Shotgun crystallization strategy for structural genomics II: crystallization conditions that produce high resolution structures for T. maritima proteins

Protein Crystallizability

Obtaining diffracting quality crystals remains a major challenge in protein structure research. We summarize and compare methods for selecting the best protein targets for crystallization, construct optimization and crystallization condition design. Target selection methods are divided into algorithms predicting the chance of successful progression through all stages of structural determination (from cloning to solving the structure) and those focusing only on the crystallization step. We tried to highlight pros and cons of different approaches examining the following aspects: data size, redundancy and representativeness, overfitting during model construction, and results evaluation. In summary, although in recent years progress was made and several sequence properties were reported to be relevant for crystallization, the successful prediction of protein crystallization behavior and selection of corresponding crystallization conditions continue to challenge structural researchers.

In Vitro Reconstitution and Crystallization of Cas9 Endonuclease Bound to a Guide RNA and a DNA Target

The programmable RNA-guided DNA cleavage activity of the bacterial CRISPR-associated endonuclease Cas9 is the basis of genome editing applications in numerous model organisms and cell types. In a binary complex with a dual crRNA:tracrRNA guide or single-molecule guide RNA, Cas9 targets double-stranded DNAs harboring sequences complementary to a 20-nucleotide segment in the guide RNA. Recent structural studies of the enzyme have uncovered the molecular mechanism of RNA-guided DNA recognition. Here, we provide protocols for electrophoretic mobility shift and fluorescence-detection size exclusion chromatography assays used to probe DNA binding by Cas9 that allowed us to reconstitute and crystallize the enzyme in a ternary complex with a guide RNA and a bona fide target DNA. The procedures can be used for further mechanistic investigations of the Cas9 endonuclease family and are potentially applicable to other multicomponent protein-nucleic acid complexes.

Crystal structure of the ALK (anaplastic lymphoma kinase) catalytic domain

ALK (anaplastic lymphoma kinase) is an RTK (receptor tyrosine kinase) of the IRK (insulin receptor kinase) superfamily, which share an YXXXYY autophosphorylation motif within their A-loops (activation loops). A common activation and regulatory mechanism is believed to exist for members of this superfamily typified by IRK and IGF1RK (insulin-like growth factor receptor kinase-1). Chromosomal translocations involving ALK were first identified in anaplastic large-cell lymphoma, a subtype of non-Hodgkin's lymphoma, where aberrant fusion of the ALK kinase domain with the NPM (nucleophosmin) dimerization domain results in autophosphosphorylation and ligand-independent activation. Activating mutations within the full-length ALK kinase domain, most commonly R1275Q and F1174L, which play a major role in neuroblastoma, were recently identified. To provide a structural framework for understanding these mutations and to guide structure-assisted drug discovery efforts, the X-ray crystal structure of the unphosphorylated ALK catalytic domain was determined in the apo, ADP- and staurosporine-bound forms. The structures reveal a partially inactive protein kinase conformation distinct from, and lacking, many of the negative regulatory features observed in inactive IGF1RK/IRK structures in their unphosphorylated forms. The A-loop adopts an inhibitory pose where a short proximal A-loop helix (alphaAL) packs against the alphaC helix and a novel N-terminal beta-turn motif, whereas the distal portion obstructs part of the predicted peptide-binding region. The structure helps explain the reported unique peptide substrate specificity and the importance of phosphorylation of the first A-loop Tyr1278 for kinase activity and NPM-ALK transforming potential. A single amino acid difference in the ALK substrate peptide binding P-1 site (where the P-site is the phosphoacceptor site) was identified that, in conjunction with A-loop sequence variation including the RAS (Arg-Ala-Ser)-motif, rationalizes the difference in the A-loop tyrosine autophosphorylation preference between ALK and IGF1RK/IRK. Enzymatic analysis of recombinant R1275Q and F1174L ALK mutant catalytic domains confirms the enhanced activity and transforming potential of these mutants. The transforming ability of the full-length ALK mutants in soft agar colony growth assays corroborates these findings. The availability of a three-dimensional structure for ALK will facilitate future structure-function and rational drug design efforts targeting this receptor tyrosine kinase.

Autoindexing with outlier rejection and identification of superimposed lattices

Constructing a model lattice to fit the observed Bragg diffraction pattern is straightforward for perfect samples, but indexing can be challenging when artifacts are present, such as poorly shaped spots, split crystals giving multiple closely aligned lattices and outright superposition of patterns from aggregated microcrystals. To optimize the lattice model against marginal data, refinement can be performed using a subset of the observations from which the poorly fitting spots have been discarded. Outliers are identified by assuming a Gaussian error distribution for the best-fitting spots and points diverging from this distribution are culled. The set of remaining observations produces a superior lattice model, while the rejected observations can be used to identify a second crystal lattice, if one is present. The prevalence of outliers provides a potentially useful measure of sample quality. The described procedures are implemented for macromolecular crystallography within the autoindexing program labelit.index (http://cci.lbl.gov/labelit).

Protein crystallizability

Obtaining well-diffracting crystals remains a major challenge in protein structure research. In this chapter, we review currently available computational methods to estimate the crystallization potential of a protein, to optimize amino acid sequences toward improved crystallization likelihood, and to design optimal crystal screen conditions.

Sequence, structure, function, immunity: structural genomics of costimulation

SUMMARY

Costimulatory receptors and ligands trigger the signaling pathways that are responsible for modulating the strength, course, and duration of an immune response. High-resolution structures have provided invaluable mechanistic insights by defining the chemical and physical features underlying costimulatory receptor:ligand specificity, affinity, oligomeric state, and valency. Furthermore, these structures revealed general architectural features that are important for the integration of these interactions and their associated signaling pathways into overall cellular physiology. Recent technological advances in structural biology promise unprecedented opportunities for furthering our understanding of the structural features and mechanisms that govern costimulation. In this review, we highlight unique insights that have been revealed by structures of costimulatory molecules from the immunoglobulin and tumor necrosis factor superfamilies and describe a vision for future structural and mechanistic analysis of costimulation. This vision includes simple strategies for the selection of candidate molecules for structure determination and highlights the critical role of structure in the design of mutant costimulatory molecules for the generation of in vivo structure-function correlations in a mammalian model system. This integrated 'atoms-to-animals' paradigm provides a comprehensive approach for defining atomic and molecular mechanisms.

Autoindexing the diffraction patterns from crystals with a pseudotranslation

Lattice patterns containing alternating strong and weak reflections can be identified by a targeted search for the weak signals, permitting a wider range of diffraction patterns to be indexed automatically.

Rotation photographs can be readily indexed if enough candidate Bragg spots are identified to properly sample the reciprocal lattice. However, while automatic indexing algorithms are widely used for macromolecular data processing, they can produce incorrect results in special situations where a subset of Bragg spots is systematically overlooked. This is a potential outcome in cases where a noncrystallographic translational symmetry operator closely mimics an exact crystallo­graphic translation. In these cases, a visual inspection of the diffraction image will reveal alternating strong and weak reflections. However, reliable detection of the weak-intensity reflections by software requires a systematic search for a diffraction signal targeted at specific reciprocal-space locations calculated a priori by considering all possible pseudotranslations. Care must be exercised to distinguish between true lattice diffraction and spurious signals contributed by neighboring overlapping Bragg spots, non-Bragg diffraction and noise. Such procedures have been implemented within the autoindexing program LABELIT and applied to known cases from publicly available data sets. Routine use of this type of signal search adds only a few seconds to the typical run time for autoindexing. The program can be downloaded from http://cci.lbl.gov/labelit.

The iron-hydrogenase of Thermotoga maritima utilizes ferredoxin and NADH synergistically: a new perspective on anaerobic hydrogen production

The hyperthermophilic and anaerobic bacterium Thermotoga maritima ferments a wide variety of carbohydrates, producing acetate, CO(2), and H(2). Glucose is degraded through a classical Embden-Meyerhof pathway, and both NADH and reduced ferredoxin are generated. The oxidation of these electron carriers must be coupled to H(2) production, but the mechanism by which this occurs is unknown. The trimeric [FeFe]-type hydrogenase that was previously purified from T. maritima does not use either reduced ferredoxin or NADH as a sole electron donor. This problem has now been resolved by the demonstration that this hydrogenase requires the presence of both electron carriers for catalysis of H(2) production. The enzyme oxidizes NADH and ferredoxin simultaneously in an approximately 1:1 ratio and in a synergistic fashion to produce H(2). It is proposed that the enzyme represents a new class of bifurcating [FeFe] hydrogenase in which the exergonic oxidation of ferredoxin (midpoint potential, -453 mV) is used to drive the unfavorable oxidation of NADH (E(0)' = -320 mV) to produce H(2) (E(0)' = -420 mV). From genome sequence analysis, it is now clear that there are two major types of [FeFe] hydrogenases: the trimeric bifurcating enzyme and the more well-studied monomeric ferredoxin-dependent [FeFe] hydrogenase. Almost one-third of the known H(2)-producing anaerobes appear to contain homologs of the trimeric bifurcating enzyme, although many of them also harbor one or more homologs of the simpler ferredoxin-dependent hydrogenase. The discovery of the bifurcating hydrogenase gives a new perspective on our understanding of the bioenergetics and mechanism of H(2) production and of anaerobic metabolism in general.

Protein crystallization in restricted geometry: advancing old ideas for modern times in structural proteomics

In the structural genomics period traditional methods for protein crystallization have been eclipsed by automation using batch or vapor diffusion equilibration to find conditions conducive for protein crystal growth. Although many globular and soluble proteins predominantly from prokaryotes have been crystallized and their structures solved by high throughput approaches, the remaining difficult proteins require more systematic and reflective methods combining miniaturization and integration of modern and traditional crystallography techniques. One of these conventional methods is growing crystals in restricted geometry, which is a historically well-known concept and a practical technique under-used by today's crystallographers. This chapter presents practical guidelines to use capillaries for microbatch crystallization screening and counter-diffusion crystallization as valuable techniques to obtain protein crystals in confined volumes. The emphasis in the authors' application is to perform broad-based screening with a microgram amount of protein, optimize crystal growth in a supersaturation gradient, and undergo in situ x-ray data analysis for x-ray crystallography without invasive manipulation. Applications and concepts presented here bring to light future prerequisites for the next generation of automation for structural genomics.

On the relevance of defining protein structures in cancer research

Are three-dimensional structures of proteins relevant in the study of cancer? The knowledge of the three-dimensional structure of a protein is crucial to gain a full understanding of its function, and structural determination has already shown its potential for guided drug design. The knowledge of the structures of proteins and their complexes with other biological macromolecules helps to elucidate functional networks and provide a better understanding of the functionally relevant behaviour of the molecular machinery of the cell. To study the cell, we must be able to work with proteins, to elucidate how they diffuse and move, to know their interacting partners, and to understand the changes induced by those interactions. Three-dimensional structures give us a picture of the protein and thereby the opportunity to introduce mutations that alter its affinity and specificity for other interactions helping us to understand the physico-chemical mechanisms that control their function. In turn these can lead to the development of novel therapies.

Strategies for improving crystallization success rates

The production of crystals suitable for high-resolution structure determination is still one of the major bottlenecks in the structure determination process. This is especially true in structural genomics (SG) consortia, where the implementation of protein-specific purification and optimization strategies is not readily implemented into the structure determination workflow. This chapter describes four strategies that have been implemented by a number of SG groups to increase the number of protein targets that resulted in atomic resolution structures: (1) orthologue screening; (2) the use of 1D (1)H NMR spectroscopy to screen for the folded state of a protein prior to crystallization; (3) deletion constructs generation, in which regions of the target protein predicted to be disordered are omitted from the construct, to maximize the likelihood of crystal formation; and (4) crystallization optimum solubility screening to identify more suitable buffers for a given protein. The implementation of these strategies can lead to a substantial increase in the number of protein structures solved. Finally, because these strategies do not require the implementation of expensive robotics, they are highly applicable not only for the SG community but also for academic laboratories.

Protein thermal stability: The role of protein structure and aqueous environment

A comprehensive bioinformatic analysis was performed on all protein homologous pairs from mesophilic and thermophilic microorganisms present in the RCSB Protein Data Bank in order to yield a clue on the role of protein structure and aqueous environment. Subsequently self-assembly and LB studies were carried out at increasing temperature by nanogravimetry with thermostable thioredoxin (Trx) from Alicyclobacillus acidocaldarius (BacTrx) versus the mesophilic Escherichia coli counterpart (EcTrx). The comparison with earlier 3D atomic structure determined on the same proteins by X-ray crystallographic diffraction and nuclear magnetic resonance confirm the role inner bound water in determining protein thermostability, as suggested by the bioinformatic and nanogravimetric analysis. The above comparative characterizations in protein solution, thin film and crystal allow to draw a possible coherent explanation for the origin and the molecular mechanisms of both heat stability and radiation resistance in proteins.