Matters Less X-ray crystallography is a central research tool for uncovering the structures of proteins and other macromolecules. However, its applicability typically requires growth of large crystals, in part because a sufficient number of molecules must be present in the lattice for the sample to withstand x-ray—induced damage. Boutet et al. (p. 362, published online 31 May) now demonstrate that the intense x-ray pulses emitted by a free-electron laser source can yield data in few enough exposures to uncover the high-resolution structure of microcrystals. A powerful x-ray laser source can probe proteins in detail using much smaller crystals than previously required. Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.
Science | 2013
Karol Nass; Daniel P. DePonte; Thomas A. White; Dirk Rehders; Anton Barty; Francesco Stellato; Mengning Liang; Thomas R. M. Barends; Sébastien Boutet; Garth J. Williams; Marc Messerschmidt; M. Marvin Seibert; Andrew Aquila; David Arnlund; Sasa Bajt; Torsten Barth; Michael J. Bogan; Carl Caleman; Tzu Chiao Chao; R. Bruce Doak; Holger Fleckenstein; Matthias Frank; Raimund Fromme; Lorenzo Galli; Ingo Grotjohann; Mark S. Hunter; Linda C. Johansson; Stephan Kassemeyer; Gergely Katona; Richard A. Kirian
Diffraction Before Destruction A bottleneck in x-ray crystallography is the growth of well-ordered crystals large enough to obtain high-resolution diffraction data within an exposure that limits radiation damage. Serial femtosecond crystallography promises to overcome these constraints by using short intense pulses that out-run radiation damage. A stream of crystals is flowed across the free-electron beam and for each pulse, diffraction data is recorded from a single crystal before it is destroyed. Redecke et al. (p. 227, published online 29 November; see the Perspective by Helliwell) used this technique to determine the structure of an enzyme from Trypanosoma brucei, the parasite that causes sleeping sickness, from micron-sized crystals grown within insect cells. The structure shows how this enzyme, which is involved in degradation of host proteins, is natively inhibited prior to activation, which could help in the development of parasite-specific inhibitors. In vivo crystallization and serial femtosecond crystallography reveal the structure of a sleeping sickness parasite protease. [Also see Perspective by Helliwell] The Trypanosoma brucei cysteine protease cathepsin B (TbCatB), which is involved in host protein degradation, is a promising target to develop new treatments against sleeping sickness, a fatal disease caused by this protozoan parasite. The structure of the mature, active form of TbCatB has so far not provided sufficient information for the design of a safe and specific drug against T. brucei. By combining two recent innovations, in vivo crystallization and serial femtosecond crystallography, we obtained the room-temperature 2.1 angstrom resolution structure of the fully glycosylated precursor complex of TbCatB. The structure reveals the mechanism of native TbCatB inhibition and demonstrates that new biomolecular information can be obtained by the “diffraction-before-destruction” approach of x-ray free-electron lasers from hundreds of thousands of individual microcrystals.
Journal of Physics D | 2008
R. B. Doak; John C. Spence; Uwe Weierstall; Daniel P. DePonte; Dmitri Starodub; Jared Scott Warner
As shown by Ganan-Calvo and co-workers, a free liquid jet can be compressed in iameter through gas-dynamic forces exerted by a co-flowing gas, obviating the need for a solid nozzle to form a microscopic liquid jet and thereby alleviating the clogging problems that plague conventional droplet sources of small diameter. We describe in this paper a novel form of droplet beam source based on this principle. The source is miniature, robust, dependable, easily fabricated, and eminently suitable for delivery of microscopic liquid droplets, including hydrated biological samples, into vacuum for analysis using vacuum instrumentation. Monodisperse, single file droplet streams are generated by triggering the device with a piezoelectric actuator. The device is essentially immune to clogging.
Nature | 2014
Jonas A. Sellberg; Congcong Huang; Trevor A. McQueen; N. D. Loh; Hartawan Laksmono; Daniel Schlesinger; Raymond G. Sierra; Dennis Nordlund; Christina Y. Hampton; Dmitri Starodub; Daniel P. DePonte; Martin Beye; Chen Chen; Andrew V. Martin; A. Barty; Kjartan Thor Wikfeldt; Thomas M. Weiss; Chiara Caronna; Jan M. Feldkamp; L. B. Skinner; M. Marvin Seibert; M. Messerschmidt; Garth J. Williams; Sébastien Boutet; Lars G. M. Pettersson; M. J. Bogan; Anders Nilsson
Water has a number of anomalous physical properties, and some of these become drastically enhanced on supercooling below the freezing point. Particular interest has focused on thermodynamic response functions that can be described using a normal component and an anomalous component that seems to diverge at about 228 kelvin (refs 1,2,3 ). This has prompted debate about conflicting theories that aim to explain many of the anomalous thermodynamic properties of water. One popular theory attributes the divergence to a phase transition between two forms of liquid water occurring in the ‘no man’s land’ that lies below the homogeneous ice nucleation temperature (TH) at approximately 232 kelvin and above about 160 kelvin, and where rapid ice crystallization has prevented any measurements of the bulk liquid phase. In fact, the reliable determination of the structure of liquid water typically requires temperatures above about 250 kelvin. Water crystallization has been inhibited by using nanoconfinement, nanodroplets and association with biomolecules to give liquid samples at temperatures below TH, but such measurements rely on nanoscopic volumes of water where the interaction with the confining surfaces makes the relevance to bulk water unclear. Here we demonstrate that femtosecond X-ray laser pulses can be used to probe the structure of liquid water in micrometre-sized droplets that have been evaporatively cooled below TH. We find experimental evidence for the existence of metastable bulk liquid water down to temperatures of kelvin in the previously largely unexplored no man’s land. We observe a continuous and accelerating increase in structural ordering on supercooling to approximately 229 kelvin, where the number of droplets containing ice crystals increases rapidly. But a few droplets remain liquid for about a millisecond even at this temperature. The hope now is that these observations and our detailed structural data will help identify those theories that best describe and explain the behaviour of water.
Optics Express | 2012
Andrew Aquila; Mark S. Hunter; R. Bruce Doak; Richard A. Kirian; Petra Fromme; Thomas A. White; Jakob Andreasson; David Arnlund; Sasa Bajt; Thomas R. M. Barends; Miriam Barthelmess; Michael J. Bogan; Christoph Bostedt; Hervé Bottin; John D. Bozek; Carl Caleman; Nicola Coppola; Jan Davidsson; Daniel P. DePonte; Veit Elser; Sascha W. Epp; Benjamin Erk; Holger Fleckenstein; Lutz Foucar; Matthias Frank; Raimund Fromme; Heinz Graafsma; Ingo Grotjohann; Lars Gumprecht; Janos Hajdu
We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
Nature Methods | 2012
Rudolf Koopmann; Karolina Cupelli; Karol Nass; Daniel P. DePonte; Thomas A. White; Francesco Stellato; Dirk Rehders; Mengning Liang; Jakob Andreasson; Andrew Aquila; Sasa Bajt; Miriam Barthelmess; Anton Barty; Michael J. Bogan; Christoph Bostedt; Sébastien Boutet; John D. Bozek; Carl Caleman; Nicola Coppola; Jan Davidsson; R. Bruce Doak; Tomas Ekeberg; Sascha W. Epp; Benjamin Erk; Holger Fleckenstein; Lutz Foucar; Heinz Graafsma; Lars Gumprecht; J. Hajdu; Christina Y. Hampton
Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo–grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.
Science | 2016
Kanupriya Pande; C. Hutchison; Gerrit Groenhof; Andy Aquila; Josef S. Robinson; Jason Tenboer; Shibom Basu; Sébastien Boutet; Daniel P. DePonte; Mengning Liang; Thomas A. White; Nadia A. Zatsepin; Oleksandr Yefanov; Dmitry Morozov; Dominik Oberthuer; Cornelius Gati; Ganesh Subramanian; Daniel James; Yun Zhao; J. D. Koralek; Jennifer Brayshaw; Christopher Kupitz; Chelsie E. Conrad; Shatabdi Roy-Chowdhury; Jesse Coe; Markus Metz; Paulraj Lourdu Xavier; Thomas D. Grant; Jason E. Koglin; Gihan Ketawala
Visualizing a response to light Many biological processes depend on detecting and responding to light. The response is often mediated by a structural change in a protein that begins when absorption of a photon causes isomerization of a chromophore bound to the protein. Pande et al. used x-ray pulses emitted by a free electron laser source to conduct time-resolved serial femtosecond crystallography in the time range of 100 fs to 3 ms. This allowed for the real-time tracking of the trans-cis isomerization of the chromophore in photoactive yellow protein and the associated structural changes in the protein. Science, this issue p. 725 The trans-to-cis isomerization of a key chromophore is characterized on ultrafast time scales. A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.
Nature Methods | 2012
Linda C. Johansson; David Arnlund; Thomas A. White; Gergely Katona; Daniel P. DePonte; Uwe Weierstall; R. Bruce Doak; Robert L. Shoeman; Lukas Lomb; Erik Malmerberg; Jan Davidsson; Karol Nass; Mengning Liang; Jakob Andreasson; Andrew Aquila; Sasa Bajt; Miriam Barthelmess; Anton Barty; Michael J. Bogan; Christoph Bostedt; John D. Bozek; Carl Caleman; Ryan Coffee; Nicola Coppola; Tomas Ekeberg; Sascha W. Epp; Benjamin Erk; Holger Fleckenstein; Lutz Foucar; Heinz Graafsma
X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.