Observation of the light-triggered binding of pyrone to chymotrypsin by Laue x-ray crystallography

The time revolution in macromolecular crystallography

Macromolecular crystallography has historically provided the atomic structures of proteins fundamental to cellular functions. However, the advent of cryo-electron microscopy for structure determination of large and increasingly smaller and flexible proteins signaled a paradigm shift in structural biology. The extensive structural and sequence data from crystallography and advanced sequencing techniques have been pivotal for training computational models for accurate structure prediction, unveiling the general fold of most proteins. Here, we present a perspective on the rise of time-resolved crystallography as the new frontier of macromolecular structure determination. We trace the evolution from the pioneering time-resolved crystallography methods to modern serial crystallography, highlighting the synergy between rapid detection technologies and state-of-the-art x-ray sources. These innovations are redefining our exploration of protein dynamics, with high-resolution crystallography uniquely positioned to elucidate rapid dynamic processes at ambient temperatures, thus deepening our understanding of protein functionality. We propose that the integration of dynamic structural data with machine learning advancements will unlock predictive capabilities for protein kinetics, revolutionizing dynamics like macromolecular crystallography revolutionized structural biology.

Mapping Enzyme Landscapes by Time-Resolved Crystallography with Synchrotron and X-Ray Free Electron Laser Light

Directly observing enzyme catalysis in real time at the molecular level has been a long-standing goal of structural enzymology. Time-resolved serial crystallography methods at synchrotron and X-ray free electron laser (XFEL) sources have enabled researchers to follow enzyme catalysis and other nonequilibrium events at ambient conditions with unprecedented time resolution. X-ray crystallography provides detailed information about conformational heterogeneity and protein dynamics, which is enhanced when time-resolved approaches are used. This review outlines the ways in which information about the underlying energy landscape of a protein can be extracted from X-ray crystallographic data, with an emphasis on new developments in XFEL and synchrotron time-resolved crystallography. The emerging view of enzyme catalysis afforded by these techniques can be interpreted as enzymes moving on a time-dependent energy landscape. Some consequences of this view are discussed, including the proposal that irreversible enzymes or enzymes that use covalent catalytic mechanisms may commonly exhibit catalysis-activated motions. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Detection of Reaction Intermediates in Mg2+-Dependent DNA Synthesis and RNA Degradation by Time-Resolved X-Ray Crystallography

Structures of enzyme-substrate/product complexes have been studied for over four decades but have been limited to either before or after a chemical reaction. Recently using in crystallo catalysis combined with X-ray diffraction, we have discovered that many enzymatic reactions in nucleic acid metabolism require additional metal ion cofactors that are not present in the substrate or product state. By controlling metal ions essential for catalysis, the in crystallo approach has revealed unprecedented details of reaction intermediates. Here we present protocols used for successful studies of Mg²⁺-dependent DNA polymerases and ribonucleases that are applicable to analyses of a variety of metal ion-dependent reactions.

Ultrafast X-Ray Crystallography and Liquidography

Time-resolved X-ray diffraction provides direct information on three-dimensional structures of reacting molecules and thus can be used to elucidate structural dynamics of chemical and biological reactions. In this review, we discuss time-resolved X-ray diffraction on small molecules and proteins with particular emphasis on its application to crystalline (crystallography) and liquid-solution (liquidography) samples. Time-resolved X-ray diffraction has been used to study picosecond and slower dynamics at synchrotrons and can now access even femtosecond dynamics with the recent arrival of X-ray free-electron lasers.

Protein-ligand interaction probed by time-resolved crystallography

Time-resolved (TR) crystallography is a unique method for determining the structures of intermediates in biomolecular reactions. The technique reached its mature stage with the development of the powerful third-generation synchrotron X-ray sources, and the advances in data processing and analysis of time-resolved Laue crystallographic data. A time resolution of 100 ps has been achieved and relatively small structural changes can be detected even from only partial reaction initiation. The remaining challenge facing the application of this technique to a broad range of biological systems is to find an efficient and rapid, system-specific method for the reaction initiation in the crystal. Other frontiers for the technique involve the continued improvement in time resolution and further advances in methods for determining intermediate structures and reaction mechanisms. The time-resolved technique, combined with trapping methods and computational approaches, holds the promise for a complete structure-based description of biomolecular reactions.

Crystal structure of gamma-chymotrypsin in complex with 7-hydroxycoumarin

The 1.8 A crystal structure of 7-hydroxycoumarin (7-HC) bound to chymotrypsin reveals that this inhibitor forms a planar cinnamate acyl-enzyme complex. The phenyl ring of the bound inhibitor forms numerous van der Waals contacts in the S1 pocket of the enzyme, with the p-hydroxyl group donating a hydrogen bond to the main-chain oxygen atom of Ser217, and the o-hydroxyl group forming a water-mediated hydrogen bond with the carbonyl oxygen of Val227. The structure of the acyl-enzyme complex suggests that the mechanism of inhibition of 7-HC involves nucleophilic attack by the Ser195 O(gamma) atom on the carbonyl carbon atom of the inhibitor, accompanied by the breaking of the 2-pyrone ring of the inhibitor, and leading to the formation of a cinnamate acyl-enzyme derivative via a tetrahedral transition state. Comparisons with structures of photoreversible cinnamates bound to chymotrypsin reveal that although 7-HC interacts with the enzyme in a similar fashion, the binding of 7-HC to chymotrypsin takes place in a productive conformation in contrast to the photoreversible cinnamates. In summary, the 7-HC-chymotrypsin complex provides basic insight into the inhibition of chymotrypsin by natural coumarins and provides a structural basis for the design of more potent mechanism-based inhibitors against a wide range of biologically important chymotrypsin-like enzymes.

Trapping reaction intermediates in macromolecular crystals for structural analyses

The development of "time-resolved" crystallographic methods, including trapping of reaction intermediates and rapid data collection, allows the comparative study of discrete structural species formed during a macromolecular reaction, such as enzymatic catalysis, ribozyme cleavage, or a protein photocycle. The primary technical details that must be addressed in such studies are the reaction initiation, the accumulation of a specific reaction species throughout the crystal, the lifetime of that species and of the crystal under the experimental conditions, and the method used to collect X-ray data. Methods of reaction initiation range from substrate diffusion, which is appropriate for the visualization of very long-lived intermediates, to photolysis, which is appropriate for the accumulation of rate-limited species with half-lives ranging from milliseconds to nanoseconds. This review discusses various methods for initiating turnover in crystals and trapping rate-limiting species for structural studies.

Crystallographic structure determination of unstable species

Crystal structures of reactive short-lived species, as occurring during chemical reactions, can be determined through time-resolved crystallography or trapping approaches. Prerequisite is the initiation and characterization of the reaction in the crystal. Ways to do this, recent results, caveats, and future prospects are discussed.

Light-activated proteins

A wide assortment of caged compounds, which are species whose biological activity can be unleashed with light, have been synthesized and used to investigate a variety of biological phenomena. In contrast, the construction of caged proteins and their application to biological systems has lagged far behind. Recent advances in the synthesis of caged proteins, as well as the development of intracellular protein delivery systems, furnish a framework upon which light-activated proteins can be designed, synthesized and employed to address questions of biological significance.

Millisecond Laue structures of an enzyme-product complex using photocaged substrate analogs

The structure of a rate-limited product complex formed during a single initial round of turnover by isocitrate dehydrogenase has been determined. Photolytic liberation of either caged substrate or caged cofactor and Laue X-ray data collection were used to visualize the complex, which has a minimum half-life of approximately 10 milliseconds. The experiment was conducted with three different photoreactive compounds, each possessing a unique mechanism leading to the formation of the enzyme-substrate (ES) complex. Photoreaction efficiency and subsequent substrate affinities and binding rates in the crystal are critical parameters for these experiments. The structure suggests that CO2 dissociation is a rapid event that may help drive product formation, and that small conformational changes may contribute to slow product release.

Structure of a protein photocycle intermediate by millisecond time-resolved crystallography

The blue-light photoreceptor photoactive yellow protein (PYP) undergoes a self-contained light cycle. The atomic structure of the bleached signaling intermediate in the light cycle of PYP was determined by millisecond time-resolved, multiwavelength Laue crystallography and simultaneous optical spectroscopy. Light-induced trans-to-cis isomerization of the 4-hydroxycinnamyl chromophore and coupled protein rearrangements produce a new set of active-site hydrogen bonds. An arginine gateway opens, allowing solvent exposure and protonation of the chromophore's phenolic oxygen. Resulting changes in shape, hydrogen bonding, and electrostatic potential at the protein surface form a likely basis for signal transduction. The structural results suggest a general framework for the interpretation of protein photocycles.

Can Laue catch Maxwell?: observation of short-lived species by Laue X-ray crystallography

Now that the Laue method has been established as a tool for protein crystallography, the main problem involved in any prospective time-resolved X-ray diffraction study is one of chemistry. The reaction or process in question must be initiated on a timescale that is fast compared with its kinetics. For most biochemical events photochemistry is the most suitable trigger, but not all substrates can be caged for photochemical release. This problem can be solved by the novel strategy of caging the enzyme with a photoreversible covalent inhibitor. The logic of this method will be discussed and its application to a time-resolved study of the reaction of a suicide substrate with the protease gamma chymotrypsin shown. The question of real-time crystallographic ‘movies’ of enzymatic reactions can now be considered. It seems likely that following a reaction in real time in a single experiment will be very difficult if not impossible in most cases, in part because even a synchronized process will rapidly become asynchronous in a protein crystal, and also because it will be very difficult to know exactly what species one is observing at any instant unless one has extremely high resolution. It seems that the best use of the Laue technique will be to study unstable species that can be accumulated in the crystal under defined conditions for short periods of time. An entire reaction sequence can then be obtained as a series of individual steps, each of which is obtained from a separate experiment.

Laue diffraction as a tool in dynamic studies: hydrolysis of a transiently stable intermediate in catalysis by trypsin

A transiently stable intermediate in trypsin catalysis, guanidinobenzoyl-Ser-195 trypsin, can be trapped and then released by control of the pH in crystals of the enzyme. This effect has been investigated by static and dynamic white-beam Laue crystallography. Comparison of structures determined before and immediately after a pH jump reveals the nature of concerted changes that accompany activation of the enzyme. Careful analysis of the results of several structure determinations gives information about the reliability of Laue results in general. A study of multiple exposures taken under differing conditions of beam intensity, crystal quality, and temperature revealed information about ways to control damage of specimens by the X-ray beam.

Art is long and time is fleeting: the current problems and future prospects for time-resolved enzyme crystallography

I offer comments on the challenges and problems of the future based on the papers in this volume. First, the requirement of the Laue technique for a very well-ordered crystal is a major obstacle to many studies. Efforts to ease this problem are needed. Secondly, the fundamental issues in time-resolved crystallography are now chemical rather than crystallographic. Methods for the rapid initiation of many reactions must be developed. Thirdly, it is imperative that the kinetics of the process in question be studied in the crystal before any diffraction experiments are done. We need better ways to make those solid state kinetic measurements. Fourthly, we should make use of combined methods, such as cryoenzymology plus Laue diffraction or site-directed mutagenesis plus Laue diffraction, to bring many processes into the time regime in which we currently can work. Fifthly, we have to be able to deconvolute diffraction data that come from a mixture of two or three discrete species. Finally, no matter how powerful our synchrotrons get, it seems to me that some of the most important events in any enzymatic reaction are not going to be accessible: consider the formation and decomposition of a transition state as an example. I close by discussing the role of computational biochemistry in filling in those frames of our enzymatic movie that we cannot observe directly by time-resolved X-ray crystallography.

The development and application of photosensitive caged compounds to aid time-resolved structure determination of macromolecules

Rapid photochemical release of biologically active molecules, typically enzyme substrates or effectors of proteins, within crystals is likely to play an important role in time-resolved macromolecular crystallography. Photosensitive or ‘caged’ compounds in which functional groups are protected by the l-(2-nitrophenyl)ethyl group are potentially useful because many such compounds are efficiently and fairly rapidly photolysed (product quantum yield ca. 0.5 and photolysis rate ca. 100 s -1 for esters of weakly acidic phosphates) and have proved effective probes of physiological mechanisms. However, their availability and successful application are unlikely to be universal, and in some cases limitations may arise because of low quantum yield, a photolysis rate that is slow compared with the mechanism being studied or the toxicity of the by-product, 2-nitrosoacetophenone. 3,5-Dinitrophenyl and 3,5'- dimethoxybenzoin esters are two other potentially useful photosensitive classes of compound (Kirby & Varvoglis, J. chem. Soc. chem. Commun. 406 (1967); Sheehan et al. , J. Am. chem. Soc . 93, 7222-7228 (1971); Baldwin et al., Tetrahedron 46, 6879-6884 (1990)). 3,5-Dinitrophenyl phosphate has a product quantum yield of 0.67 and releases P A at greater than 104 s_1. However the dinitrophenyl group is not generally photosensitive: for example the P 3-3,5-dinitrophenyl ester of ATP photolyses very inefficiently at pH 7. The S'A'-dimethoxybenzoin group is a promising photosensitive group for phosphate esters and the P 3 -3/,5'-dimethoxybenzoin ester of ATP photolyses at greater than 10 5 s -1 at neutral pH and 20 °C though with only about 4% photolysis on 347 nm pulse irradiation.

Combining Laue diffraction and molecular dynamics to study enzyme intermediates

Two separate techniques, Laue diffraction and computational molecular dynamics (MD) simulations, have been independently developed to allow the visualization and assessment of transient structural states. Recent studies on isocitrate dehydrogenase show that computational MD simulations of an enzymatic Michaelis complex are consistent with difference Fourier electron density maps of the same structure from a Laue experiment. The use of independent MD studies during crystallographic refinement has allowed us to assign with confidence a number of additional contacts and features important for hydride transfer. We find that unrestrained independent MD simulations provides a very useful method of cross-validation for highly mobile atoms in regions of experimental density that are poorly defined. Likewise, information from Laue difference maps provides information about substrate conformation and interactions that greatly facilitate MD simulations.

Laue crystallography. It's show time

New crystallographic techniques make it possible to observe directly all of the intermediates in an enzymatic reaction. Such a series of structures can be combined to create a detailed movie of enzymatic catalysis.

Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenase

Site-directed mutagenesis and Laue diffraction data to 2.5 A resolution were used to solve the structures of two sequential intermediates formed during the catalytic actions of isocitrate dehydrogenase. Both intermediates are distinct from the enzyme-substrate and enzyme-product complexes. Mutation of key catalytic residues changed the rate determining steps so that protein and substrate intermediates within the overall reaction pathway could be visualized.

Laue and monochromatic diffraction studies on catalysis in phosphorylase b crystals

The conversion of substrate, heptenitol, to product, beta-1-C-methyl, alpha-D-glucose-1-phosphate (heptulose-2-P), in crystals of glycogen phosphorylase b has been studied by Laue and monochromatic diffraction methods. The phosphorolysis reaction in the crystal was started following liberation of phosphate from a caged phosphate compound, 3,5-dinitrophenyl phosphate (DNPP). The photolysis of DNPP, stimulated by flashes from a xenon flash lamp, was monitored in the crystal with a diode array spectrophotometer. In the Laue diffraction experiments, data to 2.8 A resolution were collected and the first time shot was obtained at 3 min from the start of reaction, and data collection comprised three 800-ms exposures. Careful data processing of Laue photographs for the large enzyme resulted in electron density maps of almost comparable quality to those produced by monochromatic methods. The difference maps obtained from the Laue measurements showed that very little catalysis had occurred 3 min and 1 h after release of phosphate, and a distinct peak consistent with the position expected for phosphate, in the attacking position was observed. Data collection times with monochromatic crystallographic methods on a home source took 16 h for data to 2.3 A resolution. Sufficient phosphate was released from the caged phosphate in the crystal from 5 flashes with a xenon flashlamp within 1 min for the reaction to go to completion within the time scale of the monochromatic data collection procedures. The heptulose-2-P product complex has been refined and the model agrees with that obtained previously with the major difference that the interchange of an aspartic acid (Asp 283) by an arginine (Arg 569) was not observed at the catalytic site. This change is part of the activation process of glycogen phosphorylase and may not have taken place in the current experiments because the caged compound binds weakly at the inhibitor site, restricting conformational change, and because activators of the enzymic reaction were not present in the crystal. In experiments with monochromatic radiation in which low phosphate concentrations were generated either by fewer photons or by diffusion of known phosphate concentrations, mixtures of substrate and product were observed. It was not possible through crystallographic refinement at 2.3 A resolution to establish the fractional occupancies of the enzyme-substrate and enzyme-product complexes, but the results did indicate that the reaction was proceeding slowly, consistent with approximate calculations for the likely rate of the reaction in the crystal.(ABSTRACT TRUNCATED AT 250 WORDS)

Time-resolved protein crystallography

Advances in synchrotron radiation technology have allowed exposure times from protein crystals of the order of milliseconds to be used routinely, and in exceptional circumstances exposure times of 100 ps have been obtained. However, many data sets take seconds to record because of the slow time scale of film change or crystal reorientation or translation when more than one exposure is required. This problem has been addressed by Amemiya et al. (1989). There has been considerable progress in methods to initiate reactions in protein crystals, especially the development of photolabile caged compounds but also temperature jump, pH jump, and diffusion. Although flash lamps deliver pulses of 100 mJ/ms, often several pulses are required to release sufficient product, and reaction initiation can take several seconds. Laser illumination can provide more powerful input, but the laser must be accommodated within the restricted space at the synchrotron station. The requirement to maintain synchrony among the molecules in the crystal lattice as the reaction proceeds and to ensure that the lifetime of intermediates is longer than data collection rates emphasizes the need for chemical characterization of the reaction under study. As Ringe advocated in the studies with chymotrypsin, it may be more profitable to devise conditions under which certain intermediates along the reaction pathway accumulate in the crystal and to record these in a series of discrete steps rather than continuous monitoring of the reaction. The Laue method is limited to those proteins that give well-ordered crystals and problems of transient disorder on initiation of reaction and problems of radiation damage need to be overcome or avoided by suitable experimental protocols.(ABSTRACT TRUNCATED AT 250 WORDS)