Cryo-electron microscopy as an investigative tool: the ribosome as an example

Protein Engineering: Advances in Phage Display for Basic Science and Medical Research

Functional Protein Engineering became the hallmark in biomolecule manipulation in the new millennium, building on and surpassing the underlying structural DNA manipulation and recombination techniques developed and employed in the last decades of 20th century. Because of their prominence in almost all biological processes, proteins represent extremely important targets for engineering enhanced or altered properties that can lead to improvements exploitable in healthcare, medicine, research, biotechnology, and industry. Synthetic protein structures and functions can now be designed on a computer and/or evolved using molecular display or directed evolution methods in the laboratory. This review will focus on the recent trends in protein engineering and the impact of this technology on recent progress in science, cancer- and immunotherapies, with the emphasis on the current achievements in basic protein research using synthetic antibody (sABs) produced by phage display pipeline in the Kossiakoff laboratory at the University of Chicago (KossLab). Finally, engineering of the highly specific binding modules, such as variants of Streptococcal protein G with ultra-high orthogonal affinity for natural and engineered antibody scaffolds, and their possible applications as a plug-and-play platform for research and immunotherapy will be described.

Advanced Methods for Studying Structure and Interactions of Macrolide Antibiotics

Macrolide antibiotics are macrocyclic compounds that are clinically used and prescribed for the treatment of upper and lower respiratory tract infections. They inhibit the synthesis of bacterial proteins by reversible binding to the 23S rRNA at or near the peptidyl transferase center. However, their excellent antibacterial profile was largely compromised by the emergence of bacterial resistance. Today, fighting resistance to antibiotics is one of the greatest challenges in medicinal chemistry. Considering various physicochemical properties of macrolides, understanding their structure and interactions with macromolecular targets is crucial for the design of new antibiotics efficient against resistant pathogens. The solid-state structures of some macrolide-ribosome complexes have recently been solved, throwing new light on the macrolide binding mechanisms. On the other hand, a combination of NMR spectroscopy and molecular modeling calculations can be applied to study free and bound conformations in solution. In this article, a description of advanced physicochemical methods for elucidating the structure and interactions of macrolide antibiotics in solid state and solution will be provided, and their principal advantages and drawbacks will be discussed.

Structural insights into thermostabilization of leucine dehydrogenase from its atomic structure by cryo-electron microscopy

Leucine dehydrogenase (LDH, EC 1.4.1.9) is a NAD⁺-dependent oxidoreductase that catalyzes the deamination of branched-chain l-amino acids (BCAAs). LDH of Geobacillus stearothermophilus (GstLDH) is a highly thermostable enzyme that has been applied for the quantification or production of BCAAs. Here the cryo-electron microscopy (cryo-EM) structures of apo and NAD⁺-bound LDH are reported at 3.0 and 3.2 Å resolution, respectively. On comparing the structures, the two overall structures are almost identical, but it was observed that the partial conformational change was triggered by the interaction between Ser147 and the nicotinamide moiety of NAD⁺. NAD⁺ binding also enhanced the strength of oligomerization interfaces formed by the core domains. Such additional interdomain interaction is in good agreement with our experimental results showing that the residual activity of NAD⁺-bound form was approximately three times higher than that of the apo form after incubation at 80 °C. In addition, sequence comparison of three structurally known LDHs indicated a set of candidates for site-directed mutagenesis to improve thermostability. Subsequent mutation analysis actually revealed that non-conserved residues, including Ala94, Tyr127, and the C-terminal region, are crucial for oligomeric thermostability.

Orientation Determination of Cryo-EM Images Using Least Unsquared Deviations

A major challenge in single particle reconstruction from cryo-electron microscopy is to establish a reliable ab initio three-dimensional model using two-dimensional projection images with unknown orientations. Common-lines-based methods estimate the orientations without additional geometric information. However, such methods fail when the detection rate of common-lines is too low due to the high level of noise in the images. An approximation to the least squares global self-consistency error was obtained in [A. Singer and Y. Shkolnisky, SIAM J. Imaging Sci., 4 (2011), pp. 543-572] using convex relaxation by semidefinite programming. In this paper we introduce a more robust global self-consistency error and show that the corresponding optimization problem can be solved via semidefinite relaxation. In order to prevent artificial clustering of the estimated viewing directions, we further introduce a spectral norm term that is added as a constraint or as a regularization term to the relaxed minimization problem. The resulting problems are solved using either the alternating direction method of multipliers or an iteratively reweighted least squares procedure. Numerical experiments with both simulated and real images demonstrate that the proposed methods significantly reduce the orientation estimation error when the detection rate of common-lines is low.

Selective detection of peptide-oligonucleotide heteroconjugates utilizing capillary HPLC-ICPMS

A method for the selective detection and quantification of peptide:oligonucleotide heteroconjugates, such as those generated by protein:nucleic acid cross-links, using capillary reversed-phase high performance liquid chromatography (cap-RPHPLC) coupled with inductively coupled plasma mass spectrometry detection (ICPMS) is described. The selective detection of phosphorus as (31)P(+), the only natural isotope, in peptide-oligonucleotide heteroconjugates is enabled by the elemental detection capabilities of the ICPMS. Mobile phase conditions that allow separation of heteroconjugates while maintaining ICPMS compatibility were investigated. We found that trifluoroacetic acid (TFA) mobile phases, used in conventional peptide separations, and hexafluoroisopropanol/triethylamine (HFIP/TEA) mobile phases, used in conventional oligonucleotide separations, both are compatible with ICPMS and enable heteroconjugate separation. The TFA-based separations yielded limits of detection (LOD) of ~40 ppb phosphorus, which is nearly seven times lower than the LOD for HFIP/TEA-based separations. Using the TFA mobile phase, 1-2 pmol of a model heteroconjugate were routinely separated and detected by this optimized capLC-ICPMS method.

Ribosomal proteins and colorectal cancer

The ribosome is essential for protein synthesis. The composition and structure of ribosomes from several organisms have been determined, and it is well documented that ribosomal RNAs (rRNAs) and ribosomal proteins (RPs) constitute this important organelle. Many RPs also fill various roles that are independent of protein biosynthesis, called extraribosomal functions. These functions include DNA replication, transcription and repair, RNA splicing and modification, cell growth and proliferation, regulation of apoptosis and development, and cellular transformation. Previous investigations have revealed that RP regulation in colorectal carcinomas (CRC) differs from that found in colorectal adenoma or normal mucosa, with some RPs being up-regulated while others are down-regulated. The expression patterns of RPs are associated with the differentiation, progression or metastasis of CRC. Additionally, the recent literature has shown that the perturbation of specific RPs may promote certain genetic diseases and tumorigenesis. Because of the implications of RPs in disease, especially malignancy, our review sought to address several questions. Why do expression levels or categories of RPs differ in different diseases, most notably in CRC? Is this a cause or consequence of the diseases? What are their possible roles in the diseases? We review the known extraribosomal functions of RPs and associated changes in colorectal cancer and attempt to clarify the possible roles of RPs in colonic malignancy.

Cryo electron microscopy structures of Hsp100 proteins: crowbars in or out?

Independent cryo electron microscopy (cryo-EM) studies of the closely related protein disaggregases ClpB and Hsp104 have resulted in two different models of subunit arrangement in the active hexamer. We compare the EM maps and resulting atomic structure fits, discuss their differences, and relate them to published experimental information in an attempt to discriminate between models. In addition, we present some general assessment criteria for low-resolution cryo-EM maps to offer non-structural biologists tools to evaluate these structures.

Monolithic microfluidic mixing-spraying devices for time-resolved cryo-electron microscopy

The goal of time-resolved cryo-electron microscopy is to determine structural models for transient functional states of large macromolecular complexes such as ribosomes and viruses. The challenge of time-resolved cryo-electron microscopy is to rapidly mix reactants, and then, following a defined time interval, to rapidly deposit them as a thin film and freeze the sample to the vitreous state. Here we describe a methodology in which reaction components are mixed and allowed to react, and are then sprayed onto an EM grid as it is being plunged into cryogen. All steps are accomplished by a monolithic, microfabricated silicon device that incorporates a mixer, reaction channel, and pneumatic sprayer in a single chip. We have found that microdroplets produced by air atomization spread to sufficiently thin films on a millisecond time scale provided that the carbon supporting film is made suitably hydrophilic. The device incorporates two T-mixers flowing into a single channel of four butterfly-shaped mixing elements that ensure effective mixing, followed by a microfluidic reaction channel whose length can be varied to achieve the desired reaction time. The reaction channel is flanked by two ports connected to compressed humidified nitrogen gas (at 50 psi) to generate the spray. The monolithic mixer-sprayer is incorporated into a computer-controlled plunging apparatus. To test the mixing performance and the suitability of the device for preparation of biological macromolecules for cryo-EM, ribosomes and ferritin were mixed in the device and sprayed onto grids. Three-dimensional reconstructions of the ribosomes demonstrated retention of native structure, and 30S and 50S subunits were shown to be capable of reassociation into ribosomes after passage through the device.

Modifying the DPClus algorithm for identifying protein complexes based on new topological structures

Background

Identification of protein complexes is crucial for understanding principles of cellular organization and functions. As the size of protein-protein interaction set increases, a general trend is to represent the interactions as a network and to develop effective algorithms to detect significant complexes in such networks.

Results

Based on the study of known complexes in protein networks, this paper proposes a new topological structure for protein complexes, which is a combination of subgraph diameter (or average vertex distance) and subgraph density. Following the approach of that of the previously proposed clustering algorithm DPClus which expands clusters starting from seeded vertices, we present a clustering algorithm IPCA based on the new topological structure for identifying complexes in large protein interaction networks. The algorithm IPCA is applied to the protein interaction network of Sacchromyces cerevisiae and identifies many well known complexes. Experimental results show that the algorithm IPCA recalls more known complexes than previously proposed clustering algorithms, including DPClus, CFinder, LCMA, MCODE, RNSC and STM.

Conclusion

The proposed algorithm based on the new topological structure makes it possible to identify dense subgraphs in protein interaction networks, many of which correspond to known protein complexes. The algorithm is robust to the known high rate of false positives and false negatives in data from high-throughout interaction techniques. The program is available at .

Application of fractional mass for the identification of peptide-oligonucleotide cross-links by mass spectrometry

A method has been developed to identify oligonucleotide-peptide heteroconjugates by accurate mass measurements using MS. The fractional mass (the decimal fraction mass value following the monoisotopic nominal mass) for peptides and oligonucleotides is different due to their differing molecular compositions. This property has been used to develop the general conditions necessary to differentiate peptides and oligonucleotides from oligonucleotide-peptide heteroconjugates. Peptides and oligonucleotides generated by the theoretical digestion of various proteins and nucleic acids were plotted as nominal mass versus fractional mass. Such plots reveal that three nucleotides cross-linked to a peptide produce enough change in the fractional mass to be recognized from non-cross-linked peptides at the same nominal mass. Experimentally, a Cytochrome c digest was spiked with an oligonucleotide-peptide heteroconjugate and conditions for analyzing the sample using liquid chromatography (LC)-MS were optimized. Upon analysis of this mixture, all detected masses were plotted on a fractional mass plot and the heteroconjugate could be readily distinguished from non-cross-linked peptides. The method developed here can be incorporated into a general proteomics-like scheme for identifying protein-nucleic acid cross-links, and this method is equally applicable to characterizing cross-links generated from protein-DNA and protein-RNA complexes.

Electron microscopy of integrins

Integrins are a family of heterodimeric, cell-surface receptors that mediate interactions between the cytoskeleton and the extracellular matrix. We have used electron microscopy and single-particle image analysis combined with molecular modeling to investigate the structures of the full-length integrin alpha(IIb)beta(3) and the ectodomain of alpha(V)beta(3) in a complex with fibronectin. The full-length integrin alpha(IIb)beta(3) is purified from human platelets by ion exchange and gel filtration chromatography in buffers containing the detergent octyl-beta-D-glucopyranoside, whereas the recombinant ectodomain of alpha(V)beta(3) is soluble in aqueous buffer. Transmission electron microscopy is performed either in negative stain, where the protein is embedded in a heavy metal such as uranyl acetate, or in the frozen-hydrated state, where the sample is flash-frozen such that the buffer is vitrified and native conditions are preserved. Individual integrin particles are selected from low-dose micrographs, either by manual identification or an automated method using a cross-correlation search of the micrograph against a set of reference images. Due to the small size of integrin heterodimers (approximately 250 kDa) and the low electron dose required to minimize beam damage, the signal-to-noise level of individual particles is quite low, both by negative-stain electron microscopy and electron cryomicroscopy. Consequently, it is necessary to average many particle images with equivalent views. The particle images are subjected to reference-free alignment and classification, in which the particles are aligned to a common view and further grouped by statistical methods into classes with common orientations. Assessment of the structure from a set of two-dimensional averaged projections is often difficult, and a further three-dimensional (3D) reconstruction analysis is performed to classify each particle as belonging to a specific projection from a single 3D model. The 3D reconstruction algorithm is an iterative projection-matching routine in which the classified particles are used to construct a new, 3D map for the next iteration. Docking of known high-resolution structures of individual subdomains within the molecular envelope of the 3D EM map is used to derive a pseudoatomic model of the integrin complex. This approach of 3D EM image analysis and pseudoatomic modeling is a powerful strategy for exploring the structural biology of transmembrane signaling by integrins because it is likely that multiple conformational states will be difficult to crystallize, whereas the different states should be amenable to electron cryomicroscopy.

Coarse-grained free energy functions for studying protein conformational changes: a double-well network model

In this work, a double-well network model (DWNM) is presented for generating a coarse-grained free energy function that can be used to study the transition between reference conformational states of a protein molecule. Compared to earlier work that uses a single, multidimensional double-well potential to connect two conformational states, the DWNM uses a set of interconnected double-well potentials for this purpose. The DWNM free energy function has multiple intermediate states and saddle points, and is hence a "rough" free energy landscape. In this implementation of the DWNM, the free energy function is reduced to an elastic-network model representation near the two reference states. The effects of free energy function roughness on the reaction pathways of protein conformational change is demonstrated by applying the DWNM to the conformational changes of two protein systems: the coil-to-helix transition of the DB-loop in G-actin and the open-to-closed transition of adenylate kinase. In both systems, the rough free energy function of the DWNM leads to the identification of distinct minimum free energy paths connecting two conformational states. These results indicate that while the elastic-network model captures the low-frequency vibrational motions of a protein, the roughness in the free energy function introduced by the DWNM can be used to characterize the transition mechanism between protein conformations.

Bacteriophage T4 capsid: a unique platform for efficient surface assembly of macromolecular complexes

We report the first description of a macromolecular complex display system using bacteriophage T4. Decorated with two dispensable outer capsid proteins, Hoc (155 copies) and Soc (810 copies), the 120 nm x 86 nm T4 capsid particle offers a unique binding site-rich platform for surface assembly of hetero-oligomeric complexes. To display the 710 kDa anthrax toxin complex, two bipartite functional fusion proteins, LF-Hoc and LFn-Soc, were constructed. Using a defined in vitro binding system, sequential assembly was performed by first attaching LF-Hoc and/or LFn-Soc to hoc-soc- phage, saturating the Hoc and Soc binding sites. Trypsin-nicked PA63 was then assembled into heptamers through specific interaction with the capsid-exposed LFn domain. EF was then attached to the unoccupied sites of PA63 heptamers, completing the assembly of the tripartite anthrax toxin. Negative electron microscopy showed decoration of each capsid with a layer of heptameric PA63 rings. Up to 229 anthrax toxin complexes, equivalent to a total of 2400 protein molecules and a mass of about 133 MDa (2.7 times the mass of capsid shell), were anchored on a single particle, making it the highest density display reported on any virus. The phage T4 capsid lattice provides a stable biological platform allowing maximum display of large hetero-oligomeric complexes in vitro and offers insights for developing novel vaccines, analysis of protein-protein interactions, and structure determination of complexes.

Three-dimensional analysis of single particles by electron microscopy: sample preparation and data acquisition

Electron microscopy of single particles has recently become a very popular field in both biological and material sciences. It might be difficult for a novice researcher new to this field to know how to start tackling a new project. This chapter is designed to serve as a guideline for anyone starting a new project to determine a three-dimensional structure using single-particle techniques. The chapter describes the basic techniques necessary to prepare the samples and acquire the data to calculate a three-dimensional reconstruction in easy-to-understand, step-by-step instructions. It starts with the basic preparation of support films and the usage of a variety of staining techniques needed to assess the quality of the sample and the viability of the project. It ends with a detailed description of vitreous ice preparations designed to acquire high-resolution structural information. Guidelines and tips are given on how to record the best images with an electron microscope. Although this chapter is geared to researchers new to the field, experts might find it not only useful as a reference but also valuable because of the number of practical tips included.

Unsupervised classification of single particles by cluster tracking in multi-dimensional space

In cryo-electron microscopy (cryo-EM) single-particle reconstruction, the heterogeneity of two-dimensional projection image data resulting from the co-existence of different conformational or ligand binding states of a macromolecular complex remains a major obstacle as it impairs the validity of reconstructed density maps and limits the progress toward higher resolution. Classification of cryo-EM data according to the different conformations is difficult because of the coexistence of multiple orientations in a single dataset. Here, we present an unsupervised classification method, termed cluster tracking, which utilizes the continuity in multi-dimensional space induced by angular adjacency of projections in large datasets. In a proof of concept, the testing of cluster tracking on simulated projection data, which were generated from multiple conformations and orientations of an existing volume, produced clusters that are consistent with the conformational identity of the data. The application of the method to experimental cryo-EM projection data is found to result in a partition similar to the one generated by supervised classification.

Single particle analysis of filamentous and highly elongated macromolecular assemblies

The application of single particle techniques to the three-dimensional analysis of electron microscope images of elongated or filamentous macromolecular assemblies is evaluated, taking as an example the muscle thin filament. Although the thin filament contains local helical symmetry, because of the inherent variable twist along it, the helical coherence does not extend for large enough distances to allow the symmetry to be used for full reconstruction of the tropomyosin/troponin repeat along the filament. The muscle thin filament therefore represents a general case of a filamentous object in that it is not possible to exploit symmetry in a full analysis. Due to the nature of the imaging process in the electron microscope, only projections of the thin filament around its long axis are available without tilting the grid. Crucially, projection images around a single axis do not provide enough information to assign Euler angles ab initio using current methods. Tests with a model thin filament structure indicated that an out-of-plane tilt of approximately 20 degrees was needed for ab initio angular assignment of sufficient accuracy to calculate a 3D structure to a resolution of approximately 25 A. If no out-of-plane views are available, an alternative approach is to use a prior 3D model as a reference for the initial angle assignment. Tests with the thin filament model indicated that reasonably accurate angular assignment can be made using a reference containing actin, but lacking the regulatory proteins tropomyosin and troponin. We also found that an adaptation of the exact filtered back projection method is required to allow the correct weighting of projection images in which the particle has a very large axial ratio. This adaptation resulted in significant improvements in the reconstruction.

RNA backbone is rotameric

Despite the importance of local structural detail to a mechanistic understanding of RNA catalysis and binding functions, RNA backbone conformation has been quite recalcitrant to analysis. There are too many variable torsion angles per residue, and their raw empirical distributions are poorly clustered. This study applies quality-filtering techniques (using resolution, crystallographic B factor, and all-atom steric clashes) to the backbone torsion angle distributions from an 8,636-residue RNA database. With noise levels greatly reduced, clear signal appears for the underlying angle preferences. Half-residue torsion angle distributions for alpha-beta-gamma and for delta-epsilon-zeta are plotted and contoured in 3D; each shows about a dozen distinct peaks, which can then be combined in pairs to define complete RNA backbone conformers. Traditional nucleic acid residues are defined from phosphate to phosphate, but here we use a base-to-base (or sugar-to-sugar) division into "suites" to parse the RNA backbone repeats, both because most backbone steric clashes are within suites and because the relationship of successive bases is both reliably determined and conformationally important. A suite conformer has seven variables, with sugar pucker specified at both ends. Potential suite conformers were omitted if not represented by at least a small cluster of convincing data points after application of quality filters. The final result is a small library of 42 RNA backbone conformers, which should provide valid conformations for nearly all RNA backbone encountered in experimental structures.

Bioinformatics analysis of experimentally determined protein complexes in the yeast Saccharomyces cerevisiae

Many important cellular functions are implemented by protein complexes that act as sophisticated molecular machines of varying size and temporal stability. Here we demonstrate quantitatively that protein complexes in the yeast Saccharomyces cerevisiae are comprised of a core in which subunits are highly coexpressed, display the same deletion phenotype (essential or nonessential), and share identical functional classification and cellular localization. This core is surrounded by a functionally mixed group of proteins, which likely represent short-lived or spurious attachments. The results allow us to define the deletion phenotype and cellular task of most known complexes, and to identify with high confidence the biochemical role of hundreds of proteins with yet unassigned functionality.

Protein synthesis by single ribosomes

The ribosome is universally responsible for synthesizing proteins by translating the genetic code transcribed in mRNA into an amino acid sequence. Ribosomes use cellular accessory proteins, soluble transfer RNAs, and metabolic energy to accomplish the initiation, elongation, and termination of peptide synthesis. In translocating processively along the mRNA template during the elongation cycle, ribosomes act as supramolecular motors. Here we demonstrate that ribosomes adsorbed on a surface, as for mechanical or spectroscopic studies, are capable of polypeptide synthesis and that tethered particle analysis of fluorescent beads connected to ribosomes via polyuridylic acid can be used to estimate the rate of polyphenylalanine synthesis by individual ribosomes. This work opens the way for application of biophysical techniques, originally developed for the classical motor proteins, to the understanding of protein biosynthesis.

CPV, a stable and symmetrical machine for mRNA synthesis

The structure of cytoplasmic polyhedrosis virus (CPV), an insect pathogen from the Reoviridae family of double-strand RNA viruses, has been determined at 8 A by electron cryomicroscopy and image reconstruction. It provides new information about the functions of these viral particles as stable machines for mRNA synthesis.

Motifs in nucleic acids: molecular mechanics restraints for base pairing and base stacking

In building and refining nucleic acid structures, it is often desirable to enforce particular base pairing and/or base stacking interactions. Energy-based modeling programs with classical molecular mechanics force fields do not lend themselves to the easy imposition of penalty terms corresponding to such restraints, because the requirement that two bases lie in or near the same plane (pairing) or that they lie in parallel planes (stacking) cannot be easily expressed in terms of traditional interactions involving two atoms (bonds), three atoms (angles), or four atoms (torsions). Here we derive expressions that define a collection of pseudobonds and pseudoangles through which molecular mechanics restraints for base pairing and stacking can be imposed. We have implemented these restraints into the JUMNA package for modeling DNA and RNA structures. JUMNA scripts can specify base pairing with a variety of standard geometries (Watson-Crick, Hoogsteen, wobble, etc.), or with user-defined geometries; they can also specify stacking arrangements. We have also implemented "soft-core" functions to modify van der Waals and electrostatic interactions to avoid steric conflicts in particularly difficult refinements where two backbones need to pass through one another. Test cases are presented to show the utility of the method. The restraints could be adapted for implementation in other molecular mechanics packages.

An assay for local quality in cryo-electron micrographs of single particles

High quality of the cryo-electron micrographs is of crucial importance for the success of single particle three-dimensional reconstruction methods. In analyzing some micrographs from cryo-electron microscopy specimens, we found an extraordinary variability, within the same micrograph, in the appearance of particles. We developed a method for analyzing the variability of local image quality, using correspondence analysis of local power spectra. With this technique, we discovered a strong systematic variation of the envelope modulating an otherwise unchanged contrast transfer function. The underlying causes may be uncontrollable effects, such as variations in the thickness of ice, instability of the holey carbon, and charging. The method of assaying, resulting in "local quality maps", may be useful as a general tool for screening micrographs used as input for reconstructions.

Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory

A theory of elastic normal modes is described for the exploration of global distortions of biological structures and their assemblies based upon low-resolution image data. Structural information at low resolution, e.g. from density maps measured by cryogenic electron microscopy (cryo-EM), is used to construct discrete multi-resolution models for the electron density using the techniques of vector quantization. The elastic normal modes computed based on these discretized low-resolution models are found to compare well with the normal modes obtained at atomic resolution. The quality of the normal modes describing global displacements of the molecular system is found to depend on the resolution of the synthetic EM data and the extent of reductionism in the discretized representation. However, models that reproduce the functional rearrangements of our test set of molecules are achieved for realistic values of experimental resolution. Thus large conformational changes as occur during the functioning of biological macromolecules and assemblies can be elucidated directly from low-resolution structural data through the application of elastic normal mode theory and vector quantization.

Large-scale motions within ribosomal 50S subunits as demonstrated using photolabile oligonucleotides

Photolabile oligonucleotides (PHONTs) bind to rRNA sequences to which they are complementary and, on photolysis, incorporate into neighboring ribosomal components. Here we report on photocrosslinking results obtained with PHONTs targeting 23S rRNA nucleotides 1882-1892, in the long lateral arm of the 50S subunit (PHONT 1892), and 1085-1093, in the L11 binding domain (PHONT 1093). Photolysis of the PHONT 1892.50S and PHONT 1093.50S complexes leads to formation of 'long-range' crosslinks from C1892 to U1094/A1095 and G1950, and from G1093 to U1712/1716 and U1926, that are clearly incompatible with published crystal structures of 50S subunits. These results provide strong evidence that within the 50S subunit (a) the L11 binding domain can extend in an arm-like fashion, accessing large areas of the ribosome, and (b) the lateral arm can bend about the noncanonical helix at its center. Such motions may have functional relevance in identifying regions that undergo major conformational change as the ribosome moves through its catalytic cycle.